StringologyTimes

Papers for stringologist (2012)

• AIAI (2)(2012) [dblp]
• ALENEX(2012) [dblp]
• ANALCO(2012) [dblp]
• BCB(2012) [dblp]
• BIBM Workshops(2012) [dblp]
• COCOON(2012) [dblp]
• CPM(2012) [dblp]
• DCC(2012) [dblp]
• Developments in Language Theory(2012) [dblp]
• ECML/PKDD (2)(2012) [dblp]
• ESA(2012) [dblp]
• FAW-AAIM(2012) [dblp]
• FOCS(2012) [dblp]
• ICALP (1)(2012) [dblp]
• ISAAC(2012) [dblp]
• IWOCA(2012) [dblp]
• LATA(2012) [dblp]
• LATIN(2012) [dblp]
• MFCS(2012) [dblp]
• SEA(2012) [dblp]
• SODA(2012) [dblp]
• SOFSEM(2012) [dblp]
• SPIRE(2012) [dblp]
• STACS(2012) [dblp]
• STOC(2012) [dblp]
• SWAT(2012) [dblp]
• WABI(2012) [dblp]

• WALCOM(2012) [dblp]

• ACM Comput. Surv.(2012) [dblp]
• ACM Trans. Algorithms(2012) [dblp]
• ACM Trans. Inf. Syst.(2012) [dblp]
• Algorithmica(2012) [dblp]
• Algorithms(2012) [dblp]
• Comput. J.(2012) [dblp]
• IEEE ACM Trans. Comput. Biol. Bioinform.(2012) [dblp]
• IEEE Trans. Knowl. Data Eng.(2012) [dblp]
• IEICE Trans. Fundam. Electron. Commun. Comput. Sci.(2012) [dblp]
• Inf. Comput.(2012) [dblp]
• Inf. Process. Lett.(2012) [dblp]
• Inf. Process. Manag.(2012) [dblp]
• Inf. Retr.(2012) [dblp]
• Int. J. Found. Comput. Sci.(2012) [dblp]
• J. Comput. Syst. Sci.(2012) [dblp]
• J. Discrete Algorithms(2012) [dblp]
• SIAM J. Comput.(2012) [dblp]
• Softw. Pract. Exp.(2012) [dblp]
• Theor. Comput. Sci.(2012) [dblp]
• Theory Comput. Syst.(2012) [dblp]

Contents

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. Compressed String Dictionary Look-Up with Edit Distance One.
2. Constant-Time Word-Size String Matching.
3. Cross-Document Pattern Matching.
4. Simple and Efficient LZW-Compressed Multiple Pattern Matching.
5. Speeding Up q-Gram Mining on Grammar-Based Compressed Texts.
6. Time-Space Trade-Offs for Longest Common Extensions.
7. 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. Compressed Suffix Trees for Repetitive Texts.
2. Computing Discriminating and Generic Words.
3. Dual-Sorted Inverted Lists in Practice.
4. Efficient LZ78 Factorization of Grammar Compressed Text.
5. Faster Algorithm for Computing the Edit Distance between SLP-Compressed Strings.
6. Grammar Precompression Speeds Up Burrows-Wheeler Compression.
7. Improved Grammar-Based Compressed Indexes.
8. Ranked Document Retrieval in (Almost) No Space.
9. Smaller Self-indexes for Natural Language.
10. The Position Heap of a Trie.
11. The Wavelet Matrix.
12. 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.

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.

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.

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