WABI 2023 September 4-6, 2023, Houston, TX, USA

23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)



Djamal Belazzougui and Aïda Ouangraoua (Eds.)
ISBN 978-3-95977-294-5, LIPICS Vol. 273 ISSN 1868-8969
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Authors
  • Arasti, Shayesteh
  • Bannai, Hideo
  • Belazzougui, Djamal
  • Bohnenkämper, Leonard
  • Boucher, Christina
  • Boury, Théo
  • Chandra, Ghanshyam
  • Cáceres, Manuel
  • Dai, Junyan
  • Dhulipala, Laxman
  • Dufresne, Yoann
  • El-Kebir, Mohammed
  • Fan, Jason
  • Ferdosi, Mohsen
  • Gagie, Travis
  • Ge, Yuejun
  • Gray, Mateo
  • Gu, Xinyu
  • Górecki, Paweł
  • Han, Yunheng
  • Hong, Aaron
  • Jabbari, Hosna
  • Jain, Chirag
  • Jones, Mark
  • Julien, Esther
  • Khan, Jamshed
  • Kingsford, Carl
  • Köppl, Dominik
  • Limasset, Antoine
  • Liu, Baqiao
  • Marchet, Camille
  • Martayan, Igor
  • Medvedev, Paul
  • Mirarab, Siavash
  • Molloy, Erin
  • Molloy, Erin K.
  • Murakami, Yukihiro
  • Mykowiecka, Agnieszka
  • Mäkinen, Veli
  • Oliva, Marco
  • Ouangraoua, Aïda
  • Paszek, Jarosław
  • Patro, Rob
  • Pibiri, Giulio Ermanno
  • Ponty, Yann
  • Przytycka, Teresa M.
  • Qi, Yuanyuan
  • Qiu, Yutong
  • Rahman, Amatur
  • Rajput, Jyotshna
  • Reinharz, Vladimir
  • Rizzo, Nicola
  • Roddur, Mrinmoy Saha
  • Rouzé, Timothé
  • Rubel, Tobias
  • Rutecka, Natalia
  • Schulz, Tizian
  • Shen, Chengze
  • Shen, Yihang
  • Singh, Noor Pratap
  • Snir, Sagi
  • van Iersel, Leo
  • Warnow, Tandy
  • Wedell, Eleanor
  • Will, Sebastian
  • Williams, Kelly P.
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    Front Matter, Table of Contents, Preface, Conference Organization
    Authors: Belazzougui, Djamal ; Ouangraoua, Aïda

    Abstract | Document (462 KB) | BibTeX

    Algorithmic Approaches to Study Mutational Processes in Cancer (Invited Talk)
    Authors: Przytycka, Teresa M.

    Abstract | Document (378 KB) | BibTeX

    EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability (Abstract)
    Authors: Shen, Chengze ; Liu, Baqiao ; Williams, Kelly P. ; Warnow, Tandy

    Abstract | Document (422 KB) | BibTeX

    BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences (Abstract)
    Authors: Wedell, Eleanor ; Shen, Chengze ; Warnow, Tandy

    Abstract | Document (428 KB) | BibTeX

    Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time
    Authors: Arasti, Shayesteh ; Mirarab, Siavash

    Abstract | Document (1,805 KB) | BibTeX

    Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem
    Authors: Dai, Junyan ; Rubel, Tobias ; Han, Yunheng ; Molloy, Erin K.

    Abstract | Document (1,018 KB) | BibTeX

    Simultaneous Reconstruction of Duplication Episodes and Gene-Species Mappings
    Authors: Górecki, Paweł ; Rutecka, Natalia ; Mykowiecka, Agnieszka ; Paszek, Jarosław

    Abstract | Document (947 KB) | BibTeX

    Making a Network Orchard by Adding Leaves
    Authors: van Iersel, Leo ; Jones, Mark ; Julien, Esther ; Murakami, Yukihiro

    Abstract | Document (1,303 KB) | BibTeX

    Quartets Enable Statistically Consistent Estimation of Cell Lineage Trees Under an Unbiased Error and Missingness Model (Abstract)
    Authors: Han, Yunheng ; Molloy, Erin K.

    Abstract | Document (422 KB) | BibTeX

    Inferring Temporally Consistent Migration Histories
    Authors: Roddur, Mrinmoy Saha ; Snir, Sagi ; El-Kebir, Mohammed

    Abstract | Document (1,343 KB) | BibTeX

    Finding Maximal Exact Matches in Graphs
    Authors: Rizzo, Nicola ; Cáceres, Manuel ; Mäkinen, Veli

    Abstract | Document (810 KB) | BibTeX

    Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants
    Authors: Qiu, Yutong ; Shen, Yihang ; Kingsford, Carl

    Abstract | Document (1,569 KB) | BibTeX

    Co-Linear Chaining on Pangenome Graphs
    Authors: Rajput, Jyotshna ; Chandra, Ghanshyam ; Jain, Chirag

    Abstract | Document (1,811 KB) | BibTeX

    Acceleration of FM-Index Queries Through Prefix-Free Parsing
    Authors: Hong, Aaron ; Oliva, Marco ; Köppl, Dominik ; Bannai, Hideo ; Boucher, Christina ; Gagie, Travis

    Abstract | Document (1,046 KB) | BibTeX

    Exact Sketch-Based Read Mapping
    Authors: Schulz, Tizian ; Medvedev, Paul

    Abstract | Document (839 KB) | BibTeX

    Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching
    Authors: Rouzé, Timothé ; Martayan, Igor ; Marchet, Camille ; Limasset, Antoine

    Abstract | Document (1,934 KB) | BibTeX

    Fast, Parallel, and Cache-Friendly Suffix Array Construction
    Authors: Khan, Jamshed ; Rubel, Tobias ; Dhulipala, Laxman ; Molloy, Erin ; Patro, Rob

    Abstract | Document (979 KB) | BibTeX

    Compression Algorithm for Colored de Bruijn Graphs
    Authors: Rahman, Amatur ; Dufresne, Yoann ; Medvedev, Paul

    Abstract | Document (790 KB) | BibTeX

    Fulgor: A Fast and Compact {k-mer} Index for Large-Scale Matching and Color Queries
    Authors: Fan, Jason ; Singh, Noor Pratap ; Khan, Jamshed ; Pibiri, Giulio Ermanno ; Patro, Rob

    Abstract | Document (2,082 KB) | BibTeX

    SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles
    Authors: Gray, Mateo ; Will, Sebastian ; Jabbari, Hosna

    Abstract | Document (1,987 KB) | BibTeX

    Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique
    Authors: Boury, Théo ; Ponty, Yann ; Reinharz, Vladimir

    Abstract | Document (2,797 KB) | BibTeX

    Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design
    Authors: Gu, Xinyu ; Qi, Yuanyuan ; El-Kebir, Mohammed

    Abstract | Document (5,838 KB) | BibTeX

    Bridging Disparate Views on the DCJ-Indel Model for a Capping-Free Solution to the Natural Distance Problem
    Authors: Bohnenkämper, Leonard

    Abstract | Document (7,629 KB) | BibTeX

    Reinforcement Learning for Robotic Liquid Handler Planning
    Authors: Ferdosi, Mohsen ; Ge, Yuejun ; Kingsford, Carl

    Abstract | Document (1,460 KB) | BibTeX

    		  



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