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Selected papers from WABI 2022

New Content ItemEdited by Christina Boucher and Sven Rahmann

Algorithms for Molecular Biology is proud to publish the extended proceedings of WABI 2022. The conference's scope is:

" 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. This year it is co-located with ALGO 2022. "

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editors declare no competing interests. 


  1. We introduce a new algorithm for constructing the generalized suffix array of a collection of highly similar strings. As a first step, we construct a compressed representation of the matching statistics of the...

    Authors: Zsuzsanna Lipták, Francesco Masillo and Simon J. Puglisi
    Citation: Algorithms for Molecular Biology 2024 19:11
    Content type: Research Published on:

  2. Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequen...

    Authors: Alitzel López Sánchez and Manuel Lafond
    Citation: Algorithms for Molecular Biology 2024 19:6
    Content type: Research Published on:

  4. Although RNA secondary structure prediction is a textbook application of dynamic programming (DP) and routine task in RNA structure analysis, it remains challenging whenever pseudoknots come into play. Since t...

    Authors: Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Yann Ponty and Laurent Bulteau
    Citation: Algorithms for Molecular Biology 2023 18:18
    Content type: Research Published on:

  5. We define two new computational problems in the domain of perfect genome rearrangements, and propose three algorithms to solve them. The rearrangement scenarios modeled by the problems consider Reversal and Bl...

    Authors: Eden Ozeri, Meirav Zehavi and Michal Ziv-Ukelson
    Citation: Algorithms for Molecular Biology 2023 18:17
    Content type: Research Published on:

  6. Homologous recombination between the maternal and paternal copies of a chromosome is a key mechanism for human inheritance and shapes population genetic properties of our species. However, a similar mechanism ...

    Authors: Konstantinn Bonnet, Tobias Marschall and Daniel Doerr
    Citation: Algorithms for Molecular Biology 2023 18:15
    Content type: Research Published on:

    The Correction to this article has been published in Algorithms for Molecular Biology 2023 18:20

  7. Recently we developed a gene orthology inference tool based on genome rearrangements (Journal of Bioinformatics and Computational Biology 19:6, 2021). Given a set of genomes our method first computes all pairwise...

    Authors: Diego P. Rubert and Marília D. V. Braga
    Citation: Algorithms for Molecular Biology 2023 18:14
    Content type: Research Published on:

  9. Many bioinformatics applications involve bucketing a set of sequences where each sequence is allowed to be assigned into multiple buckets. To achieve both high sensitivity and precision, bucketing methods are ...

    Authors: Ke Chen and Mingfu Shao
    Citation: Algorithms for Molecular Biology 2023 18:7
    Content type: Research Published on:

  13. We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the...

    Authors: Taher Mun, Naga Sai Kavya Vaddadi and Ben Langmead
    Citation: Algorithms for Molecular Biology 2023 18:2
    Content type: Software Published on: