StringologyTimes

WABI for Stringologist

WABI 2022

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

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

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

WABI 2013

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

WABI 2012

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

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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