StringologyTimes

WABI for Stringologist

WABI 2022

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

WABI 2021

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

WABI 2020

  1. Linear Time Construction of Indexable Founder Block Graphs.

WABI 2019

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

WABI 2018

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

WABI 2017

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

WABI 2016

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

WABI 2015

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

WABI 2014

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

WABI 2013

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

WABI 2012

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

WABI 2010

  1. Swiftly Computing Center Strings.

WABI 2009

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

WABI 2004

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