StringologyTimes

WABI for Stringologist

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. Toward Optimal Fingerprint Indexing for Large Scale Genomics.
  4. Haplotype Threading Using the Positional Burrows-Wheeler Transform.
  5. Suffix Sorting via Matching Statistics.
  6. phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering.
  7. On Weighted k-mer Dictionaries.
  8. Prefix-Free Parsing for Building Large Tunnelled Wheeler Graphs.
  9. Locality-Sensitive Bucketing Functions for the Edit Distance.

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

WABI 2017

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

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.

WABI 2015

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

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. Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes.
  2. Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter.
  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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