Workshop on Algorithms in Bioinformatics (WABI) 2023, September 4-6

The Workshop on Algorithms in Bioinformatics (WABI), established in 2001, is one of the major annual conferences on algorithms in bioinformatics.


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 colocated with ACM-BCB 2023.

Important dates

  • Paper submission deadline: May 4, 2023
  • Paper notification: June 8, 2023
  • Camera ready: June 20, 2023
  • Invitations to authors of selected papers for the WABI 2023 series in AMB: July 12, 2023
  • Poster abstract submission deadline: July 14, 2023 (extended)
  • Poster notification: July 17, 2023 (extended)
  • Conference: September 4-6, 2023
  • Extended paper submission deadline (AMB): October 31, 2023


The workshop schedule is now available for download.

Call for papers/posters

Paper submission (closed)

Submissions must be formatted in LaTeX using the LIPIcs style and must not exceed 15 pages excluding references. For details please see the information for authors. Each paper must contain a succinct statement of the issues and of their motivation, a summary of the main results, and a brief explanation of their significance, all accessible to non-specialist readers. All submissions must be made online, through the EasyChair submission system, at:


For scientific information, please contact one of the WABI program committee co-chairs, Aïda Ouangraoua (aida.ouangraoua[at]usherbrooke[dot]ca) or Djamal Belazzougui (dbelazzougui[at]cerist[dot]dz). For organizational information, please refer to the ACM-BCB 2023 website.

You will need to register on the EasyChair web site before submitting. A standard .pdf file must be received by May 4, 2023 (time zone of your choice) in order for your submission to be considered. Re-submission of already submitted papers will be possible until May 9, 2023 (time zone of your choice). Simultaneous submission to another conference with published proceedings is not permitted, but simultaneous submission to a journal is allowed, provided that the authors notify the program chairs; if published in a journal, such a contribution will be published as a short abstract in the WABI proceedings. Depositing in arxiv.org or biorxiv.org is allowed.

By submitting a paper the authors acknowledge that in case of acceptance at least one of the authors must register at ACM-BCB 2023, attend the conference, and present the paper.

Accepted papers will be published in WABI proceedings in the LIPIcs Leibniz International Proceedings in Informatics.

Selected papers will be invited for an extended publication in a thematic series in Algorithms for Molecular Biology (AMB).

Poster submission (closed)

WABI 2023 invites the submission of abstracts of your work for presentation in a poster session. The poster can describe existing published or "in press" research, or can describe new work. Submissions must contain an abstract (about 200 words, plain justified text in 10pt character size, formatted to fit A4: 21 x 29.7 cm, including title, author(s), affiliation, e-mail, a link to the published journal version (if any), and the identity of the presenter (in case of a multi-authored poster), followed by the abstract text. A standard .pdf file must be received by July 14, 2023 (time zone of your choice) in order for your submission to be considered. All submissions must be sent by email to: wabi2023@easychair.org

Program committee

The PC is co-chaired by Aïda Ouangraoua and Djamal Belazzougui.
  • Tatsuya Akutsu, Kyoto University, Japan
  • Jasmijn Baaijens, TU Delft, Netherlands
  • Djamal Belazzougui, CERIST, Algeria (co-chair)
  • Anne Bergeron, Université du Québec à Montréal, Canada
  • Paola Bonizzoni, Universita di Milano-Bicocca, Italy
  • Christina Boucher, University of Florida, USA
  • Marília Braga, Bielefeld University, Germany
  • Cédric Chauve, Simon Fraser University, Canada
  • Rayan Chikhi, CNRS & Institut Pasteur, France
  • Daniel Doerr, University of Duesseldorf, Germany
  • Mohammed El-Kebir, University of Illinois at Urbana-Champaign, USA
  • Nadia El-Mabrouk, University of Montreal, Canada
  • Anna Gambin, Warsaw University, Poland
  • Bjarni Halldorsson, deCODE genetics and Reykjavik University, Iceland
  • Katharina Huber, University of East Anglia, UK
  • Gregory Kucherov, University of Paris Est, France
  • Manuel Lafond, Université de Sherbrooke, Canada
  • Elodie Laine, Sorbonne Université, France
  • Veli Makinen, University of Helsinki, Finland
  • Erin Molloy, University of Maryland College Park, USA
  • Vincent Moulton, University of East Anglia, UK
  • Francesca Nadalin, EMBL-EBI / ITT, Italy, England
  • Gonzalo Navarro, University of Chile, Chile
  • Aïda Ouangraoua, Université de Sherbrooke, Canada (co-chair)
  • Yann Ponty, CNRS & École poly technique, France
  • Teresa Przytycka, NCBI, NIH, USA
  • Nadia Pisanti, University of Pisa, Italy
  • Solon Pissis, CWI Amsterdam, the Netherlands
  • Alberto Policriti, University of Udine, Italy
  • Sven Rahmann, Saarland University, Germany
  • Knut Reinert, FU Berlin, Germany
  • Eric Rivals, LIRMM & Université de Montpellier, France
  • Giovanna Rosone, University of Pisa, Italy
  • Mikaël Salson, Université de Lille, France
  • Alexander Schoenhuth, Bielefeld University, Germany
  • Mingfu Shao, Penn State, US
  • Blerina Sinaimeri, Université Lyon I & INRIA, France
  • Krister Swenson, CNRS & Universite de Montpellier, France
  • Sharma Thankachan, University of Central Florida, USA
  • Alexandru Tomescu, University of Helsinki, Finland
  • Hélène Touzet, CNRS & Université de Lille, France
  • Gianluca Della Vedova, University of Milano-Bicocca, Italy
  • Tomas Vinar, Comenius University, Slovakia
  • Jérôme Waldispühl, McGill University, Canada
  • Tandy Warnow, University of Illinois at Urbana-Champaign, USA
  • Prudence W.H.Wong, University of Liverpool, UK
  • Michal Ziv-Ukelson, Ben Gurion University of the Negev, Israel
  • Louxin Zhang, National University of Singapore, Singapore

Steering committee

Keynote speaker

Teresa Przytycka is a Senior Principal Investigator at the National Center for Biotechnology Information in NLM (National Library of Medicine). The research in her group focuses on computational methods advancing the understanding of biomolecular systems and the emergence of complex phenotypes, such as cancer. Her group also develops new computational approaches to study gene regulation including methods to reconstruct Gene Regulatory Networks, single cell analysis, network-based approaches to study mutational processes in cancer and drug response. In addition to genome-wide systems level analysis, her group develops algorithms that help to utilize HT-SELEX technology for the identification of RNA binding motifs and drug design. In 2021 Przytycka was named a Fellow of the International Society for Computational Biology. She serves as an editor of serval computational biology journals including PloS Computational Biology, Bioinformatics, BMC Algorithms for Molecular Biology, among other journals. She is also a member of the steering committee of Research in Computational Molecular Biology (RECOMB) – one of the most prestigious algorithmic computational biology conferences bridging the areas of computational, mathematical, statistical, and biological sciences.

“Delineating relation between mutagenic signatures, cellular processes, and environment through computational approaches“

Cancer genomes accumulate many somatic mutations resulting from carcinogenic exposures, cancer related aberrations of DNA maintenance machinery, and normal stochastic events. These processes often lead to distinctive patterns of mutations, called mutational signatures. However interpreting mutation patterns represented by such signatures is often challenging. This talk will focus on computational methods to elucidate the relations between mutational signatures and cellular and environmental processes developed in my group. In particular, I will discuss computational methods to untangle the contributions of DNA damage and repair processes to mutation signatures and network based approaches to uncover the interactions between mutational signatures and biological processes.

Highlight talks

This year's WABI will for the first time feature highlight talks presenting recently published works which had or are expected to have a high impact in the field. For this edition, we have invited the following two speakers:
Christina Boucher
  • Pangenome Alignment via Recursive Prefix-free Parsing
  • Based on two papers, respectively presented at DCC 2023 and published in Journal of Computational Biolology (2022)
  • Co-authors: Travis Gagie, Ben Langmead, Marco Oliva, Massimiliano Rossi
Travis Gagie
  • The r-index and friends
  • Based on a paper published in the Journal of the ACM (2020) and subsequent related papers
  • Co-authors: Hideo Bannai, Andrej Baláz, Christina Boucher, Adrián Goga, Simon Heumos, Tomohiro I, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Marco Oliva, Alessia Petescia, Nicola Prezza, Massimiliano Rossi, Jouni Sirén

Accepted papers (in submission order)

  • BATCH-SCAMPP: Scaling phylogenetic placement methods to place many sequences. Eleanor Wedell, Chengze Shen and Tandy Warnow (Full version)
  • EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability. Chengze Shen, Baqiao Liu, Kelly P. Williams and Tandy Warnow (Full version)
  • Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model. Yunheng Han and Erin K. Molloy (Full version)
  • Finding Maximal Exact Matches in Graphs. Nicola Rizzo, Manuel Cáceres and Veli Mäkinen (Full version)
  • Bridging Disparate Views on the DCJ-indel model for a Capping-free Solution to the Natural Distance Problem. Leonard Bohnenkämper
  • Leveraging constraints plus dynamic programming for the large Dollo parsimony problem. Junyan Dai, Tobias Rubel, Yunheng Han and Erin K. Molloy
  • Compression algorithm for colored de Bruijn graphs. Amatur Rahman, Yoann Dufresne and Paul Medvedev (Full version)
  • Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants. Yutong Qiu, Yihang Shen and Carl Kingsford (Full version)
  • Co-linear Chaining on Pangenome Graphs. Jyotshna Rajput, Ghanshyam Chandra and Chirag Jain
  • Acceleration of FM-index Queries Through Prefix-free Parsing. Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher and Travis Gagie (Full version)
  • Making a Network Orchard by Adding Leaves. Leo van Iersel, Mark Jones, Esther Julien and Yukihiro Murakami
  • Automatic exploration of the natural variability of RNA non-canonical geometric patterns with a parameterized sampling technique. Théo Boury, Yann Ponty and Vladimir Reinharz (Full version)
  • Exact Sketch-Based Read Mapping. Tizian Schulz and Paul Medvedev
  • Fulgor: A fast and compact k-mer index for large-scale matching and color queries. Jason Fan, Noor Pratap Singh, Jamshed Khan, Giulio Ermanno Pibiri and Robert Patro (Full version)
  • Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching. Timothé Rouzé, Igor Martayan, Camille Marchet and Antoine Limasset
  • Inferring Temporally Consistent Migration Histories. Mrinmoy Saha Roddur, Sagi Snir and Mohammed El-Kebir
  • Simultaneous reconstruction of duplication episodes and gene-species mappings. Paweł Górecki, Natalia Rutecka, Agnieszka Mykowiecka and Jarosław Paszek
  • Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. Xinyu Gu, Yuanyuan Qi and Mohammed El-Kebir
  • Optimal Subtree Prune and Regraft for Quartet Score in Sub-quadratic Time. Shayesteh Arasti and Siavash Mirarab
  • SparseRNAFolD: Sparse RNA pseudoknot-free Folding including Dangles. Mateo Gray, Sebastian Will and Hosna Jabbari (Full version)
  • Fast, Parallel and Cache-friendly Suffix Array Construction. Jamshed Khan, Tobias Rubel, Laxman Dhulipala, Erin K. Molloy and Robert Patro
  • Reinforcement Learning for Robotic Liquid Handler Planning. Mohsen Ferdosi, Yuejun Ge and Carl Kingsford

Accepted posters

  • Application of Metaheuristic Algorithms for Pharmacokinetic and Pharmacodynamic Parameter Estimation. Shyam Sundar Das and Pritish Ranjan
  • Literature-based Drug Repurposing using Medical Subject Headings terms and Clustering Algorithms. Shyam Sundar Das and Pritish Ranjan
  • A Markov constraint to uniquely identify elementary flux mode weights in unimolecular metabolic networks. Justin G. Chitpin and Theodore J. Perkins
  • Orienting undirected phylogenetic networks to tree-child networks. Shunsuke Maeda, Yusuke Kaneko, Hideaki Muramatsu, Yukihiro Murakami and Momoko Hayamizu
  • Using Ctrl-F to Find Transcription Factor Binding Sites Across Wide Affinity Ranges. Zachery Mielko and Raluca Gordân
  • GEGEE: A pretrained Graph Encoder for Generalized Genomic Embeddings. Ghulam Murtaza, Justin Wagner, Justin Zook and Ritambhara Singh
  • Verkko’s approaches for one-button T2T resolution for diploid human-sized genomes. Dmitry Antipov, Adam Phillippy and Sergey Koren
  • Sa-TTCA: An SVM-based Approach for Tumor T-Cell Antigen Classification Using Features Extracted from Biological Sequencing and Natural Language Processing. Thi-Oanh Tran and Nguyen Quoc Khanh Le
  • EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability. Chengze Shen, Baqiao Liu, Kelly P. Williams and Tandy Warnow
  • Towards a Computational Approach to Quantification of Allele Specific Expression at Population Level. Roberto Pagliarini, Fabio Marroni, Giovanni Gabelli, Gabriele Magris, Gabriele Di Gaspero, Carla Piazza, Michele Morgante and Alberto Policriti
  • Sorting Strings by Flanked Block-Interchanges. Tiantian Li, Haitao Jiang, Binhai Zhu, Lusheng Wang and Daming Zhu
  • Transcript Assembly and Annotations. Bias and Adjustment. Qimin Zhang and Mingfu Shao
  • Inferring Temporally Consistent Migration Histories. Mrinmoy Saha Roddur, Sagi Snir and Mohammed El-Kebir