StringologyTimes

Papers for stringologist

Table of Contents

Contents

CALDAM 2024

  1. Consecutive Occurrences with Distance Constraints.

CPM 2024

  1. A Class of Heuristics for Reducing the Number of BWT-Runs in the String Ordering Problem.
  2. A Data Structure for the Maximum-Sum Segment Problem with Offsets.
  3. Algorithms for Galois Words: Detection, Factorization, and Rotation.
  4. BAT-LZ out of hell.
  5. Closing the Gap: Minimum Space Optimal Time Distance Labeling Scheme for Interval Graphs.
  6. Computing the LCP Array of a Labeled Graph.
  7. Connecting de Bruijn Graphs.
  8. Construction of Sparse Suffix Trees and LCE Indexes in Optimal Time and Space.
  9. Efficient Construction of Long Orientable Sequences.
  10. Exploiting New Properties of String Net Frequency for Efficient Computation.
  11. Faster Sliding Window String Indexing in Streams.
  12. Finding Diverse Strings and Longest Common Subsequences in a Graph.
  13. Front Matter, Table of Contents, Preface, Conference Organization.
  14. Hairpin Completion Distance Lower Bound.
  15. Internal Pattern Matching in Small Space and Applications.
  16. Maintaining the Size of LZ77 on Semi-Dynamic Strings.
  17. Minimizing the Minimizers via Alphabet Reordering.
  18. Online Context-Free Recognition in OMv Time.
  19. Random Wheeler Automata.
  20. Reconstructing General Matching Graphs.
  21. Searching 2D-Strings for Matching Frames.
  22. Shortest Cover After Edit.
  23. Simplified Tight Bounds for Monotone Minimal Perfect Hashing.
  24. Solving the Minimal Positional Substring Cover Problem in Sublinear Space.
  25. Subsequences with Generalised Gap Constraints: Upper and Lower Complexity Bounds.
  26. The Rational Construction of a Wheeler DFA.
  27. Tight Bounds for Compressing Substring Samples.
  28. Walking on Words.
  29. When Is the Normalized Edit Distance over Non-Uniform Weights a Metric?

EvoStar 2024

  1. A Neural Network Based Guidance for a BRKGA: An Application to the Longest Common Square Subsequence Problem.

FUN 2024

  1. Baba Is Universal.
  2. Snake in Optimal Space and Time.
  3. The Great Textual Hoax: Boosting Sampled String Matching with Fake Samples.

ICCS (5) 2024

  1. Efficient Search Algorithms for the Restricted Longest Common Subsequence Problem.

TAMC 2024

  1. Quantum Path Parallelism: A Circuit-Based Approach to Text Searching.

ACM Trans. Algorithms 2024

  1. Generic Non-recursive Suffix Array Construction.

Algorithmica 2024

  1. Pattern Masking for Dictionary Matching: Theory and Practice.

Algorithms 2024

  1. Computing RF Tree Distance over Succinct Representations.

Inf. Comput. 2024

  1. Constructing and indexing the bijective and extended Burrows-Wheeler transform.

Inf. Syst. 2024

  1. CoCo-trie: Data-aware compression and indexing of strings.

Knowl. Based Syst. 2024

  1. Dynamic-MLCS: Fast searching for dynamic multiple longest common subsequences in sequence stream data.

Theor. Comput. Sci. 2024

  1. Faster space-efficient STR-IC-LCS computation.

VLDB J. 2024

  1. Optimizing RPQs over a compact graph representation.

ALENEX 2023

  1. LZ77 via Prefix-Free Parsing.
  2. Lower Bounds for Sorting 16, 17, and 18 Elements.
  3. Multiway Powersort.
  4. PaCHash: Packed and Compressed Hash Tables.
  5. SicHash - Small Irregular Cuckoo Tables for Perfect Hashing.

COCOA (1) 2023

  1. V-Words, Lyndon Words and Substring circ-UMFFs.

COCOA (2) 2023

  1. On Problems Related to Absent Subsequences.

CPM 2023

  1. Approximation Algorithms for the Longest Run Subsequence Problem.
  2. Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications.
  3. Compressed Indexing for Consecutive Occurrences.
  4. Computing MEMs on Repetitive Text Collections.
  5. Encoding Hard String Problems with Answer Set Programming.
  6. Faster Algorithms for Computing the Hairpin Completion Distance and Minimum Ancestor.
  7. Faster Prefix-Sorting Algorithms for Deterministic Finite Automata.
  8. From Bit-Parallelism to Quantum String Matching for Labelled Graphs.
  9. Front Matter, Table of Contents, Preface, Conference Organization.
  10. Improving the Sensitivity of MinHash Through Hash-Value Analysis.
  11. L-Systems for Measuring Repetitiveness.
  12. Linear-Time Computation of Cyclic Roots and Cyclic Covers of a String.
  13. MONI Can Find k-MEMs.
  14. MUL-Tree Pruning for Consistency and Compatibility.
  15. Merging Sorted Lists of Similar Strings.
  16. On Distances Between Words with Parameters.
  17. On the Complexity of Parameterized Local Search for the Maximum Parsimony Problem.
  18. On the Impact of Morphisms on BWT-Runs.
  19. Optimal LZ-End Parsing Is Hard.
  20. Optimal Near-Linear Space Heaviest Induced Ancestors.
  21. Order-Preserving Squares in Strings.
  22. PalFM-Index: FM-Index for Palindrome Pattern Matching.
  23. Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond.
  24. Sliding Window String Indexing in Streams.
  25. String Factorization via Prefix Free Families.
  26. Suffix-Prefix Queries on a Dictionary.
  27. Trie-Compressed Adaptive Set Intersection.

DCC 2023

  1. Augmented Thresholds for MONI.
  2. Bit-Parallel (Compressed) Wavelet Tree Construction.
  3. Computing matching statistics on Wheeler DFAs.
  4. Computing the optimal BWT of very large string collections.
  5. Constructing the CDAWG CFG using LCP-Intervals.
  6. Contextual Pattern Matching in Less Space.
  7. FM-Directories: Extending the Burrows-Wheeler Transform for String Labeled Vertex Graphs of (Almost) Arbitrary Topology.
  8. JARVIS2: a data compressor for large genome sequences.
  9. LZ4r - A New Fast Compression Algorithm for High-Speed Data Storage Systems.
  10. Measuring the Similarity of Files by Data Compression.
  11. Model Compression for Data Compression: Neural Network Based Lossless Compressor Made Practical.
  12. Permutation coding using divide-and-conquer strategy.
  13. Practical Implementations of Compressed RAM.
  14. RNA secondary structures: from ab initio prediction to better compression, and back.
  15. Recursive Prefix-Free Parsing for Building Big BWTs.
  16. SnappyR: A New High-Speed Lossless Data Compression Algorithm.

DLT 2023

  1. Bit Catastrophes for the Burrows-Wheeler Transform.

ISBRA 2023

  1. CSA-MEM: Enhancing Circular DNA Multiple Alignment Through Text Indexing Algorithms.

ITCS 2023

  1. An Algorithmic Bridge Between Hamming and Levenshtein Distances.

SISAP 2023

  1. Runs of Side-Sharing Tandems in Rectangular Arrays.

SODA 2023

  1. 4D Range Reporting in the Pointer Machine Model in Almost-Optimal Time.
  2. A Nearly-Tight Analysis of Multipass Pairing Heaps.
  3. A Tight Analysis of Slim Heaps and Smooth Heaps.
  4. Breaking the 𝒪(n)-Barrier in the Construction of Compressed Suffix Arrays and Suffix Trees.
  5. Optimal Square Detection Over General Alphabets.
  6. Quantum Speed-ups for String Synchronizing Sets, Longest Common Substring, and k-mismatch Matching.
  7. Simple, deterministic, fast (but weak) approximations to edit distance and Dyck edit distance.
  8. Simplex Range Searching Revisited: How to Shave Logs in Multi-Level Data Structures.
  9. Tight Bounds for Monotone Minimal Perfect Hashing.
  10. Tiny Pointers.

SOFSEM 2023

  1. Space-Efficient STR-IC-LCS Computation.
  2. The k-Centre Problem for Classes of Cyclic Words.

SOSA 2023

  1. An Optimal Lower Bound for Simplex Range Reporting.
  2. Optimal resizable arrays.
  3. Splay Top Trees.

SPIRE 2023

  1. A Simple Grammar-Based Index for Finding Approximately Longest Common Substrings.
  2. Algorithms and Hardness for the Longest Common Subsequence of Three Strings and Related Problems.
  3. Approximate Cartesian Tree Matching: An Approach Using Swaps.
  4. Approximation and Fixed Parameter Algorithms for the Approximate Cover Problem.
  5. Binary Mixed-Digit Data Compression Codes.
  6. CAGE: Cache-Aware Graphlet Enumeration.
  7. Chaining of Maximal Exact Matches in Graphs.
  8. Compacting Massive Public Transport Data.
  9. Compressibility Measures for Two-Dimensional Data.
  10. Computing All-vs-All MEMs in Grammar-Compressed Text.
  11. Constant Time and Space Updates for the Sigma-Tau Problem.
  12. Count-Min Sketch with Variable Number of Hash Functions: An Experimental Study.
  13. Data Structures for SMEM-Finding in the PBWT.
  14. Dynamic Compact Planar Embeddings.
  15. Efficient Parameterized Pattern Matching in Sublinear Space.
  16. Engineering a Textbook Approach to Index Massive String Dictionaries.
  17. Evaluating Regular Path Queries on Compressed Adjacency Matrices.
  18. Frequency-Constrained Substring Complexity.
  19. From de Bruijn Graphs to Variation Graphs - Relationships Between Pangenome Models.
  20. Largest Repetition Factorization of Fibonacci Words.
  21. Linear-Time Computation of Generalized Minimal Absent Words for Multiple Strings.
  22. Longest Common Prefix Arrays for Succinct k-Spectra.
  23. New Advances in Rightmost Lempel-Ziv.
  24. Non-overlapping Indexing in BWT-Runs Bounded Space.
  25. On Suffix Tree Detection.
  26. On the Number of Factors in the LZ-End Factorization.
  27. Optimal Wheeler Language Recognition.
  28. Optimally Computing Compressed Indexing Arrays Based on the Compact Directed Acyclic Word Graph.
  29. Space-Time Trade-Offs for the LCP Array of Wheeler DFAs.
  30. String Covers of a Tree Revisited.
  31. Sublinear Time Lempel-Ziv (LZ77) Factorization.

STACS 2023

  1. Dynamic Binary Search Trees: Improved Lower Bounds for the Greedy-Future Algorithm.
  2. Dynamic Data Structures for Parameterized String Problems.
  3. Real Numbers Equally Compressible in Every Base.
  4. Reconstructing Words Using Queries on Subwords or Factors.

STOC 2023

  1. Approximating Binary Longest Common Subsequence in Almost-Linear Time.
  2. External Memory Fully Persistent Search Trees.
  3. Locally Consistent Decomposition of Strings with Applications to Edit Distance Sketching.
  4. Weighted Edit Distance Computation: Strings, Trees, and Dyck.

WALCOM 2023

  1. Efficient Non-isomorphic Graph Enumeration Algorithms for Subclasses of Perfect Graphs.
  2. Energy Efficient Sorting, Selection and Searching.
  3. Finding the Cyclic Covers of a String.
  4. Inferring Strings from Position Heaps in Linear Time.
  5. Internal Longest Palindrome Queries in Optimal Time.
  6. Parity Permutation Pattern Matching.

WORDS 2023

  1. Smallest and Largest Block Palindrome Factorizations.
  2. String Attractors for Factors of the Thue-Morse Word.
  3. String Attractors of Fixed Points of k-Bonacci-Like Morphisms.

ACM Trans. Algorithms 2023

  1. On the Complexity of String Matching for Graphs.

Algorithmica 2023

  1. Fast Exact Dynamic Time Warping on Run-Length Encoded Time Series.

Bioinform. 2023

  1. μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.

Comput. Sci. Rev. 2023

  1. Abelian combinatorics on words: A survey.

IEEE Trans. Commun. 2023

  1. Reconstruction of Sets of Strings From Prefix/Suffix Compositions.

IEEE Trans. Inf. Theory 2023

  1. Toward a Definitive Compressibility Measure for Repetitive Sequences.

IEEE Trans. Knowl. Data Eng. 2023

  1. Bidirectional String Anchors for Improved Text Indexing and Top-$K$ Similarity Search.

Inf. Comput. 2023

  1. Compact representations of spatial hierarchical structures with support for topological queries.
  2. Sensitivity of string compressors and repetitiveness measures.

Inf. Process. Lett. 2023

  1. Longest bordered and periodic subsequences.
  2. Order-preserving pattern matching with scaling.
  3. Space-efficient Huffman codes revisited.

Int. J. Comput. Geom. Appl. 2023

  1. Fully Dynamic No-Back-Edge-Traversal Forest via 2D-Range Queries.

J. Comput. Biol. 2023

  1. Efficient Colored de Bruijn Graph for Indexing Reads.

Multim. Tools Appl. 2023

  1. Scalable thread based index construction using wavelet tree.

Theor. Comput. Sci. 2023

  1. Compact suffix automata representations for searching long patterns.
  2. Improved characters distance sampling for online and offline text searching.
  3. Linear-space S-table algorithms for the longest common subsequence problem.
  4. Maximal degenerate palindromes with gaps and mismatches.

CPM 2022

  1. A Theoretical and Experimental Analysis of BWT Variants for String Collections.
  2. An FPT-Algorithm for Longest Common Subsequence Parameterized by the Maximum Number of Deletions.
  3. Arbitrary-Length Analogs to de Bruijn Sequences.
  4. Back-To-Front Online Lyndon Forest Construction.
  5. Beyond the Longest Letter-Duplicated Subsequence Problem.
  6. Bi-Directional r-Indexes.
  7. Cartesian Tree Subsequence Matching.
  8. Compact Text Indexing for Advanced Pattern Matching Problems: Parameterized, Order-Isomorphic, 2D, etc. (Invited Talk).
  9. Efficient Construction of the BWT for Repetitive Text Using String Compression.
  10. Front Matter, Table of Contents, Preface, Conference Organization.
  11. Indexable Elastic Founder Graphs of Minimum Height.
  12. Invitation to Combinatorial Reconfiguration (Invited Talk).
  13. Linear-Time Computation of Shortest Covers of All Rotations of a String.
  14. Longest Palindromic Substring in Sublinear Time.
  15. Making de Bruijn Graphs Eulerian.
  16. Mechanical Proving with Walnut for Squares and Cubes in Partial Words.
  17. Minimal Absent Words on Run-Length Encoded Strings.
  18. On Strings Having the Same Length- k Substrings.
  19. Parallel Algorithm for Pattern Matching Problems Under Substring Consistent Equivalence Relations.
  20. Partial Permutations Comparison, Maintenance and Applications.
  21. Permutation Pattern Matching for Doubly Partially Ordered Patterns.
  22. Polynomial-Time Equivalences and Refined Algorithms for Longest Common Subsequence Variants.
  23. Rectangular Tile Covers of 2D-Strings.
  24. Reduction Ratio of the IS-Algorithm: Worst and Random Cases.
  25. Reordering a Tree According to an Order on Its Leaves.
  26. The Dynamic k-Mismatch Problem.
  27. The Fine-Grained Complexity of Episode Matching.
  28. The Normalized Edit Distance with Uniform Operation Costs Is a Metric.
  29. Using Automata and a Decision Procedure to Prove Results in Pattern Matching (Invited Talk).
  30. {RePair} Grammars Are the Smallest Grammars for Fibonacci Words.

DCC 2022

  1. A Benchmark of Entropy Coders for the Compression of Genome Sequencing Data.
  2. Burrows-Wheeler Transform on Purely Morphic Words.
  3. CSTs for Terabyte-Sized Data.
  4. Compressing the Tree of Canonical Huffman Coding.
  5. Computing Lexicographic Parsings.
  6. Computing Matching Statistics on Repetitive Texts.
  7. Converting RLBWT to LZ77 in smaller space.
  8. FM-Indexing Grammars Induced by Suffix Sorting for Long Patterns.
  9. Fast Coding of Haar Wavelet Trees.
  10. Graphs can be succinctly indexed for pattern matching in $O(\vert E\vert ^{2}+\vert V\vert ^{5/2})$ time.
  11. HOLZ: High-Order Entropy Encoding of Lempel-Ziv Factor Distances.
  12. Linear-time Minimization of Wheeler DFAs.
  13. Lower Bounds for Lexicographical DFS Data Structures.
  14. On Dynamic Bitvector Implementations.
  15. On different variants of the Burrows-Wheeler-Transform of string collections.
  16. RLBWT Tricks.
  17. Selective Weighted Adaptive Coding.
  18. Simple Worst-Case Optimal Adaptive Prefix-Free Coding.
  19. Succinct Data Structure for Path Graphs.
  20. x3: Lossless Data Compressor.

DLT 2022

  1. Logarithmic Equal-Letter Runs for BWT of Purely Morphic Words.
  2. Prefix Palindromic Length of the Sierpinski Word.

ESA 2022

  1. An Improved Algorithm for Finding the Shortest Synchronizing Words.
  2. Approximate Circular Pattern Matching.
  3. Approximating Dynamic Time Warping Distance Between Run-Length Encoded Strings.
  4. Computing NP-Hard Repetitiveness Measures via MAX-SAT.
  5. Distinct Elements in Streams: An Algorithm for the (Text) Book.
  6. Insertion Time of Random Walk Cuckoo Hashing below the Peeling Threshold.
  7. Lyndon Arrays Simplified.
  8. Simple Worst-Case Optimal Adaptive Prefix-Free Coding.

FOCS 2022

  1. Estimating the Longest Increasing Subsequence in Nearly Optimal Time.
  2. Faster Pattern Matching under Edit Distance : A Reduction to Dynamic Puzzle Matching and the Seaweed Monoid of Permutation Matrices.
  3. Gap Edit Distance via Non-Adaptive Queries: Simple and Optimal.
  4. Online List Labeling: Breaking the log2n Barrier.
  5. Strong XOR Lemma for Communication with Bounded Rounds : (extended abstract).
  6. Õ(n+poly(k))-time Algorithm for Bounded Tree Edit Distance.

ICALP 2022

  1. An Optimal-Time RLBWT Construction in BWT-Runs Bounded Space.
  2. Fully Functional Parameterized Suffix Trees in Compact Space.
  3. Galloping in Fast-Growth Natural Merge Sorts.
  4. Improved Approximation Algorithms for Dyck Edit Distance and RNA Folding.
  5. Improved Sublinear-Time Edit Distance for Preprocessed Strings.
  6. Listing, Verifying and Counting Lowest Common Ancestors in DAGs: Algorithms and Fine-Grained Lower Bounds.

ISAAC 2022

  1. Computing Palindromes on a Trie in Linear Time.
  2. External-Memory Dictionaries with Worst-Case Update Cost.
  3. On the Complexity of Tree Edit Distance with Variables.
  4. Simple Order-Isomorphic Matching Index with Expected Compact Space.
  5. Succinct List Indexing in Optimal Time.

ISBRA 2022

  1. Optimal Sequence Alignment to ED-Strings.

IWCIA 2022

  1. Lyndon Partial Words and Arrays with Applications.

IWOCA 2022

  1. Computing Longest (Common) Lyndon Subsequences.
  2. Linear Time Construction of Indexable Elastic Founder Graphs.
  3. Practical Space-Efficient Index for Structural Pattern Matching.
  4. Shortest Unique Palindromic Substring Queries in Semi-dynamic Settings.
  5. Space-Efficient B Trees via Load-Balancing.

LATIN 2022

  1. Elastic-Degenerate String Matching with 1 Error.
  2. Near-Optimal Search Time in δ-Optimal Space.
  3. Space-Efficient Data Structure for Next/Previous Larger/Smaller Value Queries.
  4. String Attractors and Infinite Words.

MFCS 2022

  1. On Uniformization in the Full Binary Tree.
  2. Streaming Word Problems.

SEA 2022

  1. Computing Maximal Unique Matches with the r-Index.
  2. RLBWT Tricks.

SODA 2022

  1. A Lower Bound for the n-queens Problem.
  2. An Improved Algorithm for The k-Dyck Edit Distance Problem.
  3. An Upper Bound and Linear-Space Queries on the LZ-End Parsing.
  4. Average Sensitivity of Dynamic Programming.
  5. Enumerating k-SAT functions.
  6. How Compression and Approximation Affect Efficiency in String Distance Measures.
  7. How many Clusters? - An algorithmic answer.
  8. Pattern Matching on Grammar-Compressed Strings in Linear Time.
  9. Selectable Heaps and Optimal Lazy Search Trees.
  10. Simulating a stack using queues.
  11. Splay trees on trees.
  12. Streaming Regular Expression Membership and Pattern Matching.

SOSA 2022

  1. Faster Exponential Algorithm for Permutation Pattern Matching.
  2. Simpler Adjacency Labeling for Planar Graphs with B-Trees.

SPIRE 2022

  1. Accessing the Suffix Array via φ -1-Forest.
  2. Balancing Run-Length Straight-Line Programs.
  3. Compressed String Dictionaries via Data-Aware Subtrie Compaction.
  4. Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads.
  5. Computing the Parameterized Burrows-Wheeler Transform Online.
  6. Engineering Compact Data Structures for Rank and Select Queries on Bit Vectors.
  7. Genome Comparison on Succinct Colored de Bruijn Graphs.
  8. How Train-Test Leakage Affects Zero-Shot Retrieval.
  9. Internal Masked Prefix Sums and Its Connection to Fully Internal Measurement Queries.
  10. KATKA: A KRAKEN-Like Tool with k Given at Query Time.
  11. Matching Patterns with Variables Under Edit Distance.
  12. Maximal Closed Substrings.
  13. On Representing the Degree Sequences of Sublogarithmic-Degree Wheeler Graphs.
  14. On the Hardness of Computing the Edit Distance of Shallow Trees.
  15. On the Optimisation of the GSACA Suffix Array Construction Algorithm.
  16. Online Algorithms for Finding Distinct Substrings with Length and Multiple Prefix and Suffix Conditions.
  17. Pattern Matching Under DTW Distance.
  18. Quantum Time Complexity and Algorithms for Pattern Matching on Labeled Graphs.
  19. Reconstructing Parameterized Strings from Parameterized Suffix and LCP Arrays.
  20. Sorting Genomes by Prefix Double-Cut-and-Joins.
  21. Subsequence Covers of Words.
  22. Substring Complexities on Run-Length Compressed Strings.
  23. The Complexity of the Co-occurrence Problem.

STACS 2022

  1. Existential Definability over the Subword Ordering.
  2. Probabilistic vs Deterministic Gamblers.

STOC 2022

  1. Almost-optimal sublinear-time edit distance in the low distance regime.
  2. Dynamic suffix array with polylogarithmic queries and updates.
  3. Explicit binary tree codes with sub-logarithmic size alphabet.
  4. Improved approximation guarantees for shortest superstrings using cycle classification by overlap to length ratios.
  5. On the optimal time/space tradeoff for hash tables.

SWAT 2022

  1. Predecessor on the Ultra-Wide Word RAM.
  2. Unit-Disk Range Searching and Applications.

WABI 2022

  1. Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time.
  2. Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables.
  3. Haplotype Threading Using the Positional Burrows-Wheeler Transform.
  4. Locality-Sensitive Bucketing Functions for the Edit Distance.
  5. On Weighted k-mer Dictionaries.
  6. Prefix-Free Parsing for Building Large Tunnelled Wheeler Graphs.
  7. Suffix Sorting via Matching Statistics.
  8. Toward Optimal Fingerprint Indexing for Large Scale Genomics.
  9. phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering.

ACM Comput. Surv. 2022

  1. Indexing Highly Repetitive String Collections, Part I: Repetitiveness Measures.
  2. Indexing Highly Repetitive String Collections, Part II: Compressed Indexes.

ACM J. Exp. Algorithmics 2022

  1. Grammar Compression by Induced Suffix Sorting.

ACM Trans. Algorithms 2022

  1. A Simple Algorithm for Optimal Search Trees with Two-way Comparisons.

Algorithmica 2022

  1. A Faster Reduction of the Dynamic Time Warping Distance to the Longest Increasing Subsequence Length.
  2. Adaptive Succinctness.
  3. Computing Minimal Unique Substrings for a Sliding Window.
  4. Efficient Computation of Sequence Mappability.
  5. Fast and Longest Rollercoasters.
  6. Space Efficient Merging of de Bruijn Graphs and Wheeler Graphs.
  7. Streaming Dictionary Matching with Mismatches.

Algorithms Mol. Biol. 2022

  1. Space-efficient representation of genomic k-mer count tables.

Appl. Soft Comput. 2022

  1. Graph search and variable neighborhood search for finding constrained longest common subsequences in artificial and real gene sequences.

Bioinform. 2022

  1. Fast and compact matching statistics analytics.

CoRR 2022

  1. A New Class of String Transformations for Compressed Text Indexing.
  2. A theoretical and experimental analysis of BWT variants for string collections.
  3. Almost-Optimal Sublinear-Time Edit Distance in the Low Distance Regime.
  4. An Optimal-Time RLBWT Construction in BWT-runs Bounded Space.
  5. An n Hk-compressed searchable partial-sums data structure for static sequences of sublogarithmic positive integers.
  6. Approximate Circular Pattern Matching.
  7. Cartesian Tree Subsequence Matching.
  8. Computing Longest (Common) Lyndon Subsequences.
  9. Computing NP-hard Repetitiveness Measures via MAX-SAT.
  10. Computing maximal generalized palindromes.
  11. Dynamic Suffix Array with Polylogarithmic Queries and Updates.
  12. Efficient Construction of the BWT for Repetitive Text Using String Compression.
  13. Faster Pattern Matching under Edit Distance.
  14. Improving Matrix-vector Multiplication via Lossless Grammar-Compressed Matrices.
  15. LCP-dropout: Compression-based Multiple Subword Segmentation for Neural Machine Translation.
  16. Linear Time Construction of Indexable Elastic Founder Graphs.
  17. Logarithmic equal-letter runs for BWT of purely morphic words.
  18. Longest (Sub-)Periodic Subsequence.
  19. MONI can find k-MEMs.
  20. Memory Efficient Tries for Sequential Pattern Mining.
  21. Minimal Absent Words on Run-Length Encoded Strings.
  22. Multiple Genome Analytics Framework: The Case of All SARS-CoV-2 Complete Variants.
  23. Near-Optimal Search Time in δ-Optimal Space.
  24. Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches.
  25. OSM-tree: A Sortedness-Aware Index.
  26. Online List Labeling: Breaking the log2n Barrier.
  27. Online algorithms for finding distinct substrings with length and multiple prefix and suffix conditions.
  28. Õ(n+poly(k))-time Algorithm for Bounded Tree Edit Distance.
  29. Predecessor on the Ultra-Wide Word RAM.
  30. RePair Grammars are the Smallest Grammars for Fibonacci Words.
  31. Safety and Completeness in Flow Decompositions for RNA Assembly.
  32. Shortest Unique Palindromic Substring Queries in Semi-dynamic Settings.
  33. Space-Efficient STR-IC-LCS Computation.
  34. Standard Vs Uniform Binary Search and Their Variants in Learned Static Indexing: The Case of the Searching on Sorted Data Benchmarking Software Platform.
  35. Substring Complexities on Run-length Compressed Strings.
  36. The Efficiency of the ANS Entropy Encoding.
  37. What Does Dynamic Optimality Mean in External Memory?
  38. X3: Lossless Data Compressor.

Commun. ACM 2022

  1. Resolution of the burrows-wheeler transform conjecture.
  2. The compression power of the BWT: technical perspective.

IEEE Access 2022

  1. Compressing and Querying Integer Dictionaries Under Linearities and Repetitions.

Inf. Comput. 2022

  1. A periodicity lemma for partial words.
  2. Efficient representation and counting of antipower factors in words.
  3. LZRR: LZ77 parsing with right reference.
  4. Order-preserving pattern matching indeterminate strings.
  5. c-trie++: A dynamic trie tailored for fast prefix searches.

Inf. Process. Lett. 2022

  1. All-pairs suffix/prefix in optimal time using Aho-Corasick space.
  2. Palindromic trees for a sliding window and its applications.

Inf. Retr. J. 2022

  1. Applying burst-tries for error-tolerant prefix search.

J. Comput. Biol. 2022

  1. Finding Maximal Exact Matches Using the r-Index.
  2. MONI: A Pangenomic Index for Finding Maximal Exact Matches.

J. Comput. Sci. 2022

  1. A sorting algorithm based on ordered block insertions.

SN Comput. Sci. 2022

  1. Combining Forward Compression with PPM.
  2. Correction to: Graph Compression for Adjacency-Matrix Multiplication.
  3. Graph Compression for Adjacency-Matrix Multiplication.

Theor. Comput. Sci. 2022

  1. A data structure for substring-substring LCS length queries.
  2. An efficient algorithm for the longest common palindromic subsequence problem.
  3. Combinatorics of minimal absent words for a sliding window.
  4. Efficient and compact representations of some non-canonical prefix-free codes.
  5. In-place initializable arrays.
  6. Internal shortest absent word queries in constant time and linear space.
  7. Parameterized DAWGs: Efficient constructions and bidirectional pattern searches.
  8. Partial sums on the ultra-wide word RAM.

Theory Comput. Syst. 2022

  1. Factorizing Strings into Repetitions.

ALENEX 2021

  1. A “Learned” Approach to Quicken and Compress Rank/Select Dictionaries.
  2. PFP Compressed Suffix Trees.

CIAA 2021

  1. Approximate Hashing for Bioinformatics.

CIAC 2021

  1. The Parameterized Suffix Tray.

COCOA 2021

  1. Succinct Data Structures for Series-Parallel, Block-Cactus and 3-Leaf Power Graphs.

CPM 2021

  1. A Compact Index for Cartesian Tree Matching.
  2. A Fast and Small Subsampled R-Index.
  3. A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs.
  4. AWLCO: All-Window Length Co-Occurrence.
  5. An Invertible Transform for Efficient String Matching in Labeled Digraphs.
  6. Compressed Weighted de Bruijn Graphs.
  7. Computing Covers of 2D-Strings.
  8. Computing Edit Distance (Invited Talk).
  9. Constructing Strings Avoiding Forbidden Substrings.
  10. Constructing the Bijective and the Extended Burrows-Wheeler Transform in Linear Time.
  11. Data Structures for Categorical Path Counting Queries.
  12. Disorders and Permutations.
  13. Efficient Algorithms for Counting Gapped Palindromes.
  14. Front Matter, Table of Contents, Preface, Conference Organization.
  15. Gapped Indexing for Consecutive Occurrences.
  16. Internal Shortest Absent Word Queries.
  17. On-Line Pattern Matching on D-Texts (Invited Talk).
  18. Optimal Completion and Comparison of Incomplete Phylogenetic Trees Under Robinson-Foulds Distance.
  19. Optimal Construction of Hierarchical Overlap Graphs.
  20. R-enum: Enumeration of Characteristic Substrings in BWT-runs Bounded Space.
  21. Ranking Bracelets in Polynomial Time.
  22. Repetitions in Strings: A “Constant” Problem (Invited Talk).
  23. String Sanitization Under Edit Distance: Improved and Generalized.
  24. The Longest Run Subsequence Problem: Further Complexity Results.
  25. The k-Mappability Problem Revisited.
  26. Weighted Ancestors in Suffix Trees Revisited.

DCC 2021

  1. A Disk-Based Index for Trajectories with an In-Memory Compressed Cache.
  2. A grammar compressor for collections of reads with applications to the construction of the BWT.
  3. Accelerating Knuth-Morris-Pratt String Matching over LZ77 Compressed Text.
  4. Approximate Hashing for Bioinformatics.
  5. Backward Weighted Coding.
  6. Compact Representation of Spatial Hierarchies and Topological Relationships.
  7. DZip: improved general-purpose loss less compression based on novel neural network modeling.
  8. Efficiently Merging r-indexes.
  9. End-to-End optimized image compression for machines, a study.
  10. Improved LZ77 Compression.
  11. Improving Run Length Encoding by Preprocessing.
  12. Neural Networks Optimally Compress the Sawbridge.
  13. On Elias-Fano for Rank Queries in FM-Indexes.
  14. On Random Editing in LZ-End.
  15. PHONI: Streamed Matching Statistics with Multi-Genome References.
  16. Parallel Processing of Grammar Compression.
  17. Smaller RLZ-Compressed Suffix Arrays.
  18. Succinct Data Structures for Small Clique-Width Graphs.
  19. Succinct representations of Intersection Graphs on a Circle.
  20. ndzip: A High-Throughput Parallel Lossless Compressor for Scientific Data.

DLT 2021

  1. Upper Bounds on Distinct Maximal (Sub-)Repetitions in Compressed Strings.
  2. Weighted Prefix Normal Words: Mind the Gap.

ESA 2021

  1. Bidirectional String Anchors: A New String Sampling Mechanism.
  2. Compression by Contracting Straight-Line Programs.
  3. Dynamic Colored Orthogonal Range Searching.
  4. Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing.
  5. Faster Algorithms for Longest Common Substring.
  6. Hypersuccinct Trees - New Universal Tree Source Codes for Optimal Compressed Tree Data Structures and Range Minima.
  7. Lyndon Words Accelerate Suffix Sorting.
  8. Minimum Common String Partition: Exact Algorithms.
  9. Space Efficient Two-Dimensional Orthogonal Colored Range Counting.

FOCS 2021

  1. Breaking the Cubic Barrier for (Unweighted) Tree Edit Distance.
  2. Small-space and streaming pattern matching with $k$ edits.

ICALP 2021

  1. A Linear-Time n0.4-Approximation for Longest Common Subsequence.
  2. An Almost Optimal Edit Distance Oracle.
  3. Analysis of Smooth Heaps and Slim Heaps.
  4. Faster Algorithms for Bounded Tree Edit Distance.
  5. Fine-Grained Hardness for Edit Distance to a Fixed Sequence.
  6. Improved Approximation for Longest Common Subsequence over Small Alphabets.
  7. LF Successor: Compact Space Indexing for Order-Isomorphic Pattern Matching.
  8. Linear Time Runs Over General Ordered Alphabets.
  9. New Sublinear Algorithms and Lower Bounds for LIS Estimation.
  10. Optimal-Time Queries on BWT-Runs Compressed Indexes.
  11. Sorting Short Integers.
  12. Streaming and Small Space Approximation Algorithms for Edit Distance and Longest Common Subsequence.

ISAAC 2021

  1. Algorithms and Complexity on Indexing Elastic Founder Graphs.
  2. Inverse Suffix Array Queries for 2-Dimensional Pattern Matching in Near-Compact Space.
  3. Pattern Masking for Dictionary Matching.
  4. Repetition- and Linearity-Aware Rank/Select Dictionaries.
  5. Resilient Level Ancestor, Bottleneck, and Lowest Common Ancestor Queries in Dynamic Trees.
  6. Streaming Pattern Matching (Invited Talk).

IWOCA 2021

  1. The Tandem Duplication Distance Problem Is Hard over Bounded Alphabets.

LATA 2021

  1. Cadences in Grammar-Compressed Strings.
  2. Succinct Representations for (Non)Deterministic Finite Automata.

MFCS 2021

  1. Matching Patterns with Variables Under Hamming Distance.

RP 2021

  1. Absent Subsequences in Words.

SEA 2021

  1. Document Retrieval Hacks.
  2. Engineering Predecessor Data Structures for Dynamic Integer Sets.

SODA 2021

  1. A Lower Bound for Dynamic Fractional Cascading.
  2. Beating the probabilistic lower bound on perfect hashing.
  3. Competitive Data-Structure Dynamization.
  4. New Data Structures for Orthogonal Range Reporting and Range Minima Queries.
  5. On Indexing and Compressing Finite Automata.
  6. On Locating Paths in Compressed Tries.
  7. Optimal Oblivious Priority Queues.

SOFSEM 2021

  1. A Normal Sequence Compressed by PPM* But Not by Lempel-Ziv 78.
  2. Blocksequences of k-local Words.
  3. Novel Results on the Number of Runs of the Burrows-Wheeler-Transform.

SOSA 2021

  1. Modular Subset Sum, Dynamic Strings, and Zero-Sum Sets.
  2. Soft Sequence Heaps.

SPIRE 2021

  1. A Separation of γ and b via Thue-Morse Words.
  2. All Instantiations of the Greedy Algorithm for the Shortest Common Superstring Problem are Equivalent.
  3. An LMS-Based Grammar Self-index with Local Consistency Properties.
  4. Computing the Original eBWT Faster, Simpler, and with Less Memory.
  5. Exploiting Pseudo-locality of Interchange Distance.
  6. Extracting the Sparse Longest Common Prefix Array from the Suffix Binary Search Tree.
  7. Grammar Index by Induced Suffix Sorting.
  8. Improved Topic Modeling in Twitter Through Community Pooling.
  9. Longest Common Rollercoasters.
  10. Lower Bounds for the Number of Repetitions in 2D Strings.
  11. Minimal Unique Palindromic Substrings After Single-Character Substitution.
  12. On Stricter Reachable Repetitiveness Measures.
  13. On the Approximation Ratio of LZ-End to LZ77.
  14. Permutation-Constrained Common String Partitions with Applications.
  15. Position Heaps for Cartesian-Tree Matching on Strings and Tries.
  16. String Covers of a Tree.
  17. TSXor: A Simple Time Series Compression Algorithm.
  18. Unicode at Gigabytes per Second.
  19. findere: Fast and Precise Approximate Membership Query.
  20. r-Indexing the eBWT.

STACS 2021

  1. Efficiently Testing Simon’s Congruence.
  2. Finding an Optimal Alphabet Ordering for Lyndon Factorization Is Hard.
  3. The Edit Distance to k-Subsequence Universality.

STOC 2021

  1. Fully dynamic approximation of LIS in polylogarithmic time.
  2. Improved dynamic algorithms for longest increasing subsequence.
  3. Subcubic algorithms for Gomory-Hu tree in unweighted graphs.

Stringology 2021

  1. Automata Approach to Inexact Tree Pattern Matching Using 1-degree Edit Distance.
  2. Computational Substantiation of the d-step Conjecture for Distinct Squares Revisited.
  3. Counting Lyndon Subsequences.
  4. Pitfalls of Algorithm Comparison.
  5. Refined Upper Bounds on the Size of the Condensed Neighbourhood of Sequences.
  6. Searching with Extended Guard and Pivot Loop.
  7. The n-ary Initial Literal and Literal Shuffle.
  8. Towards an Efficient Text Sampling Approach for Exact and Approximate Matching.

WABI 2021

  1. Compressing and Indexing Aligned Readsets.
  2. Space-Efficient Representation of Genomic k-Mer Count Tables.

ACM Comput. Surv. 2021

  1. Predecessor Search.

ACM J. Exp. Algorithmics 2021

  1. Engineering Practical Lempel-Ziv Tries.

ACM Trans. Algorithms 2021

  1. Optimal Substring Equality Queries with Applications to Sparse Text Indexing.
  2. Optimal-Time Dictionary-Compressed Indexes.

ACM Trans. Knowl. Discov. Data 2021

  1. Combinatorial Algorithms for String Sanitization.

Algorithmica 2021

  1. Internal Dictionary Matching.
  2. Range Majorities and Minorities in Arrays.
  3. Top Tree Compression of Tries.

Algorithms 2021

  1. Compressed Communication Complexity of Hamming Distance.
  2. Lempel-Ziv Parsing for Sequences of Blocks.
  3. Non-Overlapping LZ77 Factorization and LZ78 Substring Compression Queries with Suffix Trees.
  4. Re-Pair in Small Space.
  5. Reversed Lempel-Ziv Factorization with Suffix Trees.
  6. Subpath Queries on Compressed Graphs: A Survey.

Bioinform. 2021

  1. Accurate spliced alignment of long RNA sequencing reads.

CoRR 2021

  1. $r$-indexing Wheeler graphs.
  2. A Bloom Filter Survey: Variants for Different Domain Applications.
  3. A Conditional Lower Bound for Episode Matching.
  4. A Fast and Small Subsampled R-index.
  5. A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs.
  6. A New Lossless Data Compression Algorithm Exploiting Positional Redundancy.
  7. A Separation of γ and b via Thue-Morse Words.
  8. A Simple Algorithm for Optimal Search Trees with Two-Way Comparisons.
  9. A Tight Analysis of Slim Heaps and Smooth Heaps.
  10. A new compressed cover tree guarantees a near linear parameterized complexity for all $k$-nearest neighbors search in metric spaces.
  11. A new distance based on minimal absent words and applications to biological sequences.
  12. APMF < APSP? Gomory-Hu Tree for Unweighted Graphs in Almost-Quadratic Time.
  13. Abelian Repetition Threshold Revisited.
  14. Absent Subsequences in Words.
  15. Algorithms and Complexity on Indexing Founder Graphs.
  16. Algorithms and Hardness for Multidimensional Range Updates and Queries.
  17. All instantiations of the greedy algorithm for the shortest superstring problem are equivalent.
  18. An Almost Optimal Edit Distance Oracle.
  19. An Improved Algorithm for The k-Dyck Edit Distance Problem.
  20. An O(k log n) algorithm for prefix based ranked autocomplete.
  21. An efficient way to manage blocks of data with Wise Red-Black Trees.
  22. Analysis of Smooth Heaps and Slim Heaps.
  23. Approximate Membership Query Filters with a False Positive Free Set.
  24. Approximating LCS and Alignment Distance over Multiple Sequences.
  25. Approximating Length-Restricted Means under Dynamic Time Warping.
  26. Approximating the Longest Common Subsequence problem within a sub-polynomial factor in linear time.
  27. Approximation Algorithms for LCS and LIS with Truly Improved Running Times.
  28. Arbitrary-length analogs to de Bruijn sequences.
  29. Beyond Single-Deletion Correcting Codes: Substitutions and Transpositions.
  30. Beyond the Longest Letter-duplicated Subsequence Problem.
  31. Binary Dynamic Time Warping in Linear Time.
  32. Boosting the Search Performance of B+-tree for Non-volatile Memory with Sentinels.
  33. Breaking the Cubic Barrier for (Unweighted) Tree Edit Distance.
  34. Breaking the O(n)-Barrier in the Construction of Compressed Suffix Arrays.
  35. Burrows Wheeler Transform on a Large Scale: Algorithms Implemented in Apache Spark.
  36. Cantor Mapping Technique.
  37. Checking whether a word is Hamming-isometric in linear time.
  38. Chunk List: Concurrent Data Structures.
  39. Closed Ziv-Lempel factorization of the m-bonacci words.
  40. Combinatorics of minimal absent words for a sliding window.
  41. Compact Euler Tours of Trees with Small Maximum Degree.
  42. Complex Event Forecasting with Prediction Suffix Trees: Extended Technical Report.
  43. Compressed Communication Complexity of Hamming Distance.
  44. Compression by Contracting Straight-Line Programs.
  45. Computing Matching Statistics on Repetitive Texts.
  46. Computing the original eBWT faster, simpler, and with less memory.
  47. Conditional Lower Bounds for Variants of Dynamic LIS.
  48. Construction of Sparse Suffix Trees and LCE Indexes in Optimal Time and Space.
  49. Counting Lyndon Subsequences.
  50. Counting and Verifying Abelian Border Arrays of Binary Words.
  51. Critical factorisation in square-free words.
  52. Defeating duplicates: A re-design of the LearnedSort algorithm.
  53. Deriving monadic quicksort (Declarative Pearl).
  54. Does Preprocessing help in Fast Sequence Comparisons?
  55. Dynamic Longest Increasing Subsequence and the Erdös-Szekeres Partitioning Problem.
  56. Dynamic Range Mode Enumeration.
  57. Dynamic Suffix Array with Sub-linear update time and Poly-logarithmic Lookup Time.
  58. Efficient construction of the extended BWT from grammar-compressed DNA sequencing reads.
  59. Empirically Improved Tokuda Gap Sequence in Shellsort.
  60. Engineering Predecessor Data Structures for Dynamic Integer Sets.
  61. Entropy of Mersenne-Twisters.
  62. Estimating the Longest Increasing Subsequence in Nearly Optimal Time.
  63. ExtendedHyperLogLog: Analysis of a new Cardinality Estimator.
  64. FM-Indexing Grammars Induced by Suffix Sorting for Long Patterns.
  65. Fast Succinct Retrieval and Approximate Membership using Ribbon.
  66. Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing.
  67. Fast direct access to variable length codes.
  68. Faster Algorithms for Bounded Tree Edit Distance.
  69. Faster Algorithms for Longest Common Substring.
  70. Faster Exponential Algorithm for Permutation Pattern Matching.
  71. Friendly Cut Sparsifiers and Faster Gomory-Hu Trees.
  72. From Bit-Parallelism to Quantum: Breaking the Quadratic Barrier.
  73. Gap Edit Distance via Non-Adaptive Queries: Simple and Optimal.
  74. Gapped Indexing for Consecutive Occurrences.
  75. Grammar Index By Induced Suffix Sorting.
  76. Graphs can be succinctly indexed for pattern matching in $ O(│E│^2 + │V│^{5 / 2}) $ time.
  77. HINT: A Hierarchical Index for Intervals in Main Memory.
  78. HOLZ: High-Order Entropy Encoding of Lempel-Ziv Factor Distances.
  79. Hardness of Detecting Abelian and Additive Square Factors in Strings.
  80. Hierarchical Bitmap Indexing for Range and Membership Queries on Multidimensional Arrays.
  81. How Compression and Approximation Affect Efficiency in String Distance Measures.
  82. Hypersuccinct Trees - New universal tree source codes for optimal compressed tree data structures.
  83. Improved Approximation Algorithms for Dyck Edit Distance and RNA Folding.
  84. Improved Approximation Guarantees for Shortest Superstrings using Cycle Classification by Overlap to Length Ratios.
  85. Improved Approximation for Longest Common Subsequence over Small Alphabets.
  86. Improving Run Length Encoding by Preprocessing.
  87. Internal Shortest Absent Word Queries in Constant Time and Linear Space.
  88. Is this the simplest (and most surprising) sorting algorithm ever?
  89. Learned Sorted Table Search and Static Indexes in Small Space: Methodological and Practical Insights via an Experimental Study.
  90. Linear Approximate Pattern Matching Algorithm.
  91. Linear Time Runs over General Ordered Alphabets.
  92. Linear-time Minimization of Wheeler DFAs.
  93. Load-Balancing Succinct B Trees.
  94. Lower Bounds and Improved Algorithms for Asymmetric Streaming Edit Distance and Longest Common Subsequence.
  95. Lower Bounds for the Number of Repetitions in 2D Strings.
  96. Matching Patterns with Variables under Hamming Distance.
  97. Memory-Optimality for Non-Blocking Containers.
  98. Minimal unique palindromic substrings after single-character substitution.
  99. N-ary Huffman Encoding Using High-Degree Trees - A Performance Comparison.
  100. Near-Optimal Quantum Algorithms for String Problems.
  101. Nearly Tight Lower Bounds for Succinct Range Minimum Query.
  102. Number Parsing at a Gigabyte per Second.
  103. On (co-lex) Ordering Automata.
  104. On Arithmetically Progressed Suffix Arrays and related Burrows-Wheeler Transforms.
  105. On Solving the Minimum Common String Partition Problem by Decision Diagrams.
  106. On Specialization of a Program Model of Naive Pattern Matching in Strings (Extended Abstract).
  107. On Stricter Reachable Repetitiveness Measures.
  108. On the Cost of Unsuccessful Searches in Search Trees with Two-way Comparisons.
  109. On the Optimal Time/Space Tradeoff for Hash Tables.
  110. On the approximation ratio of LZ-End to LZ77.
  111. Optimal Gap Sequences in Shellsort for n≤6 Elements.
  112. Optimal Sorting Circuits for Short Keys.
  113. Optimal Space and Time for Streaming Pattern Matching.
  114. PTHash: Revisiting FCH Minimal Perfect Hashing.
  115. Parallel Batch-Dynamic kd-Trees.
  116. Parallel Batched Interpolation Search Tree.
  117. Parallel and External-Memory Construction of Minimal Perfect Hash Functions with PTHash.
  118. Pattern Matching on Grammar-Compressed Strings in Linear Time.
  119. Pattern-defeating Quicksort.
  120. Position Heaps for Cartesian-tree Matching on Strings and Tries.
  121. Practical evaluation of Lyndon factors via alphabet reordering.
  122. Prefixes of the Fibonacci word that end with a cube.
  123. RLBWT Tricks.
  124. Range Minimum Queries in Minimal Space.
  125. Reconstruction of Sets of Strings from Prefix/Suffix Compositions.
  126. Resilient Level Ancestor, Bottleneck, and Lowest Common Ancestor Queries in Dynamic Trees.
  127. Ruler Wrapping.
  128. SIMD-Optimized Search Over Sorted Data.
  129. Scalable Hash Table for NUMA Systems.
  130. Sensitivity of string compressors and repetitiveness measures.
  131. SetSketch: Filling the Gap between MinHash and HyperLogLog.
  132. Simple Worst-Case Optimal Adaptive Prefix-Free Coding.
  133. Small space and streaming pattern matching with k edits.
  134. Solving one variable word equations in the free group in cubic time.
  135. Sorted Range Reporting.
  136. Sorting Short Integers.
  137. Space Efficient Two-Dimensional Orthogonal Colored Range Counting.
  138. Space-Efficient Huffman Codes Revisited.
  139. Spanner Evaluation over SLP-Compressed Documents.
  140. Stochastic and Worst-Case Generalized Sorting Revisited.
  141. Strictly In-Place Algorithms for Permuting and Inverting Permutations.
  142. String Comparison on a Quantum Computer Using Hamming Distance.
  143. String Sampling with Bidirectional String Anchors.
  144. Succinct Data Structure for Path Graphs.
  145. Succinct Data Structures for Series-Parallel, Block-Cactus and 3-Leaf Power Graphs.
  146. Support Optimality and Adaptive Cuckoo Filters.
  147. Text Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations.
  148. The Dynamic k-Mismatch Problem.
  149. The k-mappability problem revisited.
  150. Tiny Pointers.
  151. Tree Edit Distance with Variables. Measuring the Similarity between Mathematical Formulas.
  152. Weighted Ancestors in Suffix Trees Revisited.
  153. Weighted Burrows-Wheeler Compression.
  154. Which Regular Languages can be Efficiently Indexed?

Comput. J. 2021

  1. Smaller Compressed Suffix Arrays†.

IEEE Trans. Inf. Theory 2021

  1. On the Approximation Ratio of Ordered Parsings.
  2. The Smallest Grammar Problem Revisited.

Inf. Comput. 2021

  1. Efficient pattern matching in elastic-degenerate strings.
  2. On the cost of unsuccessful searches in search trees with two-way comparisons.
  3. Wheeler languages.

Inf. Process. Lett. 2021

  1. Longest previous overlapping factor array.

Int. J. Geogr. Inf. Sci. 2021

  1. An index for moving objects with constant-time access to their compressed trajectories.

J. Comput. Syst. Sci. 2021

  1. Block trees.
  2. Circular pattern matching with k mismatches.
  3. Grammar-compressed indexes with logarithmic search time.

J. Inf. Process. 2021

  1. Towards a Complete Perspective on Labeled Tree Indexing: New Size Bounds, Efficient Constructions, and Beyond.

J. King Saud Univ. Comput. Inf. Sci. 2021

  1. A survey on data compression techniques: From the perspective of data quality, coding schemes, data type and applications.

Theor. Comput. Sci. 2021

  1. Adaptive learning of compressible strings.
  2. Computing longest palindromic substring after single-character or block-wise edits.
  3. Efficiently computing runs on a trie.
  4. Maximal unbordered factors of random strings.
  5. Space-efficient construction of compressed suffix trees.
  6. Tight upper and lower bounds on suffix tree breadth.
  7. When a dollar makes a BWT.

Theory Comput. Syst. 2021

  1. Constructing Antidictionaries of Long Texts in Output-Sensitive Space.

ALENEX 2020

  1. Constructing the Wavelet Tree and Wavelet Matrix in Distributed Memory.
  2. Engineering Top-Down Weight-Balanced Trees.
  3. RecSplit: Minimal Perfect Hashing via Recursive Splitting.
  4. Reverse-Safe Data Structures for Text Indexing.

APPROX-RANDOM 2020

  1. Improved Circular k-Mismatch Sketches.
  2. Lp Pattern Matching in a Stream.

BCB 2020

  1. SMART: SuperMaximal approximate repeats tool.

CPM 2020

  1. Algebraic Algorithms for Finding Patterns in Graphs (Invited Talk).
  2. Approximating Longest Common Substring with k mismatches: Theory and Practice.
  3. Approximating Text-To-Pattern Distance via Dimensionality Reduction.
  4. Chaining with Overlaps Revisited.
  5. Compressed Orthogonal Search on Suffix Arrays with Applications to Range LCP.
  6. Counting Distinct Patterns in Internal Dictionary Matching.
  7. DAWGs for Parameterized Matching: Online Construction and Related Indexing Structures.
  8. Detecting k-(Sub-)Cadences and Equidistant Subsequence Occurrences.
  9. Double String Tandem Repeats.
  10. Dynamic String Alignment.
  11. Efficient Tree-Structured Categorical Retrieval.
  12. FM-Index Reveals the Reverse Suffix Array.
  13. Faster Binary Mean Computation Under Dynamic Time Warping.
  14. Finding the Anticover of a String.
  15. Front Matter, Table of Contents, Preface, Conference Organization.
  16. Genomic Problems Involving Copy Number Profiles: Complexity and Algorithms.
  17. In-Place Bijective Burrows-Wheeler Transforms.
  18. Longest Common Subsequence on Weighted Sequences.
  19. On Extensions of Maximal Repeats in Compressed Strings.
  20. On Indeterminate Strings Matching.
  21. On Two Measures of Distance Between Fully-Labelled Trees.
  22. Parameterized Algorithms for Matrix Completion with Radius Constraints.
  23. String Factorizations Under Various Collision Constraints.
  24. String Sanitization Under Edit Distance.
  25. Summarizing Diverging String Sequences, with Applications to Chain-Letter Petitions.
  26. Text Indexing and Searching in Sublinear Time.
  27. The Streaming k-Mismatch Problem: Tradeoffs Between Space and Total Time.
  28. Time-Space Tradeoffs for Finding a Long Common Substring.
  29. Unary Words Have the Smallest Levenshtein k-Neighbourhoods.
  30. k-Approximate Quasiperiodicity under Hamming and Edit Distance.

CSR 2020

  1. Optimal Skeleton Huffman Trees Revisited.

CiE 2020

  1. Faster Online Computation of the Succinct Longest Previous Factor Array.

DCC 2020

  1. Approximating Optimal Bidirectional Macro Schemes.
  2. Bitvectors with Runs and the Successor/Predecessor Problem.
  3. Compact Representation of Graphs with Small Bandwidth and Treedepth.
  4. Compressing and Randomly Accessing Sequences (note).
  5. Decompressing Lempel-Ziv Compressed Text.
  6. Edge Minimization in de Bruijn Graphs.
  7. Grammar Compression with Probabilistic Context-Free Grammar.
  8. On Dynamic Succinct Graph Representations.
  9. Pattern Search in Grammar-Compressed Graphs.
  10. Practical Repetition-Aware Grammar Compression.
  11. Re-Pair in Small Space.
  12. Revisiting Compact RDF Stores Based on k2-Trees.
  13. Semantrix: A Compressed Semantic Matrix.
  14. Towards Better Compressed Representations.
  15. c-Trie++: A Dynamic Trie Tailored for Fast Prefix Searches.

DLT 2020

  1. Scattered Factor-Universality of Words.

ESA 2020

  1. Efficient Computation of 2-Covers of a String.
  2. Fast Preprocessing for Optimal Orthogonal Range Reporting and Range Successor with Applications to Text Indexing.
  3. New Binary Search Tree Bounds via Geometric Inversions.
  4. On the Complexity of BWT-Runs Minimization via Alphabet Reordering.
  5. Practical Performance of Space Efficient Data Structures for Longest Common Extensions.
  6. The Fine-Grained Complexity of Median and Center String Problems Under Edit Distance.
  7. The Number of Repetitions in 2D-Strings.

Euro-Par 2020

  1. LCP-Aware Parallel String Sorting.

FOCS 2020

  1. Edit Distance in Near-Linear Time: it’s a Constant Factor.
  2. Faster Approximate Pattern Matching: A Unified Approach.
  3. Lazy Search Trees.
  4. On One-way Functions and Kolmogorov Complexity.
  5. Resolution of the Burrows-Wheeler Transform Conjecture.
  6. Sublinear-Time Algorithms for Computing & Embedding Gap Edit Distance.

FSTTCS 2020

  1. String Indexing for Top-k Close Consecutive Occurrences.

ICALP 2020

  1. Dynamic Longest Common Substring in Polylogarithmic Time.
  2. Space Efficient Construction of Lyndon Arrays in Linear Time.

ICDT 2020

  1. Optimal Joins Using Compact Data Structures.

ISAAC 2020

  1. A Faster Subquadratic Algorithm for the Longest Common Increasing Subsequence Problem.
  2. A Reduction of the Dynamic Time Warping Distance to the Longest Increasing Subsequence Length.
  3. Counting 4-Patterns in Permutations Is Equivalent to Counting 4-Cycles in Graphs.
  4. Distance Oracles for Interval Graphs via Breadth-First Rank/Select in Succinct Trees.
  5. Efficient Labeling for Reachability in Directed Acyclic Graphs.
  6. Enumerating Range Modes.
  7. Random Access in Persistent Strings.
  8. Update Query Time Trade-Off for Dynamic Suffix Arrays.

ITCS 2020

  1. Unexpected Power of Random Strings.

IWOCA 2020

  1. Optimal In-place Algorithms for Basic Graph Problems.

LATA 2020

  1. Lyndon Words versus Inverse Lyndon Words: Queries on Suffixes and Bordered Words.
  2. On Collapsing Prefix Normal Words.

LATIN 2020

  1. Batched Predecessor and Sorting with Size-Priced Information in External Memory.
  2. On the Collection of Fringe Subtrees in Random Binary Trees.
  3. Suffix Trees, DAWGs and CDAWGs for Forward and Backward Tries.
  4. Towards a Definitive Measure of Repetitiveness.

SEA 2020

  1. Fast and Linear-Time String Matching Algorithms Based on the Distances of q-Gram Occurrences.
  2. Fast and Simple Compact Hashing via Bucketing.
  3. Indexing Compressed Text: A Tale of Time and Space (Invited Talk).
  4. Pattern Discovery in Colored Strings.
  5. Zipping Segment Trees.

SODA 2020

  1. A Lower Bound for Jumbled Indexing.
  2. Better Data Structures for Colored Orthogonal Range Reporting.
  3. Combinatorial generation via permutation languages.
  4. Competitive Online Search Trees on Trees.
  5. Improved Algorithms for Edit Distance and LCS: Beyond Worst Case.
  6. Locally Consistent Parsing for Text Indexing in Small Space.
  7. Reducing approximate Longest Common Subsequence to approximate Edit Distance.
  8. Regular Languages meet Prefix Sorting.

SOFSEM 2020

  1. Fast Indexes for Gapped Pattern Matching.
  2. Faster STR-EC-LCS Computation.
  3. Minimal Unique Substrings and Minimal Absent Words in a Sliding Window.
  4. Parallel Duel-and-Sweep Algorithm for the Order-Preserving Pattern Matching.

SOSA 2020

  1. Bucket Oblivious Sort: An Extremely Simple Oblivious Sort.

SPIRE 2020

  1. A Comparison of Empirical Tree Entropies.
  2. Adaptive Exact Learning in a Mixed-Up World: Dealing with Periodicity, Errors and Jumbled-Index Queries in String Reconstruction.
  3. An Efficient Elastic-Degenerate Text Index? Not Likely.
  4. Approximating the Anticover of a String.
  5. Computing Covers Under Substring Consistent Equivalence Relations.
  6. Contextual Pattern Matching.
  7. Efficient Construction of Hierarchical Overlap Graphs.
  8. Efficient Enumeration of Distinct Factors Using Package Representations.
  9. Internal Quasiperiod Queries.
  10. Longest Square Subsequence Problem Revisited.
  11. Lyndon Words, the Three Squares Lemma, and Primitive Squares.
  12. Measuring Controversy in Social Networks Through NLP.
  13. Multidimensional Period Recovery.
  14. Navigating Forest Straight-Line Programs in Constant Time.
  15. On Repetitiveness Measures of Thue-Morse Words.
  16. Practical Random Access to SLP-Compressed Texts.
  17. Pre-indexing Pruning Strategies.
  18. Relative Lempel-Ziv Compression of Suffix Arrays.
  19. Smaller Fully-Functional Bidirectional BWT Indexes.
  20. Tailoring r-index for Document Listing Towards Metagenomics Applications.
  21. Towards Efficient Interactive Computation of Dynamic Time Warping Distance.

STACS 2020

  1. A Sub-Quadratic Algorithm for the Longest Common Increasing Subsequence Problem.
  2. Generalised Pattern Matching Revisited.
  3. Non-Rectangular Convolutions and (Sub-)Cadences with Three Elements.
  4. String Indexing with Compressed Patterns.
  5. Using Statistical Encoding to Achieve Tree Succinctness Never Seen Before.

STOC 2020

  1. Approximating text-to-pattern Hamming distances.
  2. Constant factor approximations to edit distance on far input pairs in nearly linear time.
  3. Constant-factor approximation of near-linear edit distance in near-linear time.
  4. Lower bound for succinct range minimum query.
  5. Nearly optimal static Las Vegas succinct dictionary.

SWAT 2020

  1. Space-Efficient Data Structures for Lattices.

SoCG 2020

  1. Four-Dimensional Dominance Range Reporting in Linear Space.
  2. Further Results on Colored Range Searching.

Stringology 2020

  1. Conversion of Finite Tree Automata to Regular Tree Expressions By State Elimination.
  2. Enumerative Data Compression with Non-Uniquely Decodable Codes.
  3. Fast Exact Pattern Matching in a Bitstream and 256-ary Strings.
  4. Fast Practical Computation of the Longest Common Cartesian Substrings of Two Strings.
  5. Forward Linearised Tree Pattern Matching Using Tree Pattern Border Array.
  6. Greedy versus Optimal Analysis of Bounded Size Dictionary Compression and On-the-Fly Distributed Computing.
  7. Left Lyndon Tree Construction.
  8. New Compression Schemes for Natural Number Sequences.
  9. On Arithmetically Progressed Suffix Arrays.
  10. Pointer-Machine Algorithms for Fully-Online Construction of Suffix Trees and DAWGs on Multiple Strings.
  11. Re-Pair in Small Space.
  12. Reducing Time and Space in Indexed String Matching by Characters Distance Text Sampling.
  13. Simple KMP Pattern-Matching on Indeterminate Strings.
  14. Tune-up for the Dead-Zone Algorithm.

TAMC 2020

  1. Partial Sums on the Ultra-Wide Word RAM.

WABI 2020

  1. Linear Time Construction of Indexable Founder Block Graphs.

WALCOM 2020

  1. Fast Multiple Pattern Cartesian Tree Matching.
  2. Faster Privacy-Preserving Computation of Edit Distance with Moves.
  3. Generalized Dictionary Matching Under Substring Consistent Equivalence Relations.
  4. Shortest Covers of All Cyclic Shifts of a String.

ACM J. Exp. Algorithmics 2020

  1. Dynamic Path-decomposed Tries.
  2. Property Suffix Array with Applications in Indexing Weighted Sequences.

ACM Trans. Algorithms 2020

  1. A Linear-Time Algorithm for Seeds Computation.
  2. Deterministic Sparse Suffix Sorting in the Restore Model.
  3. Linear-time String Indexing and Analysis in Small Space.
  4. Tree Edit Distance Cannot be Computed in Strongly Subcubic Time (Unless APSP Can).

Algorithmica 2020

  1. Compressed Dynamic Range Majority and Minority Data Structures.
  2. Computational Aspects of Ordered Integer Partitions with Bounds.
  3. Dynamic and Internal Longest Common Substring.
  4. Fast Compressed Self-indexes with Deterministic Linear-Time Construction.
  5. Fully-Online Suffix Tree and Directed Acyclic Word Graph Construction for Multiple Texts.
  6. Lempel-Ziv-Like Parsing in Small Space.

Algorithms 2020

  1. A New Lossless DNA Compression Algorithm Based on A Single-Block Encoding Scheme.
  2. Editorial: Special Issue on Data Compression Algorithms and Their Applications.
  3. Efficient Data Structures for Range Shortest Unique Substring Queries.
  4. More Time-Space Tradeoffs for Finding a Shortest Unique Substring.
  5. Practical Grammar Compression Based on Maximal Repeats.

Algorithms Mol. Biol. 2020

  1. Finding all maximal perfect haplotype blocks in linear time.
  2. gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections.

BMC Bioinform. 2020

  1. Variable-order reference-free variant discovery with the Burrows-Wheeler Transform.

Bioinform. 2020

  1. SMART: SuperMaximal approximate repeats tool.

CoRR 2020

  1. $O(\log \log n)$ Worst-Case Local Decoding and Update Efficiency for Data Compression.
  2. 2-Dimensional Palindromes with k Mismatches.
  3. A Big Data Approach for Sequences Indexing on the Cloud via Burrows Wheeler Transform.
  4. A Case for Partitioned Bloom Filters.
  5. A Data-Structure for Approximate Longest Common Subsequence of A Set of Strings.
  6. A Dynamic Space-Efficient Filter with Constant Time Operations.
  7. A Fast Algorithm for Online k-servers Problem on Trees.
  8. A Fast Randomized Algorithm for Finding the Maximal Common Subsequences.
  9. A Faster Subquadratic Algorithm for the Longest Common Increasing Subsequence Problem.
  10. A Hybrid Approach to Temporal Pattern Matching.
  11. A New Approach to Regular & Indeterminate Strings.
  12. A New Upper Bound for Separating Words.
  13. A Normal Sequence Compressed by PPM* but not by Lempel-Ziv 78.
  14. A Pedagogically Sound yet Efficient Deletion algorithm for Red-Black Trees: The Parity-Seeking Delete Algorithm.
  15. A Simple Sublinear Algorithm for Gap Edit Distance.
  16. A Tale of Two Trees: New Analysis for AVL Tree and Binary Heap.
  17. A grammar compressor for collections of reads with applications to the construction of the BWT.
  18. A reduction of the dynamic time warping distance to the longest increasing subsequence length.
  19. Access-Adaptive Priority Search Tree.
  20. Adaptive Fibonacci and Pairing Heaps.
  21. Age-Partitioned Bloom Filters.
  22. An Efficient Implementation of Manacher’s Algorithm.
  23. An Improved Algorithm for Dynamic Set Cover.
  24. An Improved Sketching Bound for Edit Distance.
  25. An inequality for the number of periods in a word.
  26. Analysis and Evaluation of Non-Blocking Interpolation Search Trees.
  27. Approximating LCS in Linear Time: Beating the √n Barrier.
  28. Approximating Optimal Bidirectional Macro Schemes.
  29. Approximating Text-to-Pattern Distance via Dimensionality Reduction.
  30. Approximating Text-to-Pattern Hamming Distances.
  31. Approximating longest common substring with $k$ mismatches: Theory and practice.
  32. Arithmetic Binary Search Trees: Static Optimality in the Matching Model.
  33. Beyond the Worst-Case Analysis of Algorithms (Introduction).
  34. Bitvectors with runs and the successor/predecessor problem.
  35. Black-White Array: A New Data Structure for Dynamic Data Sets.
  36. Blocksequences of k-local Words.
  37. Breadth-First Rank/Select in Succinct Trees and Distance Oracles for Interval Graphs.
  38. Bucket Oblivious Sort: An Extremely Simple Oblivious Sort.
  39. Cadences in Grammar-Compressed Strings.
  40. Chaining with overlaps revisited.
  41. Chronofold: a data structure for versioned text.
  42. Classical and Quantum Algorithms for Constructing Text from Dictionary Problem.
  43. Communication-Efficient String Sorting.
  44. Competitive Data-Structure Dynamization.
  45. Compressed Data Structures for Binary Relations in Practice.
  46. Compression with wildcards: All spanning trees.
  47. Computing Covers under Substring Consistent Equivalence Relations.
  48. Computing Palindromic Trees for a Sliding Window and Its Applications.
  49. Computing the rearrangement distance of natural genomes.
  50. Concurrent Disjoint Set Union.
  51. Contextual Pattern Matching.
  52. Counting 4-Patterns in Permutations Is Equivalent to Counting 4-Cycles in Graphs.
  53. Counting Distinct Patterns in Internal Dictionary Matching.
  54. Counting ternary square-free words quickly.
  55. DAWGs for parameterized matching: online construction and related indexing structures.
  56. Data Structure Primitives on Persistent Memory: An Evaluation.
  57. Decode efficient prefix codes.
  58. Detecting k-(Sub-)Cadences and Equidistant Subsequence Occurrences.
  59. Dynamic Boundary Time Warping for Sub-sequence Matching with Few Examples.
  60. Dynamic Longest Common Substring in Polylogarithmic Time.
  61. Dynamic Similarity Search on Integer Sketches.
  62. Edit Distance in Near-Linear Time: it’s a Constant Factor.
  63. Efficient Constrained Pattern Mining Using Dynamic Item Ordering for Explainable Classification.
  64. Efficient Semi-External Depth-First Search.
  65. Efficient and Effective Query Auto-Completion.
  66. Efficient constructions of the Prefer-same and Prefer-opposite de Bruijn sequences.
  67. Efficient tree-structured categorical retrieval.
  68. Efficiently Testing Simon’s Congruence.
  69. Engineering Faster Sorters for Small Sets of Items.
  70. Enumeration of LCP values, LCP intervals and Maximal repeats in BWT-runs Bounded Space.
  71. Erdös-Szekeres Partitioning Problem.
  72. Extremal overlap-free and extremal β-free binary words.
  73. Fast Generation of Big Random Binary Trees.
  74. Fast Indexes for Gapped Pattern Matching.
  75. Fast Preprocessing for Optimal Orthogonal Range Reporting and Range Successor with Applications to Text Indexing.
  76. Fast and Simple Modular Subset Sum.
  77. Fast and linear-time string matching algorithms based on the distances of q-gram occurrences.
  78. Faster Approximate Pattern Matching: A Unified Approach.
  79. Faster Binary Mean Computation Under Dynamic Time Warping.
  80. Faster Queries on BWT-runs Compressed Indexes.
  81. Faster STR-EC-LCS Computation.
  82. Fine-Grained Complexity of Regular Expression Pattern Matching and Membership.
  83. Four-Dimensional Dominance Range Reporting in Linear Space.
  84. Fully Dynamic Approximation of LIS in Polylogarithmic Time.
  85. Further Results on Colored Range Searching.
  86. Galloping in natural merge sorts.
  87. Generalised Pattern Matching Revisited.
  88. Generalized Sorting with Predictions.
  89. Generating a Gray code for prefix normal words in amortized polylogarithmic time per word.
  90. Grammar Compression By Induced Suffix Sorting.
  91. Grammar compression with probabilistic context-free grammar.
  92. Grammar-Compressed Indexes with Logarithmic Search Time.
  93. Grammar-compressed Self-index with Lyndon Words.
  94. Greedy-reduction from Shortest Linear Superstring to Shortest Circular Superstring.
  95. Hidden Words Statistics for Large Patterns.
  96. Huskysort.
  97. Impossibility Results for Grammar-Compressed Linear Algebra.
  98. Improved Circular k-Mismatch Sketches.
  99. Improved Dynamic Algorithms for Longest Increasing Subsequence.
  100. In-Place Bijective Burrows-Wheeler Transforms.
  101. Incremental Multiple Longest Common Sub-Sequences.
  102. Indexing Highly Repetitive String Collections.
  103. Integer Division by Constants: Optimal Bounds.
  104. Internal Quasiperiod Queries.
  105. LCP-Aware Parallel String Sorting.
  106. Lazy Search Trees.
  107. Learning Directly from Grammar Compressed Text.
  108. Learning Halfspaces With Membership Queries.
  109. Left Lyndon tree construction.
  110. Lengths of extremal square-free ternary words.
  111. Linear Time Construction of Indexable Founder Block Graphs.
  112. Local Editing in LZ-End Compressed Data.
  113. Locality-Sensitive Hashing Scheme based on Longest Circular Co-Substring.
  114. Longest Common Subsequence in Sublinear Space.
  115. Longest Square Subsequence Problem Revisited.
  116. Lossless Compression of Deep Neural Networks.
  117. Lower Bound for Succinct Range Minimum Query.
  118. Lyndon Words, the Three Squares Lemma, and Primitive Squares.
  119. Multiset Synchronization with Counting Cuckoo Filters.
  120. Near-Linear Time Edit Distance for Indel Channels.
  121. New Algorithms and Lower Bounds for LIS Estimation.
  122. New Approximation Algorithms for Maximum Asymmetric Traveling Salesman and Shortest Superstring.
  123. New Data Structures for Orthogonal Range Reporting and Range Minima Queries.
  124. No Repetition: Fast Streaming with Highly Concentrated Hashing.
  125. Notes on Randomized Algorithms.
  126. Novel Results on the Number of Runs of the Burrows-Wheeler-Transform.
  127. On Extensions of Maximal Repeats in Compressed Strings.
  128. On Indexing and Compressing Finite Automata.
  129. On Locating Paths in Compressed Cardinal Trees.
  130. On One-way Functions and Kolmogorov Complexity.
  131. On Rearrangement of Items Stored in Stacks.
  132. On Two Measures of Distance between Fully-Labelled Trees.
  133. On Weighted Prefix Normal Words.
  134. On prefix palindromic length of automatic words.
  135. On repetitiveness measures of Thue-Morse words.
  136. On the binomial equivalence classes of finite words.
  137. On the improvement of the in-place merge algorithm parallelization.
  138. On the parameterized complexity of the Minimum Path Cover problem in DAGs.
  139. Optimal Entropy Compression and Purification in Quantum Bits.
  140. Optimal Skeleton Huffman Trees Revisited.
  141. Optimal construction of a layer-ordered heap.
  142. Optimal selection on X+Y simplified with layer-ordered heaps.
  143. PFP Data Structures.
  144. PHONI: Streamed Matching Statistics with Multi-Genome References.
  145. Palindromic Length of Words with Many Periodic Palindromes.
  146. Palindromic k-Factorization in Pure Linear Time.
  147. Pattern Discovery in Colored Strings.
  148. Pattern Masking for Dictionary Matching.
  149. Pointer-Machine Algorithms for Fully-Online Construction of Suffix Trees and DAWGs on Multiple Strings.
  150. Primitive Sets of Words.
  151. Pushdown and Lempel-Ziv Depth.
  152. Quantum Algorithm for Lexicographically Minimal String Rotation.
  153. Quantum Algorithms for the Most Frequently String Search, Intersection of Two String Sequences and Sorting of Strings Problems.
  154. Quantum Lower and Upper Bounds for 2D-Grid and Dyck Language.
  155. Quantum string comparison method.
  156. Random Access in Persistent Strings.
  157. Reconstructing Words from Right-Bounded-Block Words.
  158. Revisiting compact RDF stores based on k2-trees.
  159. SARS-CoV-2 Coronavirus Data Compression Benchmark.
  160. SOPanG 2: online searching over a pan-genome without false positives.
  161. Scattered Factor-Universality of Words.
  162. Scout Algorithm For Fast Substring Matching.
  163. Searching and Sorting with O(n2) processors in O(1) time.
  164. Selectable Heaps and Optimal Lazy Search Trees.
  165. Semantrix: A Compressed Semantic Matrix.
  166. Shorter Labels for Routing in Trees.
  167. Simulation computation in grammar-compressed graphs.
  168. Small Longest Tandem Scattered Subsequences.
  169. Soft Sequence Heaps.
  170. Solving Shisen-Sho boards.
  171. Sorting Lists with Equal Keys Using Mergesort in Linear Time.
  172. Sorting Short Keys in Circuits of Size o(n log n).
  173. Space Efficient Deterministic Approximation of String Measures.
  174. Space efficient merging of de Bruijn graphs and Wheeler graphs.
  175. Space/time-efficient RDF stores based on circular suffix sorting.
  176. Splay trees on trees.
  177. Still Simpler Static Level Ancestors.
  178. Storing Set Families More Compactly with Top ZDDs.
  179. Streaming with Oracle: New Streaming Algorithms for Edit Distance and LCS.
  180. String Attractors for Automatic Sequences.
  181. String Indexing for Top-k Close Consecutive Occurrences.
  182. String Sanitization Under Edit Distance: Improved and Generalized.
  183. Subcubic Algorithms for Gomory-Hu Tree in Unweighted Graphs.
  184. Sublinear-Time Algorithms for Computing & Embedding Gap Edit Distance.
  185. Subpath Queries on Compressed Graphs: a Survey.
  186. Substring Complexity in Sublinear Space.
  187. Substring Query Complexity of String Reconstruction.
  188. Succinct Dynamic Ordered Sets with Random Access.
  189. Succinct Trit-array Trie for Scalable Trajectory Similarity Search.
  190. Sumsets of Wythoff Sequences, Fibonacci Representation, and Beyond.
  191. TADOC: Text Analytics Directly on Compression.
  192. Tailoring r-index for metagenomics.
  193. The Bloom Tree.
  194. The Edit Distance to k-Subsequence Universality.
  195. The K-Centre Problem for Necklaces.
  196. The Longest Run Subsequence Problem: Further Complexity Results.
  197. The Number of Repetitions in 2D-Strings.
  198. The Parameterized Suffix Tray.
  199. The Simplest Binary Word with Only Three Squares.
  200. The Streaming k-Mismatch Problem: Tradeoffs between Space and Total Time.
  201. The n-dimensional k-vector and its application to orthogonal range searching.
  202. Tight Bound for the Number of Distinct Palindromes in a Tree.
  203. Time-Space Tradeoffs for Finding a Long Common Substring.
  204. Towards Efficient Interactive Computation of Dynamic Time Warping Distance.
  205. Translating Between Wavelet Tree and Wavelet Matrix Construction.
  206. Two halves of a meaningful text are statistically different.
  207. Uniform Linked Lists Contraction.
  208. Update Query Time Trade-off for dynamic Suffix Arrays.
  209. Wheeler Languages.
  210. Zipping Segment Trees.
  211. Zuckerli: A New Compressed Representation for Graphs.
  212. k-Approximate Quasiperiodicity under Hamming and Edit Distance.

Discret. Appl. Math. 2020

  1. A brief history of parameterized matching problems.
  2. A formal framework for Stringology.
  3. A resource-frugal probabilistic dictionary and applications in bioinformatics.
  4. Accelerated partial decoding in wavelet trees.
  5. Direct merging of delta encoded files.
  6. Dynamic determination of variable sizes of chunks in a deduplication system.
  7. Dynamic index and LZ factorization in compressed space.
  8. Generating all minimal petri net unsolvable binary words.
  9. Improved online algorithms for jumbled matching.
  10. On approximate enhanced covers under Hamming distance.
  11. On the computational complexity of closest genome problems.
  12. Preface: Stringology Algorithms.
  13. The order-preserving pattern matching problem in practice.

Fundam. Informaticae 2020

  1. Comparing Degenerate Strings.

Inf. 2020

  1. On the Randomness of Compressed Data.

Inf. Comput. 2020

  1. A compressed dynamic self-index for highly repetitive text collections.
  2. Absent words in a sliding window with applications.
  3. Compact and succinct data structures for multidimensional orthogonal range searching.
  4. Computation over compressed data.
  5. Indexing weighted sequences: Neat and efficient.
  6. Online recognition of dictionary with one gap.
  7. Streaming k-mismatch with error correcting and applications.
  8. String periods in the order-preserving model.

Int. J. Found. Comput. Sci. 2020

  1. Efficient Identification of k-Closed Strings.

J. ACM 2020

  1. Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space.

J. Comput. Biol. 2020

  1. Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.
  2. Matching Reads to Many Genomes with the r-Index.

J. Signal Process. Syst. 2020

  1. An Efficient High-Throughput LZ77-Based Decompressor in Reconfigurable Logic.

Proc. VLDB Endow. 2020

  1. The PGM-index: a fully-dynamic compressed learned index with provable worst-case bounds.

Theor. Comput. Sci. 2020

  1. A linear-space data structure for range-LCP queries in poly-logarithmic time.
  2. Approximate pattern matching on elastic-degenerate text.
  3. Compressed range minimum queries.
  4. Efficient computation of longest single-arm-gapped palindromes in a string.
  5. Faster algorithms for 1-mappability of a sequence.
  6. Finding patterns and periods in Cartesian tree matching.
  7. Generating a Gray code for prefix normal words in amortized polylogarithmic time per word.
  8. Lightweight merging of compressed indices based on BWT variants.
  9. Longest property-preserved common factor: A new string-processing framework.
  10. Parallel computation of the Burrows Wheeler Transform in compact space.
  11. Refining the r-index.
  12. Space-efficient algorithms for computing minimal/shortest unique substrings.
  13. The Alternating BWT: An algorithmic perspective.
  14. Tree path majority data structures.
  15. Two-dimensional maximal repetitions.
  16. Universal reconstruction of a string.

Theory Comput. Syst. 2020

  1. Fast Algorithms for the Shortest Unique Palindromic Substring Problem on Run-Length Encoded Strings.

ALENEX 2019

  1. Lightweight Distributed Suffix Array Construction.

CIAC 2019

  1. The Parameterized Position Heap of a Trie.

CIKM 2019

  1. Improved Compressed String Dictionaries.

CPM 2019

  1. A 2-Approximation Algorithm for the Complementary Maximal Strip Recovery Problem.
  2. A New Class of Searchable and Provably Highly Compressible String Transformations.
  3. A Rearrangement Distance for Fully-Labelled Trees.
  4. Approximating Approximate Pattern Matching.
  5. Cartesian Tree Matching and Indexing.
  6. Compressed Multiple Pattern Matching.
  7. Computing Runs on a Trie.
  8. Computing the Antiperiod(s) of a String.
  9. Conversion from RLBWT to LZ77.
  10. Dichotomic Selection on Words: A Probabilistic Analysis.
  11. Entropy Lower Bounds for Dictionary Compression.
  12. Faster Queries for Longest Substring Palindrome After Block Edit.
  13. Finding a Small Number of Colourful Components.
  14. Front Matter, Table of Contents, Preface, Conference Organization.
  15. Fully-Functional Bidirectional Burrows-Wheeler Indexes and Infinite-Order De Bruijn Graphs.
  16. Hamming Distance Completeness.
  17. How to Exploit Periodicity (Invited Talk).
  18. Indexing the Bijective BWT.
  19. Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding.
  20. On Maximal Repeats in Compressed Strings.
  21. On the Size of Overlapping Lempel-Ziv and Lyndon Factorizations.
  22. Online Algorithms for Constructing Linear-Size Suffix Trie.
  23. Optimal Rank and Select Queries on Dictionary-Compressed Text.
  24. Quasi-Linear-Time Algorithm for Longest Common Circular Factor.
  25. Quasi-Periodicity in Streams.
  26. Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding.
  27. Searching Long Repeats in Streams.
  28. Simulating the DNA Overlap Graph in Succinct Space.
  29. Some Variations on Lyndon Words (Invited Talk).
  30. Space-Efficient Computation of the LCP Array from the Burrows-Wheeler Transform.
  31. Streaming Dictionary Matching with Mismatches.
  32. Stringology Combats Microbiological Threats (Invited Talk).
  33. Sufficient Conditions for Efficient Indexing Under Different Matchings.

DCC 2019

  1. A Compact Representation of Raster Time Series.
  2. A New Technique for Lossless Compression of Color Images Based on Hierarchical Prediction, Inversion and Context Adaptive Coding.
  3. BWT Tunnel Planning is Hard But Manageable.
  4. Better Than Optimal Huffman Coding?
  5. Constructing Antidictionaries in Output-Sensitive Space.
  6. Dv2v: A Dynamic Variable-to-Variable Compressor.
  7. Generalized Word Equations: A New Approach to Data Compresion.
  8. LZRR: LZ77 Parsing with Right Reference.
  9. Light Field Image Compression with Random Access.
  10. MR-RePair: Grammar Compression Based on Maximal Repeats.
  11. Multidimensional Compression with Pattern Matching.
  12. Numerical Pattern Mining Through Compression.
  13. On Lempel-Ziv Decompression in Small Space.
  14. On the Randomness of Compressed Data.
  15. Parameterized Text Indexing with One Wildcard.
  16. Practical Indexing of Repetitive Collections Using Relative Lempel-Ziv.
  17. RePair in Compressed Space and Time.
  18. Regular Expression Search on Compressed Text.
  19. Selective Dynamic Compression.
  20. Space-Efficient Computation of the Burrows-Wheeler Transform.
  21. Tunneling on Wheeler Graphs.
  22. Vectorizing Fast Compression.

DEXA (2) 2019

  1. Succinct BWT-Based Sequence Prediction.

DLT 2019

  1. Computing the k-binomial Complexity of the Thue-Morse Word.
  2. First Lower Bounds for Palindromic Length.
  3. On Palindromic Length of Sturmian Sequences.
  4. On the Length of Shortest Strings Accepted by Two-Way Finite Automata.
  5. Separating Many Words by Counting Occurrences of Factors.
  6. The Relative Edit-Distance Between Two Input-Driven Languages.
  7. k-Spectra of Weakly-c-Balanced Words.

ECML/PKDD (1) 2019

  1. String Sanitization: A Combinatorial Approach.

ESA 2019

  1. Bidirectional Text Compression in External Memory.
  2. Longest Common Substring Made Fully Dynamic.
  3. On the Hardness and Inapproximability of Recognizing Wheeler Graphs.
  4. Repetition Detection in a Dynamic String.

FCT 2019

  1. Circular Pattern Matching with k Mismatches.

FOCS 2019

  1. Approximation Algorithms for LCS and LIS with Truly Improved Running Times.
  2. Balancing Straight-Line Programs.
  3. Optimal Document Exchange and New Codes for Insertions and Deletions.
  4. Sublinear Algorithms for Gap Edit Distance.
  5. Why are Proof Complexity Lower Bounds Hard?

ICALP 2019

  1. Dynamic Ordered Sets with Approximate Queries, Approximate Heaps and Soft Heaps.
  2. Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication.

INNSBDDL (Tutorials) 2019

  1. Learned Data Structures.

ISAAC 2019

  1. An Improved Data Structure for Left-Right Maximal Generic Words Problem.
  2. Internal Dictionary Matching.
  3. On Approximate Range Mode and Range Selection.
  4. Top Tree Compression of Tries.

ITCS 2019

  1. Testing Local Properties of Arrays.

IWOCA 2019

  1. Burrows-Wheeler Transform of Words Defined by Morphisms.
  2. Finding Periods in Cartesian Tree Matching.
  3. Shortest Unique Palindromic Substring Queries on Run-Length Encoded Strings.

LATA 2019

  1. Automata over Infinite Sequences of Reals.
  2. Efficient Representation and Counting of Antipower Factors in Words.
  3. Generalized Register Context-Free Grammars.
  4. On the Maximum Number of Distinct Palindromic Sub-arrays.
  5. Palindromic Subsequences in Finite Words.
  6. Recurrence in Multidimensional Words.
  7. Regular Matching and Inclusion on Compressed Tree Patterns with Context Variables.

MFCS 2019

  1. A Constant-Time Colored Choice Dictionary with Almost Robust Iteration.
  2. From Regular Expression Matching to Parsing.
  3. Indexing Graph Search Trees and Applications.
  4. RLE Edit Distance in Near Optimal Time.
  5. The Power Word Problem.
  6. Uniform Random Expressions Lack Expressivity.
  7. Upper Bounds on the Length of Minimal Solutions to Certain Quadratic Word Equations.

RECOMB 2019

  1. Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.

SEA² 2019

  1. Searching for Best Karatsuba Recurrences.

SODA 2019

  1. Efficiently Approximating Edit Distance Between Pseudorandom Strings.
  2. Few Matches or Almost Periodicity: Faster Pattern Matching with Mismatches in Compressed Texts.
  3. List Decoding with Double Samplers.
  4. Lower Bounds for Oblivious Data Structures.
  5. Lower bounds for text indexing with mismatches and differences.
  6. Optimal Construction of Compressed Indexes for Highly Repetitive Texts.
  7. Synchronization Strings: Highly Efficient Deterministic Constructions over Small Alphabets.
  8. The streaming k-mismatch problem.

SOFSEM 2019

  1. On Infinite Prefix Normal Words.

SPIRE 2019

  1. A New Linear-Time Algorithm for Centroid Decomposition.
  2. A Practical Alphabet-Partitioning Rank/Select Data Structure.
  3. Adaptive Succinctness.
  4. An Index for Sequencing Reads Based on the Colored de Bruijn Graph.
  5. An Optimal Algorithm to Find Champions of Tournament Graphs.
  6. Approximation Ratios of RePair, LongestMatch and Greedy on Unary Strings.
  7. BM25 Beyond Query-Document Similarity.
  8. Bounds and Estimates on the Average Edit Distance.
  9. COBS: A Compact Bit-Sliced Signature Index.
  10. Compact Data Structures for Shortest Unique Substring Queries.
  11. Direct Linear Time Construction of Parameterized Suffix and LCP Arrays for Constant Alphabets.
  12. Fast Cartesian Tree Matching.
  13. Fast Identification of Heavy Hitters by Cached and Packed Group Testing.
  14. Fast, Small, and Simple Document Listing on Repetitive Text Collections.
  15. Faster Dynamic Compressed d-ary Relations.
  16. Faster Repetition-Aware Compressed Suffix Trees Based on Block Trees.
  17. Implementing the Topological Model Succinctly.
  18. Inducing the Lyndon Array.
  19. Linear Time Maximum Segmentation Problems in Column Stream Model.
  20. Lossless Image Compression Using List Update Algorithms.
  21. Minimal Absent Words in Rooted and Unrooted Trees.
  22. Network-Based Pooling for Topic Modeling on Microblog Content.
  23. On Longest Common Property Preserved Substring Queries.
  24. On the Computation of Longest Previous Non-overlapping Factors.
  25. Online Algorithms on Antipowers and Antiperiods.
  26. Parallel External Memory Wavelet Tree and Wavelet Matrix Construction.
  27. Polynomial-Delay Enumeration of Maximal Common Subsequences.
  28. Position Bias Estimation for Unbiased Learning-to-Rank in eCommerce Search.
  29. Range Shortest Unique Substring Queries.
  30. Rpair: Rescaling RePair with Rsync.
  31. Run-Length Encoding in a Finite Universe.
  32. SACABench: Benchmarking Suffix Array Construction.
  33. Searching Runs in Streams.
  34. Space- and Time-Efficient Storage of LiDAR Point Clouds.
  35. Space-Efficient Merging of Succinct de Bruijn Graphs.
  36. Weighted Shortest Common Supersequence Problem Revisited.

STACS 2019

  1. Constant-Time Retrieval with O(log m) Extra Bits.
  2. Depth First Search in the Semi-streaming Model.
  3. Fast and Longest Rollercoasters.

STOC 2019

  1. Local decodability of the Burrows-Wheeler transform.
  2. Optimal succinct rank data structure via approximate nonnegative tensor decomposition.
  3. String synchronizing sets: sublinear-time BWT construction and optimal LCE data structure.

Stringology 2019

  1. k-Abelian Pattern Matching: Revisited, Corrected, and Extended.
  2. A Fast SIMD-Based Chunking Algorithm.
  3. Algorithms to Compute the Lyndon Array Revisited.
  4. An Improvement of the Franek-Jennings-Smyth Pattern Matching Algorithm.
  5. Bidirectional Adaptive Compression.
  6. Computing Maximal Palindromes and Distinct Palindromes in a Trie.
  7. Lexicalized Syntactic Analysis by Restarting Automata.
  8. Online Parameterized Dictionary Matching with One Gap.
  9. Optimal Time and Space Construction of Suffix Arrays and LCP Arrays for Integer Alphabets.
  10. Pattern Matching on Weighted Strings.
  11. Selective Dynamic Compression.
  12. Translating Between Wavelet Tree and Wavelet Matrix Construction.

WABI 2019

  1. Finding All Maximal Perfect Haplotype Blocks in Linear Time.

WADS 2019

  1. Dynamic Dictionary Matching in the Online Model.
  2. Orthogonal Range Reporting and Rectangle Stabbing for Fat Rectangles.

WALCOM 2019

  1. Applications of V-Order: Suffix Arrays, the Burrows-Wheeler Transform & the FM-index.

WORDS 2019

  1. Generalized Lyndon Factorizations of Infinite Words.
  2. Matching Patterns with Variables.
  3. Repetitions in Infinite Palindrome-Rich Words.

ACM J. Exp. Algorithmics 2019

  1. Better External Memory LCP Array Construction.

ACM Trans. Algorithms 2019

  1. Sparse Dynamic Programming on DAGs with Small Width.

ACM Trans. Inf. Syst. 2019

  1. Brotli: A General-Purpose Data Compressor.

Algorithmica 2019

  1. Can We Recover the Cover?
  2. Correction to: Longest Common Substring with Approximately k Mismatches.
  3. Fixed Block Compression Boosting in FM-Indexes: Theory and Practice.
  4. Longest Common Substring with Approximately k Mismatches.
  5. Mind the Gap! - Online Dictionary Matching with One Gap.
  6. Tight Tradeoffs for Real-Time Approximation of Longest Palindromes in Streams.

Algorithms 2019

  1. Compaction of Church Numerals.
  2. Space-Efficient Fully Dynamic DFS in Undirected Graphs.

Algorithms Mol. Biol. 2019

  1. External memory BWT and LCP computation for sequence collections with applications.
  2. Linear time minimum segmentation enables scalable founder reconstruction.
  3. Prefix-free parsing for building big BWTs.
  4. SNPs detection by eBWT positional clustering.

Bioinform. 2019

  1. A framework for space-efficient variable-order Markov models.
  2. Compressed filesystem for managing large genome collections.
  3. Fully-sensitive seed finding in sequence graphs using a hybrid index.

CoRR 2019

  1. 3SUM with Preprocessing: Algorithms, Lower Bounds and Cryptographic Applications.
  2. A Compact Representation of Raster Time Series.
  3. A Detailed Analysis of Quicksort Algorithms with Experimental Mathematics.
  4. A Memory-Efficient Sketch Method for Estimating High Similarities in Streaming Sets.
  5. A New Class of Searchable and Provably Highly Compressible String Transformations.
  6. A New Deterministic Algorithm for Dynamic Set Cover.
  7. A New Lower Bound for Semigroup Orthogonal Range Searching.
  8. A Simple Reduction for Full-Permuted Pattern Matching Problems on Multi-Track Strings.
  9. A Simple Solution to the Level-Ancestor Problem.
  10. A fast algorithm for constructing balanced binary search trees.
  11. A multidimensional analog to the Burrows-Wheeler transform.
  12. A randomized strategy in the mirror game.
  13. A study for Image compression using Re-Pair algorithm.
  14. A sub-quadratic algorithm for the longest common increasing subsequence problem.
  15. ALLSAT compressed with wildcards: Frequent Set Mining.
  16. Abelian periods of factors of Sturmian words.
  17. Abelian-square factors and binary words.
  18. About Fibonacci trees. I.
  19. Algorithms to compute the Burrows-Wheeler Similarity Distribution.
  20. An Average-Compress Algorithm for the Sample Mean Problem under Dynamic Time Warping.
  21. An Efficient Word Lookup System by using Improved Trie Algorithm.
  22. An Incompressibility Theorem for Automatic Complexity.
  23. An Index for Sequencing Reads Based on The Colored de Bruijn Graph.
  24. An efficient sorting algorithm - Ultimate Heapsort(UHS).
  25. An in-place, subquadratic algorithm for permutation inversion.
  26. Analyzing Trade-offs in Reversible Linear and Binary Search Algorithms.
  27. Apply Sorting Algorithms to FAST Problem.
  28. Approximate Similarity Search Under Edit Distance Using Locality-Sensitive Hashing.
  29. Approximating the Geometric Edit Distance.
  30. Balancing Straight-Line Programs.
  31. Belga B-trees.
  32. Beyond the Inverted Index.
  33. Bidirectional Text Compression in External Memory.
  34. Bloom filter variants for multiple sets: a comparative assessment.
  35. Borders, Palindrome Prefixes, and Square Prefixes.
  36. Cache-Friendly Search Trees; or, In Which Everything Beats std: : set.
  37. Cartesian Tree Matching and Indexing.
  38. Characteristic Parameters and Special Trapezoidal Words.
  39. Circ-Tree: A B+-Tree Variant with Circular Design for Persistent Memory.
  40. Circular Pattern Matching with k Mismatches.
  41. Communication cost of consensus for nodes with limited memory.
  42. Compact Data Structures for Shortest Unique Substring Queries.
  43. Compact Fenwick trees for dynamic ranking and selection.
  44. Compacted binary trees admit a stretched exponential.
  45. Competitive Online Search Trees on Trees.
  46. Compressed Indexes for Fast Search of Semantic Data.
  47. Compressed Range Minimum Queries.
  48. Computing runs on a trie.
  49. Constant Delay Traversal of Grammar-Compressed Graphs with Bounded Rank.
  50. Constant factor approximations to edit distance on far input pairs in nearly linear time.
  51. Constant-factor approximation of near-linear edit distance in near-linear time.
  52. Constrained Orthogonal Segment Stabbing.
  53. Constructing Antidictionaries in Output-Sensitive Space.
  54. Constructing the Bijective BWT.
  55. Conversion from RLBWT to LZ77.
  56. Convex Graph Invariant Relaxations For Graph Edit Distance.
  57. Counting Small Permutation Patterns.
  58. Data structures to represent sets of k-long DNA sequences.
  59. DeepCABAC: A Universal Compression Algorithm for Deep Neural Networks.
  60. Depth First Search in the Semi-streaming Model.
  61. Determining satisfiability of 3-SAT in polynomial time.
  62. Direct Linear Time Construction of Parameterized Suffix and LCP Arrays for Constant Alphabets.
  63. Don’t Persist All : Efficient Persistent Data Structures.
  64. Dv2v: A Dynamic Variable-to-Variable Compressor.
  65. Dynamic Optimality Refuted - For Tournament Heaps.
  66. Dynamic Packed Compact Tries Revisited.
  67. Dynamic Palindrome Detection.
  68. Dynamic Partition Bloom Filters: A Bounded False Positive Solution For Dynamic Set Membership (Extended Abstract).
  69. Dynamic Path-Decomposed Tries.
  70. E2FM: an encrypted and compressed full-text index for collections of genomic sequences.
  71. ER-index: a referential index for encrypted genomic databases.
  72. Edge minimization in de Bruijn graphs.
  73. Efficient Online String Matching Based on Characters Distance Text Sampling.
  74. Efficient computation of the Jacobi symbol.
  75. Efficient processing of raster and vector data.
  76. Encoding 3SUM.
  77. Energy consumption in compact integer vectors: A study case.
  78. Engineering Faster Sorters for Small Sets of Items.
  79. Engineering Top-Down Weight-Balanced Trees.
  80. Entropy Bounds for Grammar-Based Tree Compressors.
  81. Entropy Trees and Range-Minimum Queries In Optimal Average-Case Space.
  82. Enumerating Range Modes.
  83. Enumerative Data Compression with Non-Uniquely Decodable Codes.
  84. Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication.
  85. Every nonnegative real number is an abelian critical exponent.
  86. EvoZip: Efficient Compression of Large Collections of Evolutionary Trees.
  87. Exhaustive Exact String Matching: The Analysis of the Full Human Genome.
  88. Extending General Compact Querieable Representations to GIS Applications.
  89. Fast Cartesian Tree Matching.
  90. Fast Concurrent Data Sketches.
  91. Fast Exact Dynamic Time Warping on Run-Length Encoded Time Series.
  92. Fast Fibonacci heaps with worst case extensions.
  93. Fast Multiple Pattern Cartesian Tree Matching.
  94. Fast Sequence Segmentation using Log-Linear Models.
  95. Fast hashing with Strong Concentration Bounds.
  96. Fast, Small, and Simple Document Listing on Repetitive Text Collections.
  97. Faster Dynamic Compressed d-ary Relations.
  98. Faster Integer Multiplication Using Preprocessing.
  99. Faster Privacy-Preserving Computation of Edit Distance with Moves.
  100. Faster Repetition-Aware Compressed Suffix Trees based on Block Trees.
  101. Faster and simpler algorithms for finding large patterns in permutations.
  102. Faster queries for longest substring palindrome after block edit.
  103. Finding First and Most-Beautiful Queens by Integer Programming.
  104. Finding monotone patterns in sublinear time.
  105. Finite test sets for morphisms which are square-free on some of Thue’s square-free ternary words.
  106. Flat combined Red Black Trees.
  107. Fully-Dynamic Space-Efficient Dictionaries and Filters with Constant Number of Memory Accesses.
  108. Fully-functional bidirectional Burrows-Wheeler indexes.
  109. Gardens of Eden in the Game of Life.
  110. Generalized Dictionary Matching under Substring Consistent Equivalence Relations.
  111. Generalized de Bruijn words and the state complexity of conjugate sets.
  112. GraCT: A Grammar-based Compressed Index for Trajectory Data.
  113. Grammar Compressed Sequences with Rank/Select Support.
  114. Heuristic algorithms for the Longest Filled Common Subsequence Problem.
  115. How far away must forced letters be so that squares are still avoidable?
  116. How to Store a Random Walk.
  117. Implementing the Topological Model Succinctly.
  118. Improved Compressed String Dictionaries.
  119. Improved local search for graph edit distance.
  120. In Search of the Fastest Concurrent Union-Find Algorithm.
  121. In oder Aus.
  122. Indexing Graph Search Trees and Applications.
  123. Inducing the Lyndon Array.
  124. Internal Dictionary Matching.
  125. It is high time we let go of the Mersenne Twister.
  126. LISA: Towards Learned DNA Sequence Search.
  127. Learning Multi-dimensional Indexes.
  128. Learning Sublinear-Time Indexing for Nearest Neighbor Search.
  129. Lempel-Ziv-like Parsing in Small Space.
  130. Leyenda: An Adaptive, Hybrid Sorting Algorithm for Large Scale Data with Limited Memory.
  131. Lightweight merging of compressed indices based on BWT variants.
  132. Linear-size Suffix Tries for Parameterized Strings.
  133. Listing Conflicting Triples in Optimal Time.
  134. Local Decode and Update for Big Data Compression.
  135. Lock-Free Hopscotch Hashing.
  136. Longest Common Subsequence on Weighted Sequences.
  137. Loop Programming Practices that Simplify Quicksort Implementations.
  138. Lp Pattern Matching in a Stream.
  139. Lyndon words versus inverse Lyndon words: queries on suffixes and bordered words.
  140. Matching Patterns with Variables.
  141. Matching reads to many genomes with the r-index.
  142. Matching strings in encoded sequences.
  143. Memory Lower Bounds for Self-Stabilization.
  144. Mergeable Dictionaries With Shifts.
  145. Minimal Absent Words in Rooted and Unrooted Trees.
  146. Minimal Unique Substrings and Minimal Absent Words in a Sliding Window.
  147. Multiple Set Matching and Pre-Filtering with Bloom Multifilters.
  148. Multiplication method for factoring natural numbers.
  149. Nearly Optimal Static Las Vegas Succinct Dictionary.
  150. New Bounds on Antipowers in Binary Words.
  151. New Paths from Splay to Dynamic Optimality.
  152. New results on pseudosquare avoidance.
  153. Non-Rectangular Convolutions and (Sub-)Cadences with Three Elements.
  154. On Approximate Range Mode and Range Selection.
  155. On Greedy Algorithms for Binary de Bruijn Sequences.
  156. On Huang and Wong’s Algorithm for Generalized Binary Split Trees.
  157. On Longest Common Property Preserved Substring Queries.
  158. On Occupancy Moments and Bloom Filter Efficiency.
  159. On Prefix-Sorting Finite Automata.
  160. On Slicing Sorted Integer Sequences.
  161. On dynamic succinct graph representations.
  162. On long words avoiding Zimin patterns.
  163. On the Average Case of MergeInsertion.
  164. On the Complexity of BWT-runs Minimization via Alphabet Reordering.
  165. On the Complexity of Exact Pattern Matching in Graphs: Binary Strings and Bounded Degree.
  166. On the Complexity of Exact Pattern Matching in Graphs: Determinism and Zig-Zag Matching.
  167. On the Hardness and Inapproximability of Recognizing Wheeler Graphs.
  168. On the Reproducibility of Experiments of Indexing Repetitive Document Collections.
  169. On the cyclic regularities of strings.
  170. Online Algorithms for Constructing Linear-size Suffix Trie.
  171. Optimal Adaptive Detection of Monotone Patterns.
  172. Optimal In-place Algorithms for Basic Graph Problems.
  173. Optimal Joins using Compact Data Structures.
  174. Order-Preserving Pattern Matching Indeterminate Strings.
  175. Orthogonal Range Reporting and Rectangle Stabbing for Fat Rectangles.
  176. Padovan heaps.
  177. Palindromic Subsequences in Finite Words.
  178. Palindromic Ziv-Lempel and Crochemore Factorizations of m-Bonacci Infinite Words.
  179. Parallel Finger Search Structures.
  180. Parallel decompression of gzip-compressed files and random access to DNA sequences.
  181. Partial Sums on the Ultra-Wide Word RAM.
  182. Pinning Down the Strong Wilber 1 Bound for Binary Search Trees.
  183. Practical Repetition-Aware Grammar Compression.
  184. Prefix Block-Interchanges on Binary and Ternary Strings.
  185. Proving tree algorithms for succinct data structures.
  186. Pseudo-solutions of word equations.
  187. Quantum Computing: Lecture Notes.
  188. Quasi-Linear-Time Algorithm for Longest Common Circular Factor.
  189. QuickSort: Improved right-tail asymptotics for the limiting distribution, and large deviations.
  190. Quotient Hash Tables - Efficiently Detecting Duplicates in Streaming Data.
  191. RAMBO: Repeated And Merged Bloom Filter for Multiple Set Membership Testing (MSMT) in Sub-linear time.
  192. RECIPE : Converting Concurrent DRAM Indexes to Persistent-Memory Indexes.
  193. RLE edit distance in near optimal time.
  194. Re-Pair In-Place.
  195. RecSplit: Minimal Perfect Hashing via Recursive Splitting.
  196. Reducing approximate Longest Common Subsequence to approximate Edit Distance.
  197. Repetitions in infinite palindrome-rich words.
  198. Resolution of the Burrows-Wheeler Transform Conjecture.
  199. Revisiting Consistent Hashing with Bounded Loads.
  200. Rpair: Rescaling RePair with Rsync.
  201. Run-Length Encoding in a Finite Universe.
  202. SOSD: A Benchmark for Learned Indexes.
  203. Selection on X1+X2+⋅⋅⋅ + Xm with layer-ordered heaps.
  204. Separate Chaining Meets Compact Hashing.
  205. Separating many words by counting occurrences of factors.
  206. Set Cover in Sub-linear Time.
  207. Shed More Light on Bloom Filter’s Variants.
  208. Shortest Unique Palindromic Substring Queries on Run-Length Encoded Strings.
  209. Simulating the DNA String Graph in Succinct Space.
  210. Sorted Top-k in Rounds.
  211. Space Efficient Algorithms for Breadth-Depth Search.
  212. Space Efficient Construction of Lyndon Arrays in Linear Time.
  213. Space-Efficient Computation of the LCP Array from the Burrows-Wheeler Transform.
  214. Space-Efficient Construction of Compressed Suffix Trees.
  215. Space-Efficient Data Structures for Lattices.
  216. Space-efficient merging of succinct de Bruijn graphs.
  217. Sparse Regular Expression Matching.
  218. Speeding up the Karatsuba algorithm.
  219. Splaying Preorders and Postorders.
  220. Stack Sorting with Increasing and Decreasing Stacks.
  221. Stack sorting with restricted stacks.
  222. String Attractors and Combinatorics on Words.
  223. String Indexing with Compressed Patterns.
  224. String Sanitization: A Combinatorial Approach.
  225. String Synchronizing Sets: Sublinear-Time BWT Construction and Optimal LCE Data Structure.
  226. String factorisations with maximum or minimum dimension.
  227. Sublinear Algorithms for Gap Edit Distance.
  228. Succinct Data Structures for Families of Interval Graphs.
  229. Succinct Representation for (Non)Deterministic Finite Automata.
  230. Suffix Trees, DAWGs and CDAWGs for Forward and Backward Tries.
  231. Superset Technique for Approximate Recovery in One-Bit Compressed Sensing.
  232. Survey of Information Encoding Techniques for DNA.
  233. Techniques for Inverted Index Compression.
  234. The Alternating BWT: an algorithmic perspective.
  235. The Bloom Clock.
  236. The One-Way Communication Complexity of Dynamic Time Warping Distance.
  237. The PGM-index: a multicriteria, compressed and learned approach to data indexing.
  238. The Parameterized Position Heap of a Trie.
  239. The Strong 3SUM-INDEXING Conjecture is False.
  240. The Tandem Duplication Distance is NP-hard.
  241. The Weak Circular Repetition Threshold Over Large Alphabets.
  242. The k-d tree data structure and a proof for neighborhood computation in expected logarithmic time.
  243. The power word problem.
  244. The repetition threshold for binary rich words.
  245. The smallest grammar problem revisited.
  246. Top Tree Compression of Tries.
  247. Towards Better Compressed Representations.
  248. Towards a Definitive Measure of Repetitiveness.
  249. Tree-Shape Grammars for Random Access.
  250. Unconstrained Church-Turing thesis cannot possibly be true.
  251. Weighted Shortest Common Supersequence Problem Revisited.
  252. What Storage Access Privacy is Achievable with Small Overhead?
  253. When a Dollar Makes a BWT.
  254. Words Avoiding Reversed Factors, Revisited.
  255. Words With Few Palindromes, Revisited.
  256. Xor Filters: Faster and Smaller Than Bloom and Cuckoo Filters.
  257. k-Spectra of c-Balanced Words.
  258. scaleBF: A High Scalable Membership Filter using 3D Bloom Filter.

Comput. J. 2019

  1. Context Sensitive Rewriting Codes for Flash Memory†.
  2. Edit Distance with Multiple Block Operations†.

Dagstuhl Reports 2019

  1. 25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241).

IEEE Trans. Inf. Theory 2019

  1. RePair and All Irreducible Grammars are Upper Bounded by High-Order Empirical Entropy.

Inf. Comput. 2019

  1. Lempel-Ziv compressed structures for document retrieval.
  2. On-line weighted pattern matching.

Inf. Process. Lett. 2019

  1. Applying the Positional Burrows-Wheeler Transform to all-pairs Hamming distance.
  2. Comparison of LZ77-type parsings.

Inf. Sci. 2019

  1. GraCT: A Grammar-based Compressed Index for Trajectory Data.

Inf. Syst. 2019

  1. On the reproducibility of experiments of indexing repetitive document collections.

J. Comb. Optim. 2019

  1. Efficient enumeration of non-equivalent squares in partial words with few holes.

J. Comput. Syst. Sci. 2019

  1. Hide and seek with repetitions.

Rev. Socionetwork Strateg. 2019

  1. Storing Partitions of Integers in Sublinear Space.

SIAM J. Comput. 2019

  1. Bicriteria Data Compression.
  2. Truly Subcubic Algorithms for Language Edit Distance and RNA Folding via Fast Bounded-Difference Min-Plus Product.

SIAM J. Discret. Math. 2019

  1. Rollercoasters: Long Sequences without Short Runs.

Softw. Pract. Exp. 2019

  1. A compact index for order-preserving pattern matching.

Theor. Comput. Sci. 2019

  1. A substring-substring LCS data structure.
  2. Algorithms to compute the Burrows-Wheeler Similarity Distribution.
  3. Approximate cover of strings.
  4. Document listing on repetitive collections with guaranteed performance.
  5. Efficient dynamic dictionary matching with DAWGs and AC-automata.
  6. Improved upper bounds on all maximal α-gapped repeats and palindromes.
  7. Maximal common subsequence algorithms.
  8. On overabundant words and their application to biological sequence analysis.
  9. On the size of the smallest alphabet for Lyndon trees.
  10. Path queries on functions.
  11. Universal compressed text indexing.

Theory Comput. Syst. 2019

  1. Pattern Matching and Consensus Problems on Weighted Sequences and Profiles.

AIAI (Workshops) 2018

  1. How Much Different Are Two Words with Different Shortest Periods.

ALENEX 2018

  1. Adaptive Cuckoo Filters.
  2. Hybrid Indexing Revisited.
  3. Simple, Fast and Lightweight Parallel Wavelet Tree Construction.

COCOON 2018

  1. A Linear-Space Data Structure for Range-LCP Queries in Poly-Logarithmic Time.

CPM 2018

  1. A Simple Linear-Time Algorithm for Computing the Centroid and Canonical Form of a Plane Graph and Its Applications.
  2. A Succinct Four Russians Speedup for Edit Distance Computation and One-against-many Banded Alignment.
  3. Can a permutation be sorted by best short swaps?.
  4. Computing longest common square subsequences.
  5. Dualities in Tree Representations.
  6. Fast Matching-based Approximations for Maximum Duo-Preservation String Mapping and its Weighted Variant.
  7. Faster Online Elastic Degenerate String Matching.
  8. Front Matter, Table of Contents, Preface, Conference Organization.
  9. Linear-Time Algorithm for Long LCF with k Mismatches.
  10. Linear-time algorithms for the subpath kernel.
  11. Locally Maximal Common Factors as a Tool for Efficient Dynamic String Algorithms.
  12. Longest Lyndon Substring After Edit.
  13. Longest substring palindrome after edit.
  14. Lyndon Factorization of Grammar Compressed Texts Revisited.
  15. Maximal Common Subsequence Algorithms.
  16. Nearest constrained circular words.
  17. Non-Overlapping Indexing - Cache Obliviously.
  18. On Undetected Redundancy in the Burrows-Wheeler Transform.
  19. On the Maximum Colorful Arborescence Problem and Color Hierarchy Graph Structure.
  20. Online LZ77 Parsing and Matching Statistics with RLBWTs.
  21. Order-Preserving Pattern Matching Indeterminate Strings.
  22. Quasi-Periodicity Under Mismatch Errors.
  23. Slowing Down Top Trees for Better Worst-Case Compression.
  24. Superstrings with multiplicities.
  25. The Heaviest Induced Ancestors Problem Revisited.

DCC 2018

  1. A Dynamic Compressed Self-Index for Highly Repetitive Text Collections.
  2. A Grammar Compression Algorithm Based on Induced Suffix Sorting.
  3. A Hybrid Approach for Wind Tunnel Data Compression.
  4. Compact Encoding for Galled-Trees and Its Applications.
  5. Compact Representations of Event Sequences.
  6. Compaction of Church Numerals for Higher-Order Compression.
  7. Compressed Hierarchical Clustering.
  8. Constant Delay Traversal of Compressed Graphs.
  9. Delta-Huffman Coding of Unbounded Integers.
  10. Efficient Processing of top-K Vector-Raster Queries Over Compressed Data.
  11. Engineering Compressed Static Functions.
  12. Exploiting Computation-Friendly Graph Compression Methods for Adjacency-Matrix Multiplication.
  13. Fast and Efficient Compression of Next Generation Sequencing Data.
  14. Fibonacci Based Compressed Suffix Array.
  15. K-Means Algorithm Over Compressed Binary Data.
  16. LZ77 Like Lossy Transformation of Quality Scores.
  17. Lapped Transforms Based Image Recovery for Block Compressed Sensing.
  18. Optimal In-Place Suffix Sorting.
  19. Practical Succinct Text Indexes in External Memory.
  20. Run Compressed Rank/Select for Large Alphabets.
  21. The Bits Between Proteins.
  22. Two-Dimensional Block Trees.

DLT 2018

  1. Block Sorting-Based Transformations on Words: Beyond the Magic BWT.
  2. The Runs Theorem and Beyond.

ESA 2018

  1. Dynamic Trees with Almost-Optimal Access Cost.
  2. Edit Distance with Block Operations.
  3. Improved Time and Space Bounds for Dynamic Range Mode.
  4. Nearly-Optimal Mergesorts: Fast, Practical Sorting Methods That Optimally Adapt to Existing Runs.
  5. On the Decision Tree Complexity of String Matching.
  6. On the Worst-Case Complexity of TimSort.
  7. String Attractors: Verification and Optimization.
  8. Two-Dimensional Maximal Repetitions.

FOCS 2018

  1. Approximating Edit Distance within Constant Factor in Truly Sub-Quadratic Time.
  2. Bloom Filters, Adaptivity, and the Dictionary Problem.
  3. PanORAMa: Oblivious RAM with Logarithmic Overhead.

FSTTCS 2018

  1. Sketching, Streaming, and Fine-Grained Complexity of (Weighted) LCS.

ICALP 2018

  1. Edit Distance between Unrooted Trees in Cubic Time.

IEEE BigData 2018

  1. Scalable Construction of Text Indexes with Thrill.

ISAAC 2018

  1. Encoding Two-Dimensional Range Top-k Queries Revisited.
  2. Longest Unbordered Factor in Quasilinear Time.
  3. Multi-Finger Binary Search Trees.
  4. Succinct Data Structures for Chordal Graphs.
  5. Tree Path Majority Data Structures.

ITCS 2018

  1. Fast and Deterministic Constant Factor Approximation Algorithms for LCS Imply New Circuit Lower Bounds.

IWOCA 2018

  1. An Efficient Representation of Partitions of Integers.
  2. LZ-ABT: A Practical Algorithm for α-Balanced Grammar Compression.
  3. On the Expected Number of Distinct Gapped Palindromic Factors.

KDD 2018

  1. Node Similarity with q -Grams for Real-World Labeled Networks.

LATA 2018

  1. Bubble-Flip - A New Generation Algorithm for Prefix Normal Words.
  2. On Periodicity Lemma for Partial Words.

LATIN 2018

  1. Compressed Indexing with Signature Grammars.
  2. On the Approximation Ratio of Lempel-Ziv Parsing.
  3. Property Suffix Array with Applications.

MFCS 2018

  1. Extra Space during Initialization of Succinct Data Structures and Dynamical Initializable Arrays.
  2. Fast Entropy-Bounded String Dictionary Look-Up with Mismatches.

SEA 2018

  1. Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line.
  2. Fast matching statistics in small space.

SISAP 2018

  1. Privacy-Preserving String Edit Distance with Moves.

SODA 2018

  1. Improved bounds for testing Dyck languages.
  2. In-Place Sparse Suffix Sorting.
  3. Labeling Schemes for Nearest Common Ancestors through Minor-Universal Trees.
  4. Lempel-Ziv: a “one-bit catastrophe” but not a tragedy.
  5. Multivariate Fine-Grained Complexity of Longest Common Subsequence.
  6. Optimal Dynamic Strings.
  7. Optimal-Time Text Indexing in BWT-runs Bounded Space.
  8. The Entropy of Backwards Analysis.
  9. Time and Space Efficient Representations of Distributive Lattices.
  10. Tree Edit Distance Cannot be Computed in Strongly Subcubic Time (unless APSP can).

SOFSEM 2018

  1. Duel and Sweep Algorithm for Order-Preserving Pattern Matching.
  2. Longest Common Prefixes with k-Mismatches and Applications.
  3. New Variants of Pattern Matching with Constants and Variables.

SOSA 2018

  1. A Simple Algorithm for Approximating the Text-To-Pattern Hamming Distance.

SPIRE 2018

  1. 3DGraCT: A Grammar-Based Compressed Representation of 3D Trajectories.
  2. Adaptive Computation of the Discrete Fréchet Distance.
  3. Better Heuristic Algorithms for the Repetition Free LCS and Other Variants.
  4. Block Palindromes: A New Generalization of Palindromes.
  5. Compressed Communication Complexity of Longest Common Prefixes.
  6. Compressed Range Minimum Queries.
  7. Computing Burrows-Wheeler Similarity Distributions for String Collections.
  8. Early Commenting Features for Emotional Reactions Prediction.
  9. Efficient Computation of Sequence Mappability.
  10. Fast Wavelet Tree Construction in Practice.
  11. Fast and Effective Neural Networks for Translating Natural Language into Denotations.
  12. Faster Recovery of Approximate Periods over Edit Distance.
  13. Faster and Smaller Two-Level Index for Network-Based Trajectories.
  14. Indexed Dynamic Programming to Boost Edit Distance and LCSS Computation.
  15. Linear-Time Online Algorithm Inferring the Shortest Path from a Walk.
  16. Longest Common Prefixes with k-Errors and Applications.
  17. Longest Property-Preserved Common Factor.
  18. Maximal Motif Discovery in a Sliding Window.
  19. New Structures to Solve Aggregated Queries for Trips over Public Transportation Networks.
  20. On Extended Special Factors of a Word.
  21. Optimal In-Place Suffix Sorting.
  22. Recoloring the Colored de Bruijn Graph.
  23. Recovering, Counting and Enumerating Strings from Forward and Backward Suffix Arrays.
  24. Searching for a Modified Pattern in a Changing Text.
  25. The Colored Longest Common Prefix Array Computed via Sequential Scans.
  26. Towards a Compact Representation of Temporal Rasters.
  27. Trickier XBWT Tricks.
  28. Truncated DAWGs and Their Application to Minimal Absent Word Problem.

STACS 2018

  1. An Improved Bound for Random Binary Search Trees with Concurrent Insertions.
  2. Computing the Longest Common Prefix of a Context-free Language in Polynomial Time.
  3. Improving the Upper Bound on the Length of the Shortest Reset Word.
  4. Relations Between Greedy and Bit-Optimal LZ77 Encodings.
  5. Space-Efficient Algorithms for Longest Increasing Subsequence.
  6. String Periods in the Order-Preserving Model.
  7. Succinct Oblivious RAM.
  8. Sums of Palindromes: an Approach via Automata.
  9. Upper and Lower Bounds for Dynamic Data Structures on Strings.

STOC 2018

  1. At the roots of dictionary compression: string attractors.
  2. Explicit binary tree codes with polylogarithmic size alphabet.
  3. Smooth heaps and a dual view of self-adjusting data structures.
  4. Synchronization strings: explicit constructions, local decoding, and applications.

SWAT 2018

  1. Succinct Dynamic One-Dimensional Point Reporting.

Stringology 2018

  1. A Faster V-order String Comparison Algorithm.
  2. Constrained Approximate Subtree Matching by Finite Automata.
  3. Discovery of Regulatory Motifs in DNA.
  4. Fast and Simple Algorithms for Computing both LCSk and LCSk+.
  5. Fibonacci Based Compressed Suffix Array.
  6. O(n log n)-time Text Compression by LZ-style Longest First Substitution.
  7. On Baier’s Sort of Maximal Lyndon Substrings.
  8. Parameterized Dictionary Matching with One Gap.
  9. Right-to-left Online Construction of Parameterized Position Heaps.
  10. Synchronizing Dynamic Huffman Codes.
  11. Three Strategies for the Dead-Zone String Matching Algorithm.

TFPIE@TFP 2018

  1. Vector Programming Using Generative Recursion.

WABI 2018

  1. A Multi-labeled Tree Edit Distance for Comparing “Clonal Trees” of Tumor Progression.
  2. A Succinct Solution to Rmap Alignment.
  3. Degenerate String Comparison and Applications.
  4. Detecting Mutations by eBWT.
  5. External memory BWT and LCP computation for sequence collections with applications.
  6. Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time.
  7. PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats.
  8. Prefix-Free Parsing for Building Big BWTs.

WALCOM 2018

  1. On Multiple Longest Common Subsequence and Common Motifs with Gaps (Extended Abstract).

Algorithmica 2018

  1. Crochemore’s Partitioning on Weighted Strings and Applications.
  2. Dynamic Path Queries in Linear Space.
  3. Dynamic Relative Compression, Dynamic Partial Sums, and Substring Concatenation.
  4. Guest Editorial: Special Issue on Compact Data Structures.
  5. LZ77 Computation Based on the Run-Length Encoded BWT.
  6. Lempel-Ziv Factorization Powered by Space Efficient Suffix Trees.
  7. Lempel-Ziv-78 Compressed String Dictionaries.

Algorithms 2018

  1. DenseZDD: A Compact and Fast Index for Families of Sets.
  2. Sliding Suffix Tree.

BMC Bioinform. 2018

  1. STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow.

Bioinform. 2018

  1. CNEFinder: finding conserved non-coding elements in genomes.
  2. Practical dynamic de Bruijn graphs.

CoRR 2018

  1. A Compact Representation for Trips over Networks built on self-indexes.
  2. A Fast Combination of AES Encryption and LZ4 Compression Algorithms.
  3. A Faster External Memory Priority Queue with DecreaseKeys.
  4. A Grammar-based Compressed Representation of 3D Trajectories.
  5. A Simple Algorithm for Computing the Document Array.
  6. A Simple and Space Efficient Segment Tree Implementation.
  7. A Weighted Generalization of the Graham-Diaconis Inequality for Ranked List Similarity.
  8. ALLSAT compressed with wildcards: Partitionings and face-numbers of simplicial complexes.
  9. Adaptive Shivers Sort: An Alternative Sorting Algorithm.
  10. Algorithms for Anti-Powers in Strings.
  11. Alignment-free sequence comparison using absent words.
  12. An O(N) Sorting Algorithm: Machine Learning Sorting.
  13. An optimized Parallel Failure-less Aho-Corasick algorithm for DNA sequence matching.
  14. Another Proof of Cuckoo hashing with New Variants.
  15. Approximate Nearest Neighbors in Limited Space.
  16. Approximate Online Pattern Matching in Sub-linear Time.
  17. Approximate Query Processing over Static Sets and Sliding Windows.
  18. Approximating Approximate Pattern Matching.
  19. Approximating Edit Distance Within Constant Factor in Truly Sub-Quadratic Time.
  20. Approximating Edit Distance in Truly Subquadratic Time: Quantum and MapReduce.
  21. Assembling Omnitigs using Hidden-Order de Bruijn Graphs.
  22. BDDs Naturally Represent Boolean Functions, and ZDDs Naturally Represent Sets of Sets.
  23. Beating Fredman-Komlós for perfect k-hashing.
  24. Block Palindromes: A New Generalization of Palindromes.
  25. Calculation of extended gcd by normalization.
  26. Cardinality Estimators do not Preserve Privacy.
  27. Collapsing Superstring Conjecture.
  28. Compact Representations of Event Sequences.
  29. Compound Binary Search Tree and Algorithms.
  30. Compressed Communication Complexity of Longest Common Prefixes.
  31. Compressed Multiple Pattern Matching.
  32. Computing the k-binomial complexity of the Thue-Morse word.
  33. CuCoTrack: Cuckoo Filter Based Connection Tracking.
  34. DeepZip: Lossless Data Compression using Recurrent Neural Networks.
  35. Design and Implementation of Dynamic Memory Management in a Reversible Object-Oriented Programming Language.
  36. Detecting Mutations by eBWT.
  37. Deterministic Document Exchange Protocols, and Almost Optimal Binary Codes for Edit Errors.
  38. Distinct Sampling on Streaming Data with Near-Duplicates.
  39. Dualities in Tree Representations.
  40. Dynamic Trees with Almost-Optimal Access Cost.
  41. Dynamic all scores matrices for LCS score.
  42. Edit Distance between Unrooted Trees in Cubic Time.
  43. Efficient Computation of Sequence Mappability.
  44. Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.
  45. Efficient Genomic Interval Queries Using Augmented Range Trees.
  46. Efficient Representation and Counting of Antipower Factors in Words.
  47. Efficient Single Writer Concurrency.
  48. Efficiently Approximating Edit Distance Between Pseudorandom Strings.
  49. Eleven Simple Algorithms to Compute Fibonacci Numbers.
  50. Encoding two-dimensional range top-k queries revisited.
  51. Enhanced string factoring from alphabet orderings.
  52. Entropy bounds for grammar compression.
  53. Enumerating Cryptarithms Using Deterministic Finite Automata.
  54. External memory BWT and LCP computation for sequence collections with applications.
  55. Extra Space during Initialization of Succinct Data Structures and of Dynamical Initializable Arrays.
  56. Fast Breadth-First Search in Still Less Space.
  57. Fast Lempel-Ziv Decompression in Linear Space.
  58. Fast Locality Sensitive Hashing for Beam Search on GPU.
  59. Fast Prefix Search in Little Space, with Applications.
  60. Fast and Longest Rollercoasters.
  61. Fast entropy-bounded string dictionary look-up with mismatches.
  62. Faster Approximate(d) Text-to-Pattern L1 Distance.
  63. Faster Attractor-Based Indexes.
  64. Faster Recovery of Approximate Periods over Edit Distance.
  65. Fault Tolerant and Fully Dynamic DFS in Undirected Graphs: Simple Yet Efficient.
  66. Finding a Small Number of Colourful Components.
  67. Fine-Grained Complexity of Analyzing Compressed Data: Quantifying Improvements over Decompress-And-Solve.
  68. Flexible and Efficient Algorithms for Abelian Matching in Strings.
  69. From Regular Expression Matching to Parsing.
  70. Fully-Functional Suffix Trees and Optimal Text Searching in BWT-runs Bounded Space.
  71. Generalized Leapfrogging Samplesort: A Class of O(n log2n) Worst-Case Complexity and O(n log n) Average-Case Complexity Sorting Algorithms.
  72. Grammar-based Compression of Unranked Trees.
  73. Graph Pattern Matching Preserving Label-Repetition Constraints.
  74. Graph Sketching Against Adaptive Adversaries Applied to the Minimum Degree Algorithm.
  75. Guidesort: Simpler Optimal Deterministic Sorting for the Parallel Disk Model.
  76. Haplotype-aware graph indexes.
  77. Improved Parallel Cache-Oblivious Algorithms for Dynamic Programming and Linear Algebra.
  78. Improved Time and Space Bounds for Dynamic Range Mode.
  79. Improved Upper Bounds on all Maximal α-gapped Repeats and Palindromes.
  80. Improved bounds for multipass pairing heaps and path-balanced binary search trees.
  81. Improving Similarity Search with High-dimensional Locality-sensitive Hashing.
  82. Indexed Dynamic Programming to boost Edit Distance and LCSS Computation.
  83. Know When to Fold ‘Em: Self-Assembly of Shapes by Folding in Oritatami.
  84. LZRR: LZ77 Parsing with Right Reference.
  85. Linear-Time Algorithm for Long LCF with k Mismatches.
  86. Linear-Time In-Place DFS and BFS in the Restore Model.
  87. List Decoding with Double Samplers.
  88. Local Decodability of the Burrows-Wheeler Transform.
  89. Locally Consistent Parsing for Text Indexing in Small Space.
  90. Longest Common Factor Made Fully Dynamic.
  91. Longest Common Prefixes with k-Errors and Applications.
  92. Longest Increasing Subsequence under Persistent Comparison Errors.
  93. Longest Property-Preserved Common Factor.
  94. Longest Unbordered Factor in Quasilinear Time.
  95. Lower Bounds for Oblivious Data Structures.
  96. Lower bounds for text indexing with mismatches and differences.
  97. MR-RePair: Grammar Compression based on Maximal Repeats.
  98. Massively Parallel Dynamic Programming on Trees.
  99. MinJoin: Efficient Edit Similarity Joins via Local Hash Minimums.
  100. Minimum Segmentation for Pan-genomic Founder Reconstruction in Optimal Time.
  101. Minuet: A method to solve Sudoku puzzles by hand.
  102. Multi-finger binary search trees.
  103. Multidimensional segment trees can do range queries and updates in logarithmic time.
  104. Multivariate Fine-Grained Complexity of Longest Common Subsequence.
  105. Near-Linear Time Insertion-Deletion Codes and (1+ε)-Approximating Edit Distance via Indexing.
  106. Nearly Optimal Space Efficient Algorithm for Depth First Search.
  107. Nearly-Optimal Mergesorts: Fast, Practical Sorting Methods That Optimally Adapt to Existing Runs.
  108. Non-Empty Bins with Simple Tabulation Hashing.
  109. O(n log n)-time text compression by LZ-style longest first substitution.
  110. On Abelian Longest Common Factor with and without RLE.
  111. On Computing Average Common Substring Over Run Length Encoded Sequences.
  112. On Estimating Edit Distance: Alignment, Dimension Reduction, and Embeddings.
  113. On Infinite Prefix Normal Words.
  114. On Periodicity Lemma for Partial Words.
  115. On Undetected Redundancy in the Burrows-Wheeler Transform.
  116. On improving the approximation ratio of the r-shortest common superstring problem.
  117. On the Approximation Ratio of Greedy Parsings.
  118. On the Diameter of Tree Associahedra.
  119. On the Worst-Case Complexity of TimSort.
  120. On the discrepancy of random low degree set systems.
  121. On the tails of the limiting QuickSort density.
  122. Online LZ77 Parsing and Matching Statistics with RLBWTs.
  123. Optimal Algorithm for Profiling Dynamic Arrays with Finite Values.
  124. Optimal Ball Recycling.
  125. Optimal Document Exchange and New Codes for Small Number of Insertions and Deletions.
  126. Optimal Hashing in External Memory.
  127. Optimal Rank and Select Queries on Dictionary-Compressed Text.
  128. Optimal Sorting with Persistent Comparison Errors.
  129. Optimal Substring-Equality Queries with Applications to Sparse Text Indexing.
  130. Optimal Succinct Rank Data Structure via Approximate Nonnegative Tensor Decomposition.
  131. Optimal streaming and tracking distinct elements with high probability.
  132. Optimizing Bloom Filter: Challenges, Solutions, and Comparisons.
  133. Orthogonal Point Location and Rectangle Stabbing Queries in 3-d.
  134. Parallel Range and Segment Queries with Augmented Maps.
  135. Parallel Working-Set Search Structures.
  136. Parallel Write-Efficient Algorithms and Data Structures for Computational Geometry.
  137. Parallelism in Randomized Incremental Algorithms.
  138. Periodicity in Data Streams with Wildcards.
  139. Pivot Sampling in QuickXSort: Precise Analysis of QuickMergesort and QuickHeapsort.
  140. Practical Access to Dynamic Programming on Tree Decompositions.
  141. Prefix-Free Parsing for Building Big BWTs.
  142. Push-Down Trees: Optimal Self-Adjusting Complete Trees.
  143. QuickMergesort: Practically Efficient Constant-Factor Optimal Sorting.
  144. QuickXsort - A Fast Sorting Scheme in Theory and Practice.
  145. Randen - fast backtracking-resistant random generator with AES+Feistel+Reverie.
  146. RePair in Compressed Space and Time.
  147. Reconstructing Strings from Substrings: Optimal Randomized and Average-Case Algorithms.
  148. Red-Black Trees with Constant Update Time.
  149. Relative compression of trajectories.
  150. Restructuring expression dags for efficient parallelization.
  151. Revisiting the tree edit distance and its backtracing: A tutorial.
  152. Right-to-left online construction of parameterized position heaps.
  153. Round-Hashing for Data Storage: Distributed Servers and External-Memory Tables.
  154. Scalable String and Suffix Sorting: Algorithms, Techniques, and Tools.
  155. Sesquickselect: One and a half pivots for cache-efficient selection.
  156. Simple Concurrent Labeling Algorithms for Connected Components.
  157. Simple and Fast BlockQuicksort using Lomuto’s Partitioning Scheme.
  158. Sketching, Streaming, and Fine-Grained Complexity of (Weighted) LCS.
  159. Sliding Suffix Tree.
  160. Small Uncolored and Colored Choice Dictionaries.
  161. Smooth heaps and a dual view of self-adjusting data structures.
  162. Some comments on the structure of the best known networks sorting 16 elements.
  163. Sorting Real Numbers in O(n√(log n)) Time and Linear Space.
  164. Space-Efficient DFS and Applications: Simpler, Leaner, Faster.
  165. Static Data Structure Lower Bounds Imply Rigidity.
  166. Strategies for Stable Merge Sorting.
  167. Streaming dictionary matching with mismatches.
  168. String Attractors: Verification and Optimization.
  169. String Periods in the Order-Preserving Model.
  170. Strong link between BWT and XBW via Aho-Corasick automaton and applications to Run-Length Encoding.
  171. Sub-O(log n) Out-of-Order Sliding-Window Aggregation.
  172. Succinct Oblivious RAM.
  173. Succinct data structure for dynamic trees with faster queries.
  174. Survey and Taxonomy of Lossless Graph Compression and Space-Efficient Graph Representations.
  175. Synchronization Strings: Efficient and Fast Deterministic Constructions over Small Alphabets.
  176. Synchronization Strings: List Decoding for Insertions and Deletions.
  177. The Read-Optimized Burrows-Wheeler Transform.
  178. The colored longest common prefix array computed via sequential scans.
  179. The effective entropy of next/previous larger/smaller value queries.
  180. The entropy of lies: playing twenty questions with a liar.
  181. Tree Path Majority Data Structures.
  182. Tunneling on Wheeler Graphs.
  183. Two Algorithms to Find Primes in Patterns.
  184. Two-Dimensional Block Trees.
  185. Universal Compressed Text Indexing.
  186. Upper and lower bounds for dynamic data structures on strings.
  187. Using Compressed Suffix-Arrays for a Compact Representation of Temporal-Graphs.
  188. Using statistical encoding to achieve tree succinctness never seen before.
  189. Vectorized Character Counting for Faster Pattern Matching.
  190. Weighted dynamic finger in binary search trees.
  191. Wormhole: A Fast Ordered Index for In-memory Data Management.
  192. Worst-Case Efficient Sorting with QuickMergesort.
  193. Xorshift1024*, Xorshift1024+, Xorshift128+ and Xoroshiro128+ Fail Statistical Tests for Linearity.
  194. Zip Trees.
  195. copMEM: Finding maximal exact matches via sampling both genomes.
  196. k-Maximum Subarrays for Small k: Divide-and-Conquer made simpler.

Comput. J. 2018

  1. Relative Suffix Trees.

Dagstuhl Reports 2018

  1. Synergies between Adaptive Analysis of Algorithms, Parameterized Complexity, Compressed Data Structures and Compressed Indices (Dagstuhl Seminar 18281).

Fundam. Informaticae 2018

  1. On Abelian Longest Common Factor with and without RLE.

IEICE Trans. Inf. Syst. 2018

  1. Approximate Frequent Pattern Discovery in Compressed Space.

Inf. Comput. 2018

  1. Alignment-free sequence comparison using absent words.

Inf. Process. Lett. 2018

  1. A hardness result and new algorithm for the longest common palindromic subsequence problem.
  2. Algorithms for anti-powers in strings.

Int. J. Found. Comput. Sci. 2018

  1. Bidirectional Variable-Order de Bruijn Graphs.
  2. Diverse Palindromic Factorization is NP-Complete.
  3. Dynamic RLE-Compressed Edit Distance Tables Under General Weighted Cost Functions.
  4. Fast Average-Case Pattern Matching on Weighted Sequences.
  5. Palindromic Decompositions with Gaps and Errors.
  6. m-Bonsai: A Practical Compact Dynamic Trie.

J. Discrete Algorithms 2018

  1. A faster implementation of online RLBWT and its application to LZ77 parsing.
  2. A separation between RLSLPs and LZ77.
  3. Algorithms and combinatorial properties on shortest unique palindromic substrings.
  4. Lyndon array construction during Burrows-Wheeler inversion.

Theor. Comput. Sci. 2018

  1. Advances in Algorithms & Combinatorics on Strings (Honoring 60th birthday for Prof. Costas S. Iliopoulos).
  2. Efficient algorithms for shortest partial seeds in words.
  3. Period recovery of strings over the Hamming and edit distances.
  4. The nearest colored node in a tree.
  5. Time-space trade-offs for Lempel-Ziv compressed indexing.

Theory Comput. Syst. 2018

  1. Finger Search in Grammar-Compressed Strings.
  2. Tighter Bounds and Optimal Algorithms for All Maximal α-gapped Repeats and Palindromes - Finding All Maximal α-gapped Repeats and Palindromes in Optimal Worst Case Time on Integer Alphabets.

ALENEX 2017

  1. CSA++: Fast Pattern Search for Large Alphabets.
  2. Compact Dynamic Rewritable (CDRW) Arrays.
  3. Elias-Fano meets Single-Term Top-k Document Retrieval.
  4. Engineering External Memory Induced Suffix Sorting.
  5. Engineering a Distributed Full-Text Index.

COCOA (2) 2017

  1. Faster Algorithms for 1-Mappability of a Sequence.

COCOON 2017

  1. Efficient Enumeration of Non-Equivalent Squares in Partial Words with Few Holes.

CPM 2017

  1. A Family of Approximation Algorithms for the Maximum Duo-Preservation String Mapping Problem.
  2. Approximate Cover of Strings.
  3. Beyond Adjacency Maximization: Scaffold Filling for New String Distances.
  4. Can We Recover the Cover?.
  5. Clique-Based Lower Bounds for Parsing Tree-Adjoining Grammars.
  6. Communication and Streaming Complexity of Approximate Pattern Matching.
  7. Computing All Distinct Squares in Linear Time for Integer Alphabets.
  8. Deterministic Indexing for Packed Strings.
  9. Document Listing on Repetitive Collections with Guaranteed Performance.
  10. Dynamic Elias-Fano Representation.
  11. Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings.
  12. Faster STR-IC-LCS Computation via RLE.
  13. From LZ77 to the Run-Length Encoded Burrows-Wheeler Transform, and Back.
  14. Front Matter, Table of Contents, Preface, Conference Organization, External Reviewers.
  15. Gapped Pattern Statistics.
  16. Lempel-Ziv Compression in a Sliding Window.
  17. Longest Common Extensions with Recompression.
  18. On the Weighted Quartet Consensus Problem.
  19. On-Line Pattern Matching on Similar Texts.
  20. Optimal Omnitig Listing for Safe and Complete Contig Assembly.
  21. Palindromic Length in Linear Time.
  22. Path Queries on Functions.
  23. Position Heaps for Parameterized Strings.
  24. Recompression of SLPs.
  25. Representing the Suffix Tree with the CDAWG.
  26. Revisiting the Parameterized Complexity of Maximum-Duo Preservation String Mapping.
  27. Shortest Superstring.
  28. Synergistic Solutions on MultiSets.
  29. The Longest Filled Common Subsequence Problem.
  30. Tight Bounds on the Maximum Number of Shortest Unique Substrings.
  31. Time-Space Trade-Offs for Lempel-Ziv Compressed Indexing.
  32. Wheeler Graphs: Variations on a Theme by Burrows and Wheeler.

CSR 2017

  1. Palindromic Decompositions with Gaps and Errors.

CiE 2017

  1. Flexible Indexing of Repetitive Collections.

DCC 2017

  1. A Compact Index for Order-Preserving Pattern Matching.
  2. A Succinct Data Structure for Multidimensional Orthogonal Range Searching.
  3. Complementary Contextual Models with FM-Index for DNA Compression.
  4. Compressed Dynamic Range Majority Data Structures.
  5. Content Adaptive Embedded Compression.
  6. Full Compressed Affix Tree Representations.
  7. Improved Parallel Construction of Wavelet Trees and Rank/Select Structures.
  8. Improvements on Re-Pair Grammar Compressor.
  9. LZ-End Parsing in Compressed Space.
  10. Making Compression Algorithms for Unicode Text.
  11. Marlin: A High Throughput Variable-to-Fixed Codec Using Plurally Parsable Dictionaries.
  12. Optimize Genomics Data Compression with Hardware Accelerator.
  13. Space-Efficient Re-Pair Compression.
  14. Stabbing Colors in One Dimension.
  15. Streaming K-Mismatch with Error Correcting and Applications.
  16. Symmetry-Compressible Graphs.

DLT 2017

  1. On the Number of Rich Words.

EANN 2017

  1. Efficient Computation of Palindromes in Sequences with Uncertainties.
  2. Efficient Identification of k-Closed Strings.

ESA 2017

  1. A Space-Optimal Grammar Compression.
  2. An Encoding for Order-Preserving Matching.
  3. Dynamic Space Efficient Hashing.
  4. Fast Dynamic Arrays.
  5. LZ-End Parsing in Linear Time.
  6. Real-Time Streaming Multi-Pattern Search for Constant Alphabet.

FCT 2017

  1. Minimal Absent Words in a Sliding Window and Applications to On-Line Pattern Matching.

FOCS 2017

  1. Fine-Grained Complexity of Analyzing Compressed Data: Quantifying Improvements over Decompress-and-Solve.

ICALP 2017

  1. Dynamic Time Warping and Geometric Edit Distance: Breaking the Quadratic Barrier.
  2. String Inference from Longest-Common-Prefix Array.

ISAAC 2017

  1. Almost Linear Time Computation of Maximal Repetitions in Run Length Encoded Strings.
  2. Fast Compressed Self-Indexes with Deterministic Linear-Time Construction.
  3. On-the-Fly Array Initialization in Less Space.
  4. Structural Pattern Matching - Succinctly.
  5. Succinct Color Searching in One Dimension.

IWOCA 2017

  1. A Faster Implementation of Online Run-Length Burrows-Wheeler Transform.
  2. Computing Abelian String Regularities Based on RLE.
  3. How to Answer a Small Batch of RMQs or LCA Queries in Practice.
  4. Shortest Unique Palindromic Substring Queries in Optimal Time.

LATA 2017

  1. Efficient Pattern Matching in Elastic-Degenerate Texts.
  2. Integrated Encryption in Dynamic Arithmetic Compression.
  3. Two-Dimensional Palindromes and Their Properties.

MFCS 2017

  1. Binary Search in Graphs Revisited.
  2. Small-Space LCE Data Structure with Constant-Time Queries.
  3. The Hardness of Solving Simple Word Equations.

SEA 2017

  1. A Framework of Dynamic Data Structures for String Processing.
  2. Compression with the tudocomp Framework.
  3. Engineering External Memory LCP Array Construction: Parallel, In-Place and Large Alphabet.
  4. Fast and Scalable Minimal Perfect Hashing for Massive Key Sets.
  5. Online Construction of Wavelet Trees.
  6. Practical Range Minimum Queries Revisited.
  7. The Quantile Index - Succinct Self-Index for Top-k Document Retrieval.

SISAP 2017

  1. Practical Space-Efficient Data Structures for High-Dimensional Orthogonal Range Searching.
  2. Scalable Similarity Search for Molecular Descriptors.
  3. Succinct Quadtrees for Road Data.

SODA 2017

  1. File Maintenance: When in Doubt, Change the Layout!
  2. Hardness of Permutation Pattern Matching.
  3. Space-Efficient Construction of Compressed Indexes in Deterministic Linear Time.
  4. Sparse Suffix Tree Construction in Optimal Time and Space.
  5. pBWT: Achieving Succinct Data Structures for Parameterized Pattern Matching and Related Problems.

SOFSEM 2017

  1. Computing Longest Single-arm-gapped Palindromes in a String.
  2. Edit-Distance Between Visibly Pushdown Languages.
  3. Longest Common Subsequence in at Least k Length Order-Isomorphic Substrings.

SPIRE 2017

  1. A Self-index on Block Trees.
  2. Constructing a Consensus Phylogeny from a Leaf-Removal Distance (Extended Abstract).
  3. Counting Palindromes in Substrings.
  4. Detecting One-Variable Patterns.
  5. Distinct Squares in Circular Words.
  6. Efficient Compression and Indexing of Trajectories.
  7. Fast Construction of Compressed Web Graphs.
  8. Fast Label Extraction in the CDAWG.
  9. Faster Practical Block Compression for Rank/Select Dictionaries.
  10. Greedy Shortest Common Superstring Approximation in Compact Space.
  11. LZ78 Compression in Low Main Memory Space.
  12. Lightweight BWT and LCP Merging via the Gap Algorithm.
  13. Linear-Size CDAWG: New Repetition-Aware Indexing and Grammar Compression.
  14. Listing Maximal Independent Sets with Minimal Space and Bounded Delay.
  15. Longest Common Factor After One Edit Operation.
  16. Mining Bit-Parallel LCS-length Algorithms.
  17. On Suffix Tree Breadth.
  18. On Two LZ78-style Grammars: Compression Bounds and Compressed-Space Computation.
  19. Optimal Skeleton Huffman Trees.
  20. Order Preserving Pattern Matching on Trees and DAGs.
  21. Pattern Matching on Elastic-Degenerate Text with Errors.
  22. Practical Evaluation of Lempel-Ziv-78 and Lempel-Ziv-Welch Tries.
  23. Practical Implementation of Space-Efficient Dynamic Keyword Dictionaries.
  24. Regular Abelian Periods and Longest Common Abelian Factors on Run-Length Encoded Strings.
  25. Succinct Partial Sums and Fenwick Trees.
  26. Tight Bounds for Top Tree Compression.

STACS 2017

  1. On Long Words Avoiding Zimin Patterns.
  2. On the Size of Lempel-Ziv and Lyndon Factorizations.

STOC 2017

  1. Synchronization strings: codes for insertions and deletions approaching the Singleton bound.

Stringology 2017

  1. A Family of Exact Pattern Matching Algorithms with Multiple Adjacent Search Windows.
  2. A Lempel-Ziv-style Compression Method for Repetitive Texts.
  3. Counting Mismatches with SIMD.
  4. Dismantling DivSufSort.
  5. Dynamic Succinct Data Structures and Compressed Random Access Memory.
  6. Faster Batched Range Minimum Queries.
  7. Many-MADFAct: Concurrently Constructing MADFAs.
  8. On Reverse Engineering the Lyndon Tree.
  9. Online Recognition of Dictionary with One Gap.
  10. Range Queries Using Huffman Wavelet Trees.
  11. Regular Expressions with Backreferences Re-examined.
  12. Speeding Up String Matching by Weak Factor Recognition.
  13. The Linear Equivalence of the Suffix Array and the Partially Sorted Lyndon Array.
  14. Trade-offs in Query and Target Indexing for the Selection of Candidates in Protein Homology Searches.

WABI 2017

  1. Optimal Computation of Overabundant Words.
  2. Rainbowfish: A Succinct Colored de Bruijn Graph Representation.

WADS 2017

  1. Optimal Query Time for Encoding Range Majority.

WALCOM 2017

  1. A Space-Efficient Algorithm for the Dynamic DFS Problem in Undirected Graphs.

WORDS 2017

  1. A de Bruijn Sequence Construction by Concatenating Cycles of the Complemented Cycling Register.
  2. Burrows-Wheeler Transform and Run-Length Enconding.
  3. Minimal Forbidden Factors of Circular Words.

ACM J. Exp. Algorithmics 2017

  1. Practical Compact Indexes for Top-k Document Retrieval.

Algorithmica 2017

  1. A Framework for Space-Efficient String Kernels.
  2. Compressed Subsequence Matching and Packed Tree Coloring.
  3. Efficient Computation of Substring Equivalence Classes with Suffix Arrays.
  4. Efficient Indexes for Jumbled Pattern Matching with Constant-Sized Alphabet.
  5. On the Succinct Representation of Equivalence Classes.
  6. String Powers in Trees.
  7. Top-k Term-Proximity in Succinct Space.

Algorithms Mol. Biol. 2017

  1. On avoided words, absent words, and their application to biological sequence analysis.

BMC Bioinform. 2017

  1. A framework for space-efficient read clustering in metagenomic samples.

Bioinform. 2017

  1. Succinct colored de Bruijn graphs.
  2. emMAW: computing minimal absent words in external memory.

CoRR 2017

  1. A Faster Implementation of Online Run-Length Burrows-Wheeler Transform.
  2. A Framework of Dynamic Data Structures for String Processing.
  3. A Grammar Compression Algorithm based on Induced Suffix Sorting.
  4. A Separation Between Run-Length SLPs and LZ77.
  5. A compressed dynamic self-index for highly repetitive text collections.
  6. A family of approximation algorithms for the maximum duo-preservation string mapping problem.
  7. A local search 2.917-approximation algorithm for duo-preservation string mapping.
  8. A succinct data structure for self-indexing ternary relations.
  9. Alphabet-dependent Parallel Algorithm for Suffix Tree Construction for Pattern Searching.
  10. Approximation ratio of RePair.
  11. Assembling sequences of DNA using an on-line algorithm based on DeBruijn graphs.
  12. At the Roots of Dictionary Compression: String Attractors.
  13. B-slack trees: Highly Space Efficient B-trees.
  14. Better Labeling Schemes for Nearest Common Ancestors through Minor-Universal Trees.
  15. Biased Predecessor Search.
  16. Bloom Filters, Adaptivity, and the Dictionary Problem.
  17. Bubble-Flip - A New Generation Algorithm for Prefix Normal Words.
  18. Cartesian trees and Lyndon trees.
  19. Closing in on Time and Space Optimal Construction of Compressed Indexes.
  20. Compaction of Church Numerals for Higher-Order Compression.
  21. Comparison of LZ77-type Parsings.
  22. Compressed Indexing with Signature Grammars.
  23. Compressed Representation of Dynamic Binary Relations with Applications.
  24. Compression with the tudocomp Framework.
  25. Computing Abelian regularities on RLE strings.
  26. Dismantling DivSufSort.
  27. Distinct Squares in Circular Words.
  28. Document Listing on Repetitive Collections with Guaranteed Performance.
  29. Duel and sweep algorithm for order-preserving pattern matching.
  30. Efficient Compression and Indexing of Trajectories.
  31. Efficient Dynamic Dictionary Matching with DAWGs and AC-automata.
  32. Efficient pattern matching in degenerate strings with the Burrows-Wheeler transform.
  33. Even faster sorting of (not only) integers.
  34. Exact Mean Computation in Dynamic Time Warping Spaces.
  35. Exploiting Computation-Friendly Graph Compression Methods.
  36. FAMOUS: Fast Approximate string Matching using OptimUm search Schemes.
  37. FMtree: A fast locating algorithm of FM-indexes for genomic data.
  38. Fast Compressed Self-Indexes with Deterministic Linear-Time Construction.
  39. Fast Computation of Graph Edit Distance.
  40. Fast Dynamic Arrays.
  41. Fast Label Extraction in the CDAWG.
  42. Fast Locating with the RLBWT.
  43. Fast and Simple Jumbled Indexing for Binary RLE Strings.
  44. Fast and Simple Parallel Wavelet Tree and Matrix Construction.
  45. Faster STR-IC-LCS computation via RLE.
  46. Faster algorithms for 1-mappability of a sequence.
  47. Faster batched range minimum queries.
  48. Faster range minimum queries.
  49. Faster truncated integer multiplication.
  50. From LZ77 to the Run-Length Encoded Burrows-Wheeler Transform, and Back.
  51. Grammar-Based Graph Compression.
  52. Greedy Shortest Common Superstring Approximation in Compact Space.
  53. How to answer a small batch of RMQs or LCA queries in practice.
  54. Hybridizing Non-dominated Sorting Algorithms: Divide-and-Conquer Meets Best Order Sort.
  55. HyperMinHash: Jaccard index sketching in LogLog space.
  56. Improved Average Complexity for Comparison-Based Sorting.
  57. Improved Bounds for Testing Forbidden Order Patterns.
  58. Improved bounds for testing Dyck languages.
  59. In-Place Initializable Arrays.
  60. Indexing Weighted Sequences: Neat and Efficient.
  61. Inverse Lyndon words and Inverse Lyndon factorizations of words.
  62. Lempel-Ziv: a “one-bit catastrophe” but not a tragedy.
  63. Linear-size CDAWG: new repetition-aware indexing and grammar compression.
  64. Longest common substring with approximately k mismatches.
  65. Lyndon Array Construction during Burrows-Wheeler Inversion.
  66. Maximal Unbordered Factors of Random Strings.
  67. Multiresolution Priority Queues.
  68. Near-Optimal Compression for the Planar Graph Metric.
  69. Near-optimal linear decision trees for k-SUM and related problems.
  70. New Cardinality Estimation Methods for HyperLogLog Sketches.
  71. New Variants of Pattern Matching with Constants and Variables.
  72. New cardinality estimation algorithms for HyperLogLog sketches.
  73. On Two LZ78-style Grammars: Compression Bounds and Compressed-Space Computation.
  74. On the Decision Tree Complexity of String Matching.
  75. On-line Assembling Mitochondrial DNA from de novo transcriptome.
  76. On-the-Fly Array Initialization in Less Space.
  77. Optimal Computation of Overabundant Words.
  78. Optimal Time and Space Construction of Suffix Arrays and LCP Arrays for Integer Alphabets.
  79. Optimal top dag compression.
  80. Optimal trade-offs for pattern matching with k mismatches.
  81. Order preserving pattern matching on trees and DAGs.
  82. Ordered Dags: HypercubeSort.
  83. Orthogonal Vectors Indexing.
  84. Palindromic Decompositions with Gaps and Errors.
  85. Persistent Cache-oblivious Streaming Indexes.
  86. Position Heaps for Parameterized Strings.
  87. Practical Evaluation of Lempel-Ziv-78 and Lempel-Ziv-Welch Tries.
  88. Practical and Effective Re-Pair Compression.
  89. Probabilistic Analysis of the Dual-Pivot Quicksort “Count”.
  90. Relations Between Greedy and Bit-Optimal LZ77 Encodings.
  91. Reoptimization of the Closest Substring Problem under Pattern Length Modification.
  92. Representing the suffix tree with the CDAWG.
  93. Run Compressed Rank/Select for Large Alphabets.
  94. Small-space encoding LCE data structure with constant-time queries.
  95. Space-Efficient Algorithms for Longest Increasing Subsequence.
  96. Space-efficient K-MER algorithm for generalized suffix tree.
  97. Streaming Pattern Matching with d Wildcards.
  98. Streaming Periodicity with Mismatches.
  99. String Attractors.
  100. Succinct Approximate Rank Queries.
  101. Succinct Partial Sums and Fenwick Trees.
  102. Text Indexing and Searching in Sublinear Time.
  103. The Case for Learned Index Structures.
  104. The Compressed Overlap Index.
  105. The Hidden Binary Search Tree: A Balanced Rotation-Free Search Tree in the AVL RAM Model.
  106. The complexity of the Multiple Pattern Matching Problem for random strings.
  107. The streaming k-mismatch problem.
  108. Time-Space Trade-Offs for Lempel-Ziv Compressed Indexing.
  109. Tree Edit Distance Cannot be Computed in Strongly Subcubic Time (unless APSP can).
  110. Trie Compression for GPU Accelerated Multi-Pattern Matching.
  111. Truly Sub-cubic Algorithms for Language Edit Distance and RNA Folding via Fast Bounded-Difference Min-Plus Product.
  112. Twin Sort Technique.
  113. Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs.
  114. m-Bonsai: a Practical Compact Dynamic Trie.

IEEE ACM Trans. Comput. Biol. Bioinform. 2017

  1. Benchmark Dataset for Whole Genome Sequence Compression.

IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 2017

  1. Packed Compact Tries: A Fast and Efficient Data Structure for Online String Processing.

Inf. Process. Lett. 2017

  1. Optimal suffix sorting and LCP array construction for constant alphabets.
  2. Tight lower bounds for the longest common extension problem.
  3. Two strings at Hamming distance 1 cannot be both quasiperiodic.

Inf. Retr. J. 2017

  1. Document retrieval on repetitive string collections.

Inf. Syst. 2017

  1. Compressed representation of dynamic binary relations with applications.

J. Comput. Syst. Sci. 2017

  1. Fast algorithms for Abelian periods in words and greatest common divisor queries.
  2. Fingerprints in compressed strings.

J. Discrete Algorithms 2017

  1. A space efficient direct access data structure.
  2. A succinct data structure for self-indexing ternary relations.
  3. Burrows-Wheeler transform and LCP array construction in constant space.
  4. Grammar compressed sequences with rank/select support.
  5. Preface - Compact Data Structures.
  6. Subsequence automata with default transitions.

Math. Comput. Sci. 2017

  1. Block Graphs in Practice.
  2. Compressed Spaced Suffix Arrays.
  3. Engineering a Lightweight External Memory Suffix Array Construction Algorithm.

Math. Struct. Comput. Sci. 2017

  1. Fast circular dictionary-matching algorithm.

Pattern Recognit. Lett. 2017

  1. A faster and more accurate heuristic for cyclic edit distance computation.

SIAM J. Comput. 2017

  1. The “Runs” Theorem.
  2. Time-Optimal Top-k Document Retrieval.

Theor. Comput. Sci. 2017

  1. Covering problems for partial words and for indeterminate strings.
  2. Inducing enhanced suffix arrays for string collections.
  3. Inferring strings from Lyndon factorization.
  4. String cadences.
  5. Wheeler graphs: A framework for BWT-based data structures.

ALENEX 2016

  1. A General Framework for Dynamic Succinct and Compressed Data Structures.

COCOA 2016

  1. On-Line Pattern Matching on Uncertain Sequences and Applications.

CPM 2016

  1. A 7/2-Approximation Algorithm for the Maximum Duo-Preservation String Mapping Problem.
  2. A Linear-Time Algorithm for the Copy Number Transformation Problem.
  3. Boxed Permutation Pattern Matching.
  4. Color-Distance Oracles and Snippets.
  5. Deterministic Sub-Linear Space LCE Data Structures With Efficient Construction.
  6. Efficient Index for Weighted Sequences.
  7. Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost.
  8. Encoding Two-Dimensional Range Top-k Queries.
  9. Estimating Statistics on Words Using Ambiguous Descriptions.
  10. Factorizing a String into Squares in Linear Time.
  11. Fast Compatibility Testing for Rooted Phylogenetic Trees.
  12. Faster Longest Common Extension Queries in Strings over General Alphabets.
  13. Finding Maximal 2-Dimensional Palindromes.
  14. Front Matter, Table of Contents, Preface.
  15. Fully-online Construction of Suffix Trees for Multiple Texts.
  16. Genomic Scaffold Filling Revisited.
  17. Graph Motif Problems Parameterized by Dual.
  18. Hardness of RNA Folding Problem With Four Symbols.
  19. Linear-time Suffix Sorting - A New Approach for Suffix Array Construction.
  20. Longest Common Substring with Approximately k Mismatches.
  21. Minimal Suffix and Rotation of a Substring in Optimal Time.
  22. On Almost Monge All Scores Matrices.
  23. On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching.
  24. Optimal Prefix Free Codes with Partial Sorting.
  25. Reconstruction of Trees from Jumbled and Weighted Subtrees.
  26. Space-Efficient Dictionaries for Parameterized and Order-Preserving Pattern Matching.
  27. Succinct Online Dictionary Matching with Improved Worst-Case Guarantees.
  28. The Nearest Colored Node in a Tree.
  29. Tight Tradeoffs for Real-Time Approximation of Longest Palindromes in Streams.
  30. Truly Subquadratic-Time Extension Queries and Periodicity Detection in Strings with Uncertainties.

DCC 2016

  1. A Simple and Efficient Approach for Adaptive Entropy Coding over Large Alphabets.
  2. A Space Efficient Direct Access Data Structure.
  3. Analysis of a Rewriting Compression System for Flash Memory.
  4. Approximate String Matching for Self-Indexes.
  5. Burrows-Wheeler Transform for Terabases.
  6. CS2A: A Compressed Suffix Array-Based Method for Short Read Alignment.
  7. Compressing Combinatorial Objects.
  8. Computing LZ77 in Run-Compressed Space.
  9. Efficient Compression of Genomic Sequences.
  10. Efficient Environmental Temperature Monitoring Using Compressed Sensing.
  11. Faster, Minuter.
  12. Grammatical Ziv-Lempel Compression: Achieving PPM-Class Text Compression Ratios with LZ-Class Decompression Speed.
  13. Hardware Based Compression in Big Data.
  14. Improved Range Minimum Queries.
  15. Induced Suffix Sorting for String Collections.
  16. Lempel-Ziv Computation in Compressed Space (LZ-CICS).
  17. Linear Time Succinct Indexable Dictionary Construction with Applications.
  18. Lossy Compression of Unordered Rooted Trees.
  19. Online Grammar Transformation Based on Re-Pair Algorithm.
  20. Parallel Lightweight Wavelet Tree, Suffix Array and FM-Index Construction.
  21. Positional Inverted Self-index.
  22. Quick Access to Compressed Data in Storage Systems.
  23. Self-Indexing RDF Archives.
  24. Shortest DNA Cyclic Cover in Compressed Space.
  25. Small Polygon Compression.
  26. Timeliness in Lossless Block Coding.
  27. When Less is More - Using Restricted Repetition Search in Fast Compressors.

DLT 2016

  1. Ternary Square-Free Partial Words with Many Wildcards.

ESA 2016

  1. BlockQuicksort: Avoiding Branch Mispredictions in Quicksort.
  2. Faster External Memory LCP Array Construction.
  3. Streaming Pattern Matching with d Wildcards.

FOCS 2016

  1. Edit Distance: Sketching, Streaming, and Document Exchange.

FSTTCS 2016

  1. Finger Search in Grammar-Compressed Strings.
  2. LZ77 Factorisation of Trees.

ICALP 2016

  1. Approximate Hamming Distance in a Stream.
  2. Data Structure Lower Bounds for Document Indexing Problems.
  3. Towards Tight Lower Bounds for Range Reporting on the RAM.

ISAAC 2016

  1. Dynamic Relative Compression, Dynamic Partial Sums, and Substring Concatenation.
  2. Mind the Gap: Essentially Optimal Algorithms for Online Dictionary Matching with One Gap.
  3. Pattern Matching and Consensus Problems on Weighted Sequences and Profiles.
  4. Space-Time Trade-Offs for the Shortest Unique Substring Problem.

ITCS 2016

  1. Is There an Oblivious RAM Lower Bound?

IWOCA 2016

  1. Finding Gapped Palindromes Online.
  2. Packed Compact Tries: A Fast and Efficient Data Structure for Online String Processing.
  3. Partial Covering Arrays: Algorithms and Asymptotics.

KDD 2016

  1. Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices.

LATA 2016

  1. On Del-Robust Primitive Partial Words with One Hole.
  2. Optimal Bounds for Computing \alpha α -gapped Repeats.

LATIN 2016

  1. Bidirectional Variable-Order de Bruijn Graphs.
  2. Compressing Bounded Degree Graphs.
  3. Deterministic Sparse Suffix Sorting on Rewritable Texts.
  4. Linear-Time Sequence Comparison Using Minimal Absent Words & Applications.
  5. The Grandmama de Bruijn Sequence for Binary Strings.
  6. Tree Compression Using String Grammars.

MFCS 2016

  1. Computing DAWGs and Minimal Absent Words in Linear Time for Integer Alphabets.
  2. Dividing by Zero - How Bad Is It, Really?.
  3. Fully Dynamic Data Structure for LCE Queries in Compressed Space.
  4. Shortest Unique Substring Queries on Run-Length Encoded Strings.

SEA 2016

  1. CHICO: A Compressed Hybrid Index for Repetitive Collections.
  2. Fast Scalable Construction of (Minimal Perfect Hash) Functions.
  3. Lempel-Ziv Decoding in External Memory.
  4. Practical Dynamic Entropy-Compressed Bitvectors with Applications.
  5. Practical Variable Length Gap Pattern Matching.
  6. Worst-Case-Efficient Dynamic Arrays in Practice.

SIGIR 2016

  1. Fast and Compact Hamming Distance Index.
  2. Succinct Data Structures in Information Retrieval: Theory and Practice.

SODA 2016

  1. Range Predecessor and Lempel-Ziv Parsing.
  2. The k-mismatch problem revisited.
  3. Weighted dynamic finger in binary search trees.

SOFSEM 2016

  1. Compacting a Dynamic Edit Distance Table by RLE Compression.
  2. Subsequence Automata with Default Transitions.

SPIRE 2016

  1. A Linear-Space Algorithm for the Substring Constrained Alignment Problem.
  2. AC-Automaton Update Algorithm for Semi-dynamic Dictionary Matching.
  3. Analyzing Relative Lempel-Ziv Reference Construction.
  4. Bookmarks in Grammar-Compressed Strings.
  5. Compact Trip Representation over Networks.
  6. Dynamic and Approximate Pattern Matching in 2D.
  7. Efficient Representation of Multidimensional Data over Hierarchical Domains.
  8. Efficient and Compact Representations of Some Non-canonical Prefix-Free Codes.
  9. Fast Classification of Protein Structures by an Alignment-Free Kernel.
  10. Fragmented BWT: An Extended BWT for Full-Text Indexing.
  11. Fully Dynamic de Bruijn Graphs.
  12. GraCT: A Grammar Based Compressed Representation of Trajectories.
  13. Inverse Range Selection Queries.
  14. LCP Array Construction Using O(sort(n)) (or Less) I/Os.
  15. Lexical Matching of Queries and Ads Bid Terms in Sponsored Search.
  16. Longest Common Abelian Factors and Large Alphabets.
  17. Low Space External Memory Construction of the Succinct Permuted Longest Common Prefix Array.
  18. Maximal Unbordered Factors of Random Strings.
  19. Near-Optimal Computation of Runs over General Alphabet via Non-Crossing LCE Queries.
  20. Parallel Computation for the All-Pairs Suffix-Prefix Problem.
  21. Parallel Lookups in String Indexes.
  22. Pattern Matching for Separable Permutations.
  23. RLZAP: Relative Lempel-Ziv with Adaptive Pointers.
  24. The Smallest Grammar Problem Revisited.
  25. XBWT Tricks.

STACS 2016

  1. Efficiently Finding All Maximal alpha-gapped Repeats.
  2. External Memory Three-Sided Range Reporting and Top-k Queries with Sublogarithmic Updates.
  3. Periods and Borders of Random Words.

STOC 2016

  1. Streaming algorithms for embedding and computing edit distance in the low distance regime.

SWAT 2016

  1. A Framework for Dynamic Parameterized Dictionary Matching.
  2. A Simple Mergeable Dictionary.
  3. Cuckoo Filter: Simplification and Analysis.
  4. Lower Bounds for Approximation Schemes for Closest String.

Stringology 2016

  1. A Family of Data Compression Codes with Multiple Delimiters.
  2. A Resource-frugal Probabilistic Dictionary and Applications in (Meta)Genomics.
  3. Accelerated Partial Decoding in Wavelet Trees.
  4. Algorithms to Compute the Lyndon Array.
  5. Computing All Approximate Enhanced Covers with the Hamming Distance.
  6. Computing Smallest and Largest Repetition Factorizations in O(n log n) Time.
  7. Dynamic Index and LZ Factorization in Compressed Space.
  8. Fast Full Permuted Pattern Matching Algorithms on Multi-track Strings.
  9. Forced Repetitions over Alphabet Lists.
  10. Generating All Minimal Petri Net Unsolvable Binary Words.
  11. Interpreting the Subset Construction Using Finite Sublanguages.
  12. Jumbled Matching with SIMD.
  13. The String Matching Algorithms Research Tool.
  14. The Use and Usefulness of Fibonacci Codes.
  15. Using Human Computation in Dead-zone based 2D Pattern Matching.

WABI 2016

  1. A Graph Extension of the Positional Burrows-Wheeler Transform and Its Applications.
  2. A Natural Encoding of Genetic Variation in a Burrows-Wheeler Transform to Enable Mapping and Genome Inference.
  3. Optimal Computation of Avoided Words.

ACM J. Exp. Algorithmics 2016

  1. Faster Compressed Suffix Trees for Repetitive Collections.
  2. Inducing Suffix and LCP Arrays in External Memory.
  3. LCP Array Construction in External Memory.
  4. Lazy Lempel-Ziv Factorization Algorithms.

ACM Trans. Algorithms 2016

  1. Compressed Cache-Oblivious String B-Tree.
  2. Data Structures for Path Queries.
  3. Sparse Text Indexing in Small Space.

ACM Trans. Archit. Code Optim. 2016

  1. Yet Another Compressed Cache: A Low-Cost Yet Effective Compressed Cache.

Algorithmica 2016

  1. Compressed String Dictionary Search with Edit Distance One.
  2. Optimal Encodings for Range Majority Queries.

Algorithms 2016

  1. siEDM: An Efficient String Index and Search Algorithm for Edit Distance with Moves.

Algorithms Mol. Biol. 2016

  1. Circular sequence comparison: algorithms and applications.
  2. Erratum to: Circular sequence comparison: algorithms and applications.

BMC Bioinform. 2016

  1. libFLASM: a software library for fixed-length approximate string matching.

CoRR 2016

  1. A Memory Bandwidth-Efficient Hybrid Radix Sort on GPUs.
  2. A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings.
  3. A Self-Index on Block Trees.
  4. A Simpler Bit-parallel Algorithm for Swap Matching.
  5. A family of fast exact pattern matching algorithms.
  6. A hardness result and new algorithm for the longest common palindromic subsequence problem.
  7. A loopless and branchless $O(1)$ algorithm to generate the next Dyck word.
  8. Access Time Tradeoffs in Archive Compression.
  9. Aggregated 2D Range Queries on Clustered Points.
  10. Algorithms to Compute the Lyndon Array.
  11. An Estimation of the Size of Non-Compact Suffix Trees.
  12. An Optimal Algorithm for Range Search on Multidimensional Points.
  13. Approximate Hamming distance in a stream.
  14. Asymmetric Rényi Problem and PATRICIA Tries.
  15. Average Size of a Suffix Tree for Markov Sources.
  16. Bidirectional Conditional Insertion Sort algorithm; An efficient progress on the classical insertion sort.
  17. Burrows-Wheeler transform and LCP array construction in constant space.
  18. CSA++: Fast Pattern Search for Large Alphabets.
  19. Comments on Dumitrescu’s “A Selectable Sloppy Heap”.
  20. Compressed Dynamic Range Majority Data Structures.
  21. Compressing Graphs and Indexes with Recursive Graph Bisection.
  22. Compressing and Indexing Stock Market Data.
  23. Computing All Distinct Squares in Linear Time for Integer Alphabets.
  24. Computing Longest Increasing Subsequence Over Sequential Data Streams.
  25. Computing longest single-arm-gapped palindromes in a string.
  26. Data Structure Lower Bounds for Document Indexing Problems.
  27. Designing optimal- and fast-on-average pattern matching algorithms.
  28. Detecting Unary Patterns.
  29. Deterministic Indexing for Packed Strings.
  30. Deterministic sub-linear space LCE data structures with efficient construction.
  31. Distortion-Resistant Hashing for rapid search of similar DNA subsequence.
  32. Document Retrieval on Repetitive String Collections.
  33. Dual-Pivot Quicksort: Optimality, Analysis and Zeros of Associated Lattice Paths.
  34. Dynamic Time Warping: Breaking the Quadratic Barrier.
  35. Dynamic index and LZ factorization in compressed space.
  36. Edit Distance: Sketching, Streaming and Document Exchange.
  37. Efficient Index Maintenance Under Dynamic Genome Modification.
  38. Efficient Index for Weighted Sequences.
  39. Efficient Pattern Matching in Elastic-Degenerate Strings.
  40. Efficient Representation of Multidimensional Data over Hierarchical Domains.
  41. Efficient and Compact Representations of Some Non-Canonical Prefix-Free Codes.
  42. Encoding Arguments.
  43. Energy-Efficient Algorithms.
  44. Engineering a Distributed Full-Text Index.
  45. Fast Longest Common Extensions in Small Space.
  46. Faster Longest Common Extension Queries in Strings over General Alphabets.
  47. From H&M to Gap for Lightweight BWT Merging.
  48. Fully Dynamic de Bruijn Graphs.
  49. Fully dynamic data structure for LCE queries in compressed space.
  50. Games from Basic Data Structures.
  51. GateKeeper: Enabling Fast Pre-Alignment in DNA Short Read Mapping with a New Streaming Accelerator Architecture.
  52. GraCT: A Grammar based Compressed representation of Trajectories.
  53. Hardness of Permutation Pattern Matching.
  54. Improved Space efficient algorithms for BFS, DFS and applications.
  55. In-Place Longest Common Extensions.
  56. LZ-End Parsing in Compressed Space.
  57. Lempel-Ziv Decoding in External Memory.
  58. Lightweight LCP Construction for Very Large Collections of Strings.
  59. Linear-time string indexing and analysis in small space.
  60. Longest Common Extensions with Recompression.
  61. Longest Common Subsequence in at Least k Length Order-isomorphic Substrings.
  62. Low Space External Memory Construction of the Succinct Permuted Longest Common Prefix Array.
  63. Minimal Suffix and Rotation of a Substring in Optimal Time.
  64. Monte Carlo Sort for unreliable human comparisons.
  65. Multi-view pattern matching.
  66. Near-Optimal Computation of Runs over General Alphabet via Non-Crossing LCE Queries.
  67. New Error Tolerant Method to Search Long Repeats in Symbol Sequences.
  68. Oblivious Sorting and Queues.
  69. On pattern matching with k mismatches and few don’t cares.
  70. On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching.
  71. On the Size of Lempel-Ziv and Lyndon Factorizations.
  72. On the circuit complexity of the standard and the Karatsuba methods of multiplying integers.
  73. Online Grammar Compression for Frequent Pattern Discovery.
  74. Optimal Computation of Avoided Words.
  75. Optimal In-Place Suffix Sorting.
  76. Optimal Prefix Free Codes With Partial Sorting.
  77. Optimizing run-length algorithm using octonary repetition tree.
  78. Pachinko.
  79. Packed Compact Tries: A Fast and Efficient Data Structure for Online String Processing.
  80. Parameterized Pattern Matching - Succinctly.
  81. Practical Data Compression for Modern Memory Hierarchies.
  82. Practical combinations of repetition-aware data structures.
  83. RLZAP: Relative Lempel-Ziv with Adaptive Pointers.
  84. Randomized Ternary Search Tries.
  85. Range Majorities and Minorities in Arrays.
  86. Rank and select: Another lesson learned.
  87. Representing Pattern Matching Algorithms by Polynomial-Size Automata.
  88. Scalable Construction of Text Indexes.
  89. Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices.
  90. Shortest unique palindromic substring queries in optimal time.
  91. Simple and Efficient Fully-Functional Succinct Trees.
  92. Sort Race.
  93. Sort well with energy-constrained comparisons.
  94. Sorting Discrete i.i.d. Inputs: Quicksort is Optimal.
  95. Space-Efficient Construction of Compressed Indexes in Deterministic Linear Time.
  96. Space-Efficient Re-Pair Compression.
  97. Sparse Suffix Tree Construction in Optimal Time and Space.
  98. Streaming Algorithms For Computing Edit Distance Without Exploiting Suffix Trees.
  99. Streaming k-mismatch with data recovery and applications.
  100. String Cadences.
  101. String Inference from the LCP Array.
  102. Succinct Choice Dictionaries.
  103. Succinct data-structure for nearest colored node in a tree.
  104. Suffix arrays with a twist.
  105. The Generalized Smallest Grammar Problem.
  106. The complexity of bit retrieval.
  107. The landscape of bounds for binary search trees.
  108. Tight Lower Bounds for the Longest Common Extension Problem.
  109. Tight Tradeoffs for Real-Time Approximation of Longest Palindromes in Streams.
  110. Tight bound on the maximum number of shortest unique substrings.
  111. Toward a Succinct Index for Order-Preserving Pattern Matching.
  112. Twenty (simple) questions.
  113. Two-stage algorithms for covering array construction.
  114. TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes.
  115. Universal Indexes for Highly Repetitive Document Collections.
  116. Variance of the Internal Profile in Suffix Trees.
  117. Word Existence Algorithm.
  118. siEDM: an efficient string index and search algorithm for edit distance with moves.

Dagstuhl Reports 2016

  1. Computation over Compressed Structured Data (Dagstuhl Seminar 16431).

Discret. Appl. Math. 2016

  1. A computational substantiation of the d-step approach to the number of distinct squares problem.
  2. A multiobjective optimization algorithm for the weighted LCS.
  3. A note on easy and efficient computation of full abelian periods of a word.
  4. Closed factorization.
  5. Computing covers using prefix tables.
  6. Editorial: Stringology Algorithms.
  7. New tabulation and sparse dynamic programming based techniques for sequence similarity problems.
  8. Optimal partitioning of data chunks in deduplication systems.
  9. Random access to Fibonacci encoded files.
  10. Sequence binary decision diagram: Minimization, relationship to acyclic automata, and complexities of Boolean set operations.
  11. Similarity based deduplication with small data chunks.
  12. The New Periodicity Lemma revisited.
  13. The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings.

IEEE ACM Trans. Comput. Biol. Bioinform. 2016

  1. Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data.

IEEE Trans. Parallel Distributed Syst. 2016

  1. A Survey Of Architectural Approaches for Data Compression in Cache and Main Memory Systems.

Inf. 2016

  1. Lazy Management for Frequency Table on Hardware-Based Stream Lossless Data Compression.

Inf. Process. Lett. 2016

  1. Computing runs on a general alphabet.
  2. On the greedy algorithm for the Shortest Common Superstring problem with reversals.

Inf. Syst. 2016

  1. Aggregated 2D range queries on clustered points.
  2. New dynamic metric indices for secondary memory.
  3. Practical compressed string dictionaries.
  4. Universal indexes for highly repetitive document collections.

J. Discrete Algorithms 2016

  1. An improved algorithm for the all-pairs suffix-prefix problem.

SIAM J. Discret. Math. 2016

  1. Efficient Ranking of Lyndon Words and Decoding Lexicographically Minimal de Bruijn Sequence.

Softw. Pract. Exp. 2016

  1. Improving a lightweight LZ77 computation algorithm for running faster.

Theor. Comput. Sci. 2016

  1. A really simple approximation of smallest grammar.
  2. Computing minimal and maximal suffixes of a substring.
  3. Document retrieval with one wildcard.
  4. Dynamic range majority data structures.
  5. Fast computation of abelian runs.
  6. Fast construction of wavelet trees.
  7. Faster Lyndon factorization algorithms for SLP and LZ78 compressed text.
  8. Finding the leftmost critical factorization on unordered alphabet.
  9. Generalized pattern matching and periodicity under substring consistent equivalence relations.
  10. Linear-time computation of prefix table for weighted strings & applications.
  11. Linear-time superbubble identification algorithm for genome assembly.
  12. Longest common extensions in trees.
  13. Maximum number of distinct and nonequivalent nonstandard squares in a word.
  14. Order-preserving indexing.
  15. Order-preserving pattern matching with k mismatches.
  16. Permuted scaled matching.
  17. Reporting consecutive substring occurrences under bounded gap constraints.
  18. Simple and efficient fully-functional succinct trees.
  19. Tighter bounds for the sum of irreducible LCP values.

ALENEX 2015

  1. A Data-Aware FM-index.
  2. Faster Linear-space Orthogonal Range Searching in Arbitrary Dimensions.
  3. Improved Single-Term Top-k Document Retrieval.

BCB 2015

  1. Fast and efficient compression of high-throughput sequencing reads.

BPOE 2015

  1. Stream-Based Lossless Data Compression Hardware Using Adaptive Frequency Table Management.

CIAC 2015

  1. An Opportunistic Text Indexing Structure Based on Run Length Encoding.

CPM 2015

  1. A Framework for Space-Efficient String Kernels.
  2. A Probabilistic Analysis of the Reduction Ratio in the Suffix-Array IS-Algorithm.
  3. Alphabet-Dependent String Searching with Wexponential Search Trees.
  4. Combinatorial RNA Design: Designability and Structure-Approximating Algorithm.
  5. Compact Indexes for Flexible Top- k k Retrieval.
  6. Composite Repetition-Aware Data Structures.
  7. Dictionary Matching with Uneven Gaps.
  8. Efficient Construction of a Compressed de Bruijn Graph for Pan-Genome Analysis.
  9. Encoding Nearest Larger Values.
  10. Encodings of Range Maximum-Sum Segment Queries and Applications.
  11. Fast String Dictionary Lookup with One Error.
  12. Greedy Conjecture for Strings of Length 4.
  13. Improved Algorithms for the Boxed-Mesh Permutation Pattern Matching Problem.
  14. LZD Factorization: Simple and Practical Online Grammar Compression with Variable-to-Fixed Encoding.
  15. Lempel Ziv Computation in Small Space (LZ-CISS).
  16. Longest Common Extensions in Sublinear Space.
  17. Longest Common Extensions in Trees.
  18. On Maximal Unbordered Factors.
  19. On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction Problem.
  20. On the Hardness of Optimal Vertex Relabeling and Restricted Vertex Relabeling.
  21. On the Readability of Overlap Digraphs.
  22. Online Detection of Repetitions with Backtracking.
  23. Parallel External Memory Suffix Sorting.
  24. Parameterized Complexity of Superstring Problems.
  25. Partition into Heapable Sequences, Heap Tableaux and a Multiset Extension of Hammersley’s Process.
  26. Range Minimum Query Indexes in Higher Dimensions.
  27. Ranked Document Retrieval with Forbidden Pattern.
  28. Reporting Consecutive Substring Occurrences Under Bounded Gap Constraints.
  29. Semi-dynamic Compact Index for Short Patterns and Succinct van Emde Boas Tree.
  30. Sorting by Cuts, Joins and Whole Chromosome Duplications.
  31. String Powers in Trees.
  32. Succinct Non-overlapping Indexing.
  33. The Approximability of Maximum Rooted Triplets Consistency with Fan Triplets and Forbidden Triplets.
  34. Tighter Bounds for the Sum of Irreducible LCP Values.

DCC 2015

  1. Bi-Directional Context Modeling with Combinatorial Structuring for Genome Sequence Compression.
  2. Compressing Yahoo Mail.
  3. Compression for Similarity Identification: Computing the Error Exponent.
  4. Compression of Next Generation Sequencing Data.
  5. Compression-Aware Algorithms for Massive Datasets.
  6. Data Compression Cost Optimization.
  7. Document Counting in Compressed Space.
  8. Efficient Set Operations over k2-Trees.
  9. Enhanced Direct Access to Huffman Encoded Files.
  10. Faster Compressed Quadtrees.
  11. Geometric Compression of Orientation Signals for Fast Gesture Analysis.
  12. Improving PPM with Dynamic Parameter Updates.
  13. Incremental Locality and Clustering-Based Compression.
  14. On Probability Estimation via Relative Frequencies and Discount.
  15. OnlineRePair: A Recompressor for XML Structures.
  16. Parallel Wavelet Tree Construction.
  17. Queries on LZ-Bounded Encodings.
  18. Range Selection Queries in Data Aware Space and Time.
  19. Serializing RDF in Compressed Space.
  20. Smaller and Faster: Parallel Processing of Compressed Graphs with Ligra+.
  21. Universal Compression of Memoryless Sources over Large Alphabets via Independent Component Analysis.
  22. Variable-Order de Bruijn Graphs.

DEXA Workshops 2015

  1. Longest Previous Non-overlapping Factors Computation.

DLT 2015

  1. Diverse Palindromic Factorization Is NP-complete.
  2. Grammar-Based Tree Compression.
  3. Squareable Words.
  4. State Complexity of Neighbourhoods and Approximate Pattern Matching.
  5. Transfinite Lyndon Words.
  6. Unary Patterns with Permutations.

ESA 2015

  1. Access, Rank, and Select in Grammar-compressed Strings.
  2. Approximating LZ77 via Small-Space Multiple-Pattern Matching.
  3. Compressed Data Structures for Dynamic Sequences.
  4. Dictionary Matching in a Stream.

FCT 2015

  1. Longest α-Gapped Repeat and Palindrome.

FOCS 2015

  1. Pattern-Avoiding Access in Binary Search Trees.
  2. Quadratic Conditional Lower Bounds for String Problems and Dynamic Time Warping.
  3. Tight Hardness Results for LCS and Other Sequence Similarity Measures.

ICALP (1) 2015

  1. Hollow Heaps.
  2. Optimal Encodings for Range Top- k k , Selection, and Min-Max.
  3. Replacing Mark Bits with Randomness in Fibonacci Heaps.

ISAAC 2015

  1. An In-place Framework for Exact and Approximate Shortest Unique Substring Queries.
  2. Inferring Strings from Full Abelian Periods.
  3. Multidimensional Range Selection.
  4. On the Succinct Representation of Unlabeled Permutations.
  5. Optimal Search Trees with 2-Way Comparisons.

IWOCA 2015

  1. Computing the BWT and the LCP Array in Constant Space.
  2. EERTREE: An Efficient Data Structure for Processing Palindromes in Strings.
  3. Longest Common Extensions in Partial Words.

LATA 2015

  1. Average Linear Time and Compressed Space Construction of the Burrows-Wheeler Transform.
  2. Average-Case Optimal Approximate Circular String Matching.
  3. Backward Linearised Tree Pattern Matching.
  4. Compressed Data Structures for Range Searching.
  5. Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree.
  6. Coverability in Two Dimensions.
  7. Equation x^iy^jx^k=u^iv^ju^k in Words.
  8. On the Language of Primitive Partial Words.
  9. On the Number of Closed Factors in a Word.
  10. Online Computation of Abelian Runs.
  11. Square-Free Words over Partially Commutative Alphabets.

MFCS (1) 2015

  1. Longest Gapped Repeats and Palindromes.
  2. Strong Inapproximability of the Shortest Reset Word.

MFCS (2) 2015

  1. Faster Lightweight Lempel-Ziv Parsing.

PPAM (2) 2015

  1. Parallelising the Computation of Minimal Absent Words.

SEA 2015

  1. A Bulk-Parallel Priority Queue in External Memory with STXXL.
  2. Huffman Codes versus Augmented Non-Prefix-Free Codes.
  3. Parallel Construction of Succinct Trees.
  4. Tree Compression with Top Trees Revisited.

SODA 2015

  1. A new characterization of maximal repetitions by Lyndon trees.
  2. Approximate Range Emptiness in Constant Time and Optimal Space.
  3. Cell-probe bounds for online edit distance and other pattern matching problems.
  4. Internal Pattern Matching Queries in a Text and Applications.
  5. The amortized cost of finding the minimum.
  6. Wavelet Trees Meet Suffix Trees.

SPIRE 2015

  1. A Compact RDF Store Using Suffix Arrays.
  2. A Faster Algorithm for Computing Maximal \alpha -gapped Repeats in a String.
  3. Adaptive Computation of the Swap-Insert Correction Distance.
  4. Assessing the Efficiency of Suffix Stripping Approaches for Portuguese Stemming.
  5. Beyond the Runs Theorem.
  6. Chaining Fragments in Sequences: to Sweep or Not (Extended Abstract).
  7. Computing the Longest Unbordered Substring.
  8. DeShaTo: Describing the Shape of Cumulative Topic Distributions to Rank Retrieval Systems Without Relevance Judgments.
  9. Efficient Algorithms for Longest Closed Factor Array.
  10. Efficient Term Set Prediction Using the Bell-Wigner Inequality.
  11. Evaluating Geographical Knowledge Re-Ranking, Linguistic Processing and Query Expansion Techniques for Geographical Information Retrieval.
  12. Fast Online Lempel-Ziv Factorization in Compressed Space.
  13. Faster Exact Search Using Document Clustering.
  14. Feasibility of Word Difficulty Prediction.
  15. Filtration Algorithms for Approximate Order-Preserving Matching.
  16. Fishing in Read Collections: Memory Efficient Indexing for Sequence Assembly.
  17. How Big is that Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra.
  18. Improved Practical Compact Dynamic Tries.
  19. Induced Sorting Suffixes in External Memory with Better Design and Less Space.
  20. Longest Common Prefix with Mismatches.
  21. On Prefix/Suffix-Square Free Words.
  22. Online Self-Indexed Grammar Compression.
  23. Parallel Construction of Succinct Representations of Suffix Tree Topologies.
  24. Prefix and Suffix Reversals on Strings.
  25. Range LCP Queries Revisited.
  26. Relative Select.
  27. Sampling the Suffix Array with Minimizers.
  28. Selective Labeling and Incomplete Label Mitigation for Low-Cost Evaluation.
  29. ShRkC: Shard Rank Cutoff Prediction for Selective Search.
  30. Space-Efficient Detection of Unusual Words.
  31. Temporal Analysis of CHAVE Collection.
  32. Temporal Query Classification at Different Granularities.
  33. Tight Bound for the Number of Distinct Palindromes in a Tree.
  34. Transforming XML Streams with References.

STACS 2015

  1. Lempel-Ziv Factorization May Be Harder Than Computing All Runs.
  2. Pattern Matching with Variables: Fast Algorithms and New Hardness Results.
  3. Space-efficient Basic Graph Algorithms.

STOC 2015

  1. Edit Distance Cannot Be Computed in Strongly Subquadratic Time (unless SETH is false).

Stringology 2015

  1. A Faster Longest Common Extension Algorithm on Compressed Strings and its Applications.
  2. A Formal Framework for Stringology.
  3. Alternative Algorithms for Order-Preserving Matching.
  4. An Efficient Skip-Search Approach to the Order-Preserving Pattern Matching Problem.
  5. Combinatorics of the Interrupted Period.
  6. Computing Left-Right Maximal Generic Words.
  7. Controlling the Chunk-Size in Deduplication Systems.
  8. Efficient Algorithm for δ-Approximate Jumbled Pattern Matching.
  9. Enhanced Extraction from Huffman Encoded Files.
  10. Parameterized Matching: Solutions and Extensions.
  11. Quantum Leap Pattern Matching.
  12. Refined Tagging of Complex Verbal Phrases for the Italian Language.
  13. Tuning Algorithms for Jumbled Matching.

WABI 2015

  1. Bloom Filter Trie - A Data Structure for Pan-Genome Storage.
  2. Circular Sequence Comparison with q-grams.
  3. Optimizing Read Reversals for Sequence Compression - (Extended Abstract).

WADS 2015

  1. Universal Reconstruction of a String.

WALCOM 2015

  1. A Practical Succinct Data Structure for Tree-Like Graphs.
  2. Non-repetitive Strings over Alphabet Lists.

WORDS 2015

  1. Arithmetics on Suffix Arrays of Fibonacci Words.
  2. Linear-Time Computation of Prefix Table for Weighted Strings.

WWW 2015

  1. Compressed Indexes for String Searching in Labeled Graphs.

ACM Trans. Algorithms 2015

  1. Optimal Lower and Upper Bounds for Representing Sequences.

Algorithmica 2015

  1. Binary Jumbled Pattern Matching on Trees and Tree-Like Structures.
  2. Fast Algorithm for Partial Covers in Words.
  3. Improved Space-Time Tradeoffs for Approximate Full-Text Indexing with One Edit Error.
  4. Linked Dynamic Tries with Applications to LZ-Compression in Sublinear Time and Space.
  5. Space-Time Trade-offs for Stack-Based Algorithms.

BMC Bioinform. 2015

  1. Fast randomized approximate string matching with succinct hash data structures.

Bioinform. 2015

  1. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
  2. Ultrafast SNP analysis using the Burrows-Wheeler transform of short-read data.

CoRR 2015

  1. A Bloom filter based semi-index on q-grams.
  2. A Compressed-Gap Data-Aware Measure for Indexable Dictionaries.
  3. A Fast Heuristic for Exact String Matching.
  4. A Lower Bound on Supporting Predecessor Search in k sorted Arrays.
  5. A Note on Easy and Efficient Computation of Full Abelian Periods of a Word.
  6. A Practical O(Rlog log n+n) time Algorithm for Computing the Longest Common Subsequence.
  7. A Quadratic Assignment Formulation of the Graph Edit Distance.
  8. A Review on the Tree Edit Distance Problem and Related Path-Decomposition Algorithms.
  9. A Study on Splay Trees.
  10. A framework for space-efficient string kernels.
  11. A note on the longest common Abelian factor problem.
  12. A numerical analysis of Quicksort: How many cases are bad cases?
  13. Adaptive Search over Sorted Sets.
  14. Algorithms for Longest Common Abelian Factors.
  15. Amortized Rotation Cost in AVL Trees.
  16. An Efficient Dynamic Programming Algorithm for STR-IC-SEQ-EC-LCS Problem.
  17. An efficient dynamic programming algorithm for the generalized LCS problem with multiple substring inclusive constraints.
  18. Approximating LZ77 in Small Space.
  19. Approximating LZ77 via Small-Space Multiple-Pattern Matching.
  20. Binary Coding in Stream.
  21. Burrows-Wheeler transform for terabases.
  22. Communication Complexity (for Algorithm Designers).
  23. Composite repetition-aware data structures.
  24. Compressed Data Structures for Dynamic Sequences.
  25. Compressed Tree Canonization.
  26. Computing LZ77 in Run-Compressed Space.
  27. Computing Runs on a General Alphabet.
  28. Constructing LZ78 Tries and Position Heaps in Linear Time for Large Alphabets.
  29. Deterministic Sparse Suffix Sorting on Rewritable Texts.
  30. Dictionary matching in a stream.
  31. Diverse Palindromic Factorization is NP-Complete.
  32. Dual pivot Quicksort.
  33. Dynamic Data Structures for Document Collections and Graphs.
  34. Dynamic Relative Compression.
  35. Dynamic concurrent van Emde Boas array.
  36. Dynamic index, LZ factorization, and LCE queries in compressed space.
  37. Efficient Algorithms for the Order Preserving Pattern Matching Problem.
  38. Efficient Deterministic Single Round Document Exchange for Edit Distance.
  39. Efficient Ranking of Lyndon Words and Decoding Lexicographically Minimal de Bruijn Sequence.
  40. Efficiently Finding All Maximal $α$-gapped Repeats.
  41. Enhanced Covers of Regular & Indeterminate Strings using Prefix Tables.
  42. Error Tree: A Tree Structure for Hamming & Edit Distances & Wildcards Matching.
  43. External Memory Three-Sided Range Reporting and Top-$k$ Queries with Sublogarithmic Updates.
  44. FM-index for dummies.
  45. Fast Algorithms for Exact String Matching.
  46. Fast Algorithms for Finding Pattern Avoiders and Counting Pattern Occurrences in Permutations.
  47. Fast Average-Case Pattern Matching on Weighted Sequences.
  48. Fast Computation of Abelian Runs.
  49. Fast and Powerful Hashing using Tabulation.
  50. Fast and Vectorizable Alternatives to Binary Search.
  51. Faster Lightweight Lempel-Ziv Parsing.
  52. Finding the Leftmost Critical Factorization on Unordered Alphabet.
  53. Finger Search, Random Access, and Longest Common Extensions in Grammar-Compressed Strings.
  54. Full-text and Keyword Indexes for String Searching.
  55. Fully-online construction of suffix trees and DAWGs for multiple texts.
  56. How Good is Multi-Pivot Quicksort?
  57. Implementation of BT-trees.
  58. Layered Heaps Beating Standard and Fibonacci Heaps in Practice.
  59. Lempel Ziv Computation In Compressed Space (LZ-CICS).
  60. Lempel Ziv Computation In Small Space (LZ-CISS).
  61. Linear Algorithm for Conservative Degenerate Pattern Matching.
  62. Linear Algorithms for Computing the Lyndon Border Array and the Lyndon Suffix Array.
  63. Linear-Time Sequence Comparison Using Minimal Absent Words & Applications.
  64. Linear-Time Superbubble Identification Algorithm.
  65. Longest Common Extensions in Sublinear Space.
  66. Longest Gapped Repeats and Palindromes.
  67. Lower bounds for approximation schemes for Closest String.
  68. Mespotine-RLE-basic v0.9 - An overhead-reduced and improved Run-Length-Encoding Method.
  69. Multiple sequence alignment for short sequences.
  70. On Longest Repeat Queries.
  71. On Maximal Unbordered Factors.
  72. On The Average-Case Complexity of Shellsort.
  73. On the Greedy Algorithm for the Shortest Common Superstring Problem with Reversals.
  74. Online Computation of Abelian Runs.
  75. Online Dictionary Matching with One Gap.
  76. Online Self-Indexed Grammar Compression.
  77. Optimal Dynamic Strings.
  78. Optimal search trees with equality tests.
  79. Parallel Query in the Suffix Tree.
  80. Parameterized Complexity of Superstring Problems.
  81. Pattern-avoiding access in binary search trees.
  82. Permutations sortable by two stacks in series.
  83. Practical Concurrent Priority Queues.
  84. Probabilistic Threshold Indexing for Uncertain Strings.
  85. Quadratic Conditional Lower Bounds for String Problems and Dynamic Time Warping.
  86. Quadratic-Time Hardness of LCS and other Sequence Similarity Measures.
  87. Range Predecessor and Lempel-Ziv Parsing.
  88. Read Mapping on de Bruijn graph.
  89. Relative Compressed Suffix Trees.
  90. Relative Select.
  91. Space-efficient detection of unusual words.
  92. Strictly Implicit Priority Queues: On the Number of Moves and Worst-Case Time.
  93. Subsequence Automata with Default Transitions.
  94. Testing k-binomial equivalence.
  95. The Complexity of Pattern Matching for 321-Avoiding and Skew-Merged Permutations.
  96. The complexity of computation in bit streams.
  97. The k-mismatch problem revisited.
  98. Traversing Grammar-Compressed Trees with Constant Delay.
  99. Tree Compression with Top Trees Revisited.
  100. Tree compression using string grammars.
  101. Triple State QuickSort, A replacement for the C/C++ library qsort.

IEEE Trans. Inf. Theory 2015

  1. Efficient and Compact Representations of Prefix Codes.

Inf. Comput. 2015

  1. Approximate periodicity.
  2. Detecting regularities on grammar-compressed strings.
  3. Tree compression with top trees.

Inf. Process. Lett. 2015

  1. Constructing LZ78 tries and position heaps in linear time for large alphabets.

Inf. Syst. 2015

  1. The wavelet matrix: An efficient wavelet tree for large alphabets.

J. Discrete Algorithms 2015

  1. A suffix tree or not a suffix tree?
  2. An efficient Variable-to-Fixed length encoding using multiplexed parse trees.
  3. Approximate pattern matching in LZ77-compressed texts.
  4. Bottom-k document retrieval.
  5. Computing the Burrows-Wheeler transform in place and in small space.
  6. Dynamic edit distance table under a general weighted cost function.
  7. Improved and extended locating functionality on compressed suffix arrays.

Knowl. Inf. Syst. 2015

  1. Compressed vertical partitioning for efficient RDF management.

SIAM J. Comput. 2015

  1. Random Access to Grammar-Compressed Strings and Trees.

SIAM J. Discret. Math. 2015

  1. String Reconstruction from Substring Compositions.

Softw. Pract. Exp. 2015

  1. Fast in-memory XPath search using compressed indexes.

Theor. Comput. Sci. 2015

  1. Compressed automata for dictionary matching.
  2. Dictionary matching with a few gaps.
  3. Global and local sequence alignment with a bounded number of gaps.
  4. On hardness of several string indexing problems.

ALENEX 2014

  1. Multi-Pivot Quicksort: Theory and Experiments.
  2. Top-k Substring Matching for Auto-Completion.

CPM 2014

  1. A really Simple Approximation of Smallest Grammar.
  2. An Improved Query Time for Succinct Dynamic Dictionary Matching.
  3. Approximate On-line Palindrome Recognition, and Applications.
  4. Approximate String Matching Using a Bidirectional Index.
  5. Compactness-Preserving Mapping on Trees.
  6. Compressed Subsequence Matching and Packed Tree Coloring.
  7. Computing Minimal and Maximal Suffixes of a Substring Revisited.
  8. Computing Palindromic Factorizations and Palindromic Covers On-line.
  9. Computing k-th Lyndon Word and Decoding Lexicographically Minimal de Bruijn Sequence.
  10. Dictionary Matching with One Gap.
  11. Efficient Algorithms for Shortest Partial Seeds in Words.
  12. Encodings for Range Majority Queries.
  13. From Indexing Data Structures to de Bruijn Graphs.
  14. Indexed Geometric Jumbled Pattern Matching.
  15. Most Recent Match Queries in On-Line Suffix Trees.
  16. On Combinatorial Generation of Prefix Normal Words.
  17. On Hardness of Several String Indexing Problems.
  18. On the DCJ Median Problem.
  19. On the Efficiency of the Hamming C-Centerstring Problems.
  20. Order-Preserving Pattern Matching with k Mismatches.
  21. Parameterized Complexity Analysis for the Closest String with Wildcards Problem.
  22. Permuted Scaled Matching.
  23. Randomized and Parameterized Algorithms for the Closest String Problem.
  24. Reversal Distances for Strings with Few Blocks or Small Alphabets.
  25. Searching of Gapped Repeats and Subrepetitions in a Word.
  26. Shortest Unique Substring Query Revisited.
  27. String Range Matching.
  28. The Worst Case Complexity of Maximum Parsimony.

DCC 2014

  1. A Practical Implementation of Compressed Suffix Arrays with Applications to Self-Indexing.
  2. Adaptive Dictionary Sharing Method for Re-Pair Algorithm.
  3. Alignment Free Sequence Similarity with Bounded Hamming Distance.
  4. Better Compression through Better List Update Algorithms.
  5. Boosting the Compression of Rewriting on Flash Memory.
  6. Combining Deduplication and Delta Compression to Achieve Low-Overhead Data Reduction on Backup Datasets.
  7. Compressing Sets and Multisets of Sequences.
  8. Compressing Similar Biological Sequences Using FM-Index.
  9. Compression Schemes for Similarity Queries.
  10. Direct Access to Variable-to-Fixed Length Codes with a Succinct Index.
  11. Entropy Reduction Using Context Transformations.
  12. Fast Fully-Compressed Suffix Trees.
  13. Fully Online Grammar Compression in Constant Space.
  14. Hybrid Compression of Bitvectors for the FM-Index.
  15. Information Profiles for DNA Pattern Discovery.
  16. Interleaved K2-Tree: Indexing and Navigating Ternary Relations.
  17. LZ-Compressed String Dictionaries.
  18. Lempel-Ziv Parsing in External Memory.
  19. Relative Lempel-Ziv with Constant-Time Random Access.
  20. Space Efficient Linear Time Lempel-Ziv Factorization for Small Alphabets.
  21. Towards Markup-Aware Text Compression.
  22. Universal Text Preprocessing and Postprocessing for PPM Using Alphabet Adjustment.

Developments in Language Theory 2014

  1. On k-Abelian Palindromic Rich and Poor Words.
  2. k-Abelian Pattern Matching.

ESA 2014

  1. Amortized Bounds for Dynamic Orthogonal Range Reporting.
  2. Bicriteria Data Compression: Efficient and Usable.
  3. Document Retrieval on Repetitive Collections.
  4. Equivalence between Priority Queues and Sorting in External Memory.
  5. Sublinear Space Algorithms for the Longest Common Substring Problem.
  6. The Batched Predecessor Problem in External Memory.
  7. Weighted Ancestors in Suffix Trees.

FOCS 2014

  1. Dynamic Integer Sets with Optimal Rank, Select, and Predecessor Search.
  2. The Dyck Language Edit Distance Problem in Near-Linear Time.

FSTTCS 2014

  1. Asymptotically Optimal Encodings for Range Selection.

HPCA 2014

  1. MemZip: Exploring unconventional benefits from memory compression.

ICALP (1) 2014

  1. Deterministic Rectangle Enclosure and Offline Dominance Reporting on the RAM.
  2. On Hardness of Jumbled Indexing.

ISAAC 2014

  1. Depth-First Search Using O(n) Bits.
  2. Hashing and Indexing: Succinct DataStructures and Smoothed Analysis.
  3. The Power and Limitations of Static Binary Search Trees with Lazy Finger.
  4. Top- k Term-Proximity in Succinct Space.

IWOCA 2014

  1. A Suffix Tree Or Not a Suffix Tree?
  2. Computing Primitively-Rooted Squares and Runs in Partial Words.
  3. Fast and Simple Computations Using Prefix Tables Under Hamming and Edit Distance.

JSAI-isAI Workshops 2014

  1. Finding Ambiguous Patterns on Grammar Compressed String.

LATIN 2014

  1. Biased Predecessor Search.
  2. LZ77-Based Self-indexing with Faster Pattern Matching.
  3. Multiply Balanced k -Partitioning.
  4. Quad-K-d Trees.

Language, Culture, Computation (1) 2014

  1. Hypertext Searching - A Survey.

MFCS (1) 2014

  1. Universal Lyndon Words.

MFCS (2) 2014

  1. Document Retrieval with One Wildcard.
  2. Inferring Strings from Lyndon Factorization.

SEA 2014

  1. Approximate Online Matching of Circular Strings.
  2. DenseZDD: A Compact and Fast Index for Families of Sets.
  3. Efficient Representation for Online Suffix Tree Construction.
  4. Efficient Wavelet Tree Construction and Querying for Multicore Architectures.
  5. Faster Compressed Suffix Trees for Repetitive Text Collections.
  6. From Theory to Practice: Plug and Play with Succinct Data Structures.
  7. Improved ESP-index: A Practical Self-index for Highly Repetitive Texts.
  8. Improved and Extended Locating Functionality on Compressed Suffix Arrays.
  9. LCP Array Construction in External Memory.
  10. Order-Preserving Matching with Filtration.
  11. Retrieval and Perfect Hashing Using Fingerprinting.

SISAP 2014

  1. Dynamic List of Clusters in Secondary Memory.

SODA 2014

  1. Bicriteria data compression.
  2. Concurrent Range Reporting in Two-Dimensional Space.
  3. Finding small patterns in permutations in linear time.
  4. Near-optimal labeling schemes for nearest common ancestors.
  5. Selection and Sorting in the “Restore” Model.

SOFSEM 2014

  1. Shortest Unique Substrings Queries in Optimal Time.

SPIRE 2014

  1. A 3-Approximation Algorithm for the Multiple Spliced Alignment Problem and Its Application to the Gene Prediction Task.
  2. A Compressed Suffix-Array Strategy for Temporal-Graph Indexing.
  3. Algorithms for Jumbled Indexing, Jumbled Border and Jumbled Square on Run-Length Encoded Strings.
  4. Alphabet-Independent Algorithms for Finding Context-Sensitive Repeats in Linear Time.
  5. Context-Aware Deal Size Prediction.
  6. Efficient Compressed Indexing for Approximate Top-k String Retrieval.
  7. Efficient Indexing and Representation of Web Access Logs.
  8. Fast Construction of Wavelet Trees.
  9. Grammar Compressed Sequences with Rank/Select Support.
  10. I/O-Efficient Dictionary Search with One Edit Error.
  11. Improved Filters for the Approximate Suffix-Prefix Overlap Problem.
  12. Indexed Matching Statistics and Shortest Unique Substrings.
  13. Information-Theoretic Term Selection for New Item Recommendation.
  14. K 2-Treaps: Range Top-k Queries in Compact Space.
  15. On the String Consensus Problem and the Manhattan Sequence Consensus Problem.
  16. Online Multiple Palindrome Pattern Matching.
  17. Online Pattern Matching for String Edit Distance with Moves.
  18. Order Preserving Prefix Tables.
  19. Performance Improvements for Search Systems Using an Integrated Cache of Lists+Intersections.
  20. Relative FM-Indexes.
  21. Relative Lempel-Ziv with Constant-Time Random Access.
  22. Sequence Decision Diagrams.
  23. Shortest Unique Queries on Strings.
  24. Simple and Efficient String Algorithms for Query Suggestion Metrics Computation.
  25. Strategic Pattern Search in Factor-Compressed Text.
  26. Succinct Indexes for Reporting Discriminating and Generic Words.

STACS 2014

  1. Data-Oblivious Data Structures.
  2. Faster Compact On-Line Lempel-Ziv Factorization.
  3. Faster Sparse Suffix Sorting.
  4. Space-Efficient String Indexing for Wildcard Pattern Matching.
  5. Testing Generalised Freeness of Words.
  6. Weighted Coloring in Trees.

STOC 2014

  1. Linear time construction of compressed text indices in compact space.
  2. Zig-zag sort: a simple deterministic data-oblivious sorting algorithm running in O(n log n) time.

SWAT 2014

  1. B-slack Trees: Space Efficient B-Trees.
  2. Colored Range Searching in Linear Space.
  3. Expected Linear Time Sorting for Word Size Ω(log2 n loglogn).
  4. Ranked Document Selection.

Stringology 2014

  1. A Process-Oriented Implementation of Brzozowski’s DFA Construction Algorithm.
  2. Alternative Algorithms for Lyndon Factorization.
  3. Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings.
  4. Closed Factorization.
  5. Computing Abelian Covers and Abelian Runs.
  6. Efficient Online Abelian Pattern Matching in Strings by Simulating Reactive Multi-Automata.
  7. Fast Regular Expression Matching Based On Dual Glushkov NFA.
  8. Improved Two-Way Bit-parallel Search.
  9. Metric Preserving Dense SIFT Compression.
  10. Multiple Pattern Matching Revisited.
  11. New Tabulation and Sparse Dynamic Programming Based Techniques for Sequence Similarity Problems.
  12. On the Number of Distinct Squares.
  13. Random Access to Fibonacci Codes.
  14. Reducing Squares in Suffix Arrays.
  15. Speeding up Compressed Matching with SBNDM2.
  16. Threshold Approximate Matching in Grammar-Compressed Strings.
  17. Two Simple Full-Text Indexes Based on the Suffix Array.
  18. Two Squares Canonical Factorization.
  19. Using Correctness-by-Construction to Derive Dead-zone Algorithms.

TFPIE 2014

  1. Simple Balanced Binary Search Trees.

WABI 2014

  1. Constructing String Graphs in External Memory.
  2. Manifold de Bruijn Graphs.

WALCOM 2014

  1. Alignment with Non-overlapping Inversions on Two Strings.

ACM J. Exp. Algorithmics 2014

  1. General Document Retrieval in Compact Space.
  2. Locally Compressed Suffix Arrays.

ACM Trans. Algorithms 2014

  1. Alphabet-Independent Compressed Text Indexing.
  2. Fully Functional Static and Dynamic Succinct Trees.

ACM Trans. Inf. Syst. 2014

  1. XXS: Efficient XPath Evaluation on Compressed XML Documents.

Algorithmica 2014

  1. A Framework for Succinct Labeled Ordinal Trees over Large Alphabets.
  2. Efficient Fully-Compressed Sequence Representations.
  3. Substring Range Reporting.

Algorithms 2014

  1. High-Order Entropy Compressed Bit Vectors with Rank/Select.

Algorithms Mol. Biol. 2014

  1. Fast algorithms for approximate circular string matching.
  2. Optimal computation of all tandem repeats in a weighted sequence.

BMC Bioinform. 2014

  1. Linear-time computation of minimal absent words using suffix array.

CoRR 2014

  1. $LCSk$++: Practical similarity metric for long strings.
  2. A Comparative Study on String Matching Algorithm of Biological Sequences.
  3. A Fast String Matching Algorithm Based on Lowlight Characters in the Pattern.
  4. A Parameterized Study of Maximum Generalized Pattern Matching Problems.
  5. A Subquadratic Algorithm for Minimum Palindromic Factorization.
  6. A Suffix Tree Or Not A Suffix Tree?
  7. A massively parallel algorithm for constructing the BWT of large string sets.
  8. A new characterization of maximal repetitions by Lyndon trees.
  9. A note on multipivot Quicksort.
  10. A note on the largest number of red nodes in red-black trees.
  11. A really simple approximation of smallest grammar.
  12. ARC Sort: Enhanced and Time Efficient Sorting Algorithm.
  13. Algorithms in the Ultra-Wide Word Model.
  14. Alternative Algorithms for Lyndon Factorization.
  15. Analysis of Branch Misses in Quicksort.
  16. Analysis of Pivot Sampling in Dual-Pivot Quicksort.
  17. Analysis of String Sorting using Heapsort.
  18. Approximating solution structure of the Weighted Sentence Alignment problem.
  19. Average-Case Optimal Approximate Circular String Matching.
  20. Binary Jumbled Pattern Matching via All-Pairs Shortest Paths.
  21. Building a Balanced k-d Tree in O(kn log n) Time.
  22. Combining pattern-based CRFs and weighted context-free grammars.
  23. Compact Indexes for Flexible Top-k Retrieval.
  24. Compact Subsequence Matching and Packed Tree Coloring.
  25. Compression of high throughput sequencing data with probabilistic de Bruijn graph.
  26. Compressive Mining: Fast and Optimal Data Mining in the Compressed Domain.
  27. Computing Covers Using Prefix Tables.
  28. Constructing String Graphs in External Memory.
  29. Constructing small tree grammars and small circuits for formulas.
  30. Covering Problems for Partial Words and for Indeterminate Strings.
  31. Data Compaction - Compression without Decompression.
  32. Dictionary Matching with One Gap.
  33. Disk-based genome sequencing data compression.
  34. Document Counting in Practice.
  35. Document Retrieval on Repetitive Collections.
  36. Dynamic Partial Sorting.
  37. Efficient Compressed Wavelet Trees over Large Alphabets.
  38. Efficient Representation for Online Suffix Tree Construction.
  39. Efficient and Compact Representations of Prefix Codes.
  40. Encodings of Range Maximum-Sum Segment Queries and Applications.
  41. Engineering Parallel String Sorting.
  42. Fast Algorithm for Partial Covers in Words.
  43. Fast construction of FM-index for long sequence reads.
  44. Faster Compressed Quadtrees.
  45. Faster Language Edit Distance, Connection to All-pairs Shortest Paths and Related Problems.
  46. Faster Sorting Networks for $17$, $19$ and $20$ Inputs.
  47. Fewer runs than word length.
  48. Fibonacci Heaps Revisited.
  49. Fully Online Grammar Compression in Constant Space.
  50. Fusion Tree Sorting.
  51. GCD Computation of n Integers.
  52. GPU-Accelerated BWT Construction for Large Collection of Short Reads.
  53. How Fast Can We Multiply Large Integers on an Actual Computer?
  54. How inefficient can a sort algorithm be?
  55. Improved ESP-index: a practical self-index for highly repetitive texts.
  56. Integer Set Compression and Statistical Modeling.
  57. Introduction to Dynamic Unary Encoding.
  58. Kernelization lower bound for Permutation Pattern Matching.
  59. Lempel-Ziv Factorization May Be Harder Than Computing All Runs.
  60. Linear time construction of compressed text indices in compact space.
  61. Linear-time Computation of Minimal Absent Words Using Suffix Array.
  62. Longest Common Extensions in Trees.
  63. Longest Common Subsequence in k-length substrings.
  64. Longest common substrings with k mismatches.
  65. Mathematical Programming Strategies for Solving the Minimum Common String Partition Problem.
  66. Most Recent Match Queries in On-Line Suffix Trees (with appendix).
  67. Multilevel polynomial partitions and simplified range searching.
  68. Multiple pattern matching revisited.
  69. Normal, Abby Normal, Prefix Normal.
  70. On Combinatorial Generation of Prefix Normal Words.
  71. On Hardness of Jumbled Indexing.
  72. On the Average-case Complexity of Pattern Matching with Wildcards.
  73. On the representation of de Bruijn graphs.
  74. Online Pattern Matching for String Edit Distance with Moves.
  75. Online Repetition Detection With Backtracking.
  76. Online Square Detection.
  77. Optimal Encodings for Range Majority Queries.
  78. Optimal Encodings for Range Min-Max and Top-k.
  79. Optimal Time Random Access to Grammar-Compressed Strings in Small Space.
  80. Parallel Wavelet Tree Construction.
  81. Path algebra algorithm for finding longest increasing subsequence.
  82. Pattern Matching and Local Alignment for RNA Structures.
  83. PivotCompress: Compression by Sorting.
  84. Practical Massively Parallel Sorting - Basic Algorithmic Ideas.
  85. Quantum pattern matching fast on average.
  86. Queries on LZ-Bounded Encodings.
  87. Rank, select and access in grammar-compressed strings.
  88. Reusing an FM-index.
  89. Run-Length Encoded Nondeterministic KMP and Suffix Automata.
  90. Sampling the suffix array with minimizers.
  91. Searching and Indexing Genomic Databases via Kernelization.
  92. Space-Efficient String Indexing for Wildcard Pattern Matching.
  93. String Reconstruction from Substring Compositions.
  94. Strong inapproximability of the shortest reset word.
  95. Sublinear Space Algorithms for the Longest Common Substring Problem.
  96. Suffix Arrays for Spaced-SNP Databases.
  97. The Level Ancestor Problem in Practice.
  98. The LevelArray: A Fast, Practical Long-Lived Renaming Algorithm.
  99. Tight tradeoffs for approximating palindromes in streams.
  100. Towards Tight Lower Bounds for Range Reporting on the RAM.
  101. Twenty-Five Comparators is Optimal when Sorting Nine Inputs (and Twenty-Nine for Ten).
  102. Two simple full-text indexes based on the suffix array.
  103. Variable-Order de Bruijn Graphs.
  104. Wavelet Trees Meet Suffix Trees.
  105. Weighted ancestors in suffix trees.
  106. Zig-zag Sort: A Simple Deterministic Data-Oblivious Sorting Algorithm Running in O(n log n) Time.

Comput. Geom. 2014

  1. Space efficient data structures for dynamic orthogonal range counting.

Discret. Appl. Math. 2014

  1. A d-step approach to the maximum number of distinct squares and runs in strings.
  2. A hybrid algorithm for the DNA sequencing problem.
  3. A set-covering based heuristic algorithm for the periodic vehicle routing problem.
  4. Algorithms for computing Abelian periods of words.
  5. Algorithms for nesting with defects.
  6. An ILP-refined tabu search for the Directed Profitable Rural Postman Problem.
  7. Antichains and completely separating systems - A catalogue and applications.
  8. Asymptotically optimal algorithms for geometric Max TSP and Max m-PSP.
  9. Average number of occurrences of repetitions in a necklace.
  10. Computing the number of cubic runs in standard Sturmian words.
  11. Counting unique-sink orientations.
  12. Cycle-aware minimization of acyclic deterministic finite-state automata.
  13. Editorial.
  14. Essential points of the n-cube subset partitioning characterisation.
  15. Improving deduplication techniques by accelerating remainder calculations.
  16. Improving heuristics for network modularity maximization using an exact algorithm.
  17. Inferring strings from suffix trees and links on a binary alphabet.
  18. Investigating the b-chromatic number of bipartite graphs by using the bicomplement.
  19. Lower and upper bounds for the Bin Packing Problem with Fragile Objects.
  20. Morphisms for resistive electrical networks.
  21. New simple efficient algorithms computing powers and runs in strings.
  22. On defensive alliances and strong global offensive alliances.
  23. On the minimum size of 4-uniform hypergraphs without property B.
  24. Partition into almost straight trails.
  25. Polynomial-time algorithms for special cases of the maximum confluent flow problem.
  26. Practical fixed length Lempel-Ziv coding.
  27. Preface.
  28. Rime: Repeat identification.
  29. Scheduling arc maintenance jobs in a network to maximize total flow over time.
  30. Simple tree pattern matching for trees in the prefix bar notation.
  31. String matching with lookahead.
  32. Stringology algorithms.
  33. Text searching allowing for inversions and translocations of factors.
  34. Tight and simple Web graph compression for forward and reverse neighbor queries.
  35. Tilted Sperner families.
  36. Triple arrays and related designs.
  37. Unital designs with blocking sets.

IEEE Trans. Knowl. Data Eng. 2014

  1. Large-Scale Pattern Search Using Reduced-Space On-Disk Suffix Arrays.

J. Comput. Syst. Sci. 2014

  1. Range LCP.

J. Discrete Algorithms 2014

  1. A subquadratic algorithm for minimum palindromic factorization.
  2. Cross-document pattern matching.
  3. Multi-pattern matching with bidirectional indexes.
  4. Simple and efficient LZW-compressed multiple pattern matching.
  5. Simple, compact and robust approximate string dictionary.
  6. Time-space trade-offs for longest common extensions.
  7. Wavelet trees for all.

Knowl. Inf. Syst. 2014

  1. Compressed representations for web and social graphs.

Parallel Comput. 2014

  1. Distributed text search using suffix arrays.

SIAM J. Comput. 2014

  1. Optimal Dynamic Sequence Representations.

Softw. Pract. Exp. 2014

  1. Optimized succinct data structures for massive data.

Theor. Comput. Sci. 2014

  1. Closest periodic vectors in Lp spaces.
  2. Compact q-gram profiling of compressed strings.
  3. Detecting approximate periodic patterns.
  4. Extending alignments with k-mismatches and ℓ-gaps.
  5. Fast relative Lempel-Ziv self-index for similar sequences.
  6. Less space: Indexing for queries with wildcards.
  7. New space/time tradeoffs for top-k document retrieval on sequences.
  8. Order-preserving matching.
  9. Towards optimal packed string matching.

Theory Comput. Syst. 2014

  1. String Indexing for Patterns with Wildcards.
  2. Validating the Knuth-Morris-Pratt Failure Function, Fast and Online.

ALENEX 2013

  1. Fast Packed String Matching for Short Patterns.
  2. Inducing Suffix and Lcp Arrays in External Memory.
  3. Lempel-Ziv factorization: Simple, fast, practical.

CIAA 2013

  1. Compressed Automata for Dictionary Matching.

CIAC 2013

  1. Average Optimal String Matching in Packed Strings.

CPM 2013

  1. A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm.
  2. A Constant-Space Comparison-Based Algorithm for Computing the Burrows-Wheeler Transform.
  3. A Succinct Grammar Compression.
  4. Approximating Shortest Superstring Problem Using de Bruijn Graphs.
  5. Approximation of Grammar-Based Compression via Recompression.
  6. Compact q-Gram Profiling of Compressed Strings.
  7. Converting SLP to LZ78 in almost Linear Time.
  8. Data Structure Lower Bounds on Random Access to Grammar-Compressed Strings.
  9. Discrete Methods for Image Analysis Applied to Molecular Biology.
  10. Document Listing on Repetitive Collections.
  11. Efficient All Path Score Computations on Grid Graphs.
  12. Efficient Lyndon Factorization of Grammar Compressed Text.
  13. External Memory Generalized Suffix and LCP Arrays Construction.
  14. Fast Algorithm for Partial Covers in Words.
  15. Forty Years of Text Indexing.
  16. LCP Magic.
  17. Linear Time Lempel-Ziv Factorization: Simple, Fast, Small.
  18. Local Search for String Problems: Brute Force Is Essentially Optimal.
  19. Locating All Maximal Approximate Runs in a String.
  20. New Algorithms for Position Heaps.
  21. On Minimal and Maximal Suffixes of a Substring.
  22. Pattern Matching with Variables: A Multivariate Complexity Analysis.
  23. Space-Efficient Construction Algorithm for the Circular Suffix Tree.
  24. Time-Space Trade-Offs for the Longest Common Substring Problem.

CSR 2013

  1. Alphabetic Minimax Trees in Linear Time.

CiE 2013

  1. Discovering Hidden Repetitions in Words.

DCC 2013

  1. A Simple Online Competitive Adaptation of Lempel-Ziv Compression with Efficient Random Access Support.
  2. Algorithms for Compressed Inputs.
  3. An Adaptive Difference Distribution-Based Coding with Hierarchical Tree Structure for DNA Sequence Compression.
  4. Compressed Parameterized Pattern Matching.
  5. Compressing Huffman Models on Large Alphabets.
  6. Computing Convolution on Grammar-Compressed Text.
  7. Effective Variable-Length-to-Fixed-Length Coding via a Re-Pair Algorithm.
  8. Faster Compact Top-k Document Retrieval.
  9. Faster Compressed Top-k Document Retrieval.
  10. From Run Length Encoding to LZ78 and Back Again.
  11. Partition Tree Weighting.
  12. Practical Parallel Lempel-Ziv Factorization.
  13. Quadratic Similarity Queries on Compressed Data.
  14. Random Extraction from Compressed Data - A Practical Study.
  15. Simpler and Faster Lempel Ziv Factorization.
  16. Space-Efficient Construction Algorithm for the Circular Suffix Tree.
  17. Texture Compression.
  18. The Rightmost Equal-Cost Position Problem.
  19. Variable-to-Fixed-Length Encoding for Large Texts Using Re-Pair Algorithm with Shared Dictionaries.

Developments in Language Theory 2013

  1. Abelian Repetitions in Sturmian Words.
  2. On the Number of Abelian Bordered Words.
  3. Repetition Avoidance in Circular Factors.
  4. Suffixes, Conjugates and Lyndon Words.

ESA 2013

  1. Binary Jumbled Pattern Matching on Trees and Tree-Like Structures.
  2. Compressed Cache-Oblivious String B-tree.
  3. Efficient Indexes for Jumbled Pattern Matching with Constant-Sized Alphabet.
  4. Encodings for Range Selection and Top-k Queries.
  5. Optimal Color Range Reporting in One Dimension.
  6. Parallel String Sample Sort.
  7. The Encoding Complexity of Two Dimensional Range Minimum Data Structures.
  8. Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform.

ICALP (1) 2013

  1. Combining Binary Search Trees.
  2. Dynamic Compressed Strings with Random Access.
  3. Sparse Suffix Tree Construction in Small Space.
  4. Tree Compression with Top Trees.

ICCS 2013

  1. n-step FM-Index for Faster Pattern Matching.

IEEE BigData 2013

  1. A reconfigurable stream compression hardware based on static symbol-lookup table.

ISAAC 2013

  1. Beating $\mathcal{O}(nm)$ in Approximate LZW-Compressed Pattern Matching.
  2. Faster, Space-Efficient Selection Algorithms in Read-Only Memory for Integers.
  3. Less Space: Indexing for Queries with Wildcards.
  4. Pattern Matching with Non Overlapping Reversals - Approximation and On-line Algorithms.
  5. RAM-Efficient External Memory Sorting.
  6. Single and Multiple Consecutive Permutation Motif Search.
  7. Sliding Bloom Filters.
  8. Succinct Data Structures for Representing Equivalence Classes.
  9. Top-k Document Retrieval in Compact Space and Near-Optimal Time.

IWOCA 2013

  1. An Optimal Algorithm for Computing All Subtree Repeats in Trees.
  2. Deciding Representability of Sets of Words of Equal Length in Polynomial Time.
  3. Motif Matching Using Gapped Patterns.
  4. Prefix Table Construction and Conversion.
  5. Suffix Tree of Alignment: An Efficient Index for Similar Data.

Information Theory, Combinatorics, and Search Theory 2013

  1. On the Value of Multiple Read/Write Streams for Data Compression.

LATA 2013

  1. Linear-Time Version of Holub’s Algorithm for Morphic Imprimitivity Testing.
  2. On the Number of Unbordered Factors.

MFCS 2013

  1. Detecting Regularities on Grammar-Compressed Strings.

MICRO 2013

  1. Decoupled compressed cache: exploiting spatial locality for energy-optimized compressed caching.
  2. Linearly compressed pages: a low-complexity, low-latency main memory compression framework.

PPAM (2) 2013

  1. Accelerating String Matching on MIC Architecture for Motif Extraction.

SEA 2013

  1. Lightweight Lempel-Ziv Parsing.
  2. Space-Efficient, High-Performance Rank and Select Structures on Uncompressed Bit Sequences.

SIGIR 2013

  1. Faster and smaller inverted indices with treaps.

SODA 2013

  1. Adaptive and Approximate Orthogonal Range Counting.
  2. Compressed static functions with applications.
  3. Lyndon Words and Short Superstrings.
  4. Near-Optimal Range Reporting Structures for Categorical Data.
  5. Optimal Dynamic Sequence Representations.
  6. The Space Complexity of 2-Dimensional Approximate Range Counting.
  7. Twisted Tabulation Hashing.

SOFSEM 2013

  1. Permuted Pattern Matching on Multi-track Strings.

SPIRE 2013

  1. A Lempel-Ziv Compressed Structure for Document Listing.
  2. Accurate Profiling of Microbial Communities from Massively Parallel Sequencing Using Convex Optimization.
  3. Adaptive Data Structures for Permutations and Binary Relations.
  4. Adding Compression and Blended Search to a Compact Two-Level Suffix Array.
  5. Compact Querieable Representations of Raster Data.
  6. Consolidating and Exploring Information via Textual Inference.
  7. Discovering Dense Subgraphs in Parallel for Compressing Web and Social Networks.
  8. Distributed Query Processing on Compressed Graphs Using K2-Trees.
  9. Document Listing on Versioned Documents.
  10. Efficient Approximation of Edit Distance.
  11. Faster Lyndon Factorization Algorithms for SLP and LZ78 Compressed Text.
  12. Faster Range LCP Queries.
  13. Faster Top-k Document Retrieval in Optimal Space.
  14. Fully-Online Grammar Compression.
  15. Indexes for Jumbled Pattern Matching in Strings, Trees and Graphs.
  16. Learning URL Normalization Rules Using Multiple Alignment of Sequences.
  17. Learning to Schedule Webpage Updates Using Genetic Programming.
  18. Lossless Compression of Rotated Maskless Lithography Images.
  19. Minimal Discriminating Words Problem Revisited.
  20. Nowcasting with Google Trends.
  21. On Two-Dimensional Lyndon Words.
  22. Order-Preserving Incomplete Suffix Trees and Order-Preserving Indexes.
  23. Pattern Discovery and Listing in Graphs.
  24. Position-Restricted Substring Searching over Small Alphabets.
  25. Query Processing in Highly-Loaded Search Engines.
  26. Simulation Study of Multi-threading in Web Search Engine Processors.
  27. Solving Graph Isomorphism Using Parameterized Matching.
  28. Space-Efficient Construction of the Burrows-Wheeler Transform.
  29. Suffix Array of Alignment: A Practical Index for Similar Data.
  30. Top-k Color Queries on Tree Paths.
  31. Using Mutual Influence to Improve Recommendations.
  32. You Are What You Eat: Learning User Tastes for Rating Prediction.

STACS 2013

  1. Fast Algorithms for Abelian Periods in Words and Greatest Common Divisor Queries.
  2. Finding Pseudo-repetitions.
  3. Parameterized Matching in the Streaming Model.
  4. Recompression: a simple and powerful technique for word equations.

Stringology 2013

  1. Compact Complete Inverted Files for Texts and Directed Acyclic Graphs Based on Sequence Binary Decision Diagrams .
  2. Computing Reversed Lempel-Ziv Factorization Online.
  3. Crochemore’s String Matching Algorithm: Simplification, Extensions, Applications.
  4. Deciding the Density Type of a Given Regular Language.
  5. Degenerate String Reconstruction from Cover Arrays.
  6. Finding Distinct Subpalindromes Online.
  7. Graphs and Automata.
  8. Improved and Self-Tuned Occurrence Heuristics.
  9. Maximal Palindromic Factorization.
  10. On Morphisms Generating Run-Rich Strings.
  11. Optimal Partitioning of Data Chunks in Deduplication Systems.
  12. Parallel Suffix Array Construction by Accelerated Sampling.
  13. Sorting Suffixes of a Text via its Lyndon Factorization.
  14. Swap Matching in Strings by Simulating Reactive Automata.
  15. The Sum of Exponents of Maximal Repetitions in Standard Sturmian Words.
  16. Towards a Very Fast Multiple String Matching Algorithm for Short Patterns.
  17. Weak Factor Automata: Comparing (Failure) Oracles and Storacles.

WABI 2013

  1. A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications.
  2. Probabilistic Approaches to Alignment with Tandem Repeats.
  3. Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs.

WADS 2013

  1. Better Space Bounds for Parameterized Range Majority and Minority.
  2. Compressed Persistent Index for Efficient Rank/Select Queries.
  3. Fingerprints in Compressed Strings.
  4. On (Dynamic) Range Minimum Queries in External Memory.

ACM Comput. Surv. 2013

  1. Spaces, Trees, and Colors: The algorithmic landscape of document retrieval on sequences.

ACM J. Exp. Algorithmics 2013

  1. Compressed suffix trees: Efficient computation and storage of LCP-values.

ACM Trans. Algorithms 2013

  1. Optimal Pattern Matching in LZW Compressed Strings.

Algorithmica 2013

  1. Distribution-Aware Compressed Full-Text Indexes.
  2. Sublinear Algorithms for Approximating String Compressibility.

Algorithms 2013

  1. Practical Compressed Suffix Trees.

Algorithms Mol. Biol. 2013

  1. Data compression for sequencing data.

BMC Bioinform. 2013

  1. libgapmis: extending short-read alignments.

CoRR 2013

  1. 2D Lyndon Words and Applications
  2. A Dynamic Programming Solution to a Generalized LCS Problem
  3. A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications.
  4. A Functional Approach to Standard Binary Heaps.
  5. A Note on the Longest Common Compatible Prefix Problem for Partial Words.
  6. A Succinct Grammar Compression
  7. A general definition of the big-oh notation for algorithm analysis.
  8. A simple online competitive adaptation of Lempel-Ziv compression with efficient random access support
  9. AliBI: An Alignment-Based Index for Genomic Datasets.
  10. Alphabet-Dependent String Searching with Wexponential Search Trees
  11. An Efficient Dynamic Programming Algorithm for the Generalized LCS Problem with Multiple Substring Exclusion Constrains
  12. An Elegant Algorithm for the Construction of Suffix Arrays.
  13. Approximate String Matching using a Bidirectional Index.
  14. Approximation of grammar-based compression via recompression
  15. Approximation of smallest linear tree grammar.
  16. Average Case and Distributional Analysis of Java 7’s Dual Pivot Quicksort
  17. Beating O(nm) in approximate LZW-compressed pattern matching.
  18. Bicriteria data compression.
  19. Bin Packing and Related Problems: General Arc-flow Formulation with Graph Compression.
  20. Binary Jumbled Pattern Matching on Trees and Tree-Like Structures
  21. Compact q-gram Profiling of Compressed Strings
  22. Complexity of the FIFO Stack-Up Problem.
  23. Compressed Pattern-Matching with Ranked Variables in Zimin Words.
  24. Compressed Spaced Suffix Arrays.
  25. Computing convolution on grammar-compressed text
  26. Computing the Longest Increasing Subsequence of a Sequence Subject to Dynamic Insertion.
  27. Data Structures in Classical and Quantum Computing.
  28. Detecting regularities on grammar-compressed strings
  29. Domain Specific Hierarchical Huffman Encoding.
  30. Dynamic 2D Dictionary Matching in Small Space
  31. Dynamic Gomory-Hu Tree Construction - fast and simple.
  32. ELB-Trees, An Efficient and Lock-free B-tree Derivative.
  33. Efficient Lyndon factorization of grammar compressed text
  34. Efficient algorithms for the longest common subsequence in $k$-length substrings.
  35. Efficient repeat finding via suffix arrays
  36. Efficiently Computing Edit Distance to Dyck Language.
  37. Encoding Range Minimum Queries.
  38. Engineering Small Space Dictionary Matching
  39. Estimating the longest increasing sequence in polylogarithmic time.
  40. Faster Compact On-Line Lempel-Ziv Factorization
  41. Finding Distinct Subpalindromes Online
  42. Finding small patterns in permutations in linear time.
  43. Fingerprints in Compressed Strings
  44. First-Come-First-Served for Online Slot Allocation and Huffman Coding.
  45. From Theory to Practice: Plug and Play with Succinct Data Structures.
  46. Full-fledged Real-Time Indexing for Constant Size Alphabets
  47. GPU Accelerated Multiple Deoxyribose Nucleic Acid Sequence Parallel Matching
  48. Heaviest Induced Ancestors and Longest Common Substrings
  49. Hybrid Indexes for Repetitive Datasets.
  50. Indexes for Jumbled Pattern Matching in Strings, Trees and Graphs
  51. LZ-Compressed String Dictionaries
  52. Large-Scale Pattern Search Using Reduced-Space On-Disk Suffix Arrays
  53. Lempel-Ziv Parsing in External Memory.
  54. Lightweight LCP Construction for Next-Generation Sequencing Datasets
  55. Lightweight Lempel-Ziv Parsing
  56. Minimal Indices for Successor Search.
  57. Modulated String Searching
  58. Motif matching using gapped patterns.
  59. Near-optimal labeling schemes for nearest common ancestors.
  60. On Updating and Querying Sub-arrays of Multidimensional Arrays.
  61. On a compact encoding of the swap automaton.
  62. On string matching with k mismatches.
  63. One-variable word equations in linear time
  64. Optimal Color Range Reporting in One Dimension.
  65. Optimal Partitioning for Dual Pivot Quicksort
  66. Optimal Top-k Document Retrieval.
  67. Order Preserving Matching
  68. Order-Preserving Suffix Trees and Their Algorithmic Applications
  69. Order-preserving pattern matching with k mismatches.
  70. Orthogonal Range Searching for Text Indexing.
  71. Parallel Algorithm for Longest Common Subsequence in a String.
  72. Parallel String Sample Sort
  73. Parallel Suffix Array Construction by Accelerated Sampling
  74. QuickXsort: Efficient Sorting with n log n - 1.399n +o(n) Comparisons on Average.
  75. RAM-Efficient External Memory Sorting.
  76. Regular Expression Searching in Sublinear Time.
  77. Repetition-free longest common subsequence of random sequences
  78. Set-Difference Range Queries.
  79. Shortest Unique Substring Query Revisited.
  80. Simple, compact and robust approximate string dictionary.
  81. Single and multiple consecutive permutation motif search
  82. Sorted Range Reporting Revisited.
  83. Sorting suffixes of a text via its Lyndon Factorization.
  84. Space Efficient Linear Time Lempel-Ziv Factorization on Constant~Size~Alphabets.
  85. Statistically-secure ORAM with $\tilde{O}(\log^2 n)$ Overhead.
  86. Substring Suffix Selection.
  87. Succinct data structures for representing equivalence classes.
  88. Succinct representation of labeled trees.
  89. Suffix Trays and Suffix Trists: Structures for Faster Text Indexing.
  90. Suffix Tree of Alignment: An Efficient Index for Similar Data
  91. TRANS outperforms MTF for two special types of request sequences without locality of reference.
  92. The Swap Matching Problem Revisited.
  93. The technique of in-place associative sorting.
  94. Tree Compression with Top Trees
  95. Tree-based Arithmetic and Compressed Representations of Giant Numbers
  96. Using cascading Bloom filters to improve the memory usage for de Brujin graphs
  97. Various improvements to text fingerprinting
  98. Web graph compression with fast access
  99. XML Compression via DAGs.

Eur. J. Comb. 2013

  1. Computing the Longest Previous Factor.
  2. Minimax trees in linear time with applications.

IEICE Trans. Inf. Syst. 2013

  1. Scalable Detection of Frequent Substrings by Grammar-Based Compression.

Inf. Comput. 2013

  1. Compact binary relation representations with rich functionality.
  2. Range majority in constant time and linear space.

Inf. Process. Manag. 2013

  1. DACs: Bringing direct access to variable-length codes.

Inf. Syst. 2013

  1. Space-efficient representations of rectangle datasets supporting orthogonal range querying.
  2. Succinct nearest neighbor search.

Int. J. Comput. Biol. Drug Des. 2013

  1. Querying highly similar sequences.

Int. J. Comput. Geom. Appl. 2013

  1. External Memory orthogonal Range Reporting with Fast Updates.

J. Discrete Algorithms 2013

  1. Computing the longest common prefix array based on the Burrows-Wheeler transform.
  2. ESP-index: A compressed index based on edit-sensitive parsing.
  3. Fast q-gram mining on SLP compressed strings.
  4. Improved compressed indexes for full-text document retrieval.
  5. Various improvements to text fingerprinting.

SIAM J. Comput. 2013

  1. On the Bit-Complexity of Lempel-Ziv Compression.

Theor. Comput. Sci. 2013

  1. Colored range queries and document retrieval.
  2. Enhanced string covering.
  3. On compressing and indexing repetitive sequences.
  4. On compressing permutations and adaptive sorting.
  5. On the weak prefix-search problem.
  6. Palindrome pattern matching.
  7. Space-efficient data-analysis queries on grids.
  8. Succinct encoding of arbitrary graphs.

AIAI (2) 2012

  1. GapMis-OMP: Pairwise Short-Read Alignment on Multi-core Architectures.

ALENEX 2012

  1. Computing a Consensus of Multilabeled Trees.
  2. Fast Compressed Tries through Path Decompositions.
  3. Solving the Minimum String Cover Problem.
  4. The Complexity of Partial Orders.

ANALCO 2012

  1. The Complexity of Partial Orders.

BCB 2012

  1. ERNE-BS5: aligning BS-treated sequences by multiple hits on a 5-letters alphabet.

BIBM Workshops 2012

  1. Libgapmis: An ultrafast library for short-read single-gap alignment.

COCOON 2012

  1. Multi-pattern Matching with Bidirectional Indexes.

CPM 2012

  1. A Linear Kernel for the Complementary Maximal Strip Recovery Problem.
  2. An Efficient Linear Pseudo-minimization Algorithm for Aho-Corasick Automata.
  3. Approximation Algorithms and Hardness Results for Shortest Path Based Graph Orientations.
  4. Compressed String Dictionary Look-Up with Edit Distance One.
  5. Computing the Burrows-Wheeler Transform of a String and Its Reverse.
  6. Computing the Rooted Triplet Distance between Galled Trees by Counting Triangles.
  7. Constant-Time Word-Size String Matching.
  8. Cross-Document Pattern Matching.
  9. Document Listing for Queries with Excluded Pattern.
  10. Efficient Algorithm for Circular Burrows-Wheeler Transform.
  11. Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees.
  12. Efficient Two-Dimensional Pattern Matching with Scaling and Rotation and Higher-Order Interpolation.
  13. FEMTO: Fast Search of Large Sequence Collections.
  14. Faster and Simpler Minimal Conflicting Set Identification - (Extended Abstract).
  15. Finding Longest Common Segments in Protein Structures in Nearly Linear Time.
  16. Fixed-Parameter Algorithms for Finding Agreement Supertrees.
  17. Gene Regulation, Protein Networks and Disease: A Computational Perspective.
  18. Hardness of Longest Common Subsequence for Sequences with Bounded Run-Lengths.
  19. Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots.
  20. Least Random Suffix/Prefix Matches in Output-Sensitive Time.
  21. Local Exact Pattern Matching for Non-fixed RNA Structures.
  22. Minimum Leaf Removal for Reconciliation: Complexity and Algorithms.
  23. Near Linear Time Construction of an Approximate Index for All Maximum Consecutive Sub-sums of a Sequence.
  24. On Approximating String Selection Problems with Outliers.
  25. On the Closest String via Rank Distance.
  26. Partitioning into Colorful Components by Minimum Edge Deletions.
  27. Pattern Matching in Multiple Streams.
  28. Simple and Efficient LZW-Compressed Multiple Pattern Matching.
  29. Speeding Up q-Gram Mining on Grammar-Based Compressed Texts.
  30. The Complexity of String Partitioning.
  31. The Maximum Number of Squares in a Tree.
  32. The Parameterized Complexity of the Shared Center Problem.
  33. Time-Space Trade-Offs for Longest Common Extensions.
  34. Towards an Optimal Space-and-Query-Time Index for Top-k Document Retrieval.
  35. Wavelet Trees for All.

DCC 2012

  1. A Cuckoo Hashing Variant with Improved Memory Utilization and Insertion Time.
  2. Adaptive Context Tree Weighting.
  3. Compressed Dynamic Binary Relations.
  4. Differentially Encoded Search Trees.
  5. Fast Construction of Nearly-Optimal Prefix Codes without Probability Sorting.
  6. Fast Insertion and Deletion in Compressed Texts.
  7. Gipfeli - High Speed Compression Algorithm.
  8. Mixing Strategies in Data Compression.
  9. Slashing the Time for BWT Inversion.

Developments in Language Theory 2012

  1. Fine and Wilf’s Theorem for k-Abelian Periods.
  2. Pseudoperiodic Words.
  3. Squares in Binary Partial Words.

ECML/PKDD (2) 2012

  1. General Algorithms for Mining Closed Flexible Patterns under Various Equivalence Relations.

ESA 2012

  1. Efficient Communication Protocols for Deciding Edit Distance.
  2. New Lower and Upper Bounds for Representing Sequences.
  3. Succinct Data Structures for Path Queries.
  4. Succinct Posets.

FAW-AAIM 2012

  1. Fast Relative Lempel-Ziv Self-index for Similar Sequences.

FOCS 2012

  1. On-Line Indexing for General Alphabets via Predecessor Queries on Subsets of an Ordered List.

ICALP (1) 2012

  1. CRAM: Compressed Random Access Memory.
  2. De-amortizing Binary Search Trees.
  3. Faster Fully Compressed Pattern Matching by Recompression.
  4. Succinct Indices for Range Queries with Applications to Orthogonal Range Maxima.

ISAAC 2012

  1. A Framework for Succinct Labeled Ordinal Trees over Large Alphabets.
  2. A General Method for Improving Insertion-Based Adaptive Sorting.
  3. An Improved Algorithm for Static 3D Dominance Reporting in the Pointer Machine.
  4. Computing the Longest Common Subsequence of Two Run-Length Encoded Strings.
  5. Efficient Counting of Square Substrings in a Tree.
  6. Finger Search in the Implicit Model.

IWOCA 2012

  1. A Sequential Recursive Implementation of Dead-Zone Single Keyword Pattern Matching.
  2. Border Array for Structural Strings.
  3. Computing a Longest Common Palindromic Subsequence.
  4. Indexing Highly Repetitive Collections.
  5. Range Extremum Queries.

LATA 2012

  1. A Faster Grammar-Based Self-index.
  2. Longest Common Extensions via Fingerprinting.

LATIN 2012

  1. Forbidden Patterns.
  2. Indexed Multi-pattern Matching.

MFCS 2012

  1. Abelian Pattern Avoidance in Partial Words.
  2. Computing Lempel-Ziv Factorization Online.
  3. Fine and Wilf’s Theorem and Pseudo-repetitions.
  4. How to Reconstruct a Genome.

SEA 2012

  1. Branch Mispredictions Don’t Affect Mergesort.
  2. Dynamizing Succinct Tree Representations.
  3. Fast, Small, Simple Rank/Select on Bitmaps.
  4. Space Efficient Modifications to Structator - A Fast Index-Based Search Tool for RNA Sequence-Structure Patterns.
  5. Space-Efficient Top-k Document Retrieval.

SODA 2012

  1. A linear time algorithm for seeds computation.
  2. Fully persistent B-trees.
  3. I/O-efficient data structures for colored range and prefix reporting.
  4. Top-k document retrieval in optimal time and linear space.
  5. Using hashing to solve the dictionary problem.

SOFSEM 2012

  1. Computing q-Gram Non-overlapping Frequencies on SLP Compressed Texts.

SPIRE 2012

  1. A Study on Novelty Evaluation in Biomedical Information Retrieval.
  2. A Zipf-Like Distant Supervision Approach for Multi-document Summarization Using Wikinews Articles.
  3. Active Microbloggers: Identifying Influencers, Leaders and Discussers in Microblogging Networks.
  4. Approximate Function Matching under δ- and γ- Distances.
  5. Approximate Period Detection and Correction.
  6. Basic Word Completion and Prediction for Hebrew.
  7. Characterization and Extraction of Irredundant Tandem Motifs.
  8. Clustering Heterogeneous Data with Mutual Semi-supervision.
  9. Collection Ranking and Selection for Federated Entity Search.
  10. Compressed Representation of Web and Social Networks via Dense Subgraphs.
  11. Compressed Suffix Trees for Repetitive Texts.
  12. Computing Discriminating and Generic Words.
  13. Computing Maximum Number of Runs in Strings.
  14. Computing the Maximal-Exponent Repeats of an Overlap-Free String in Linear Time.
  15. Configurations and Minority in the String Consensus Problem.
  16. Dual-Sorted Inverted Lists in Practice.
  17. Eager XPath Evaluation over XML Streams.
  18. Efficient Bubble Enumeration in Directed Graphs.
  19. Efficient Data Structures for the Factor Periodicity Problem.
  20. Efficient LZ78 Factorization of Grammar Compressed Text.
  21. Experiments on Pseudo Relevance Feedback Using Graph Random Walks.
  22. Fast Multiple String Matching Using Streaming SIMD Extensions Technology.
  23. Faster Algorithm for Computing the Edit Distance between SLP-Compressed Strings.
  24. Grammar Precompression Speeds Up Burrows-Wheeler Compression.
  25. Impact of Regionalization on Performance of Web Search Engine Result Caches.
  26. Improved Address-Calculation Coding of Integer Arrays.
  27. Improved Grammar-Based Compressed Indexes.
  28. Method of Mining Subtopics Using Dependency Structure and Anchor Texts.
  29. Parallel Suffix Array Construction for Shared Memory Architectures.
  30. Parikh Matching in the Streaming Model.
  31. Position-Aligned Translation Model for Citation Recommendation.
  32. Ranked Document Retrieval in (Almost) No Space.
  33. Relevance Feedback Method Based on Vector Space Basis Change.
  34. Semantic Document Representation: Do It with Wikification.
  35. Smaller Self-indexes for Natural Language.
  36. Space-Efficient Computation of Maximal and Supermaximal Repeats in Genome Sequences.
  37. Temporal Web Image Retrieval.
  38. The Longest Common Subsequence Problem with Crossing-Free Arc-Annotated Sequences.
  39. The Position Heap of a Trie.
  40. The Wavelet Matrix.
  41. Usage Data in Web Search: Benefits and Limitations.
  42. Variable-Length Codes for Space-Efficient Grammar-Based Compression.

STACS 2012

  1. Linear-Space Data Structures for Range Mode Query in Arrays.
  2. Tying up the loose ends in fully LZW-compressed pattern matching.

STOC 2012

  1. Strict fibonacci heaps.
  2. Tight lower bounds for the online labeling problem.

SWAT 2012

  1. A Fast Algorithm for Permutation Pattern Matching Based on Alternating Runs.
  2. Linear-Space Data Structures for Range Minority Query in Arrays.
  3. Sorted Range Reporting.
  4. String Indexing for Patterns with Wildcards.

Stringology 2012

  1. A Computational Framework for Determining Square-maximal Strings.
  2. A Multiobjective Approach to the Weighted Longest Common Subsequence Problem.
  3. An Efficient Parallel Determinisation Algorithm for Finite-state Automata.
  4. BlastGraph: Intensive Approximate Pattern Matching in Sequence Graphs and de-Bruijn Graphs.
  5. Correctness-by-Construction in Stringology.
  6. Failure Deterministic Finite Automata.
  7. LZW Data Compression on Large Scale and Extreme Distributed Systems.
  8. New and Efficient Approaches to the Quasiperiodic Characterisation of a String.
  9. Quasi-linear Time Computation of the Abelian Periods of a Word.
  10. Similarity Based Deduplication with Small Data Chunks.
  11. The Number of Cubes in Sturmian Words.

WABI 2012

  1. Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes.
  2. Distributed String Mining for High-Throughput Sequencing Data.
  3. Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter.
  4. Succinct de Bruijn Graphs.

WALCOM 2012

  1. Linear Time Inference of Strings from Cover Arrays Using a Binary Alphabet - (Extended Abstract).

ACM Comput. Surv. 2012

  1. A comparison of index-based lempel-Ziv LZ77 factorization algorithms.

ACM Trans. Algorithms 2012

  1. Succinct ordinal trees based on tree covering.

ACM Trans. Inf. Syst. 2012

  1. Word-based self-indexes for natural language text.

Algorithmica 2012

  1. Fast Arc-Annotated Subsequence Matching in Linear Space.
  2. Lightweight Data Indexing and Compression in External Memory.
  3. Stronger Lempel-Ziv Based Compressed Text Indexing.
  4. Succinct Representation of Labeled Graphs.

Algorithms 2012

  1. A Note on Sequence Prediction over Large Alphabets.
  2. An Online Algorithm for Lightweight Grammar-Based Compression.

CoRR 2012

  1. (Really) Tight bounds for dispatching binary methods
  2. A Bijective String Sorting Transform
  3. A Fast Algorithm for Permutation Pattern Matching Based on Alternating Runs
  4. A New Algorithm for Data Compression Optimization
  5. A Note on Efficient Computation of All Abelian Periods in a String
  6. A memory versus compression ratio trade-off in PPM via compressed context modeling
  7. A refined Quicksort asymptotic
  8. Adaptive Techniques to find Optimal Planar Boxes
  9. Algorithms for Computing Abelian Periods of Words
  10. Algorithms for discovering and proving theorems about permutation patterns.
  11. An Entertaining Example for the Usage of Bitwise Operations in Programming
  12. Approximate pattern matching with k-mismatches in packed text
  13. BIN@ERN: Binary-Ternary Compressing Data Coding
  14. Better Space Bounds for Parameterized Range Majority and Minority
  15. Binary Jumbled String Matching: Faster Indexing in Less Space
  16. Bouma2 - A Quasi-Stateless, Tunable Multiple String-Match Algorithm
  17. Compact Binary Relation Representations with Rich Functionality
  18. Comparison of Bucket Sort and RADIX Sort
  19. Computing Lempel-Ziv Factorization Online
  20. Counting common substrings effectively
  21. Cross-Document Pattern Matching
  22. Data Structure Lower Bounds on Random Access to Grammar-Compressed Strings
  23. Deterministic Polynomial-Time Algorithms for Designing Short DNA Words
  24. Distance Measures for Sequences
  25. Efficient Algorithms for Finding Tucker Patterns
  26. Efficient LZ78 factorization of grammar compressed text
  27. Efficient algorithms for highly compressed data: The Word Problem in Generalized Higman Groups is in P
  28. Fast Packed String Matching for Short Patterns
  29. Fast algorithm finding the shortest reset words
  30. Faster Compact Top-k Document Retrieval
  31. Grammar-Based Construction of Indexes for Binary Jumbled Pattern Matching
  32. Improved in-place associative integer sorting
  33. Improving Compressed Counting
  34. In-place associative integer sorting
  35. In-place associative permutation sort
  36. Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform
  37. Linear Time Lempel-Ziv Factorization: Simple, Fast, Small
  38. Linear-Space Substring Range Counting over Polylogarithmic Alphabets
  39. Lower bounding edit distances between permutations
  40. Lyndon Words and Short Superstrings
  41. Memory Efficient De Bruijn Graph Construction
  42. Necklaces, Convolutions, and X+Y
  43. New Algorithms for Position Heaps
  44. New algorithms for binary jumbled pattern matching
  45. Note on the Greedy Parsing Optimality for Dictionary-Based Text Compression
  46. On Approximating String Selection Problems with Outliers
  47. On Optimal Top-K String Retrieval
  48. On Top-k Search and Range Reporting
  49. On a New Method of Storing a Variable Size Array
  50. On the Complexity of Minimum Labeling Alignment of Two Genomes
  51. On the Value of Multiple Read/Write Streams for Data Compression
  52. On the combinatorics of suffix arrays
  53. On-line Indexing for General Alphabets via Predecessor Queries on Subsets of an Ordered List
  54. Optimal Dynamic Sequence Representations.
  55. Optimal compression of hash-origin prefix trees
  56. Pattern Matching in Multiple Streams
  57. Predecessor search with distance-sensitive query time
  58. Quasi-Succinct Indices
  59. Quasiperiodicities in Fibonacci strings
  60. QuickHeapsort: Modifications and improved analysis
  61. Ranked Document Retrieval in (Almost) No Space
  62. Sequential-Access FM-Indexes
  63. Simpler and Faster Lempel Ziv Factorization
  64. Simplified, stable parallel merging
  65. Some Novel Results From Analysis of Move To Front (MTF) List Accessing Algorithm
  66. Sorted Range Reporting
  67. Sorting and preimages of pattern classes
  68. Sorting distinct integer keys using in-place associative sort
  69. Sorting distinct integers using improved in-place associative sort
  70. Space-Time Trade-offs for Stack-Based Algorithms
  71. Sparse Suffix Tree Construction with Small Space
  72. SparseDTW: A Novel Approach to Speed up Dynamic Time Warping
  73. Speeding-up $q$-gram mining on grammar-based compressed texts
  74. Streaming Complexity of Checking Priority Queues
  75. String Trees
  76. Succinct Indices for Range Queries with applications to Orthogonal Range Maxima
  77. Succinct Posets
  78. TH*:Scalable Distributed Trie Hashing
  79. The Rightmost Equal-Cost Position Problem
  80. The Wavelet Trie: Maintaining an Indexed Sequence of Strings in Compressed Space
  81. Time and Space Efficient Lempel-Ziv Factorization based on Run Length Encoding
  82. Time-Space Trade-Offs for Longest Common Extensions

Comput. J. 2012

  1. Boosting Text Compression with Word-Based Statistical Encoding.
  2. The String-to-Dictionary Matching Problem.

IEEE ACM Trans. Comput. Biol. Bioinform. 2012

  1. An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence.

IEEE Trans. Knowl. Data Eng. 2012

  1. Practical Efficient String Mining.

IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 2012

  1. A Fast On-Line Algorithm for the Longest Common Subsequence Problem with Constant Alphabet.

Inf. Comput. 2012

  1. Bidirectional search in a string with wavelet trees and bidirectional matching statistics.

Inf. Process. Lett. 2012

  1. An efficient algorithm to test square-freeness of strings compressed by straight-line programs.
  2. Computing all subtree repeats in ordered trees.

Inf. Process. Manag. 2012

  1. Bidirectional delta files.

Inf. Retr. 2012

  1. Implicit indexing of natural language text by reorganizing bytecodes.

Int. J. Found. Comput. Sci. 2012

  1. Finding Characteristic Substrings from Compressed Texts.
  2. Parallel Algorithms for Mapping Short degenerate and Weighted DNA Sequences to a Reference genome.

J. Comput. Syst. Sci. 2012

  1. Ultra-succinct representation of ordered trees with applications.

J. Discrete Algorithms 2012

  1. An algorithm for mapping short reads to a dynamically changing genomic sequence.
  2. Dictionary-symbolwise flexible parsing.
  3. On left and right seeds of a string.
  4. String matching with alphabet sampling.
  5. Tree template matching in ranked ordered trees by pushdown automata.
  6. Worst-case efficient single and multiple string matching on packed texts in the word-RAM model.

SIAM J. Comput. 2012

  1. An Optimal Dynamic Data Structure for Stabbing-Semigroup Queries.

Softw. Pract. Exp. 2012

  1. Revisiting bounded context block-sorting transformations.

Theor. Comput. Sci. 2012

  1. LRM-Trees: Compressed indices, adaptive sorting, and compressed permutations.
  2. New algorithms on wavelet trees and applications to information retrieval.
  3. String matching with variable length gaps.
  4. Succinct representations of permutations and functions.

Theory Comput. Syst. 2012

  1. Faster Approximate String Matching for Short Patterns.

ALENEX 2011

  1. A Closer Look at the Closest String and Closest Substring Problem.
  2. A Simple Parallel Cartesian Tree Algorithm and its Application to Suffix Tree Construction.
  3. Exact Pattern Matching with Feed-Forward Bloom Filters.
  4. Fast and Lightweight LCP-Array Construction Algorithms.

BCB 2011

  1. Approximate string-matching with a single gap for sequence alignment.
  2. DynMap: mapping short reads to multiple related genomes.

CCP 2011

  1. A Method to Ensure the Confidentiality of the Compressed Data.
  2. An Online Algorithm for Lightweight Grammar-Based Compression.
  3. Asymptotic Optimal Lossless Compression via the CSE Technique.
  4. Backwards Search in Context Bound Text Transformations.
  5. Cache Friendly Burrows-Wheeler Inversion.
  6. Combining Non-stationary Prediction, Optimization and Mixing for Data Compression.
  7. Generalized Witness Sets.
  8. Lempel-Ziv Data Compression on Parallel and Distributed Systems.
  9. Lossless Compression of Hyperspectral Imagery.
  10. Natural Language Compression per Blocks.
  11. Pattern Matching on Sparse Suffix Trees.
  12. Quick Estimation of Data Compression and De-duplication for Large Storage Systems.
  13. Straight-Line Programs: A Practical Test.
  14. Wavelet Trees: From Theory to Practice.

CIAA 2011

  1. Chrobak Normal Form Revisited, with Applications.
  2. Tree Template Matching in Ranked Ordered Trees by Pushdown Automata.

CIKM 2011

  1. Indexes for highly repetitive document collections.

COCOON 2011

  1. On the Right-Seed Array of a String.

CPM 2011

  1. A Coarse-to-Fine Approach to Computing the k-Best Viterbi Paths.
  2. A Combinatorial Model of Phyllotaxis Perturbations in Arabidopsis thaliana.
  3. A d-Step Approach for Distinct Squares in Strings.
  4. Algorithms on Grammar-Compressed Strings.
  5. Approximation Algorithms for Orienting Mixed Graphs.
  6. Automatic Discovery of Patterns in Media Content.
  7. Computational Regulatory Genomics.
  8. Counting Colours in Compressed Strings.
  9. Edit Distance with Duplications and Contractions Revisited.
  10. Efficient Matching of Biological Sequences Allowing for Non-overlapping Inversions.
  11. Efficient Seeds Computation Revisited.
  12. Fast Error-Tolerant Quartet Phylogeny Algorithms.
  13. Faster Subsequence and Don’t-Care Pattern Matching on Compressed Texts.
  14. Filling Scaffolds with Gene Repetitions: Maximizing the Number of Adjacencies.
  15. Finding Approximate and Constrained Motifs in Graphs.
  16. Forest Alignment with Affine Gaps and Anchors.
  17. Frequent Submap Discovery.
  18. Improved MAX SNP-Hard Results for Finding an Edit Distance between Unordered Trees.
  19. LRM-Trees: Compressed Indices, Adaptive Sorting, and Compressed Permutations.
  20. Lempel-Ziv Factorization Revisited.
  21. Lightweight BWT Construction for Very Large String Collections.
  22. On Wavelet Tree Construction.
  23. On the Weak Prefix-Search Problem.
  24. Palindrome Pattern Matching.
  25. Phylogenetic Footprinting and Consistent Sets of Local Aligments.
  26. Polynomial-Time Approximation Algorithms for Weighted LCS Problem.
  27. Quick Greedy Computation for Minimum Common String Partitions.
  28. Real-Time Streaming String-Matching.
  29. Restricted Common Superstring and Restricted Common Supersequence.
  30. Self-indexing Based on LZ77.
  31. Simple Real-Time Constant-Space String Matching.
  32. Space Lower Bounds for Online Pattern Matching.
  33. Sparse and Truncated Suffix Trees on Variable-Length Codes.
  34. String Comparison and Lyndon-Like Factorization Using V-Order in Linear Time.
  35. Substring Range Reporting.
  36. Succincter Text Indexing with Wildcards.
  37. Tractability Results for the Consecutive-Ones Property with Multiplicity.
  38. Tractability and Approximability of Maximal Strip Recovery.
  39. Unique Perfect Phylogeny Is NP-Hard.

DCC 2011

  1. Coding of Sets of Words.
  2. Color Image Compression Using a Learned Dictionary of Pairs of Orthonormal Bases.
  3. Compressed Context Modeling for Text Compression.
  4. Compressed Index for Property Matching.
  5. Compressed Property Suffix Trees.
  6. Deplump for Streaming Data.
  7. Error Recovery Method for PPM Compressed Data.
  8. Improving PPM Algorithm Using Dictionaries.
  9. Lossless Data Compression Testbed: ExCom and Prague Corpus.
  10. Mixing Deduplication and Compression on Active Data Sets.
  11. On Performance of Compressed Pattern Matching on VF Codes.
  12. Search and Modification in Compressed Texts.
  13. Sequence Similarity by Gapped LZW.
  14. Sliding Window Update Using Suffix Arrays.
  15. The String-to-Dictionary Matching Problem.
  16. Tree Structure Compression with RePair.

DSL 2011

  1. Specific “scientific” data structures, and their processing

Developments in Language Theory 2011

  1. Abelian Primitive Words.
  2. Avoiding Abelian Powers in Partial Words.
  3. On Highly Repetitive and Power Free Words.
  4. On Prefix Normal Words.

Discovery Science 2011

  1. Scalable Detection of Frequent Substrings by Grammar-Based Compression.

ESA 2011

  1. Alphabet-Independent Compressed Text Indexing.
  2. Distribution-Aware Compressed Full-Text Indexes.
  3. Pattern Matching in Lempel-Ziv Compressed Strings: Fast, Simple, and Deterministic.

FSTTCS 2011

  1. Optimal Packed String Matching.

ICALP (1) 2011

  1. Range Majority in Constant Time and Linear Space.

ISAAC 2011

  1. A Dynamic Stabbing-Max Data Structure with Sub-Logarithmic Query Time.
  2. A New Algorithm for the Characteristic String Problem under Loose Similarity Criteria.
  3. Compact Representation of Posets.
  4. Dynamic Range Majority Data Structures.
  5. Dynamic Range Selection in Linear Space.
  6. Encoding 2D Range Maximum Queries.
  7. External Memory Orthogonal Range Reporting with Fast Updates.
  8. Faster Approximate Pattern Matching in Compressed Repetitive Texts.
  9. Path Queries in Weighted Trees.
  10. Range LCP.
  11. Space-Efficient Data-Analysis Queries on Grids.
  12. Succinct Indexes for Circular Patterns.

IWOCA 2011

  1. A Unifying Property for Distribution-Sensitive Priority Queues.
  2. Parameterized Longest Previous Factor.
  3. Periods in Partial Words: An Algorithm.
  4. Two Constant-Factor-Optimal Realizations of Adaptive Heapsort.
  5. p-Suffix Sorting as Arithmetic Coding.

LATA 2011

  1. Improved Alignment Based Algorithm for Multilingual Text Compression.
  2. Unary Pattern Avoidance in Partial Words Dense with Holes.

MFCS 2011

  1. Compressed Word Problems for Inverse Monoids.
  2. On Minimising Automata with Errors.
  3. Periodicity Algorithms for Partial Words.
  4. The Bounded Search Tree Algorithm for the Closest String Problem Has Quadratic Smoothed Complexity.

SEA 2011

  1. An Empirical Evaluation of Extendible Arrays.
  2. Compressed String Dictionaries.
  3. Online Dictionary Matching with Variable-Length Gaps.
  4. Practical Compressed Document Retrieval.

SIGIR 2011

  1. Sample selection for dictionary-based corpus compression.

SISAP 2011

  1. Succinct nearest neighbor search.

SODA 2011

  1. Improved Space Bounds for Cache-Oblivious Range Reporting.
  2. Optimal pattern matching in LZW compressed strings.
  3. Ordered and Unordered Top-K Range Reporting in Large Data Sets.
  4. Persistent Predecessor Search and Orthogonal point Location on the Word RAM.
  5. Random Access to grammar-Compressed Strings.
  6. Top-K Color Queries for Document Retrieval.

SOFSEM 2011

  1. An Improved B+ Tree for Flash File Systems.
  2. In-Place Sorting.

SPIRE 2011

  1. A Knowledge-Based Semantic Kernel for Text Classification.
  2. A Learned Approach for Ranking News in Real-Time Using the Blogosphere.
  3. A Multi-faceted Approach to Query Intent Classification.
  4. A New Approach for Verifying URL Uniqueness in Web Crawlers.
  5. A Succinct Index for Hypertext.
  6. Approximate Point Set Pattern Matching with L p -Norm.
  7. Approximate Regular Expression Matching with Multi-strings.
  8. Approximations and Partial Solutions for the Consensus Sequence Problem.
  9. Attribute Retrieval from Relational Web Tables.
  10. COCA Filters: Co-occurrence Aware Bloom Filters.
  11. Candidate Document Retrieval for Web-Scale Text Reuse Detection.
  12. Compressed Indexes for Aligned Pattern Matching.
  13. Compressed Text Indexing with Wildcards.
  14. Computing All Subtree Repeats in Ordered Ranked Trees.
  15. Computing the Longest Common Prefix Array Based on the Burrows-Wheeler Transform.
  16. Constructing Strings at the Nano Scale via Staged Self-assembly.
  17. Cross-Lingual Text Fragment Alignment Using Divergence from Randomness.
  18. Detecting Health Events on the Social Web to Enable Epidemic Intelligence.
  19. Discounted Cumulative Gain and User Decision Models.
  20. ESP-Index: A Compressed Index Based on Edit-Sensitive Parsing.
  21. Enhancing Document Snippets Using Temporal Information.
  22. External Query Reformulation for Text-Based Image Retrieval.
  23. Fast Computation of a String Duplication History under No-Breakpoint-Reuse - (Extended Abstract).
  24. Fast q-gram Mining on SLP Compressed Strings.
  25. Finding Frequent Elements in Compressed 2D Arrays and Strings.
  26. Fixed Block Compression Boosting in FM-Indexes.
  27. Improved Compressed Indexes for Full-Text Document Retrieval.
  28. Indexing with Gaps.
  29. Navigating the User Query Space.
  30. Near Real-Time Suffix Tree Construction via the Fringe Marked Ancestor Problem.
  31. On Suffix Extensions in Suffix Trees.
  32. On-Line Construction of Position Heaps.
  33. Persistency in Suffix Trees with Applications to String Interval Problems.
  34. Query-Sets + + : A Scalable Approach for Modeling Web Sites.
  35. Reference Sequence Construction for Relative Compression of Genomes.
  36. Space Efficient Wavelet Tree Construction.
  37. Spaced Seeds Design Using Perfect Rulers.
  38. Sparse Spatial Selection for Novelty-Based Search Result Diversification.
  39. Succinct Gapped Suffix Arrays.
  40. Weighted Shortest Common Supersequence.
  41. When Was It Written? Automatically Determining Publication Dates.

STACS 2011

  1. On Minimal Sturmian Partial Words.

STOC 2011

  1. The power of simple tabulation hashing.

Stringology 2011

  1. 2001-2010: Ten Years of Exact String Matching Algorithms.
  2. A Parameterized Formulation for the Maximum Number of Runs Problem.
  3. Algorithmics of Posets Generated by Words over Partially Commutative Alphabets.
  4. An Improved Version of the Runs Algorithm Based on Crochemore’s Partitioning Algorithm.
  5. Analyzing Edit Distance on Trees: Tree Swap Distance is Intractable.
  6. Binary Image Compression via Monochromatic Pattern Substitution: A Sequential Speed-Up.
  7. Computing Abelian Periods in Words.
  8. Computing Longest Common Substring/Subsequence of Non-linear Texts.
  9. Computing the Number of Cubic Runs in Standard Sturmian Words.
  10. Efficient Eager XPath Filtering over XML Streams.
  11. Finding Long and Multiple Repeats with Edit Distance.
  12. Improving Deduplication Techniques by Accelerating Remainder Calculations.
  13. Improving Exact Search of Multiple Patterns From a Compressed Suffix Array.
  14. Inexact Graph Matching by “Geodesic Hashing” for the Alignment of Pseudoknoted RNA Secondary Structures.
  15. Inferring Strings from Suffix Trees and Links on a Binary Alphabet.
  16. Minimization of Acyclic DFAs.
  17. Notes on Sequence Binary Decision Diagrams: Relationship to Acyclic Automata and Complexities of Binary Set Operations.
  18. Observations On Compressed Pattern-Matching with Ranked Variables in Zimin Words.
  19. On Compile Time Knuth-Morris-Pratt Precomputation.
  20. Variations of Forward-SBNDM.

WADS 2011

  1. Space Efficient Data Structures for Dynamic Orthogonal Range Counting.

WALCOM 2011

  1. De Bruijn Sequences for the Binary Strings with Maximum Density.
  2. Efficient Top-k Queries for Orthogonal Ranges.

ACM J. Exp. Algorithmics 2011

  1. Theory and practice of monotone minimal perfect hashing.

ACM Trans. Algorithms 2011

  1. Fully compressed suffix trees.
  2. Succinct indexes for strings, binary relations and multilabeled trees.
  3. The tree inclusion problem: In linear space and faster.

Algorithmica 2011

  1. On Optimally Partitioning a Text to Improve Its Compression.

Algorithms 2011

  1. Compressed Matching in Dictionaries.
  2. Edit Distance with Block Deletions.

Bioinform. 2011

  1. Compression of DNA sequence reads in FASTQ format.

CoRR 2011

  1. A Compressed Self-Index for Genomic Databases
  2. A Dynamic Stabbing-Max Data Structure with Sub-Logarithmic Query Time
  3. A Faster LZ77-Based Index
  4. A Regularity Measure for Context Free Grammars
  5. A Searchable Compressed Edit-Sensitive Parsing
  6. A Simple Linear-Space Data Structure for Constant-Time Range Minimum Query
  7. Algorithms for Jumbled Pattern Matching in Strings
  8. An Improved Move-To-Front(IMTF) Off-line Algorithm for the List Accessing Problem
  9. An implementation of range trees with fractional cascading in C++
  10. Anomaly Sequences Detection from Logs Based on Compression
  11. Approximating Edit Distance in Near-Linear Time
  12. Compressed String Dictionaries
  13. Computing a Longest Common Palindromic Subsequence
  14. Computing on Binary Strings
  15. Computing q-gram Frequencies on Collage Systems
  16. Computing q-gram Non-overlapping Frequencies on SLP Compressed Texts
  17. De-amortizing Binary Search Trees
  18. Don’t Rush into a Union: Take Time to Find Your Roots
  19. Dynamic Range Majority Data Structures
  20. Dynamic Range Selection in Linear Space
  21. Edit Distance to Monotonicity in Sliding Windows
  22. Efficient Seeds Computation Revisited
  23. Encoding 2-D Range Maximum Queries
  24. External Memory Orthogonal Range Reporting with Fast Updates
  25. Fast $q$-gram Mining on SLP Compressed Strings
  26. Faster Approximate Pattern Matching in Compressed Repetitive Texts
  27. Faster fully compressed pattern matching by recompression
  28. Fixed Block Compression Boosting in FM-Indexes
  29. Genome Halving by Block Interchange
  30. I/O-Efficient Data Structures for Colored Range and Prefix Reporting
  31. Improved Grammar-Based Compressed Indexes
  32. Improved space-time tradeoffs for approximate full-text indexing with one edit error
  33. Inducing the LCP-Array
  34. K-sort: A new sorting algorithm that beats Heap sort for n <= 70 lakhs!
  35. Linear Time Inference of Strings from Cover Arrays using a Binary Alphabet
  36. Linear pattern matching on sparse suffix trees
  37. Linear-Space Data Structures for Range Mode Query in Arrays
  38. Lossless data compression on GPGPU architectures
  39. Mining Patterns in Networks using Homomorphism
  40. New Lower and Upper Bounds for Representing Sequences
  41. On Approximability of Block Sorting
  42. On Compressing Permutations and Adaptive Sorting
  43. On Dynamic Optimality for Binary Search Trees
  44. On minimising automata with errors
  45. On the Complexity of Approximate Sum of Sorted List
  46. On-line construction of position heaps
  47. Optimal Indexes for Sparse Bit Vectors
  48. Orthogonal Range Searching on the RAM, Revisited
  49. Partial Data Compression and Text Indexing via Optimal Suffix Multi-Selection
  50. Pattern Matching under Polynomial Transformation
  51. Pattern matching in Lempel-Ziv compressed strings: fast, simple, and deterministic
  52. Practical Top-K Document Retrieval in Reduced Space
  53. Privacy-Enhanced Methods for Comparing Compressed DNA Sequences
  54. Quadratic-time Algorithm for the String Constrained LCS Problem
  55. Random input helps searching predecessors
  56. Reference Sequence Construction for Relative Compression of Genomes
  57. Relative Lempel-Ziv Factorization for Efficient Storage and Retrieval of Web Collections
  58. Restructuring Compressed Texts without Explicit Decompression
  59. Self-Index Based on LZ77
  60. Self-Index based on LZ77 (thesis)
  61. Sorting Algorithms with Restrictions
  62. Space Lower Bounds for Online Pattern Matching
  63. Space-Efficient Data-Analysis Queries on Grids
  64. SparseAssembler: de novo Assembly with the Sparse de Bruijn Graph
  65. Stratified B-trees and versioning dictionaries
  66. String Indexing for Patterns with Wildcards
  67. String Matching with Variable Length Gaps
  68. Substring Range Reporting
  69. Succinct Representations of Permutations and Functions
  70. Succincter Text Indexing with Wildcards
  71. The Cell Probe Complexity of Dynamic Range Counting
  72. Tight lower bounds for online labeling problem
  73. Towards Optimal Sorting of 16 Elements
  74. Towards an Optimal Space-and-Query-Time Index for Top-$k$ Document Retrieval
  75. Tying up the loose ends in fully LZW-compressed pattern matching
  76. Uncommon Suffix Tries
  77. Upper Bounds for Maximally Greedy Binary Search Trees

Fundam. Informaticae 2011

  1. Self-Indexed Grammar-Based Compression.

Inf. Comput. 2011

  1. Space-efficient construction of Lempel-Ziv compressed text indexes.

Inf. Process. Lett. 2011

  1. Computing Longest Previous non-overlapping Factors.

Inf. Process. Manag. 2011

  1. Improving semistatic compression via phrase-based modeling.

Inf. Syst. 2011

  1. Fully dynamic metric access methods based on hyperplane partitioning.

Int. J. Found. Comput. Sci. 2011

  1. Stronger Quickheaps.

J. Discrete Algorithms 2011

  1. Fast searching in packed strings.
  2. Missing pattern discovery.
  3. Tight bounds for online stable sorting.

Probl. Inf. Transm. 2011

  1. Computing the longest common substring with one mismatch.

Proc. VLDB Endow. 2011

  1. Relative Lempel-Ziv Factorization for Efficient Storage and Retrieval of Web Collections.

Theor. Comput. Sci. 2011

  1. Approximate string matching with stuck address bits.
  2. On-line approximate string matching with bounded errors.
  3. Succinct data structures for Searchable Partial Sums with optimal worst-case performance.
  4. Succinct representation of dynamic trees.
  5. Verifying and enumerating parameterized border arrays.

ALENEX 2010

  1. Succinct Trees in Practice.

Algorithms and Applications 2010

  1. A Parallel Algorithm for Fixed-Length Approximate String-Matching with k-mismatches.
  2. Extended Compact Web Graph Representations.
  3. Unified View of Backward Backtracking in Short Read Mapping.

BIBE 2010

  1. Compressed q-Gram Indexing for Highly Repetitive Biological Sequences.

BIBM 2010

  1. An algorithm for mapping short reads to a dynamically changing genomic sequence.

CPM 2010

  1. A Compact Representation of Nondeterministic (Suffix) Automata for the Bit-Parallel Approach.
  2. A Minimal Periods Algorithm with Applications.
  3. Affine Image Matching Is Uniform TC0-Complete.
  4. Algorithms for Forest Pattern Matching.
  5. Algorithms for Three Versions of the Shortest Common Superstring Problem.
  6. Approximate All-Pairs Suffix/Prefix Overlaps.
  7. Bidirectional Search in a String with Wavelet Trees.
  8. Bounds on the Minimum Mosaic of Population Sequences under Recombination.
  9. Breakpoint Distance and PQ-Trees.
  10. Building the Minimal Automaton of A*X in Linear Time, When X Is of Bounded Cardinality.
  11. Compression, Indexing, and Retrieval for Massive String Data.
  12. Cover Array String Reconstruction.
  13. Extended Islands of Tractability for Parsimony Haplotyping.
  14. Extension and Faster Implementation of the GRP Transform for Lossless Compression.
  15. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks.
  16. Finding Optimal Alignment and Consensus of Circular Strings.
  17. Implicit Hitting Set Problems and Multi-genome Alignment.
  18. Mod/Resc Parsimony Inference.
  19. Old and New in Stringology.
  20. On the Parameterized Complexity of Some Optimization Problems Related to Multiple-Interval Graphs.
  21. Optimizing Restriction Site Placement for Synthetic Genomes.
  22. Parallel and Distributed Compressed Indexes.
  23. Phylogeny- and Parsimony-Based Haplotype Inference with Constraints.
  24. Pseudo-realtime Pattern Matching: Closing the Gap.
  25. Sampled Longest Common Prefix Array.
  26. Small-Space 2D Compressed Dictionary Matching.
  27. Succinct Dictionary Matching with No Slowdown.
  28. Succinct Representations of Separable Graphs.
  29. The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection.
  30. The Property Suffix Tree with Dynamic Properties.
  31. Verifying a Parameterized Border Array in O(n1.5) Time.

CSR 2010

  1. Validating the Knuth-Morris-Pratt Failure Function, Fast and Online.

DASFAA Workshops 2010

  1. An Improved Algorithm for Extracting Research Communities from Bibliographic Data.

DCC 2010

  1. A New Searchable Variable-to-Variable Compressor.
  2. A Pseudo-Random Number Generator Based on LZSS.
  3. A Similarity Measure Using Smallest Context-Free Grammars.
  4. Advantages of Shared Data Structures for Sequences of Balanced Parentheses.
  5. Bidirectional Delta Files.
  6. Efficient Algorithms for Constructing Optimal Bi-directional Context Sets.
  7. File-Size Preserving LZ Encoding for Reversible Data Embedding.
  8. I/O-Efficient Compressed Text Indexes: From Theory to Practice.
  9. LZ77-Like Compression with Fast Random Access.
  10. Local Modeling for WebGraph Compression.
  11. Lossless Compression of Maps, Charts, and Graphs via Color Separation.
  12. Lossless Data Compression via Substring Enumeration.
  13. Modelling Parallel Texts for Boosting Compression.
  14. Neural Markovian Predictive Compression: An Algorithm for Online Lossless Data Compression.
  15. On Computation of Performance Bounds of Optimal Index Assignment.
  16. Optimum String Match Choices in LZSS.
  17. Xampling: Analog Data Compression.
  18. gFPC: A Self-Tuning Compression Algorithm.

Discovery Science 2010

  1. Sparse Substring Pattern Set Discovery Using Linear Programming Boosting.

ER Workshops 2010

  1. Range Queries over a Compact Representation of Minimum Bounding Rectangles.

ESA (1) 2010

  1. A Fully Compressed Algorithm for Computing the Edit Distance of Run-Length Encoded Strings.
  2. Fast Prefix Search in Little Space, with Applications.
  3. Medium-Space Algorithms for Inverse BWT.
  4. On the Huffman and Alphabetic Tree Problem with General Cost Functions.

ESA (2) 2010

  1. Data Structures: Time, I/Os, Entropy, Joules!
  2. On Space Efficient Two Dimensional Range Minimum Data Structures.
  3. Top-k Ranked Document Search in General Text Databases.

FOCS 2010

  1. A Lower Bound for Dynamic Approximate Membership Data Structures.

FUN 2010

  1. A Fun Application of Compact Data Structures to Indexing Geographic Data.

ICALP (1) 2010

  1. Interval Sorting.
  2. Mergeable Dictionaries.
  3. Optimal Trade-Offs for Succinct String Indexes.

ICDE 2010

  1. Fast in-memory XPath search using compressed indexes.

ISAAC (1) 2010

  1. Priority Range Trees.
  2. Should Static Search Trees Ever Be Unbalanced?

ISAAC (2) 2010

  1. Alphabet Partitioning for Compressed Rank/Select and Applications.
  2. Dynamic Range Reporting in External Memory.
  3. Efficient Indexes for the Positional Pattern Matching Problem and Two Related Problems over Small Alphabets.
  4. Entropy-Bounded Representation of Point Grids.
  5. Identifying Approximate Palindromes in Run-Length Encoded Strings.

IWOCA 2010

  1. Dictionary-Symbolwise Flexible Parsing.
  2. Minimum Number of Holes in Unavoidable Sets of Partial Words of Size Three.
  3. On the Maximal Sum of Exponents of Runsin a String.
  4. Skip Lift: A Probabilistic Alternative to Red-Black Trees.
  5. Worst Case Efficient Single and Multiple String Matching in the RAM Model.

LATA 2010

  1. A Fast Longest Common Subsequence Algorithm for Similar Strings.
  2. Abelian Square-Free Partial Words.
  3. Avoidable Binary Patterns in Partial Words.
  4. Choosing Word Occurrences for the Smallest Grammar Problem.
  5. Extending Stochastic Context-Free Grammars for an Application in Bioinformatics.
  6. Grammar-Based Compression in a Streaming Model.
  7. Hard Counting Problems for Partial Words.

LATIN 2010

  1. Compact Rich-Functional Binary Relation Representations.
  2. Fast Set Intersection and Two-Patterns Matching.
  3. Lightweight Data Indexing and Compression in External Memory.
  4. Optimal Succinctness for Range Minimum Queries.
  5. Sharp Separation and Applications to Exact and Parameterized Algorithms.

MFCS 2010

  1. Counting Dependent and Independent Strings.

SEA 2010

  1. Bit-Parallel Search Algorithms for Long Patterns.
  2. Experiments on Union-Find Algorithms for the Disjoint-Set Data Structure.
  3. Practical Compressed Suffix Trees.

SODA 2010

  1. Cache-Oblivious Dynamic Dictionaries with Update/Query Tradeoffs.
  2. Cell-Probe Lower Bounds for Succinct Partial Sums.
  3. Counting Inversions, Offline Orthogonal Range Counting, and Related Problems.
  4. Data Structures for Range Minimum Queries in Multidimensional Arrays.
  5. Data-Specific Analysis of String Sorting.
  6. Deletion Without Rebalancing in Balanced Binary Trees.
  7. Fully-Functional Succinct Trees.
  8. Lower Bounds for Edit Distance and Product Metrics via Poincaré-Type Inequalities.
  9. On the Cell Probe Complexity of Dynamic Membership.
  10. Randomized Shellsort: A Simple Oblivious Sorting Algorithm.
  11. Regular Expression Matching with Multi-Strings and Intervals.

SOFSEM 2010

  1. Dynamic Edit Distance Table under a General Weighted Cost Function.
  2. Efficient Algorithms for Two Extensions of LPF Table: The Power of Suffix Arrays.
  3. Fast Arc-Annotated Subsequence Matching in Linear Space.
  4. Fast and Compact Prefix Codes.

SPIRE 2010

  1. A PTAS for the Square Tiling Problem.
  2. A Self-Supervised Approach for Extraction of Attribute-Value Pairs from Wikipedia Articles.
  3. Algorithms for Finding a Minimum Repetition Representation of a String.
  4. Approximate String Matching with Stuck Address Bits.
  5. CST++.
  6. Colored Range Queries and Document Retrieval.
  7. Compressed Self-indices Supporting Conjunctive Queries on Document Collections.
  8. Computing Matching Statistics and Maximal Exact Matches on Compressed Full-Text Indexes.
  9. Counting and Verifying Maximal Palindromes.
  10. Dual-Sorted Inverted Lists.
  11. Dynamic Z-Fast Tries.
  12. Evaluation of Query Performance Prediction Methods by Range.
  13. Extracting Powers and Periods in a String from Its Runs Structure.
  14. Fast Bit-Parallel Matching for Network and Regular Expressions.
  15. Faster Compressed Dictionary Matching.
  16. Fingerprinting Ratings for Collaborative Filtering - Theoretical and Empirical Analysis.
  17. Finite Automata Based Algorithms for the Generalized Constrained Longest Common Subsequence Problems.
  18. Hypergeometric Language Model and Zipf-Like Scoring Function for Web Document Similarity Retrieval.
  19. Identifying SNPs without a Reference Genome by Comparing Raw Reads.
  20. Improved Fast Similarity Search in Dictionaries.
  21. Incremental Algorithms for Effective and Efficient Query Recommendation.
  22. Mining Large Query Induced Graphs towards a Hierarchical Query Folksonomy.
  23. Multiplication Algorithms for Monge Matrices.
  24. On Shortest Common Superstring and Swap Permutations.
  25. On Tag Spell Checking.
  26. On the Hardness of Counting and Sampling Center Strings.
  27. Parameterized Searching with Mismatches for Run-Length Encoded Strings - (Extended Abstract).
  28. Querying the Web Graph - (Invited Talk).
  29. Range Queries over Untangled Chains.
  30. Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval.
  31. Restricted LCS.
  32. Standard Deviation as a Query Hardness Estimator.
  33. String Matching with Variable Length Gaps.
  34. String Retrieval for Multi-pattern Queries.
  35. Succinct Representations of Dynamic Strings.
  36. Temporal Analysis of Document Collections: Framework and Applications.
  37. Text Comparison Using Soft Cardinality.
  38. The Gapped Suffix Array: A New Index Structure for Fast Approximate Matching.
  39. Training Parse Trees for Efficient VF Coding.
  40. Using Related Queries to Improve Web Search Results Ranking.
  41. Why Large Closest String Instances Are Easy to Solve in Practice.

STACS 2010

  1. On Equations over Sets of Integers.

SWAT 2010

  1. An O(log log n)-Competitive Binary Search Tree with Optimal Worst-Case Access Times.

Stringology 2010

  1. (In)approximability Results for Pattern Matching Problems.
  2. A Space-Efficient Implementation of the Good-Suffix Heuristic.
  3. Approximate String Matching Allowing for Inversions and Translocations.
  4. Average Number of Runs and Squares in Necklace.
  5. Binary Image Compression via Monochromatic Pattern Substitution: Effectiveness and Scalability.
  6. Bounded Number of Squares in Infinite Repetition-Constrained Binary Words.
  7. Formal Characterizations of FA-based String Processors.
  8. Improving Automata Efficiency by Stretching and Jamming.
  9. Inferring Strings from Runs.
  10. New Simple Efficient Algorithms Computing Powers and Runs in Strings.
  11. On the Complexity of Variants of the k Best Strings Problem.
  12. Practical Fixed Length Lempel Ziv Coding.
  13. Reactive Links to Save Automata States.
  14. Simple Tree Pattern Matching for Trees in the Prefix Bar Notation.
  15. The Number of Runs in a Ternary Word.
  16. Tight and Simple Web Graph Compression.
  17. Tiling Binary Matrices in Haplotyping: Complexity, Models and Algorithms.

WABI 2010

  1. Swiftly Computing Center Strings.

WSDM 2010

  1. On compressing the textual web.

ACM J. Exp. Algorithmics 2010

  1. Practical approaches to reduce the space requirement of lempel-ziv-based compressed text indices.

ACM Trans. Algorithms 2010

  1. The compressed permuterm index.

ACM Trans. Embed. Comput. Syst. 2010

  1. Online memory compression for embedded systems.

ACM Trans. Inf. Syst. 2010

  1. Dynamic lightweight text compression.

ACM Trans. Web 2010

  1. Fast and Compact Web Graph Representations.

Algorithmica 2010

  1. On Sorting, Heaps, and Minimum Spanning Trees.

Algorithms Mol. Biol. 2010

  1. Linear-time protein 3-D structure searching with insertions and deletions.

Bioinform. 2010

  1. Efficient construction of an assembly string graph using the FM-index.

CoRR 2010

  1. An Efficient Algorithm For Chinese Postman Walk on Bi-directed de Bruijn Graphs
  2. Compressed random access memory
  3. Counting Colours in Compressed Strings
  4. Document Clustering with K-tree
  5. Dynamic Range Reporting in External Memory
  6. Efficient Parallel and Out of Core Algorithms for Constructing Large Bi-directed de Bruijn Graphs
  7. Exact Analysis of Pattern Matching Algorithms with Probabilistic Arithmetic Automata
  8. Fully Dynamic Data Structure for Top-k Queries on Uncertain Data
  9. K-tree: Large Scale Document Clustering
  10. LRM-Trees: Compressed Indices, Adaptive Sorting, and Compressed Permutations
  11. Lightweight LCP-Array Construction in Linear Time
  12. Mergeable Dictionaries
  13. New Algorithms on Wavelet Trees and Applications to Information Retrieval
  14. On Finding Frequent Patterns in Directed Acyclic Graphs
  15. On the Border Length Minimization Problem (BLMP) on a Square Array
  16. Optimal Trade-Off for Succinct String Indexes
  17. Parallelization of Weighted Sequence Comparison by using EBWT
  18. Pattern Kits
  19. Permuted Common Supersequence
  20. Random Access to Grammar Compressed Strings
  21. Random Indexing K-tree
  22. Range Reporting for Moving Points on a Grid
  23. Sampled Longest Common Prefix Array
  24. Should Static Search Trees Ever Be Unbalanced?
  25. Some long-period random number generators using shifts and xors
  26. Succinct Data Structures for Assembling Large Genomes
  27. Succinct Dictionary Matching With No Slowdown
  28. Succinct Representations of Dynamic Strings
  29. The B-Skip-List: A Simpler Uniquely Represented Alternative to B-Trees
  30. The universality of iterated hashing over variable-length strings
  31. Tight and simple Web graph compression
  32. Top-K Color Queries for Document Retrieval
  33. Tree structure compression with RePair
  34. Unified Compression-Based Acceleration of Edit-Distance Computation
  35. Uses of randomness in computation
  36. Worst case efficient single and multiple string matching in the Word-RAM model

Discret. Appl. Math. 2010

  1. Sorting with networks of data structures.

IEICE Trans. Inf. Syst. 2010

  1. Context-Sensitive Grammar Transform: Compression and Pattern Matching.

Inf. Process. Lett. 2010

  1. Efficient algorithms for the all-pairs suffix-prefix problem and the all-pairs substring-prefix problem.

J. Comput. Biol. 2010

  1. Storage and Retrieval of Highly Repetitive Sequence Collections.

J. Discrete Algorithms 2010

  1. The longest common extension problem revisited and applications to approximate string searching.

Math. Comput. Sci. 2010

  1. Fast, Practical Algorithms for Computing All the Repeats in a String.

Theor. Comput. Sci. 2010

  1. Move-to-Front, Distance Coding, and Inversion Frequencies revisited.
  2. On compact representations of All-Pairs-Shortest-Path-Distance matrices.

ACISP 2009

  1. Testing Stream Ciphers by Finding the Longest Substring of a Given Density.

ALENEX 2009

  1. Theory and Practise of Monotone Minimal Perfect Hashing.

CIAA 2009

  1. Implementation and Application of Automata in String Processing.

CPM 2009

  1. An Efficient Matching Algorithm for Encoded DNA Sequences and Binary Strings.
  2. Approximate Matching for Run-Length Encoded Strings Is 3sum-Hard.
  3. Average-Case Analysis of Perfect Sorting by Reversals.
  4. CPM’s 20th Anniversary: A Statistical Retrospective.
  5. Contracted Suffix Trees: A Simple and Dynamic Text Indexing Data Structure.
  6. Deconstructing Intractability: A Case Study for Interval Constrained Coloring.
  7. Efficient Inference of Haplotypes from Genotypes on a Pedigree with Mutations and Missing Alleles (Extented Abstract).
  8. Fast RNA Structure Alignment for Crossing Input Structures.
  9. Fast Searching in Packed Strings.
  10. Faster and Space-Optimal Edit Distance “1” Dictionary.
  11. Finding All Sorting Tandem Duplication Random Loss Operations.
  12. Generalized Substring Compression.
  13. Graph Mining: Patterns, Generators and Tools.
  14. Haplotype Inference Constrained by Plausible Haplotype Data.
  15. LCS Approximation via Embedding into Local Non-repetitive Strings.
  16. Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time.
  17. Linear Time Suffix Array Construction Using D-Critical Substrings.
  18. Maximum Motif Problem in Vertex-Colored Graphs.
  19. Modeling and Algorithmic Challenges in Online Social Networks.
  20. Multiple Alignment of Biological Networks: A Flexible Approach.
  21. New Complexity Bounds for Image Matching under Rotation and Scaling.
  22. On the Value of Multiple Read/Write Streams for Data Compression.
  23. Online Approximate Matching with Non-local Distances.
  24. Periodic String Comparison.
  25. Permuted Longest-Common-Prefix Array.
  26. Quasi-distinct Parsing and Optimal Compression Methods.
  27. Reoptimization of the Shortest Common Superstring Problem.
  28. Sparse RNA Folding: Time and Space Efficient Algorithms.
  29. Statistical Properties of Factor Oracles.
  30. Text Indexing, Suffix Sorting, and Data Compression: Common Problems and Techniques.
  31. The Structure of Level-k Phylogenetic Networks.

DASFAA 2009

  1. Reducing Space Requirements for Disk Resident Suffix Arrays.

DCC 2009

  1. Low-Memory Adaptive Prefix Coding.
  2. Suffix Tree Based VF-Coding for Compressed Pattern Matching.

ECDL 2009

  1. A Compressed Self-indexed Representation of XML Documents.

ER Workshops 2009

  1. A New Point Access Method Based on Wavelet Trees.

ESA 2009

  1. On Optimally Partitioning a Text to Improve Its Compression.

Efficient Algorithms 2009

  1. Reflections on Optimal and Nearly Optimal Binary Search Trees.

ICALP (1) 2009

  1. Dynamic Succinct Ordered Trees.
  2. Faster Regular Expression Matching.

IJCBS 2009

  1. Practical and Efficient Algorithms for Degenerate and Weighted Sequences Derived from High Throughput Sequencing Technologies.

ISAAC 2009

  1. Data Structures for Approximate Orthogonal Range Counting.
  2. Deletion without Rebalancing in Multiway Search Trees.
  3. Finding All Approximate Gapped Palindromes.
  4. Interval Stabbing Problems in Small Integer Ranges.
  5. Online Sorted Range Reporting.
  6. Range Non-overlapping Indexing.
  7. Succinct Index for Dynamic Dictionary Matching.

ITW 2009

  1. Constructing optimal whole-bit recycling codes.

IWOCA 2009

  1. LPF Computation Revisited.
  2. Lightweight Parameterized Suffix Array Construction.
  3. Minimax Trees in Linear Time with Applications.
  4. Succinct Representations of Trees.

LATA 2009

  1. A Series of Run-Rich Strings.
  2. Counting Parameterized Border Arrays for a Binary Alphabet.

MFCS 2009

  1. Self-indexed Text Compression Using Straight-Line Programs.

PARCO 2009

  1. A Parallel Algorithm for the Fixed-length Approximate String Matching Problem for High Throughput Sequencing Technologies.

RECOMB 2009

  1. Storage and Retrieval of Individual Genomes.

SEA 2009

  1. An Application of Self-organizing Data Structures to Compression.
  2. Broadword Computing and Fibonacci Code Speed Up Compressed Suffix Arrays.

SISAP 2009

  1. Analyzing Metric Space Indexes: What For?
  2. Dynamic Spatial Approximation Trees for Massive Data.

SODA 2009

  1. Monotone minimal perfect hashing: searching a sorted table with O(1) accesses.

SPIRE 2009

  1. A Comparison of Data-Driven Automatic Syllabification Methods.
  2. A Compressed Enhanced Suffix Array Supporting Fast String Matching.
  3. A Last-Resort Semantic Cache for Web Queries.
  4. A Linear-Time Burrows-Wheeler Transform Using Induced Sorting.
  5. A Task-Based Evaluation of an Aggregated Search Interface.
  6. A Two-Level Structure for Compressing Aligned Bitexts.
  7. Compressed Suffix Arrays for Massive Data.
  8. Consensus Optimizing Both Distance Sum and Radius.
  9. Constant Factor Approximation of Edit Distance of Bounded Height Unordered Trees.
  10. Directly Addressable Variable-Length Codes.
  11. Efficient Index for Retrieving Top-k Most Frequent Documents.
  12. Efficient Language-Independent Retrieval of Printed Documents without OCR.
  13. Expectation of Strings with Mismatches under Markov Chain Distribution.
  14. Fast Single-Pass Construction of a Half-Inverted Index.
  15. Faster Algorithms for Sampling and Counting Biological Sequences.
  16. Generalised Matching.
  17. Identifying the Intent of a User Query Using Support Vector Machines.
  18. Improved Approximation Results on the Shortest Common Supersequence Problem.
  19. Indexing Variable Length Substrings for Exact and Approximate Matching.
  20. Novel and Generalized Sort-Based Transform for Lossless Data Compression.
  21. On Entropy-Compressed Text Indexing in External Memory.
  22. On-Demand Associative Cross-Language Information Retrieval.
  23. On-Line Construction of Parameterized Suffix Trees.
  24. Practical Algorithms for the Longest Common Extension Problem.
  25. Range Quantile Queries: Another Virtue of Wavelet Trees.
  26. Set Intersection and Sequence Matching.
  27. Sketching Algorithms for Approximating Rank Correlations in Collaborative Filtering Systems.
  28. Succinct Text Indexing with Wildcards.
  29. Syntactic Query Models for Restatement Retrieval.
  30. The Frequent Items Problem, under Polynomial Decay, in the Streaming Model.
  31. Towards a Theory of Patches.
  32. Two-Dimensional Distributed Inverted Files.
  33. Use of Co-occurrences for Temporal Expressions Annotation.
  34. k2-Trees for Compact Web Graph Representation.

STACS 2009

  1. Compressed Representations of Permutations, and Applications.

Stringology 2009

  1. Adapting Boyer-Moore-Like Algorithms for Searching Huffman Encoded Texts.
  2. An Efficient Algorithm for Approximate Pattern Matching with Swaps.
  3. An Input Sensitive Online Algorithm for LCS Computation.
  4. Asymptotic Behaviour of the Maximal Number of Squares in Standard Sturmian Words.
  5. Bit-parallel Algorithms for Computing all the Runs in a String.
  6. Combining Text Compression and String Matching: The Miracle of Self-Indexing.
  7. Compressing Bi-Level Images by Block Matching on a Tree Architecture.
  8. Constant-memory Iterative Generation of Special Strings Representing Binary Trees.
  9. Crochemore’s Repetitions Algorithm Revisited - Computing Runs.
  10. Delta Encoding in a Compressed Domain.
  11. Feature Extraction for Image Pattern Matching with Cellular Automata.
  12. Filter Based Fast Matching of Long Patterns by Using SIMD Instructions.
  13. Finding All Covers of an Indeterminate String in O(n) Time on Average.
  14. Finding Characteristic Substrings from Compressed Texts.
  15. On Bijective Variants of the Burrows-Wheeler Transform.
  16. On Minimizing Deterministic Tree Automata.
  17. On the Usefulness of Backspace.
  18. On-line Construction of a Small Automaton for a Finite Set of Words.
  19. Parallel Algorithms for Degenerate and Weighted Sequences Derived from High Throughput Sequencing Technologies.
  20. Reducing Repetitions.
  21. Searching for Jumbled Patterns in Strings.
  22. String Suffix Automata and Subtree Pushdown Automata.
  23. Taxonomies of Regular Tree Algorithms.
  24. Validation and Decomposition of Partially Occluded Images with Holes.

WABI 2009

  1. Linear-Time Protein 3-D Structure Searching with Insertions and Deletions.

WADS 2009

  1. Worst-Case Optimal Adaptive Prefix Coding.

ACM J. Exp. Algorithmics 2009

  1. Engineering a compressed suffix tree implementation.
  2. Speeding up spatial approximation search in metric spaces.

ACM Trans. Algorithms 2009

  1. Improved approximate string matching and regular expression matching on Ziv-Lempel compressed texts.

Algorithms 2009

  1. Approximate String Matching with Compressed Indexes.
  2. Linear-Time Text Compression by Longest-First Substitution.

Bioinform. 2009

  1. A fast hybrid short read fragment assembly algorithm.
  2. SHREC: a short-read error correction method.
  3. Textual data compression in computational biology: a synopsis.

CoRR 2009

  1. A Lower Bound for Succinct Rank Queries
  2. A Lower Bound on the Complexity of Approximating the Entropy of a Markov Source
  3. A Minimal Periods Algorithm with Applications
  4. A Unified Algorithm for Accelerating Edit-Distance Computation via Text-Compression
  5. Alphabet Partitioning for Compressed Rank/Select with Applications
  6. An $O(n^2)$ Algorithm for Computing Longest Common Cyclic Subsequence
  7. Analysis of the Relationships among Longest Common Subsequences, Shortest Common Supersequences and Patterns and its application on Pattern Discovery in Biological Sequences
  8. Another Virtue of Wavelet Trees
  9. Cell-Probe Lower Bounds for Prefix Sums
  10. Compressed Representations of Permutations, and Applications
  11. Data Structures for Approximate Range Counting
  12. Estimating Entropy of Data Streams Using Compressed Counting
  13. Fast Arc-Annotated Subsequence Matching in Linear Space
  14. Fast In-Memory XPath Search over Compressed Text and Tree Indexes
  15. Fast Searching in Packed Strings
  16. Fast Set Intersection and Two Patterns Matching
  17. Fast and Compact Prefix Codes
  18. Fully-Functional Static and Dynamic Succinct Trees
  19. Generating All Partitions: A Comparison Of Two Encodings
  20. Grammar-Based Compression in a Streaming Model
  21. Heaps Simplified
  22. Lightweight Data Indexing and Compression in External Memory
  23. More Haste, Less Waste: Lowering the Redundancy in Fully Indexable Dictionaries
  24. New Algorithms and Lower Bounds for Sequential-Access Data Compression
  25. On Bijective Variants of the Burrows-Wheeler Transform
  26. On Smoothed Analysis of Quicksort and Hoare’s Find
  27. On optimally partitioning a text to improve its compression
  28. On the Use of Suffix Arrays for Memory-Efficient Lempel-Ziv Data Compression
  29. Online Sorting via Searching and Selection
  30. Practical Algorithmic Techniques for Several String Processing Problems
  31. Randomized Shellsort: A Simple Oblivious Sorting Algorithm
  32. Range Non-Overlapping Indexing
  33. Re-Pair Compression of Inverted Lists
  34. Renewal theory in analysis of tries and strings
  35. Scalable Distributed-Memory External Sorting
  36. Searching a bitstream in linear time for the longest substring of any given density
  37. The Mastermind Attack on Genomic Data
  38. Tight Bounds for Online Stable Sorting
  39. Time and Memory Efficient Lempel-Ziv Compression Using Suffix Arrays
  40. Wee LCP
  41. b-Bit Minwise Hashing

Fundam. Informaticae 2009

  1. A New Algorithm for Building Alphabetic Minimax Trees.

IEICE Trans. Inf. Syst. 2009

  1. A Space-Saving Approximation Algorithm for Grammar-Based Compression.

Inf. Comput. 2009

  1. The myriad virtues of Wavelet Trees.

Inf. Process. Lett. 2009

  1. Parameterized matching on non-linear structures.

Int. J. Comput. Biol. Drug Des. 2009

  1. Algorithms for mapping short degenerate and weighted sequences to a reference genome.

J. ACM 2009

  1. Compressing and indexing labeled trees, with applications.

J. Discrete Algorithms 2009

  1. Matching subsequences in trees.

SIAM J. Comput. 2009

  1. Breaking a Time-and-Space Barrier in Constructing Full-Text Indices.

Theor. Comput. Sci. 2009

  1. Compressed depth sequences.
  2. Efficient algorithms to compute compressed longest common substrings and compressed palindromes.
  3. Efficient construction of maximal and minimal representations of motifs of a string.
  4. Faster entropy-bounded compressed suffix trees.
  5. Rank/select on dynamic compressed sequences and applications.

CPM 2008

  1. A Black Box for Online Approximate Pattern Matching.
  2. A Linear Delay Algorithm for Building Concept Lattices.
  3. An Improved Succinct Representation for Dynamic k-ary Trees.
  4. An(other) Entropy-Bounded Compressed Suffix Tree.
  5. Analysis of the Size of Antidictionary in.
  6. Approximate String Matching with Address Bit Errors.
  7. Computing Inverse ST in Linear Complexity.
  8. Constrained LCS: Hardness and Approximation.
  9. Dynamic Fully-Compressed Suffix Trees.
  10. Fast Algorithms for Computing Tree LCS.
  11. Faster Algorithm for the Set Variant of the String Barcoding Problem.
  12. Finding Additive Biclusters with Random Background.
  13. Finding Largest Well-Predicted Subset of Protein Structure Models.
  14. Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots.
  15. HP Distance Via Double Cut and Join Distance.
  16. Lower Bounds for Succinct Data Structures.
  17. Matching Integer Intervals by Minimal Sets of Binary Words with don’t cares.
  18. On Compact Representations of All-Pairs-Shortest-Path-Distance Matrices.
  19. On the Longest Common Parameterized Subsequence.
  20. On-Line Approximate String Matching with Bounded Errors.
  21. Parameterized Algorithms and Hardness Results for Some Graph Motif Problems.
  22. Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics.
  23. ReCombinatorics: Combinatorial Algorithms for Studying the History of Recombination in Populations.
  24. Searching for Gapped Palindromes.
  25. The Changing Face of Web Search.
  26. Towards a Solution to the “Runs” Conjecture.
  27. Two-Dimensional Pattern Matching with Combined Scaling and Rotation.
  28. Why Greed Works for Shortest Common Superstring Problem.

CSR 2008

  1. Computing Longest Common Substrings Via Suffix Arrays.

DCC 2008

  1. All-Match LZ77 Bit Recycling.
  2. List Update Algorithms for Data Compression.
  3. On Self-Indexing Images - Image Compression with Added Value.
  4. Re-pair Achieves High-Order Entropy.
  5. Word-Based Statistical Compressors as Natural Language Compression Boosters.

DNA 2008

  1. Speeding Up Local-Search Type Algorithms for Designing DNA Sequences under Thermodynamical Constraints.

Discovery Science 2008

  1. String Kernels Based on Variable-Length-Don’t-Care Patterns.

ESA 2008

  1. An Online Algorithm for Finding the Longest Previous Factors.
  2. Succinct Representations of Arbitrary Graphs.

ISAAC 2008

  1. Space-Time Tradeoffs for Longest-Common-Prefix Array Computation.

LATA 2008

  1. 2-Synchronizing Words.

LATIN 2008

  1. Fully-Compressed Suffix Trees.
  2. Improved Dynamic Rank-Select Entropy-Bound Structures.

SIGIR 2008

  1. Reorganizing compressed text.

SIGMOD Conference 2008

  1. Improving suffix array locality for fast pattern matching on disk.

SOFSEM 2008

  1. Computing Longest Common Substring and All Palindromes from Compressed Strings.

SPIRE 2008

  1. “Search Is a Solved Problem” and Other Annoying Fallacies.
  2. An Efficient Linear Space Algorithm for Consecutive Suffix Alignment under Edit Distance (Short Preliminary Paper).
  3. Approximate Runs - Revisited.
  4. Approximated Pattern Matching with the L1, L2 and Linfinit Metrics.
  5. Clique Analysis of Query Log Graphs.
  6. Comparison of s-gram Proximity Measures in Out-of-Vocabulary Word Translation.
  7. Context-Sensitive Grammar Transform: Compression and Pattern Matching.
  8. Engineering Radix Sort for Strings.
  9. Exact Distribution of a Spaced Seed Statistic for DNA Homology Detection.
  10. Faster Text Fingerprinting.
  11. Improved Variable-to-Fixed Length Codes.
  12. Indexed Hierarchical Approximate String Matching.
  13. Interchange Rearrangement: The Element-Cost Model.
  14. Mismatch Sampling.
  15. New Perspectives on the Prefix Array.
  16. On the Structure of Small Motif Recognition Instances.
  17. Out of the Box Phrase Indexing.
  18. Pattern Matching with Pair Correlation Distance.
  19. Practical Rank/Select Queries over Arbitrary Sequences.
  20. Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections.
  21. Self-indexing Natural Language.
  22. Sliding CDAWG Perfection.
  23. Some Approximations for Shortest Common Nonsubsequences and Supersequences.
  24. Speeding Up Pattern Matching by Text Sampling.
  25. Term Impacts as Normalized Term Frequencies for BM25 Similarity Scoring.
  26. The Effect of Weighted Term Frequencies on Probabilistic Latent Semantic Term Relationships.
  27. delta-gamma-Parameterized Matching.

SWAT 2008

  1. A Uniform Approach Towards Succinct Representation of Trees.

Stringology 2008

  1. A Concurrent Specification of an Incremental DFA Minimisation Algorithm.
  2. An Adaptive Hybrid Pattern-Matching Algorithm on Indeterminate Strings.
  3. Average Value of Sum of Exponents of Runs in Strings.
  4. Conservative String Covering of Indeterminate Strings.
  5. Dynamic Burrows-Wheeler Transform.
  6. Edit Distance with Single-Symbol Combinations and Splits by Manolis.
  7. Efficient Variants of the Backward-Oracle-Matching Algorithm.
  8. Fast Optimal Algorithms for Computing All the Repeats in a String.
  9. Huffman Coding with Non-Sorted Frequencies.
  10. In-place Update of Suffix Array while Recoding Words.
  11. Infinite Smooth Lyndon Words.
  12. Lossless Image Compression by Block Matching on Practical Massively Parallel Architectures.
  13. New Efficient Bit-Parallel Algorithms for the delta-Matching Problem with alpha-Bounded Gaps in Musical Sequences.
  14. New Lower Bounds for the Maximum Number of Runs in a String.
  15. On Regular Expression Hashing to Reduce FA Size.
  16. On the Uniform Distribution of Strings.
  17. Parameterized Suffix Arrays for Binary Strings.
  18. Speeding up Lossless Image Compression: Experimental Results on a Parallel Machine.
  19. The Road Coloring and Cerny Conjecture.
  20. The Virtual Suffix Tree: An Efficient Data Structure for Suffix Trees and Suffix Arrays.
  21. Usefulness of Directed Acyclic Subword Graphs in Problems Related to Standard Sturmian Words.

ACM J. Exp. Algorithmics 2008

  1. Compressed text indexes: From theory to practice.
  2. Implementing the LZ-index: Theory versus practice.

ACM Trans. Algorithms 2008

  1. Dynamic entropy-compressed sequences and full-text indexes.

BMC Bioinform. 2008

  1. RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.

Bioinform. 2008

  1. GENESIS: genome evolution scenarios.

CoRR 2008

  1. A Dynamic Programming Approach To Length-Limited Huffman Coding
  2. A Generic Top-Down Dynamic-Programming Approach to Prefix-Free Coding
  3. A New Algorithm for Building Alphabetic Minimax Trees
  4. Approximating General Metric Distances Between a Pattern and a Text
  5. Biased Range Trees
  6. Binar Sort: A Linear Generalized Sorting Algorithm
  7. Bit-Optimal Lempel-Ziv compression
  8. Deriving Sorting Algorithms
  9. Discovering More Accurate Frequent Web Usage Patterns
  10. Efficient Pattern Matching on Binary Strings
  11. Faster Approximate String Matching for Short Patterns
  12. How robust is quicksort average complexity?
  13. Improved Algorithms for Approximate String Matching (Extended Abstract)
  14. Low-Memory Adaptive Prefix Coding
  15. Minimax Trees in Linear Time
  16. New Lower Bounds for the Maximum Number of Runs in a String
  17. Optimal Succinctness for Range Minimum Queries
  18. Parameterized Algorithms for Partial Cover Problems
  19. Secondary Indexing in One Dimension: Beyond B-trees and Bitmap Indexes
  20. Space-Efficient Multi-Dimensional Range Reporting
  21. String algorithms and data structures
  22. Succinct Data Structures for Retrieval and Approximate Membership
  23. Succinct Geometric Indexes Supporting Point Location Queries
  24. Understanding maximal repetitions in strings
  25. Violation Heaps: A Better Substitute for Fibonacci Heaps
  26. Worst-Case Optimal Adaptive Prefix Coding

Inf. Process. Lett. 2008

  1. Computing Longest Previous Factor in linear time and applications.
  2. Sorting streamed multisets.

Inf. Retr. 2008

  1. A compressed self-index using a Ziv-Lempel dictionary.

Int. J. Found. Comput. Sci. 2008

  1. Reachability on Suffix Tree Graphs.

Math. Comput. Sci. 2008

  1. Lempel-Ziv Factorization Using Less Time & Space.

Softw. Pract. Exp. 2008

  1. New adaptive compressors for natural language text.

Theor. Comput. Sci. 2008

  1. Fast and compact regular expression matching.
  2. How many runs can a string contain?

ALENEX 2007

  1. Practical Entropy-Compressed Rank/Select Dictionary.

CPM 2007

  1. A Combinatorial Approach to Genome-Wide Ortholog Assignment: Beyond Sequence Similarity Search.
  2. A Lempel-Ziv Text Index on Secondary Storage.
  3. A New and Faster Method of Sorting by Transpositions.
  4. A Simple Construction of Two-Dimensional Suffix Trees in Linear Time.
  5. Algorithmic Problems in Scheduling Jobs on Variable-Speed Processors.
  6. Algorithms for Computing the Longest Parameterized Common Subsequence.
  7. Cache-Oblivious Index for Approximate String Matching.
  8. Common Structured Patterns in Linear Graphs: Approximation and Combinatorics.
  9. Compressed Text Indexes with Fast Locate.
  10. Computing Exact p-Value for Structured Motif.
  11. Deterministic Length Reduction: Fast Convolution in Sparse Data and Applications.
  12. Dynamic Rank-Select Structures with Applications to Run-Length Encoded Texts.
  13. Efficient Computation of Substring Equivalence Classes with Suffix Arrays.
  14. Fast and Practical Algorithms for Computing All the Runs in a String.
  15. Finding Compact Structural Motifs.
  16. Finding Witnesses by Peeling.
  17. Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem.
  18. Guided Forest Edit Distance: Better Structure Comparisons by Using Domain-knowledge.
  19. Identification of Distinguishing Motifs.
  20. Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants.
  21. Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts.
  22. Improved Sketching of Hamming Distance with Error Correcting.
  23. Longest Common Separable Pattern Among Permutations.
  24. Most Burrows-Wheeler Based Compressors Are Not Optimal.
  25. Move-to-Front, Distance Coding, and Inversion Frequencies Revisited.
  26. Non-breaking Similarity of Genomes with Gene Repetitions.
  27. On Demand String Sorting over Unbounded Alphabets.
  28. Processing Compressed Texts: A Tractability Border.
  29. Self-normalised Distance with Don’t Cares.
  30. Space-Efficient Algorithms for Document Retrieval.
  31. Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions.
  32. Stringology: Some Classic and Some Modern Problems.
  33. Suffix Arrays on Words.
  34. Tiling Periodicity.
  35. Two-Dimensional Range Minimum Queries.

DCC 2007

  1. Bit Recycling with Prefix Codes.
  2. Compressed Delta Encoding for LZSS Encoded Files.
  3. Simple Linear-Time Off-Line Text Compression by Longest-First Substitution.

DNA 2007

  1. Dynamic Neighborhood Searches for Thermodynamically Designing DNA Sequence.

FSTTCS 2007

  1. Compressed Dynamic Tries with Applications to LZ-Compression in Sublinear Time and Space.

ICALP 2007

  1. Succinct Ordinal Trees Based on Tree Covering.

ICESS 2007

  1. A Unified Compressed Cache Hierarchy Using Simple Frequent Pattern Compression and Partial Cache Line Prefetching.

ISAAC 2007

  1. Succinct Representation of Labeled Graphs.

MDAI 2007

  1. Algorithms for String Pattern Discovery.

MFCS 2007

  1. Space-Conscious Compression.

SIGIR 2007

  1. Compressed permuterm index.

SPIRE 2007

  1. A Chaining Algorithm for Mapping cDNA Sequences to Multiple Genomic Sequences.
  2. A Fast and Compact Web Graph Representation.
  3. A Filtering Algorithm for k -Mismatch with Don’t Cares.
  4. A Pocket Guide to Web History.
  5. A Web-Page Usage Prediction Scheme Using Weighted Suffix Trees.
  6. Admission Policies for Caches of Search Engine Results.
  7. Algorithms for Weighted Matching.
  8. Approximate String Matching with Lempel-Ziv Compressed Indexes.
  9. Approximate Swap and Mismatch Edit Distance.
  10. Approximating Constrained LCS.
  11. Compact Set Representation for Information Retrieval.
  12. Edge-Guided Natural Language Text Compression.
  13. Efficient Computations of l1 and linfinity Rearrangement Distances.
  14. Efficient Text Proximity Search.
  15. Enhancing Educational-Material Retrieval Using Authored-Lesson Metadata.
  16. Estimating Number of Citations Using Author Reputation.
  17. Exploiting Genre in Focused Crawling.
  18. Extending Weighting Models with a Term Quality Measure.
  19. Generalized LCS.
  20. Highly Frequent Terms and Sentence Retrieval.
  21. Implicit Compression Boosting with Applications to Self-indexing.
  22. Indexing a Dictionary for Subset Matching Queries.
  23. Jump-Matching with Errors.
  24. Local Transpositions in Alignment of Polyphonic Musical Sequences.
  25. Optimal Self-adjusting Trees for Dynamic String Data in Secondary Storage.
  26. Prefix-Shuffled Geometric Suffix Tree.
  27. Tuning Approximate Boyer-Moore for Gene Sequences.

WEA 2007

  1. Engineering a Compressed Suffix Tree Implementation.

ACM Comput. Surv. 2007

  1. A taxonomy of suffix array construction algorithms.
  2. Compressed full-text indexes.

ACM J. Exp. Algorithmics 2007

  1. An efficient, versatile approach to suffix sorting.

ACM Trans. Algorithms 2007

  1. A data structure for a sequence of string accesses in external memory.
  2. Compressed indexes for dynamic text collections.
  3. Compressed representations of sequences and full-text indexes.

Algorithmica 2007

  1. A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays.

BMC Bioinform. 2007

  1. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.

Bioinform. 2007

  1. Compressed suffix tree - a basis for genome-scale sequence analysis.

CoRR 2007

  1. A nearly tight memory-redundancy trade-off for one-pass compression
  2. Bounds for Compression in Streaming Models
  3. Compressed Text Indexes:From Theory to Practice!
  4. Dualheap Sort Algorithm: An Inherently Parallel Generalization of Heapsort
  5. Empirical entropy in context
  6. Pattern Matching in Trees and Strings
  7. Radix Sorting With No Extra Space
  8. Sublinear Algorithms for Approximating String Compressibility

Inf. Comput. 2007

  1. Rotation and lighting invariant template matching.

Inf. Process. Lett. 2007

  1. Dynamic Shannon coding.

Inf. Process. Manag. 2007

  1. Using structural contexts to compress semistructured text collections.

Inf. Retr. 2007

  1. Lightweight natural language text compression.

J. Assoc. Inf. Sci. Technol. 2007

  1. Lempel-Ziv compression of highly structured documents.

J. Discrete Algorithms 2007

  1. Edit distance with move operations.
  2. Succinct data structures for flexible text retrieval systems.

Theor. Comput. Sci. 2007

  1. A simple storage scheme for strings achieving entropy bounds.
  2. Adaptive searching in succinctly encoded binary relations and tree-structured documents.
  3. Compressed data structures: Dictionaries and data-aware measures.
  4. Fast BWT in small space by blockwise suffix sorting.
  5. Faster suffix sorting.
  6. Rank and select revisited and extended.

Theory Comput. Syst. 2007

  1. Compressed Suffix Trees with Full Functionality.

ALENEX 2006

  1. Optimal Incremental Sorting.

CIAC 2006

  1. Matching Subsequences in Trees.

CPM 2006

  1. A Compact Mathematical Programming Formulation for DNA Motif Finding.
  2. A Linear Size Index for Approximate Pattern Matching.
  3. A Simpler Analysis of Burrows-Wheeler Based Compression.
  4. Adaptive Searching in Succinctly Encoded Binary Relations and Tree-Structured Documents.
  5. Algorithms for Finding a Most Similar Subforest.
  6. An Improved Algorithm for the Macro-evolutionary Phylogeny Problem.
  7. An O(n3/2sqrt(log n)) Algorithm for Sorting by Reciprocal Translocations.
  8. Approximate Matching in Weighted Sequences.
  9. Approximation of RNA Multiple Structural Alignment.
  10. Asynchronous Pattern Matching.
  11. Common Substrings in Random Strings.
  12. Dynamic Entropy-Compressed Sequences and Full-Text Indexes.
  13. Efficient Algorithms for Regular Expression Constrained Sequence Alignment.
  14. Faster Algorithms for Computing Longest Common Increasing Subsequences.
  15. Faster Two Dimensional Scaled Matching.
  16. Finding Common RNA Pseudoknot Structures in Polynomial Time.
  17. Fingerprint Clustering with Bounded Number of Missing Values.
  18. Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures.
  19. Identifying Co-referential Names Across Large Corpora.
  20. Large Scale Matching for Position Weight Matrices.
  21. Local Alignment of RNA Sequences with Arbitrary Scoring Schemes.
  22. Longest Common Subsequences in Permutations and Maximum Cliques in Circle Graphs.
  23. New Algorithms for Text Fingerprinting.
  24. New Bounds for Motif Finding in Strong Instances.
  25. Obtaining Provably Good Performance from Suffix Trees in Secondary Storage.
  26. On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem.
  27. On-Line Linear-Time Construction of Word Suffix Trees.
  28. Property Matching and Weighted Matching.
  29. Reducing the Space Requirement of LZ-Index.
  30. SNP and Haplotype Analysis - Algorithms and Applications.
  31. Solving the Maximum Agreement SubTree and the Maximum Compatible Tree Problems on Many Bounded Degree Trees.
  32. Statistical Encoding of Succinct Data Structures.
  33. Sublinear Algorithms for Parameterized Matching.
  34. Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms.
  35. Theoretical and Practical Improvements on the RMQ-Problem, with Applications to LCA and LCE.
  36. Tiling an Interval of the Discrete Line.

DCC 2006

  1. Compressed Data Structures: Dictionaries and Data-Aware Measures.
  2. Modeling Delta Encoding of Compressed Files.

ESA 2006

  1. The Engineering of a Compression Boosting Library: Theory vs Practice in BWT Compression.

Ershov Memorial Conference 2006

  1. Improving Semistatic Compression Via Pair-Based Coding.

ICALP (1) 2006

  1. New Algorithms for Regular Expression Matching.
  2. The Myriad Virtues of Wavelet Trees.

IFIP TCS 2006

  1. An O(1) Solution to the Prefix Sum Problem on a Specialized Memory Architecture.

ISAAC 2006

  1. Improving Time and Space Complexity for Compressed Pattern Matching.

ISSAC 2006

  1. Succinct representation of finite abelian groups.

International Conference on Computational Science (1) 2006

  1. An Index Data Structure for Searching in Metric Space Databases.

LATIN 2006

  1. Position-Restricted Substring Searching.

MFCS 2006

  1. A Combinatorial Approach to Collapsing Words.

PODS 2006

  1. Cache-oblivious string B-trees.

SPIRE 2006

  1. A Compressed Self-index Using a Ziv-Lempel Dictionary.
  2. A Multiple Criteria Approach for Information Retrieval.
  3. A New Algorithm for Fast All-Against-All Substring Matching.
  4. A Statistical Model of Query Log Generation.
  5. Adaptive Query-Based Sampling of Distributed Collections.
  6. Analyzing User Behavior to Rank Desktop Items.
  7. Cluster Generation and Cluster Labelling for Web Snippets: A Fast and Accurate Hierarchical Solution.
  8. Compact Features for Detection of Near-Duplicates in Distributed Retrieval.
  9. Computing the Minimum Approximate lambda-Cover of a String.
  10. Discovering Context-Topic Rules in Search Engine Logs.
  11. Dotted Suffix Trees A Structure for Approximate Text Indexing.
  12. Efficient Algorithms for Pattern Matching with General Gaps and Character Classes.
  13. Efficient Lazy Algorithms for Minimal-Interval Semantics.
  14. English to Persian Transliteration.
  15. How to Compare Arc-Annotated Sequences: The Alignment Hierarchy.
  16. Improving Usability Through Password-Corrective Hashing.
  17. Incremental Aggregation of Latent Semantics Using a Graph-Based Energy Model.
  18. Inverted Files Versus Suffix Arrays for Locating Patterns in Primary Memory.
  19. MP-Boost: A Multiple-Pivot Boosting Algorithm and Its Application to Text Categorization.
  20. Mapping Words into Codewords on PPM.
  21. Matrix Tightness: A Linear-Algebraic Framework for Sorting by Transpositions.
  22. On-Line Repetition Detection.
  23. Output-Sensitive Autocompletion Search.
  24. Phrase-Based Pattern Matching in Compressed Text.
  25. Principal Components for Automatic Term Hierarchy Building.
  26. Sparse Directed Acyclic Word Graphs.
  27. Structured Index Organizations for High-Throughput Text Querying.
  28. The Intention Behind Web Queries.
  29. TreeBoost.MH: A Boosting Algorithm for Multi-label Hierarchical Text Categorization.
  30. Using String Comparison in Context for Improved Relevance Feedback in Different Text Media.
  31. Word-Based Correction for Retrieval of Arabic OCR Degraded Documents.

Stringology 2006

  1. 2D context-free grammars: Mathematical formulae recognition.
  2. A Markovian approach for the analysis of the gene structure.
  3. A concurrent specification of Brzozowski’s DFA construction algorithm.
  4. An asymptotic lower bound for the maximal-number-of-runs function.
  5. Can dist tables be merged in linear time - An Open Problem.
  6. Efficient algorithms for (delta, gamma, alpha)-matching.
  7. Efficient automata constructions and approximate automata.
  8. FM-KZ: An even simpler alphabet-independent FM-index.
  9. FireµSat: An algorithm to detect microsatellites in DNA.
  10. Flipping letters to minimize the support of a string.
  11. Modeling delta encoding of compressed files.
  12. On implementation and performance of table-driven DFA-based string processors.
  13. On some combinatorial problems concerning the harmonic structure of musical chord sequences.
  14. On the problem of deciding if a polyomino tiles the plane by translation.
  15. Reachability on suffix tree graphs.
  16. Song classifications for dancing.
  17. Sparse compact directed acyclic word graphs.
  18. The gapped-factor tree.
  19. Two-dimensional bitwise memory matrix: A tool for optimal parallel approximate pattern matching.
  20. Using alignment for multilingual text compression.
  21. Working with compressed concordances.

WWW 2006

  1. Compressing and searching XML data via two zips.

CoRR 2006

  1. An O(1) Solution to the Prefix Sum Problem on a Specialized Memory Architecture
  2. Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts
  3. New Algorithms for Regular Expression Matching
  4. On the space complexity of one-pass compression
  5. Practical Entropy-Compressed Rank/Select Dictionary
  6. The Tree Inclusion Problem: In Linear Space and Faster

Inf. Process. Lett. 2006

  1. Compressing probability distributions.
  2. Large alphabets and incompressibility.

Inf. Process. Manag. 2006

  1. Adapting the Knuth-Morris-Pratt algorithm for pattern matching in Huffman encoded texts.

Int. J. Found. Comput. Sci. 2006

  1. A Simple Alphabet-independent Fm-index.
  2. Compressed Pattern Matching in Jpeg Images.
  3. Flexible Music Retrieval in Sublinear Time.

SIAM J. Discret. Math. 2006

  1. A New Periodicity Lemma.

Theor. Comput. Sci. 2006

  1. A metric index for approximate string matching.
  2. The binomial transform and the analysis of skip lists.

Theory Comput. Syst. 2006

  1. Insertion Sort is O(n log n).

AMT 2005

  1. A simple extension of queriable compression for XML data.

CONIELECOMP 2005

  1. Approximate Searching on Compressed Text.

CPM 2005

  1. A Fast Algorithm for Approximate String Matching on Gene Sequences.
  2. A Linear Tree Edit Distance Algorithm for Similar Ordered Trees.
  3. A New Compressed Suffix Tree Supporting Fast Search and Its Construction Algorithm Using Optimal Working Space.
  4. A New Periodicity Lemma.
  5. A Polynomial Time Matching Algorithm of Ordered Tree Patterns Having Height-Constrained Variables.
  6. A Simple Fast Hybrid Pattern-Matching Algorithm.
  7. An Efficient Algorithm for Generating Super Condensed Neighborhoods.
  8. An Extension of the Burrows Wheeler Transform and Applications to Sequence Comparison and Data Compression.
  9. An Optimal Algorithm for Online Square Detection.
  10. An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery.
  11. Approximate Matching in the L1 Metric.
  12. Assessing the Significance of Sets of Words.
  13. Construction of Aho Corasick Automaton in Linear Time for Integer Alphabets.
  14. DNA Compression Challenge Revisited: A Dynamic Programming Approach.
  15. Exact and Approximation Algorithms for DNA Tag Set Design.
  16. Faster Algorithms for delta, gamma-Matching and Related Problems.
  17. Hardness of Optimal Spaced Seed Design.
  18. Identifying Similar Surface Patches on Proteins Using a Spin-Image Surface Representation.
  19. Incremental Inference of Relational Motifs with a Degenerate Alphabet.
  20. Inferring a Graph from Path Frequency.
  21. Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements.
  22. Linear-Time Construction of Compressed Suffix Arrays Using o(n log n)-Bit Working Space for Large Alphabets.
  23. Mass Spectra Alignments and Their Significance.
  24. On the Complexity of Sparse Exon Assembly.
  25. On the Longest Common Rigid Subsequence Problem.
  26. Parametric Analysis for Ungapped Markov Models of Evolution.
  27. Prefix-Free Regular-Expression Matching.
  28. Reducing the Size of NFAs by Using Equivalences and Preorders.
  29. Regular Expression Constrained Sequence Alignment.
  30. Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern.
  31. Speeding up Parsing of Biological Context-Free Grammars.
  32. Succinct Suffix Arrays Based on Run-Length Encoding.
  33. Text Indexing with Errors.
  34. The Median Problem for the Reversal Distance in Circular Bacterial Genomes.
  35. Two Dimensional Parameterized Matching.
  36. Using PQ Trees for Comparative Genomics.
  37. Weighted Directed Word Graph.

DCC 2005

  1. Compressed Pattern Matching in JPEG Images.
  2. Real-Time Traversal in Grammar-Based Compressed Files.
  3. The Performance of Linear Time Suffix Sorting Algorithms.

Discovery Science 2005

  1. Practical Algorithms for Pattern Based Linear Regression.

ECDL 2005

  1. Compressing Dynamic Text Collections via Phrase-Based Coding.

ENC 2005

  1. Combining Structural and Textual Contexts for Compressing Semistructured Databases.

ESA 2005

  1. Space Efficient Algorithms for the Burrows-Wheeler Backtransformation.

FCT 2005

  1. Fully Incremental LCS Computation.

FOCS 2005

  1. Structuring labeled trees for optimal succinctness, and beyond.

Federation over the Web 2005

  1. Faster Pattern Matching Algorithm for Arc-Annotated Sequences.

ICALP 2005

  1. The Tree Inclusion Problem: In Optimal Space and Faster.
  2. Towards Optimal Multiple Selection.

ISAAC 2005

  1. Space-Efficient Construction of LZ-Index.

SIGIR 2005

  1. Efficiently decodable and searchable natural language adaptive compression.

SPIRE 2005

  1. N-Gram Similarity and Distance.
  2. A Bilingual Linking Service for the Web.
  3. A Bit-Parallel Tree Matching Algorithm for Patterns with Horizontal VLDC’s.
  4. A Fast Algorithmic Technique for Comparing Large Phylogenetic Trees.
  5. A Generalization of the Method for Evaluation of Stemming Algorithms Based on Error Counting.
  6. A Model for Information Retrieval Based on Possibilistic Networks.
  7. A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison.
  8. A Partition-Based Efficient Algorithm for Large Scale Multiple-Strings Matching.
  9. An Edit Distance Between RNA Stem-Loops.
  10. Application of Clustering Technique in Multiple Sequence Alignment.
  11. Approximate Matching in the Linfinity Metric.
  12. Cache-Conscious Collision Resolution in String Hash Tables.
  13. Classifying Sentences Using Induced Structure.
  14. Comparison of Representations of Multiple Evidence Using a Functional Framework for IR.
  15. Composite Pattern Discovery for PCR Application.
  16. Compressed Perfect Embedded Skip Lists for Quick Inverted-Index Lookups.
  17. Computing Similarity of Run-Length Encoded Strings with Affine Gap Penalty.
  18. Counting Lumps in Word Space: Density as a Measure of Corpus Homogeneity.
  19. Counting Suffix Arrays and Strings.
  20. Deriving TF-IDF as a Fisher Kernel.
  21. Enhanced Byte Codes with Restricted Prefix Properties.
  22. Evaluating Hierarchical Clustering of Search Results.
  23. Experimental Analysis of a Fast Intersection Algorithm for Sorted Sequences.
  24. Fast Plagiarism Detection System.
  25. Faster Generation of Super Condensed Neighbourhoods Using Finite Automata.
  26. L1 Pattern Matching Lower Bound.
  27. Linear Time Algorithm for the Generalised Longest Common Repeat Problem.
  28. Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array.
  29. Lydia: A System for Large-Scale News Analysis.
  30. Measuring the Difficulty of Distance-Based Indexing.
  31. Multi-label Text Categorization Using K-Nearest Neighbor Approach with M-Similarity.
  32. Necklace Swap Problem for Rhythmic Similarity Measures.
  33. Normalized Similarity of RNA Sequences.
  34. Practical and Optimal String Matching.
  35. Rank-Sensitive Data Structures.
  36. Recommending Better Queries from Click-Through Data.
  37. Restricted Transposition Invariant Approximate String Matching Under Edit Distance.
  38. Retrieval Status Values in Information Retrieval Evaluation.
  39. Stemming Arabic Conjunctions and Prepositions.
  40. Towards Real-Time Suffix Tree Construction.
  41. Using the k-Nearest Neighbor Graph for Proximity Searching in Metric Spaces.
  42. Utilizing Dynamically Updated Estimates in Solving the Longest Common Subsequence Problem.
  43. XML Multimedia Retrieval.
  44. XML Retrieval with a Natural Language Interface.

Stringology 2005

  1. A missing link in root-to-frontier tree pattern matching.
  2. A simple alphabet-independent FM-index.
  3. A space efficient bit-parallel algorithm for the multiple string matching problem.
  4. A taxonomy of suffix array construction algorithms.
  5. Alphabets in generic programming.
  6. Approximation algorithm for the cyclic swap problem.
  7. Asynchronous pattern matching - Metrics.
  8. Backward pattern matching automaton.
  9. Bit-parallel computation of local similarity score matrices with unitary weights.
  10. Bounded size dictionary compression: Relaxing the LRU deletion heuristic.
  11. Compressed pattern matching in JPEG images.
  12. Context-dependent stopper encoding.
  13. Flexible music retrieval in sublinear time.
  14. From suffix trees to suffix vectors.
  15. General pattern matching on regular collage system.
  16. Incremental string correction: Towards correction of XML documents.
  17. Reconstructing a suffix array.
  18. Reordering finite automata states for fast string recognition.

ACM J. Exp. Algorithmics 2005

  1. Increased bit-parallelism for approximate and multiple string matching.

Algorithmica 2005

  1. Bit-Parallel Witnesses and Their Applications to Approximate String Matching.
  2. New Techniques for Regular Expression Searching.

CoRR 2005

  1. Compressing Probability Distributions
  2. Dynamic Shannon Coding
  3. Fast and Compact Regular Expression Matching
  4. Large Alphabets and Incompressibility
  5. Matching Subsequences in Trees
  6. Sorting a Low-Entropy Sequence

Comput. J. 2005

  1. In Place Differential File Compression.

Discret. Appl. Math. 2005

  1. On-line construction of compact directed acyclic word graphs.

Inf. Process. Lett. 2005

  1. New bounds on D-ary optimal codes.
  2. Restructuring binary search trees revisited.

Inf. Process. Manag. 2005

  1. Pattern matching in Huffman encoded texts.

Int. J. Found. Comput. Sci. 2005

  1. A fully compressed pattern matching algorithm for simple collage systems.

J. ACM 2005

  1. Boosting textual compression in optimal linear time.
  2. Indexing compressed text.

J. Algorithms 2005

  1. Lowest common ancestors in trees and directed acyclic graphs.
  2. Transposition invariant string matching.

J. Discrete Algorithms 2005

  1. A fully linear-time approximation algorithm for grammar-based compression.
  2. Bit-parallel (delta, gamma)-matching and suffix automata.
  3. Indexing text with approximate q-grams.
  4. On minimizing pattern splitting in multi-track string matching.
  5. Practical algorithms for transposition-invariant string-matching.

J. Syst. Softw. 2005

  1. Worst case constant time priority queue.

Pattern Recognit. Lett. 2005

  1. A compact space decomposition for effective metric indexing.

SIAM J. Comput. 2005

  1. Cache-Oblivious B-Trees.
  2. Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching.

SIAM J. Discret. Math. 2005

  1. Labeling Schemes for Small Distances in Trees.

Softw. Pract. Exp. 2005

  1. LZgrep: a Boyer-Moore string matching tool for Ziv-Lempel compressed text.

Theor. Comput. Sci. 2005

  1. A survey on tree edit distance and related problems.
  2. Sequential and indexed two-dimensional combinatorial template matching allowing rotations.

CATS 2004

  1. Succinct Data Structures.

CPM 2004

  1. A Combinatorial Shape Matching Algorithm for Rigid Protein Docking.
  2. A Computational Model for RNA Multiple Structural Alignment..
  3. A Fast Set Intersection Algorithm for Sorted Sequences.
  4. A Linear-Time Algorithm for Computing Translocation Distance between Signed Genomes.
  5. A Simple Optimal Representation for Balanced Parentheses.
  6. A Trie-Based Approach for Compacting Automata.
  7. Approximate Labelled Subtree Homeomorphism.
  8. Approximate Point Set Pattern Matching on Sequences and Planes.
  9. Approximate String Matching Using Compressed Suffix Arrays.
  10. Average-Case Analysis of Approximate Trie Search (Extended Abstract).
  11. Compressed Compact Suffix Arrays.
  12. Compressed Index for a Dynamic Collection of Texts.
  13. Computational Design of New and Recombinant Selenoproteins.
  14. Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs.
  15. Efficient Algorithms for Finding Submasses in Weighted Strings.
  16. Faster Two Dimensional Pattern Matching with Rotations.
  17. Finding Biclusters by Random Projections.
  18. Improved Single and Multiple Approximate String Matching.
  19. Maximal Common Connected Sets of Interval Graphs.
  20. Maximum Agreement and Compatible Supertrees (Extended Abstract).
  21. Multi-seed Lossless Filtration (Extended Abstract).
  22. New Results for the 2-Interval Pattern Problem.
  23. On the Average Sequence Complexity.
  24. On the k-Closest Substring and k-Consensus Pattern Problems.
  25. Optimizing Multiple Spaced Seeds for Homology Search.
  26. Performing Local Similarity Searches with Variable Length Seeds.
  27. Polynomial-Time Algorithms for the Ordered Maximum Agreement Subtree Problem.
  28. Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences.
  29. Real-Time String Matching in Sublinear Space.
  30. Reversal Distance without Hurdles and Fortresses.
  31. Small Phylogeny Problem: Character Evolution Trees.
  32. Sorting by Length-Weighted Reversals: Dealing with Signs and Circularity.
  33. Sorting by Reversals in Subquadratic Time.
  34. Sparse Normalized Local Alignment.
  35. The Protein Sequence Design Problem in Canonical Model on 2D and 3D Lattices.
  36. Two Algorithms for LCS Consecutive Suffix Alignment.

Data Compression Conference 2004

  1. Adapting the Knuth-Morris-Pratt Algorithm for Pattern Matching in Huffman Encoded Texts.
  2. Compressed Index for Dynamic Text.
  3. Dynamic Shannon Coding.
  4. Lempel-Ziv Compression of Structured Text.
  5. Merging Prediction by Partial Matching with Structural Contexts Model.

Developments in Language Theory 2004

  1. An Efficient Pattern Matching Algorithm on a Subclass of Context Free Grammars.

ECCV (2) 2004

  1. From a 2D Shape to a String Structure Using the Symmetry Set.

ESA 2004

  1. Dynamic Shannon Coding.

ICALP 2004

  1. Succinct Representations of Functions.

ISAAC 2004

  1. Advantages of Backward Searching - Efficient Secondary Memory and Distributed Implementation of Compressed Suffix Arrays.

LATIN 2004

  1. Rooted Maximum Agreement Supertrees.
  2. Rotation and Lighting Invariant Template Matching.

PVM/MPI 2004

  1. Neighborhood Composition: A Parallelization of Local Search Algorithms.

SPIRE 2004

  1. A New Feature Normalization Scheme Based on Eigenspace for Noisy Speech Recognition.
  2. A Scalable System for Identifying Co-derivative Documents.
  3. A Space-Saving Linear-Time Algorithm for Grammar-Based Compression.
  4. Alphabet Permutation for Differentially Encoding Text.
  5. An Alphabet-Friendly FM-Index.
  6. An Efficient Algorithm for the Longest Tandem Scattered Subsequence Problem.
  7. An Efficient Index Data Structure with the Capabilities of Suffix Trees and Suffix Arrays for Alphabets of Non-negligible Size.
  8. An Improvement and an Extension on the Hybrid Index for Approximate String Matching.
  9. Automatic Document Categorization Based on k-NN and Object-Based Thesauri.
  10. Automaton-Based Sublinear Keyword Pattern Matching.
  11. Bit-Parallel Branch and Bound Algorithm for Transposition Invariant LCS.
  12. Concurrency Control and I/O-Optimality in Bulk Insertion..
  13. Cross-Comparison for Two-Dimensional Text Categorization.
  14. DDOC: Overlapping Clustering of Words for Document Classification.
  15. Dealing with Syntactic Variation Through a Locality-Based Approach.
  16. Efficient Computation of Balancedness in Binary Sequence Generators.
  17. Efficient Extraction of Structured Motifs Using Box-Links.
  18. Efficient One Dimensional Real Scaled Matching.
  19. Evaluating Relevance Feedback and Display Strategies for Searching on Small Displays.
  20. Evaluation of Web Page Representations by Content Through Clustering.
  21. Fast Detection of Common Sequence Structure Patterns in RNAs.
  22. Finding Cross-Lingual Spelling Variants.
  23. First Huffman, Then Burrows-Wheeler: A Simple Alphabet-Independent FM-Index.
  24. Indexing Text Documents Based on Topic Identification.
  25. Inferring Query Performance Using Pre-retrieval Predictors..
  26. Information Extraction by Embedding HMM to the Set of Induced Linguistic Features.
  27. Linear Nondeterministic Dawg String Matching Algorithm.
  28. Linear Time Algorithm for the Longest Common Repeat Problem.
  29. Longest Motifs with a Functionally Equivalent Central Block.
  30. Metric Indexes for Approximate String Matching in a Dictionary.
  31. Metric Indexing for the Vector Model in Text Retrieval.
  32. Motif Extraction from Weighted Sequences.
  33. Negations and Document Length in Logical Retrieval.
  34. New Algorithms for Finding Monad Patterns in DNA Sequences.
  35. On Asymptotic Finite-State Error Repair.
  36. On Classification of Strings.
  37. On the Transformation Distance Problem.
  38. Permuted and Scaled String Matching.
  39. Processing Conjunctive and Phrase Queries with the Set-Based Model.
  40. Searching XML Documents Using Relevance Propagation.
  41. Searching for a Set of Correlated Patterns.
  42. Simple Implementation of String B-Trees..
  43. Simple, Fast, and Efficient Natural Language Adaptive Compression..
  44. Techniques for Efficient Query Expansion.

Stringology 2004

  1. A First Approach to Finding Common Motifs With Gaps.
  2. A Framework for the Dynamic Implementation of Finite Automata for Performance Enhancement.
  3. A Fully Compressed Pattern Matching Algorithm for Simple Collage Systems.
  4. A Note on Bit-Parallel Alignment Computation.
  5. A Simple Lossless Compression Heuristic for Grey Scale Images.
  6. Algorithms for the Constrained Longest Common Subsequence Problems.
  7. Arithmetic Coding in Parallel.
  8. BDD-Based Analysis of Gapped q-Gram Filters.
  9. Combinatorial Characterization of the Language Recognized by Factor and Suffix Oracles.
  10. Conditional Inequalities and the Shortest Common Superstring Problem.
  11. Efficient Algorithms for the delta-Approximate String Matching Problem in Musical Sequences.
  12. Semi-Lossless Text Compression.
  13. Sorting suffixes of two-pattern strings.
  14. Theoretical Issues of Searching Aerial Photographs: A Bird’s Eye View.

Theory Is Forever 2004

  1. On NFA Reductions.

WABI 2004

  1. Finding Missing Patterns.
  2. Finding Optimal Pairs of Patterns.

WEA 2004

  1. Increased Bit-Parallelism for Approximate String Matching.

WMPI 2004

  1. A compressed memory hierarchy using an indirect index cache.

ACM J. Exp. Algorithmics 2004

  1. Average-optimal single and multiple approximate string matching.

Algorithmica 2004

  1. Engineering a Lightweight Suffix Array Construction Algorithm.

CoRR 2004

  1. Insertion Sort is O(n log n)

Discret. Appl. Math. 2004

  1. Fun-Sort–or the chaos of unordered binary search.

J. Comput. Syst. Sci. 2004

  1. Implicit B-trees: a new data structure for the dictionary problem.

J. Discrete Algorithms 2004

  1. Compact directed acyclic word graphs for a sliding window.
  2. Indexing text using the Ziv-Lempel trie.
  3. Practical and flexible pattern matching over Ziv-Lempel compressed text.

Softw. Pract. Exp. 2004

  1. A simple and fast DNA compressor.

Theor. Comput. Sci. 2004

  1. Average complexity of exact and approximate multiple string matching.
  2. Ternary directed acyclic word graphs.
  3. The Level Ancestor Problem simplified.

CIAA 2003

  1. Ternary Directed Acyclic Word Graphs.

CPM 2003

  1. A Fully Linear-Time Approximation Algorithm for Grammar-Based Compression.
  2. A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions.
  3. Alignment between Two Multiple Alignments.
  4. An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum.
  5. An Exact and Polynomial Distance-Based Algorithm to Reconstruct Single Copy Tandem Duplication Trees.
  6. An Improved Algorithm for Generalized Comparison of Minisatellites.
  7. Analysis of Tree Edit Distance Algorithms.
  8. Average-Optimal Multiple Approximate String Matching.
  9. Complexities of the Centre and Median String Problems.
  10. Constrained Tree Inclusion.
  11. Distributed and Paged Suffix Trees for Large Genetic Databases.
  12. Efficient Data Structures and a New Randomized Approach for Sorting Signed Permutations by Reversals.
  13. Efficient Selection of Unique and Popular Oligos for Large EST Databases.
  14. Extracting Approximate Patterns.
  15. Fast Lightweight Suffix Array Construction and Checking.
  16. Haplotype Inference by Pure Parsimony.
  17. Linear-Time Construction of Suffix Arrays.
  18. More Efficient Left-to-Right Pattern Matching in Non-sequential Equational Programs.
  19. Multiple Genome Alignment: Chaining Algorithms Revisited.
  20. On Minimizing Pattern Splitting in Multi-track String Matching.
  21. Optimal Partitions of Strings: A New Class of Burrows-Wheeler Compression Algorithms.
  22. Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions.
  23. Pattern Discovery in RNA Secondary Structure Using Affix Trees.
  24. Space Efficient Linear Time Construction of Suffix Arrays.
  25. Sparse LCS Common Substring Alignment.
  26. Tuning String Matching for Huge Pattern Sets.
  27. Two-Dimensional Pattern Matching with Rotations.
  28. Working on the Problem of Sorting by Transpositions on Genome Rearrangements.

DCC 2003

  1. In-Place Differential File Compression.

ECIR 2003

  1. An Efficient Compression Code for Text Databases.
  2. Compressing Semistructured Text Databases.

ENC 2003

  1. Current Challenges in Textual Databases.

Euro-Par 2003

  1. Compression in Data Caches with Compressible Field Isolation for Recursive Data Structures.
  2. Suffix Arrays in Parallel.

FOCS 2003

  1. Breaking a Time-and-Space Barrier in Constructing Full-Text Indices.

ICALP 2003

  1. Succinct Representations of Permutations.

ISAAC 2003

  1. Constructing Compressed Suffix Arrays with Large Alphabets.
  2. New Ways to Construct Binary Search Trees.
  3. Succinct Data Structures for Searchable Partial Sums.

ISLPED 2003

  1. Non redundant data cache.

MFCS 2003

  1. Inferring Strings from Graphs and Arrays.

SPIRE 2003

  1. (S, C)-Dense Coding: An Optimized Compression Code for Natural Language Text Databases.
  2. A Bit-Parallel Suffix Automation Approach for (delta, gamma)-Matching in Music Retrieval.
  3. A Practical Index for Genome Searching.
  4. A Three Level Search Engine Index Based in Query Log Distribution.
  5. Alternative Algorithms for Bit-Parallel String Matching.
  6. An Empirical Comparison of Text Categorization Methods.
  7. BFT: Bit Filtration Technique for Approximate String Join in Biological Databases.
  8. Bit-Parallel Approximate String Matching Algorithms with Transposition.
  9. Current Challenges in Bioinformatics.
  10. Distributed Query Processing Using Suffix Arrays.
  11. FindStem: Analysis and Evaluation of a Turkish Stemming Algorithm.
  12. Flexible and Efficient Bit-Parallel Techniques for Transposition Invariant Approximate Matching in Music Retrieval.
  13. French Noun Phrase Indexing and Mining for an Information Retrieval System.
  14. Improving Text Retrieval in Medical Collections Through Automatic Categorization.
  15. Large Edit Distance with Multiple Block Operations.
  16. Linear-Time Off-Line Text Compression by Longest-First Substitution.
  17. Link Information as a Similarity Measure in Web Classification.
  18. Memory-Adaptive Dynamic Spatial Approximation Trees.
  19. New Refinement Techniques for Longest Common Subsequence Algorithms.
  20. Non-adjacent Digrams Improve Matching of Cross-Lingual Spelling Variants.
  21. Patterns on the Web.
  22. Processing of Huffman Compressed Texts with a Super-Alphabet.
  23. Ranking Structured Documents Using Utility Theory in the Bayesian Network Retrieval Model.
  24. Row-wise Tiling for the Myers’ Bit-Parallel Approximate String Matching Algorithm.
  25. SCM: Structural Contexts Model for Improving Compression in Semistructured Text Databases.
  26. The Implementation and Evaluation of a Lexicon-Based Stemmer.
  27. The Size of Subsequence Automaton.
  28. Using WordNet for Word Sense Disambiguation to Support Concept Map Construction.
  29. What’s Changed? Measuring Document Change in Web Crawling for Search Engines.

STACS 2003

  1. Algorithms for Transposition Invariant String Matching.

Stringology 2003

  1. A Linear Algorithm for the Detection of Evolutive Tandem Repeats.
  2. An Efficient Mapping for Score of String Matching.
  3. Approximate Seeds of Strings.
  4. Computing the Minimum k-Cover of a String.
  5. Computing the Repetitions in a Weighted Sequence.
  6. Constructing Factor Oracles.
  7. Forward-Fast-Search: Another Fast Variant of the Boyer-Moore String Matching Algorithm.
  8. Learning the Morphological Features of a Large Set of Words.
  9. Matching Numeric Strings under Noise.
  10. Operation L-INSERT on Factor Automaton.
  11. The Transformation Distance Problem Revisited.

Algorithmica 2003

  1. Approximate Matching of Run-Length Compressed Strings.

IEEE Trans. Inf. Theory 2003

  1. Efficient universal lossless data compression algorithms based on a greedy sequential grammar transform .2. With context models.

J. Algorithms 2003

  1. New text indexing functionalities of the compressed suffix arrays.

J. Comput. Biol. 2003

  1. Fast and Simple Character Classes and Bounded Gaps Pattern Matching, with Applications to Protein Searching.

J. Comput. Syst. Sci. 2003

  1. Two-dimensional substring indexing.

J. Discrete Algorithms 2003

  1. Approximate string matching on Ziv-Lempel compressed text.
  2. Regular expression searching on compressed text.

Theor. Comput. Sci. 2003

  1. Application of Lempel-Ziv factorization to the approximation of grammar-based compression.
  2. Collage system: a unifying framework for compressed pattern matching.
  3. Optimal binary search trees with costs depending on the access paths.

CC 2002

  1. Data Compression Transformations for Dynamically Allocated Data Structures.

COCOON 2002

  1. A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays.

CPM 2002

  1. A Better Method for Length Distribution Modeling in HMMs and Its Application to Gene Finding.
  2. Application of Lempel-Ziv Factorization to the Approximation of Grammar-Based Compression.
  3. Block Merging for Off-Line Compression.
  4. Constructing NFA s by Optimal Use of Positions in Regular Expressions.
  5. Edit Distance with Move Operations.
  6. Efficient Text Mining with Optimized Pattern Discovery.
  7. Faster Bit-Parallel Approximate String Matching.
  8. Identifying Occurrences of Maximal Pairs in Multiple Strings.
  9. Local Similarity Based Point-Pattern Matching.
  10. On the Complexity of Deriving Position Specific Score Matrices from Examples.
  11. One-Gapped q-Gram Filtersfor Levenshtein Distance.
  12. Optimal Exact and Fast Approximate Two Dimensional Pattern Matching Allowing Rotations.
  13. Pattern Matching Problems over 2-Interval Sets.
  14. Practical Software for Aligning ESTs to Human Genome.
  15. Simple and Practical Sequence Nearest Neighbors with Block Operations.
  16. Space-Economical Algorithms for Finding Maximal Unique Matches.
  17. Statistical Identification of Uniformly Mutated Segments within Repeats.
  18. String Matching with Stopper Encoding and Code Splitting.
  19. The Minimum DAWG for All Suffixes of a String and Its Applications.
  20. The Problem of Context Sensitive String Matching.
  21. Three Heuristics for delta-Matching: delta-BM Algorithms.
  22. Towards Optimally Solving the LONGEST COMMON SUBSEQUENCE Problem for Sequences with Nested Arc Annotations in Linear Time.
  23. Two-Pattern Strings.

DCC 2002

  1. Searching in Compressed Dictionaries.

Discovery Science 2002

  1. Discovering Best Variable-Length-Don’t-Care Patterns.

ESA 2002

  1. Engineering a Lightweight Suffix Array Construction Algorithm.
  2. Two Simplified Algorithms for Maintaining Order in a List.

FOCS 2002

  1. Implicit B-Trees: New Results for the Dictionary Problem.
  2. Static Optimality Theorem for External Memory String Access.

ISAAC 2002

  1. Space-Efficient Data Structures for Flexible Text Retrieval Systems.

LATIN 2002

  1. A Metric Index for Approximate String Matching.
  2. The Level Ancestor Problem Simplified.

MFCS 2002

  1. Space-Economical Construction of Index Structures for All Suffixes of a String.

Progress in Discovery Science 2002

  1. Data Compression Method Combining Properties of PPM and CTW.
  2. Efficient Data Mining from Large Text Databases.
  3. Finding Best Patterns Practically.

SCCC 2002

  1. Improved Antidictionary Based Compression.

SPIRE 2002

  1. A Framework for Generating Attribute Extractors for Web Data Sources.
  2. A Theoretical Analysis of Google’s PageRank.
  3. Compact Directed Acyclic Word Graphs for a Sliding Window.
  4. Efficient Computation of Long Similar Subsequences.
  5. Enhancing the Set-Based Model Using Proximity Information.
  6. Faster String Matching with Super-Alphabets.
  7. Firing Policies for an Arabic Rule-Based Stemmer.
  8. Focussed Structured Document Retrieval.
  9. From Searching Text to Querying XML Streams.
  10. Fully Dynamic Spatial Approximation Trees.
  11. Indexing Text Using the Ziv-Lempel Trie.
  12. Java MARIAN: From an OPAC to a Modern Digital Library System.
  13. Machine Learning Approach for Homepage Finding Task.
  14. Multiple Example Queries in Content-Based Image Retrieval.
  15. On the Size of DASG for Multiple Texts.
  16. Optimal Exact Strring Matching Based on Suffix Arrays.
  17. Pattern Matching over Multi-attribute Data Streams.
  18. Probabilistic Proximity Searching Algorithms Based on Compact Partitions.
  19. Processing Text Files as Is: Pattern Matching over Compressed Texts, Multi-byte Character Texts, and Semi-structured Texts.
  20. Sorting by Prefix Transpositions.
  21. Stemming Galician Texts.
  22. String Matching Problems from Bioinformatics Which Still Need Better Solutions (Extended Abstract).
  23. String Matching with Metric Trees Using an Approximate Distance.
  24. The DBLP Computer Science Bibliography: Evolution, Research Issues, Perspectives.
  25. Towards a More Comprehensive Comparison of Collaborative Filtering Algorithms.
  26. Tree Pattern Matching for Linear Static Terms.
  27. Web Structure, Dynamics and Page Quality.
  28. t-Spanners as a Data Structure for Metric Space Searching.

Stringology 2002

  1. A Bit-Vector Algorithm for Computing Levenshtein and Damerau Edit Distances.
  2. A Note on Crochemore’s Repetitions Algorithm a Fast Space-Efficient Approach.
  3. A Note on Randomized Algorithm for String Matching with Mismatches.
  4. A Recursive Function for Calculating the Number of Legal Strings of Parentheses and for Calculating Catalan Numbers.
  5. A Work-Optimal Parallel Implementation of Lossless Image Compression by Block Matching.
  6. Bidirectional Construction of Suffix Trees.
  7. Border Array on Bounded Alphabet.
  8. Image Recognition Using Finite Automata.
  9. Split and join for minimizing: Brzozowski’s algorithm.
  10. String Matching with Gaps for Musical Melodic Recognition.
  11. String Regularities with Don’t Cares.

Algorithmica 2002

  1. A Theoretical and Experimental Study on the Construction of Suffix Arrays in External Memory.

Bioinform. 2002

  1. DNACompress: fast and effective DNA sequence compression.

Random Struct. Algorithms 2002

  1. New and faster filters for multiple approximate string matching.

ALENEX 2001

  1. Experiments on Adaptive Set Intersections for Text Retrieval Systems.
  2. Trade Off Between Compression and Search Times in Compact Suffix Array.

CPM 2001

  1. A Fast Algorithm for Optimal Alignment between Similar Ordered Trees.
  2. A Very Elementary Presentation of the Hannenhalli-Pevzner Theory.
  3. An Extension of the Periodicity Lemma to Longer Periods (Invited Lecture).
  4. An Output-Sensitive Flexible Pattern Discovery Algorithm.
  5. Approximate Matching of Run-Length Compressed Strings.
  6. Balanced Suffix Trees (Invited Lecture).
  7. Better Filtering with Gapped q-Grams.
  8. Computing the Equation Automaton of a Regular Expression in Space and Time.
  9. Efficient Discovery of Proximity Patterns with Suffix Arrays.
  10. Efficient Experimental String Matching by Weak Factor Recognition.
  11. Episode Matching.
  12. Finding All Common Intervals of k Permutations.
  13. Fuzzy Hamming Distance: A New Dissimilarity Measure.
  14. Generalized Pattern Matching and the Complexity of Unavoidability Testing.
  15. Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications.
  16. Minimum Quartet Inconsistency Is Fixed Parameter Tractable.
  17. Multiple Pattern Matching Algorithms on Collage System.
  18. On-Line Construction of Compact Directed Acyclic Word Graphs.
  19. Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC.
  20. Parallel Lempel Ziv Coding.
  21. Regular Expression Searching over Ziv-Lempel Compressed Text.
  22. String Resemblance Systems: A Unifying Framework for String Similarity with Applications to Literature and Music.
  23. Tandem Cyclic Alignment.
  24. What to Do with All this Hardware? (Invited Lecture).

Data Compression Conference 2001

  1. Faster Approximate String Matching over Compressed Text.
  2. Pattern Matching in Huffman Encoded Texts.
  3. Space-Time Tradeoffs in the Inverse B-W Transform.

Discovery Science 2001

  1. A Practical Algorithm to Find the Best Episode Patterns.

PODS 2001

  1. Two-dimensional Substring Indexing.

RECOMB 2001

  1. Fast and simple character classes and bounded gaps pattern matching, with application to protein searching.

SPIRE 2001

  1. A Comparative Study of Topic Identification on Newspaper and E-mail.
  2. A Documental Database Query Language.
  3. A Model for the Representation and Focussed Retrieval of Structured Documents Based on Fuzzy Aggregation.
  4. A Stemming Algorithmm for the Portuguese Language.
  5. A Subquadratic Algorithm for Cluster and Outlier Detection in Massive Metric Data.
  6. Adding Security to Compressed Information Retrieval Systems.
  7. An Efficient Bottom-Up Distance between Trees.
  8. Compaction Techniques for Nextword Indexes.
  9. Design of a Graphical User Interface for Structured Documents Retrieval.
  10. Distributed Query Processing Using Partitioned Inverted Files.
  11. Evaluation of N-grams Conflation Approach in Text-Based Information Retrieval.
  12. Exact Distribution of Deletion Sizes for Unavoidable Strings.
  13. Fast Categorisation of Large Document Collections.
  14. Genome Rearrangements Distance by Fusion, Fission, and Transposition is Easy.
  15. Musical Sequence Comparison for Melodic and Rhythmic Similarities.
  16. Of Maps Bigger than the Empire (Invited Paper).
  17. On Compression of Parse Trees.
  18. On Using Two-Phase Filtering in Indexed Approximate String Matching with Application to Searching Unique Oligonucleotides.
  19. On-Line Construction of Symmetric Compact Directed Acyclic Word Graphs.
  20. Re-Store: A System for Compressing, Browsing, and Searching Large Documents (Invited Paper).
  21. Relating Web Characteristics with Link Based Web Page Ranking.
  22. Semantic Labeling - Unveiling the Main Components of Meaning of Free-Text (Invited Paper).
  23. Semantic Thesaurus for Automatic Expanded Query in Information Retrieval.
  24. Speed-up of Aho-Corasick Pattern Matching Machines by Rearranging States.
  25. Speeding-up Hirschberg and Hunt-Szymanski LCS Algorithms.
  26. Storing Semistructured Data in Relational Databases.
  27. Using Edit Distance in Point-Pattern Matching.
  28. Using Semantics for Paragraph Selection in Question Answering Systems.

Stringology 2001

  1. A linear time string matching algorithm on average with efficient text storage.
  2. Approximate String Matching in Musical Sequences.
  3. Bioinformatics: tools for analysis of biological sequences.
  4. Construction of the CDAWG for a Trie.
  5. Searching in an Efficiently Stored DNA Text Using a Hardware Solution.

ACM Comput. Surv. 2001

  1. A guided tour to approximate string matching.
  2. Searching in metric spaces.

Algorithmica 2001

  1. Improving an Algorithm for Approximate Pattern Matching.

Inf. Sci. 2001

  1. An experimental study of a compressed index.

J. ACM 2001

  1. An analysis of the Burrows-Wheeler transform.

J. Algorithms 2001

  1. Space Efficient Suffix Trees.

SIAM J. Comput. 2001

  1. Succinct Representation of Balanced Parentheses and Static Trees.

Softw. Pract. Exp. 2001

  1. NR-grep: a fast and flexible pattern-matching tool.

CIAC 2000

  1. Speeding Up Pattern Matching by Text Compression.

CPM 2000

  1. A Boyer-Moore Type Algorithm for Compressed Pattern Matching.
  2. A Dynamic Edit Distance Table.
  3. A Faster and Unifying Algorithm for Comparing Trees.
  4. A Lower Bound for the Breakpoint Phylogeny Problem.
  5. A Polynominal Time Approximation Scheme for the Closest Substring Problem.
  6. Algorithmic Aspects of Speech Recognition: A Synopsis.
  7. An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC).
  8. Approximate String Matching over Ziv-Lempel Compressed Text.
  9. Approximating the Maximum Isomorphic Agreement Subtree Is Hard.
  10. Approximation Algorithms for Hamming Clustering Problems.
  11. Boyer-Moore String Matching over Ziv-Lempel Compressed Text.
  12. Browsing around a Digital Library: Today and Tomorrow.
  13. Compact Suffix Array.
  14. Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts.
  15. Explaining and Controlling Ambiguity in Dynamic Programming.
  16. Finding Maximal Quasiperiodicities in Strings.
  17. Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments.
  18. Identifying and Filtering Near-Duplicate Documents.
  19. Improving Static Compression Schemes by Alphabet Extension.
  20. Incomplete Directed Perfect Phylogeny.
  21. Indexing Text with Approximate q-Grams.
  22. Linear Bidirectional On-Line Construction of Affix Trees.
  23. Machine Learning for Efficient Natural-Language Processing.
  24. On the Complexity of Determining the Period of a String.
  25. Parametric Multiple Sequence Alignment and Phylogeny Construction.
  26. Periods and Quasiperiods Characterization.
  27. Shift Error Detection in Standardized Exams.
  28. Simple Optimal String Matching Algorithm.
  29. Some Results on Flexible-Pattern Discovery.
  30. Structural Properties and Tractability Results for Linear Synteny.
  31. The Combinatorial Partitioning Method.
  32. The Longest Common Subsequence Problem for Arc-Annotated Sequences.
  33. Tsukuba BB: A Branch and Bound Algorithm for Local Multiple Sequence Alignment.
  34. Using Suffix Trees for Gapped Motif Discovery.

Data Compression Conference 2000

  1. A New Compression Method for Compressed Matching.
  2. Implementing the Context Tree Weighting Method for Text Compression.

Discovery Science 2000

  1. A Practical Algorithm to Find the Best Subsequence Patterns.

ESA 2000

  1. On the Competitiveness of Linear Search.

FOCS 2000

  1. Cache-Oblivious B-Trees.
  2. Opportunistic Data Structures with Applications.

IFIP TCS 2000

  1. An Index for Two Dimensional String Matching Allowing Rotations.

ISAAC 2000

  1. Compressed Text Databases with Efficient Query Algorithms Based on the Compressed Suffix Array.

LATIN 2000

  1. The LCA Problem Revisited.

RECOMB 2000

  1. A compression algorithm for DNA sequences and its applications in genome comparison.

Recent Advances in Intrusion Detection 2000

  1. A Pattern Matching Based Filter for Audit Reduction and Fast Detection of Potential Intrusions.

SPIRE 2000

  1. A Model and Software Architecture for Search Results Visualization on the WWW.
  2. A New Approach for Approximating the Tranposition Distance.
  3. A PRAM-on-Chip Vision (invited abstract).
  4. A Survey of Longest Common Subsequence Algorithms.
  5. A Word Stemming Algorithm for the Spanish Language.
  6. Adding String Processing Capabilities to Data Management Systems.
  7. An Effective Clustering Algorithm to Index High Dimensional Metric Spaces.
  8. An Image Similarity Measure Based on Graph Matching.
  9. Automatic Construction of Rule-Based Trees for Conceptual Retrieval.
  10. Bit-Parallel Approach to Approximate String Matching in Compressed Texts.
  11. Combinatorial Methods for Approximate Pattern Matching under Rotations and Translations in 3D Arrays.
  12. Computing with Membranes: P Systems with Worm-Objects.
  13. DNA Processing in Ciliates - A Computational Point of View (invited abstract).
  14. DelfosnetX: A Workbench for XML-Based Information Retrieval Systems.
  15. Experiment Analysis in Newspaper Topic Detection.
  16. Fast Calculation of Optimal Strategies for Searching with Non-Uniform Costs.
  17. Fast Multipattern Search Algorithms for Intrusion Detection.
  18. Finding Repeats with Fixed Gap.
  19. Fully Compressed Pattern Matching Algorithm for Balanced Straight-Line Programs.
  20. Hybrid Protein Model (HPM): A Method to Compact Protein 3D-Structure Information and Physicochemical Properties.
  21. Implementing Document Ranking within a Logical Framework.
  22. Learning Profile in Routing: Comparison between Relevance and Gradient Back-Propagation.
  23. Muninn: A Pragmatic Information Extraction System.
  24. NFAs with Tagged Transitions, Their Conversion to Deterministic Automata and Application to Regular Expressions.
  25. New Approaches to Information Management: Attribute-Centric Data Systems (invited paper).
  26. Online Construction of Subsequence Automata for Multiple Texts.
  27. Parallel Search Using Partitioned Inverted Files.
  28. Prosodic Stress and Topic Detection in Spoken Sentences.
  29. Rotation Invariant Histogram Filters for Similarity and Distance Measures between Digital Images.
  30. Speeding up Parallel Decoding of LZ Compressed Text on the PRAM EREW.
  31. Virtual Test Tubes: A New Methodology for Computing.

Stringology 2000

  1. A new family of Commentz-Walter-style multiple-keyword pattern matching algorithms.
  2. Computing Approximate Repetitions in Musical Sequences.
  3. Condensation Principle.
  4. Multiple Sequence Alignment as a Facility Location Problem.
  5. Repetitions in two-pattern strings.
  6. The Set-Set Closest Common Subsequence Problem.
  7. Word-based Compression Method with Direct Access.

ACM J. Exp. Algorithmics 2000

  1. An Experimental Study of Priority Queues in External Memory.
  2. Fast and Flexible String Matching by Combining Bit-Parallelism and Suffix Automata.

ACM Trans. Inf. Syst. 2000

  1. Fast and flexible word searching on compressed text.

Algorithmica 2000

  1. Binary Searching with Nonuniform Costs and Its Application to Text Retrieval.

Computer 2000

  1. Compression: A Key for Next-Generation Text Retrieval Systems.

Inf. Retr. 2000

  1. Adding Compression to Block Addressing Inverted Indexes.

J. ACM 2000

  1. On the sorting-complexity of suffix tree construction.

Proc. IEEE 2000

  1. Off-line compression by greedy textual substitution.
  2. Off-line dictionary-based compression.

Theor. Comput. Sci. 2000

  1. Improved approximate pattern matching on hypertext.

CPM 1999

  1. A Dynamic Data Structure for Reverse Lexicographically Sorted Prefixes.
  2. A General Practical Approach to Pattern Matching over Ziv-Lempel Compressed Text.
  3. A New Indexing Method for Approximate String Matching.
  4. Applying an Edit Distance to the Matching of Tree Ring Sequences in Dendrochronology.
  5. Approximate Periods of Strings.
  6. Bounds on the Number of String Subsequences.
  7. Computing Similarity between RNA Structures.
  8. Fast Multi-dimensional Approximate Pattern Matching.
  9. Finding Common RNA Secondary Structures from RNA Sequences.
  10. Finding Common Subsequences with Arcs and Pseudoknots.
  11. Finding Maximal Pairs with Bounded Gap.
  12. GESTALT: Genomic Steiner Alignments.
  13. Hybridization and Genome Rearrangement.
  14. Matching of Spots in 2D Electrophoresis Images. Point Matching Under Non-uniform Distortions.
  15. On the Complexity of Positional Sequencing by Hybridization.
  16. On the Structure of Syntenic Distance.
  17. Pattern Matching in Text Compressed by Using Antidictionaries.
  18. Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem.
  19. Shift-And Approach to Pattern Matching in LZW Compressed Text.
  20. The Compression of Subsegments of Images Described by Finite Automata.
  21. Ziv Lempel Compression of Huge Natural Language Data Tries Using Suffix Arrays.

Data Compression Conference 1999

  1. A Modified Burrows-Wheeler Transformation for Case-Insensitive Search with Application to Suffix Array Compression.
  2. Offline Dictionary-Based Compression.

ESA 1999

  1. Efficient Algorithms foe On-Line Symbol Ranking Compression.
  2. On Constructing Suffix Arrays in External Memory.

MFCS 1999

  1. Invited Lecture: The Burrows-Wheeler Transform: Theory and Practice.

RECOMB 1999

  1. q-gram based database searching using a suffix array (QUASAR).

SPIRE/CRIWG 1999

  1. A Fast Distributed Suffix Array Generation Algorithm.
  2. A Unifying Framework for Compressed Pattern Matching.

STOC 1999

  1. Multi-Method Dispatching: A Geometric Approach With Applications to String Matching Problems.

Stringology 1999

  1. A Fast String Matching Algorithm and Experimental Results.
  2. A New Practical Linear Space Algorithm for the Longest Common Subsequence Problem.
  3. Centroid Trees with Application to String Processing.
  4. On Procedures for Multiple-string Match with Respect to Two Sets.
  5. The Closest Common Subsequence Problems.

WADS 1999

  1. Representing Trees of Higer Degree.
  2. Resizable Arrays in Optimal Time and Space.

WAE 1999

  1. An Experimental Study of Priority Queues in External Memory.
  2. Fast Regular Expression Search.

Algorithmica 1999

  1. Faster Approximate String Matching.
  2. String Search in Coarse-Grained Parallel Computers.
  3. Suffix Trees on Words.

Inf. Process. Lett. 1999

  1. Very Fast and Simple Approximate String Matching.

J. ACM 1999

  1. The String B-tree: A New Data Structure for String Search in External Memory and Its Applications.

J. Algorithms 1999

  1. Improved Dynamic Text Indexing.

Parallel Process. Lett. 1999

  1. An EREW PRAM Algorithm for Updating Minimum Spanning Trees.

SIAM J. Comput. 1999

  1. Compression of Low Entropy Strings with Lempel-Ziv Algorithms.
  2. Membership in Constant Time and Almost-Minimum Space.

Theory Comput. Syst. 1999

  1. Bounding the Expected Length of Longest Common Subsequences and Forests.

CPM 1998

  1. A Bit-Parallel Approach to Suffix Automata: Fast Extended String Matching.
  2. A Dictionary Matching Algorithm Fast on the Average for Terms of Varying Length.
  3. A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming.
  4. A Rotation Invariant Filter for Two-Dimensional String Matching.
  5. A Very Fast String Matching Algorithm for Small Alphabeths and Long Patterns (Extended Abstract).
  6. Aligning Alignments.
  7. Aligning DNA Sequences to Minimize the Change in Protein (Extended Abstract).
  8. An Approximate Oracle for Distance in Metric Spaces.
  9. Approximate Word Sequence Matching over Sparse Suffix Trees.
  10. Comparison of Coding DNA.
  11. Constructing Suffix Arrays for Multi-dimensional Matrices.
  12. Efficient Parallel Algorithm for the Editing Distance between Ordered Trees.
  13. Efficient Special Cases of Pattern Matching with Swaps.
  14. Fixed Topology Alignment with Recombination.
  15. Genome Halving.
  16. Reporting Exact and Approximate Regular Expression Matches.
  17. Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version).

Data Compression Conference 1998

  1. A Fast Algorithms for Making Suffix Arrays and for Burrows-Wheeler Transformation.
  2. Multiple Pattern Matching in LZW Compressed Text.
  3. On Optimality of Varients of the Block Sorting Compression.
  4. Some Theory and Practice of Greedy Off-Line Textual Substitution.
  5. The Context Trees of Block Sorting Compression.

FOCS 1998

  1. Overcoming the Memory Bottleneck in Suffix Tree Construction.

FSTTCS 1998

  1. Space Efficient Suffix Trees.

LATIN 1998

  1. Fast Two-Dimensional Approximate Pattern Matching
  2. Improved Approximate Pattern Matching on Hypertext.

SIGIR 1998

  1. Fast Searching on Compressed Text Allowing Errors.

SPIRE 1998

  1. A Linear Time Lower Bound on Updating Algorithms for Suffix Trees.
  2. A Model and a Visual Query Language for Structured Text.
  3. An Experiment Stemming Non-Traditional Text.
  4. Direct Pattern Matching on Compressed Text.
  5. Efficient Search Techniques for the Inference of Minimum Size Finite Automata.
  6. Evidence Accumulation with Competition in Information Retrieval.
  7. Fast Approximate String Matching in a Dictionary.
  8. Hyperdictionary: A Knowledge Discovery Tool to Help Information Retrieval.
  9. In-Place Length-Restricted Prefix Coding.
  10. Information Overload - An IR Problem?
  11. New Approximation Algorithms for Longest Common Subsequences.
  12. Reversal and Transposition Distance of Linear Chromosomes.
  13. SST versus EST in Gene Recognition (Invited Paper).
  14. Searching the Web: Challenges and Partial Solutions (Invited Paper).

Stringology 1998

  1. A Fast Morphological Analysis Using the Extended AC Machine for Oriental Languages.
  2. A Highly Parallel Finite State Automaton Processor for Biological Pattern Matching.
  3. An Early-Retirement Plan for the States.
  4. Application of Sequence Alignment Methods to Multiple Structural Alignment and Superposition.
  5. Approximate String Matching by Fuzzy Automata.
  6. Directed Acyclic Subsequence Graph.
  7. Dynamic Programming for Reduced NFAs for Approximate String and Sequence Matching.
  8. Exact String Matching Animation in Java.
  9. Implementation of DAWG.
  10. Local Prediction for Lossless Image Compression.
  11. On the All Occurrences of a Word in a Text.
  12. The Factor Automaton.
  13. The Longest Restricted Common Subsequence Problem.
  14. Validating and Decomposing Partially Occluded Two-Dimensional Images (Extended Abstract).

CLEI Electron. J. 1998

  1. A Practical q -Gram Index for Text Retrieval Allowing Errors.

Inf. Comput. 1998

  1. Dynamic Dictionary Matching in External Memory.

SIAM J. Comput. 1998

  1. Optimal On-Line Search and Sublinear Time Update in String Matching.

Theor. Comput. Sci. 1998

  1. On Updating Suffix Tree Labels.

CIAC 1997

  1. A Note on Updating Suffix Tree Labels.

CIKM 1997

  1. Block Addressing Indices for Approximate Text Retrieval.

CPM 1997

  1. A Filter Method for the Weighted Local Similarity Search Problem.
  2. A New Algorithm for the Ordered Tree Inclusion Problem.
  3. Aligning Coding DNA in the Presence of Frame-Shift Errors.
  4. An Easy Case of Sorting by Reversals.
  5. An Improved Pattern Matching Algorithm for Strings in Terms of Straight-Line Programs.
  6. Approximation Algorithms for the Fixed-Topology Phylogenetic Number Problem.
  7. Banishing Bias from Consensus Sequences.
  8. Direct Construction of Compact Directed Acyclic Word Graphs.
  9. Distributed Generation of Suffix Arrays.
  10. Efficient Algorithms for Approximate String Matching with Swaps (Extended Abstract).
  11. Episode Matching.
  12. Estimating the Probability of Approximate Matches.
  13. External Inverse Pattern Matching.
  14. Flexible Identification of Structural Objects in Nucleic Acid Sequences: Palindromes, Mirror Repeats, Pseudoknots and Triple Helices.
  15. Iterative versus simultaneous Multiple Sequence Alignment (Abstract).
  16. Modern Comparative Lexicostatistics.
  17. On Incremental Computation of Transitive Closure and Greedy Alignment.
  18. On Weak Circular Squares in Binary Words.
  19. On the Complexity of Pattern Matching for Highly Compressed Two-Dimensional Texts.
  20. On the Nadeau-Taylor Theory of Conserved Chromosome Segments.
  21. Space- and Time-Efficient Decoding with Canonical Huffman Trees.
  22. Trie-Based Data Structures for Sequence Assembly.

FOCS 1997

  1. Succinct Representation of Balanced Parentheses, Static Trees and Planar Graphs.

SEQUENCES 1997

  1. Compression of low entropy strings with Lempel-Ziv algorithms.
  2. Multi-string search in BSP.
  3. Sequence sorting in secondary storage.
  4. Text compression using recency rank with context and relation to context sorting, block sorting and PPM*.

STOC 1997

  1. On Sorting Strings in External Memory (Extended Abstract).

Stringology 1997

  1. 6D Classification of Pattern Matching Problems.
  2. A Boyer-Moore (or Watson-Watson) Type Algorithm for Regular Tree Pattern Matching.
  3. A New Family of String Pattern Matching Algorithms.
  4. Algebra of Pattern Matching Problems.
  5. An Efficient Trie Hashing Method Using a Compact Binary Trie.
  6. SPARE Parts: A C++ Toolkit for String PAttern REcognition.
  7. Simulation of NFA in Approximate String and Sequence Matching.

WADS 1997

  1. Multiple Approximate String Matching.
  2. Trans-Dichotomous Algorithms Without Multiplication - Some Upper and Lower Bounds.

ACM Trans. Inf. Syst. 1997

  1. Proximal Nodes: A Model to Query Document Databases by Content and Structure.

IEEE Trans. Inf. Theory 1997

  1. On the average redundancy rate of the Lempel-Ziv code.

IEEE Trans. Knowl. Data Eng. 1997

  1. Text Compression for Dynamic Document Databases.

J. Algorithms 1997

  1. Dynamic Text Indexing under String Updates.

CPM 1996

  1. A 2 2/3-Approximation Algorithm for the Shortest Superstring Problem.
  2. A Double Combinatorial Approach to Discovering Patterns in Biological Sequences.
  3. A Faster Algorithm for Approximate String Matching.
  4. Alphabet Independent and Dictionary Scaled Matching.
  5. Analysis of Two-Dimensional Approximate Pattern Matching Algorithms.
  6. Approximate Dictionary Queries.
  7. Approximate Multiple Strings Search.
  8. Approximate Pattern Matching in Directed Graphs.
  9. Approximation Algorithms for Maximum Two-Dimensional Pattern Matching.
  10. Boyer-Moore Strategy to Efficient Approximate String Matching.
  11. Computing Discoveries in Molecular Biology (Abstract).
  12. Constructing Computer Virus Phylogenies.
  13. Docking of Conformationally Flexible Proteins.
  14. Efficient Parallel Algorithms for Tree Editing Problems.
  15. Fast Sorting by Reversal.
  16. Filtration with q-Samples in Approximate String Matching.
  17. Finite-State Computability of Annotations of Strings and Trees.
  18. Graph Traversals, Genes, and Matroids: An Efficient Case of the Travelling Salesman Problem.
  19. Improved Approximation Algorithms for Tree Alignment.
  20. Invariant Patterns in Crystal Lattices: Implications for Protein Folding Algorithms (Extended Abstract).
  21. Original Synteny.
  22. Perfect Hashing for Strings: Formalization and Algorithms.
  23. Poisson Process Approximation for Repeats in One Sequence and Its Application to Sequencing by Hybridization.
  24. Randomized Efficient Algorithms for Compressed Strings: The Finger-Print Approach (Extended Abstract).
  25. Spliced Alignment: A New Approach to Gene Recognition.
  26. Suffix Trees on Words.
  27. The Asymmetric Median Tree - A New model for Building Consensus Trees.
  28. The suffix Tree of a Tree and Minimizing Sequential Transducers.

Data Compression Conference 1996

  1. Extended Application of Suffix Trees to Data Compression.

Stringology 1996

  1. A Collection of New Regular Grammar Pattern Matching Algorithms.
  2. An Efficient Multi-Attribute Pattern Matching Machine.
  3. Approximate Regular Expression Matching.
  4. Efficiency of AC-Machine and SNFA in Practical String Matching.
  5. Fast Full Text Search Using Tree Structured[TS] File.
  6. Reduced Nondeterministic Finite Automata for Approximate String Matching.
  7. Space Complexity of Linear Time Approximate String Matching.

Algorithmica 1996

  1. Fast Stable In-Place Sorting with O (n) Data Moves.

SIGMOD Rec. 1996

  1. Integrating Contents and Structure in Text Retrieval.

Theor. Comput. Sci. 1996

  1. Selection from Read-Only Memory and Sorting with Minimum Data Movement.

CPM 1995

  1. A New Flexible Algorithm for the Longest Common Subsequence Problem.
  2. An Efficient Algorithm for Developing Topological Valid Matchings.
  3. Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree.
  4. Common Subsequences and Supersequences and Their expected Length.
  5. Computing Similarity between RNA Strings.
  6. Constant-Space String Matching with Smaller Number of Comparisons: Sequential Sampling.
  7. Dictionary Loop-Up with Small Errors.
  8. Efficient String Matching on Coded Texts.
  9. Fast Approximate Matching using Suffix Trees.
  10. Genome Analysis: Pattern Search in Biological Macromolecules.
  11. Making the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment More Space Efficient in Practice (Extended Abstract).
  12. Matching Patterns of An Automaton.
  13. Matching a Set of Strings with Variable Length Don’t Cares.
  14. Minimizing Phylogenetic Number to find Good Evolutionary Trees.
  15. Multi-Dimensional Pattern Matching with Dimensional Wildcards.
  16. Multiple Sequence Comparison: A Peptide Matching Approach.
  17. New Results and Open Problems Related to Non-Standard Stringology.
  18. Of Chicken Teeth and Mouse Eyes, or Generalized Character Compatibility.
  19. On a Technique for Parsing a String (Abstract).
  20. On the Complexity of Comparing Evolutionary Trees (Extended Abstract).
  21. On the Editing Distance between Undirected Acyclic Graphs and Related Problems.
  22. Pairwise Alignment with Scoring on Tuples.
  23. Pattern Matching in Directed Graphs.
  24. Pattern-Matching for Strings with Short Descriptions.
  25. Polynomial-time Algorithm for Computing Translocation Distance between Genomes.
  26. Smaller Representations for Finite-State Transducers and Finite-State Automata.
  27. String Matching in Hypertext.
  28. Suffix Cactus: A Cross between Suffix Tree and Suffix Array.
  29. Three-Dimensional Pattern Matching in Protein Structure Analysis.

ESA 1995

  1. Optimized Binary Search and Text Retrieval.
  2. The Binomial Transform and its Application to the Analysis of Skip Lists.

IWMM 1995

  1. Dynamic Storage Allocation: A Survey and Critical Review

SIGIR 1995

  1. A Language for Queries on Structure and Contents of Textual.

SIAM J. Comput. 1995

  1. Permuting in Place.

CPM 1994

  1. A Context Dependent Method for Comparing Sequences.
  2. A Lossy Data Compression Based on String Matching: Preliminary Analysis and Suboptimal Algorithms.
  3. A Space Efficient Algorithm for Finding the Best Non-Overlapping Alignment Score.
  4. A Text Compression Scheme That Allows Fast Searching Directly in the Compressed File.
  5. Alignment of Trees - An Alternative to Tree Edit.
  6. An Alphabet-Independent Optimal Parallel Search for Three Dimensional Pattern.
  7. Approximate String Matching and Local Similarity.
  8. Approximate String Matching with Don’t Care Characters.
  9. Approximation Algorithms for Multiple Sequence Alignment.
  10. Computation of Squares in a String (Preliminary Version).
  11. Computing all Suboptimal Alignments in Linear Space.
  12. Dictionary-Matching on Unbounded Alphabets: Uniform Length Dictionaries.
  13. Efficient Bounds for Oriented Chromosome Inversion Distance.
  14. Fast Identification of Approximately Matching Substrings.
  15. Matching with Matrix Norm Minimization.
  16. Maximal Common Subsequences and Minimal Common Supersequences.
  17. Minimization of Sequential Transducers.
  18. Multiple Matching of Parameterized Patterns.
  19. Parametric Recomuting in Alignment Graphs.
  20. Polynomial-Time Algorithms for Computing Characteristic Strings.
  21. Proximity Matching Using Fixed-Queries Trees.
  22. Query Primitives for Tree-Structured Data.
  23. Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars.
  24. Shortest Common Superstrings for Strings of Random Letters.
  25. The Parameterized Complexity of Sequence Alignment and Consensus.
  26. Unit Route Upper Bound for String-Matching on Hypercube.

ESA 1994

  1. Membership in Constant Time and Minimum Space.

Inf. Process. Manag. 1994

  1. A New Challenge for Compression Algorithms: Genetic Sequences.

Proc. IEEE 1994

  1. The sliding-window Lempel-Ziv algorithm is asymptotically optimal.

CPM 1993

  1. 3-D Docking of Protein Molecules.
  2. A Fast Filtration Algorithm for the Substring Matching Problem.
  3. A Linear Time Pattern Matching Algorithm Between a String and a Tree.
  4. A New Editing based Distance between Unordered Labeled Trees.
  5. A Unifying Look at d-Dimensional Periodicities and Space Coverings.
  6. An Algorithm for Approximate Tandem Repeats.
  7. An Algorithm for Locating Non-Overlapping Regions of Maximum Alignment Score.
  8. Analysis of a String Edit Problem in a Probabilistic Framework (Extended Abstract).
  9. Approximate String-Matching over Suffix Trees.
  10. Covering a String.
  11. Detecting False Matches in String Matching Algorithms.
  12. Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes.
  13. Minimal Separators of Two Words.
  14. Multiple Sequence Comparison and n-Dimensional Image Reconstruction.
  15. On Suboptimal Alignments of Biological Sequences.
  16. On the Worst-Case Behaviour of Some Approximation Algorithms for the Shortest Common Supersequence of k Strings.
  17. The Maximum Weight Trace Problem in Multiple Sequence Alignment.
  18. Tight Comparison Bounds for the String Prefix-Matching Problem.
  19. Two Dimensional Pattern Matching in a Digitized Image.

CPM 1992

  1. 3-D Substructure Matching in Protein Molecules.
  2. A Language Approach to String Searching Evaluation.
  3. Approximate Regular Expression Pattern Matching with Concave Gap Penalties.
  4. Color Set Size Problem with Application to String Matching.
  5. Computing Display Conflicts in String and Circular String Visualization.
  6. DZ: A Text Compression Algorithm For Natural Languages.
  7. Dynamic Dictionary Matching with Failure Functions (Extended Abstract).
  8. Edit Distances for Genome Comparisons Based on Non-Local Operations.
  9. Efficient Randomized Dictionary Matching Algorithms (Extended Abstract).
  10. Fast Multiple Keyword Searching.
  11. Fast Serial and Parallel Algorithms for Approximate Tree Matching with VLDC’s.
  12. Fast and Practical Approximate String Matching.
  13. From Regular Expressions to DFA’s Using Compressed NFA’s.
  14. Grammatical Tree Matching.
  15. Heaviest Increasing/Common Subsequence Problems.
  16. Identifying Periodic Occurrences of a Template with Applications to Protein Structures.
  17. Matrix Longest Common Subsequence Problem, Duality and Hibert Bases.
  18. Multiple Alignment with Guaranteed Error Bounds and Communication Cost.
  19. Pattern Matching With Mismatches: A Probabilistic Analysis and a Randomized Algorithm (Extended Abstract).
  20. Probabilistic Analysis of Generalized Suffix Trees (Extended Abstract).
  21. Theoretical and Empirical Comparisons of Approximate String Matching Algorithms.
  22. Two Algorithms for the Longest Common Subsequence of Three (or More) Strings.

FSTTCS 1992

  1. Selection from Read-Only Memory and Sorting with Optimum Data Movement.

BIT 1992

  1. Average Search and Update Costs in Skip Lists.

J. Algorithms 1992

  1. Sorting with Minimum Data Movement.

FSTTCS 1991

  1. Fast Sorting In-Place Sorting with O(n) Data.

WADS 1991

  1. A Case Study in Comparison Based Complexity: Finding the Nearest Value(s).
  2. Sorting Multisets and Vectors In-Place.

Inf. Comput. 1991

  1. Fringe Analysis for Extquick: An in Situ Distributive External Sorting Algorithm

J. Comput. Syst. Sci. 1991

  1. An Implicit Data Structure for Searching a Multikey Table in Logarithmic Time.

FOCS 1990

  1. Permuting

SWAT 1990

  1. Analysis of the Expected Search Cost in Skip Lists.

Algorithmica 1990

  1. Analysis of the Standard Deletion Algorithms in Exact Fit Domain Binary Search Trees.

BIT 1990

  1. Stable in Situ Sorting and Minimum Data Movement.

Comput. J. 1989

  1. Explaining the Behaviour of Binary Search Trees Under Prolonged Updates: A Model and Simulations.

SWAT 1988

  1. An Implicit Binomial Queue with Constant Insertion Time.

SIAM J. Comput. 1988

  1. A Functional Approach to Data Structures and Its Use in Multidimensional Searching.

STOC 1987

  1. Searching a Two Key Table Under a Single Key

BIT 1987

  1. Searchability in Merging and Implicit Data Structures.

MFCS 1986

  1. Developing Implicit Data Structures.

SCG 1986

  1. Linear Data Structures for Two Types of Range Search.

Algorithmica 1986

  1. Fractional Cascading: I. A Data Structuring Technique.
  2. Fractional Cascading: II. Applications.

J. Comput. Syst. Sci. 1986

  1. An Implicit Data Structure Supporting Insertion, Deletion, and Search in O(log² n) Time.

SIAM J. Comput. 1986

  1. Filtering Search: A New Approach to Query-Answering.
  2. Heaps on Heaps.

FOCS 1985

  1. Robin Hood Hashing (Preliminary Report)

J. Algorithms 1985

  1. The Analysis of a Fringe Heuristic for Binary Search Trees.

PODS 1983

  1. A Discipline for Robustness or Storage Reduction in Binary Search Trees.

Comput. Vis. Graph. Image Process. 1983

  1. Direct dynamic structures for some line segment problems.

ICALP 1982

  1. Heaps on Heaps.

J. ACM 1982

  1. Data compression via textual substitution.

STOC 1981

  1. A Linear Probing Sort and its Analysis (Preliminary Draft)

SIAM J. Comput. 1981

  1. Exegesis of Self-Organizing Linear Search.

J. Comput. Syst. Sci. 1980

  1. Implicit Data Structures for Fast Search and Update.

FOCS 1979

  1. Toward Self-Organizing Linear Search (Preliminary Draught)

STOC 1979

  1. Implicit Data Structures (Preliminary Draft)

SIAM J. Comput. 1979

  1. Efficient Ordering of Hash Tables.

FOCS 1978

  1. Selection and Sorting with Limited Storage

J. ACM 1978

  1. Self-Organizing Binary Search Trees.

STOC 1977

  1. The Analysis of an Improved Hashing Technique

FOCS 1976

  1. Self-Organizing Binary Search Trees

SIAM J. Comput. 1976

  1. Sorting and Searching in Multisets.
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