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Selected papers from WABI 2020

New Content ItemEdited by Carl Kingsford and Nadia Pisanti

Algorithms for Molecular Biology is proud to publish the extended proceedings of WABI 2020. 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 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.

View all collections published in Algorithms for Molecular Biology.

  1. Prediction of drug resistance and identification of its mechanisms in bacteria such as Mycobacterium tuberculosis, the etiological agent of tuberculosis, is a challenging problem. Solving this problem requires a ...

    Authors: Hooman Zabeti, Nick Dexter, Amir Hosein Safari, Nafiseh Sedaghat, Maxwell Libbrecht and Leonid Chindelevitch
    Citation: Algorithms for Molecular Biology 2021 16:17
    Content type: Research Published on:

  2. Gene clusters are groups of genes that are co-locally conserved across various genomes, not necessarily in the same order. Their discovery and analysis is valuable in tasks such as gene annotation and predicti...

    Authors: Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi and Michal Ziv-Ukelson
    Citation: Algorithms for Molecular Biology 2021 16:16
    Content type: Research Published on:

  3. In the context of biomarker discovery and molecular characterization of diseases, laser capture microdissection is a highly effective approach to extract disease-specific regions from complex, heterogeneous ti...

    Authors: Leonie Selbach, Tobias Kowalski, Klaus Gerwert, Maike Buchin and Axel Mosig
    Citation: Algorithms for Molecular Biology 2021 16:15
    Content type: Research Published on:

  5. Directed evolution (DE) is a technique for protein engineering that involves iterative rounds of mutagenesis and screening to search for sequences that optimize a given property, such as binding affinity to a ...

    Authors: Trevor S. Frisby and Christopher James Langmead
    Citation: Algorithms for Molecular Biology 2021 16:13
    Content type: Research Published on:

  6. One of the Grand Challenges in Science is the construction of the Tree of Life, an evolutionary tree containing several million species, spanning all life on earth. However, the construction of the Tree of Life i...

    Authors: Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy and Tandy Warnow
    Citation: Algorithms for Molecular Biology 2021 16:12
    Content type: Research Published on:

  7. Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to ob...

    Authors: Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger and Gunnar W. Klau
    Citation: Algorithms for Molecular Biology 2021 16:11
    Content type: Research Published on:

  8. K-mer based methods have become prevalent in many areas of bioinformatics. In applications such as database search, they often work with large multi-terabyte-sized datasets. Storing such large datasets is a de...

    Authors: Amatur Rahman, Rayan Chikhi and Paul Medvedev
    Citation: Algorithms for Molecular Biology 2021 16:10
    Content type: Research Published on:

  9. Mutation trees are rooted trees in which nodes are of arbitrary degree and labeled with a mutation set. These trees, also referred to as clonal trees, are used in computational oncology to represent the mutati...

    Authors: Katharina Jahn, Niko Beerenwinkel and Louxin Zhang
    Citation: Algorithms for Molecular Biology 2021 16:9
    Content type: Research Published on:

  10. Advances in genome sequencing over the last years have lead to a fundamental paradigm shift in the field. With steadily decreasing sequencing costs, genome projects are no longer limited by the cost of raw seq...

    Authors: Thomas Gatter, Sarah von Löhneysen, Jörg Fallmann, Polina Drozdova, Tom Hartmann and Peter F. Stadler
    Citation: Algorithms for Molecular Biology 2021 16:8
    Content type: Research Published on:

  11. Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which...

    Authors: Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela and Christina Boucher
    Citation: Algorithms for Molecular Biology 2021 16:6
    Content type: Research Published on:

  12. The probability of sequencing a set of RNA-seq reads can be directly modeled using the abundances of splice junctions in splice graphs instead of the abundances of a list of transcripts. We call this model gra...

    Authors: Cong Ma, Hongyu Zheng and Carl Kingsford
    Citation: Algorithms for Molecular Biology 2021 16:5
    Content type: Research Published on:

  13. A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. Th...

    Authors: Diego P. Rubert, Fábio V. Martinez and Marília D. V. Braga
    Citation: Algorithms for Molecular Biology 2021 16:4
    Content type: Research Published on:

  15. With an increasing number of patient-derived xenograft (PDX) models being created and subsequently sequenced to study tumor heterogeneity and to guide therapy decisions, there is a similarly increasing need fo...

    Authors: Jens Zentgraf and Sven Rahmann
    Citation: Algorithms for Molecular Biology 2021 16:2
    Content type: Research Published on: