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Selected papers from WABI 2023

Guest Editors:
Aïda Ouangraoua, MSc, Université de Sherbrooke, Canada
Djamal Belazzougui, PhD, CERIST, Algeria

Submission Status: Closed   |   Submission Deadline: 30 May 2024


This collection is no longer accepting submissions.


Algorithms for Molecular Biology is proud to publish the extended proceedings of WABI 2023. WABI is an international conference covering research in algorithmic work in bioinformatics, computational biology and systems biology. The emphasis is mainly on discrete algorithms and machine-learning methods that address important problems in molecular biology, that are founded on sound models, that are computationally efficient, and that provide evidence of their potential usefulness in practice, preferably by testing on appropriately chosen simulated or real datasets. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research.

Image credit: tadamichi / stock.adobe.com

  1. A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs are used in a variety of applications, including variant call...

    Authors: Amatur Rahman, Yoann Dufresne and Paul Medvedev
    Citation: Algorithms for Molecular Biology 2024 19:20
    Content type: Research Published on:

  2. Given a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a “similar sequence”. Traditionally, “similar sequence” was defined as having a high alignme...

    Authors: Tizian Schulz and Paul Medvedev
    Citation: Algorithms for Molecular Biology 2024 19:19
    Content type: Research Published on:

  4. String indexes such as the suffix array (sa) and the closely related longest common prefix (lcp) array are fundamental objects in bioinformatics and have a wide variety of applications. Despite their importance i...

    Authors: Jamshed Khan, Tobias Rubel, Erin Molloy, Laxman Dhulipala and Rob Patro
    Citation: Algorithms for Molecular Biology 2024 19:16
    Content type: Research Published on:

  5. FM-indexes are crucial data structures in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [1] observed in 2007 that word-b...

    Authors: Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher and Travis Gagie
    Citation: Algorithms for Molecular Biology 2024 19:15
    Content type: Research Published on:

  7. We study the problem of finding maximal exact matches (MEMs) between a query string Q and a labeled graph G. MEMs are an important class of seeds, often used in seed-chain-extend type of practical alignment metho...

    Authors: Nicola Rizzo, Manuel Cáceres and Veli Mäkinen
    Citation: Algorithms for Molecular Biology 2024 19:10
    Content type: Research Published on:

  10. We present a novel problem, called MetaEC, which aims to infer gene-species assignments in a collection of partially leaf-labeled gene trees labels by minimizing the size of duplication episode clustering (EC)...

    Authors: Paweł Górecki, Natalia Rutecka, Agnieszka Mykowiecka and Jarosław Paszek
    Citation: Algorithms for Molecular Biology 2024 19:7
    Content type: Research Published on:

  11. Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to t...

    Authors: Jyotshna Rajput, Ghanshyam Chandra and Chirag Jain
    Citation: Algorithms for Molecular Biology 2024 19:4
    Content type: Research Published on:

  12. The problem of sequence identification or matching—determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence—is relevant for many imp...

    Authors: Jason Fan, Jamshed Khan, Noor Pratap Singh, Giulio Ermanno Pibiri and Rob Patro
    Citation: Algorithms for Molecular Biology 2024 19:3
    Content type: Research Published on:

  13. The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal wi...

    Authors: Junyan Dai, Tobias Rubel, Yunheng Han and Erin K. Molloy
    Citation: Algorithms for Molecular Biology 2024 19:2
    Content type: Research Published on:

  14. Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed usin...

    Authors: Chengze Shen, Baqiao Liu, Kelly P. Williams and Tandy Warnow
    Citation: Algorithms for Molecular Biology 2023 18:21
    Content type: Research Published on:

  15. Cancer progression and treatment can be informed by reconstructing its evolutionary history from tumor cells. Although many methods exist to estimate evolutionary trees (called phylogenies) from molecular sequ...

    Authors: Yunheng Han and Erin K. Molloy
    Citation: Algorithms for Molecular Biology 2023 18:19
    Content type: Research Published on:

Submission Guidelines

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This Collection welcomes submission of original Research Articles and Reviews. Should you wish to submit a different article type, please read our submission guidelines to confirm that type is accepted by the journal. Articles for this Collection should be submitted via our submission system, Snapp. During the submission process you will be asked whether you are submitting to a Collection, please select "Selected papers from WABI 2023" from the dropdown menu.

Articles will undergo the journal’s standard peer-review process and are subject to all of the journal’s standard policies. Articles will be added to the Collection as they are published.

The Guest Editors have no competing interests with the submissions which they handle through the peer review process. The peer review of any submissions for which the Guest Editors have competing interests is handled by another Editorial Board Member who has no competing interests.