WABI 2026

SCOPE

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.

IMPORTANT DATES

  • Paper submission deadline:
    • Abstract deadline: May 11, 2026 (AoE) May 14, 2026 (AoE)
    • Full paper deadline: May 14, 2026 (AoE) May 21, 2026 (AoE)
  • Author notifications: June 25, 2026
  • Camera ready versions of accepted papers due: July 2, 2026
  • Conference: August 31 – September 2, 2026

PAPER SUBMISSION

Submissions must be formatted in LaTeX using the LIPIcs style and must not exceed 15 pages excluding the front page (authors, affiliation, keywords, abstract, …), references and a brief appendix (of up to 5 pages). For details please see the information for authors https://submission.dagstuhl.de/series/details/LIPIcs#author.

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:

https://easychair.org/conferences/?conf=wabi2026

For scientific information, please contact one of the WABI program committee co-chairs, Nadia El-Mabrouk (mabrouk@iro.umontreal.ca) or Fabio Vandin (fabio.vandin@unipd.it). For additional organizational information, please refer to the ALGO 2026 website, or contact the local organizers at algo2026@univaq.onmicrosoft.com.

An abstract of the paper must be received in EasyChair by May 11, 2026 (AoE) in order for your submission to be considered. Submission of full versions for already submitted papers will be possible until May 14, 2026 (AoE). 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 encouraged.

By submitting a paper, the authors acknowledge that, in case of acceptance at least one of the authors must register for WABI 2026 and present the paper.

Accepted papers will be published in the 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).

SUBMISSION LINK

You can submit your work to WABI here.

ACCEPTED PAPERS

  • Junyan Dai and Erin Molloy. Is level-1 blob reconstruction under the network multispecies coalescent easy?
  • Ryosuke Yamano and Tetsuo Shibuya. Improved Approximation Algorithms and Hardness Results for Shortest Common Superstring with Reverse Complements
  • Aurélien Berthier, Emile Benoist, Guillaume Fertin and Géraldine Jean. GSI: A New Approach to the Protein Inference Problem
  • Diego Diaz, Pierfrancesco Martinello, Taku Onodera, Simon Puglisi and Leena Salmela. Contig model for variable-order de Bruijn graphs
  • Arseny Shur, Ido Tziony and Yaron Orenstein. 10-minimizers: a promising class of constant-space minimizers
  • Ke Chen, Abhishek Talesara, Sanchal Thakkar and Mingfu Shao. Minimum flow decomposition guided by saturating subflows
  • Jarno Alanko and Simon Puglisi. Construction of distinct k-mer color sets via set fingerprinting
  • Masahito Tsukahara and Tetsuo Shibuya. Theoretically and Practically Faster Algorithms for Protein Structure Alignment
  • Denys Andrukhovskyi, Martin Madzin, Luca Denti, Tomas Vinar and Broňa Brejová. Efficient Algorithms for Pangenome Personalization
  • Zhezheng Xander Song and Carl Kingsford. Quantum Closest-Pair Search for Biological Sequences via k-mer Distribution Statistics
  • Juan Luque, Arjun Subramanian, Aravind Srinivasan, Salem Malikic and S. Cenk Sahinalp. Exact and Efficient Inference of Tumor Phylogenies via Novel Pruning Techniques
  • Samuel Gardelle, Laurent Bulteau and Yann Ponty. FTP Learning of Sparse, Robust and Interpretable Generative models of RNA evolution
  • Théo Boury, Laurent Bulteau and Yann Ponty. RNA Inverse Folding Under Stacked Base Pairs Maximization
  • Nicola Rizzo and Ragnar Groot Koerkamp. Anchored Edit Distance in O(n log log n)-time using Colinear Chaining
  • Steffen Schüler, Antonia Schmidt and Matthias Müller-Hannemann. Quick 2.0: Efficient Large-Scale DNA Barcode Calling
  • Leonard Bohnenkämper and Daria Frolova. Towards a Unified Exact Solution of Rearrangement Small Parsimony for Natural Genomes
  • Johanna Elena Schmitz and Sven Rahmann. DivQuant: Estimation of Species Richness and Entropy from Small Samples
  • Michał Ciach, Elissavet Zacharopoulou, Michał Startek, Błażej Miasojedow and Panagiotis Alexiou. Discriminative learning of substitution matrices and gap penalties for pairwise alignment of biological sequences
  • Jarno Alanko, Lore Depuydt, Camille Marchet and Simon Puglisi. Fast Set Operations for Compact k-mer Sets
  • Luís Felipe Cunha, Thiago Nascimento, Marília Braga and Jens Stoye. On the complexity of the (l, k)-Median Problems
  • Shane Elder, Guillaume Marçais and Carl Kingsford. Turnpike with Uncertain Measurements: Triangle-Equality Integer Programming with a Deterministic Recovery Guarantee.
  • Moein Karami, Jens Zentgraf and Sven Rahmann. Designing exact k-mer filters based on hits and coverage
  • Ragnar Groot Koerkamp. The anti-lexicographic SUS-anchor: a near-optimal k=1 sampling scheme
  • Gryte Satas, Matthew Myers and Sohrab Shah. Statistical Inconsistency of Error-correction Objectives for Perfect Phylogenies
  • Finn Archinuk and Hosna Jabbari. CoSTAR: Coarse Stem-Topology Alignment of Pseudoknotted RNA Structures by Relation-Constrained Search
  • Manuel Lafond. Constructing Incompatibility Graphs of Pairs of Trees in Optimal Output-Sensitive Time
  • Ariel Bruner and Mona Singh. FBApro: A fast, simple linear transformation for diverse metabolic modeling tasks
  • Jarno Alanko, Elena Biagi and Simon Puglisi. Finimap: fast approximate single-species bacterial pseudoalignment with finimizers
  • Or Zuk. Selecting Chromosomes for Polygenic Traits: Algorithms and Complexity
  • Anna Lisiecka, Adam Cicherski and Norbert Dojer. Reconciling and comparing variation graphs using homology relations
  • Mateo Gray, Sebastian Will and Hosna Jabbari. PRISM: Partition-Function Decomposition into Structural Classes for Hierarchically Constrained RNA Pseudoknot Ensembles

POSTER ABSTRACT SUBMISSION

We invite researchers to submit their latest results that fall into the general area of algorithms in bioinformatics in the form of a poster. Therefore they are requested to submit an abstract that must be in plain text and no longer than 500 words, not including bibliographic references.

You can submit your poster here.

The poster session will be in the afternoon of Wednesday, September 2. The format will be A0 portrait.

At least one author of each accepted poster is required to register for and attend the workshop.

POSTER KEY DATES:

  • Poster submission deadline: August 9, 2026 (AoE) August 16, 2026 (AoE)
  • Notification of poster acceptance: August 16, 2026 (AoE) August 18, 2026 (AoE)

PROGRAM COMMITTEE CHAIRS

  • Nadia El-Mabrouk
  • Fabio Vandin

PROGRAM COMMITTEE

  • Tatsuya Akutsu, Kyoto University
  • Jarno Alanko, University of Helsinki
  • Lorraine Ayad, Brunel University London
  • Broňa Brejová, Comenius University in Bratislava
  • Manuel Cáceres, Aalto University
  • Yao-Ban Chan, The University of Melbourne
  • Panagiotis Charalampopoulos, King’s College London
  • Daniel Doerr, Heinrich Heine University Düsseldorf
  • Mohammed El-Kebir, University of Illinois at Urbana-Champaign
  • Jonas Ellert, DIENS, École Normale Supérieure, Paris, France
  • Anna Gambin, Institute of Informatics, Warsaw University
  • Ragnar Groot Koerkamp, ETH Zurich
  • Momoko Hayamizu, Waseda University
  • Hosna Jabbari, University of Alberta
  • Gregory Kucherov, CNRS/LIGM, France
  • Manuel Lafond , Université de Sherbrooke
  • Benjamin Langmead, Johns Hopkins University
  • Stefano Leucci , University of L’Aquila
  • Yuri Pirola, DISCo, Univ. degli Studi di Milano-Bicocca
  • Solon Pissis, The Cyprus Institute, Cyprus
  • Cinzia Pizzi, University of Padova
  • Nicola Prezza, Ca’ Foscari University
  • Sven Rahmann, Saarland University
  • Leena Salmela, University of Helsinki
  • Mingfu  Shao, Carnegie Mellon University
  • Wing-Kin Sung, Chinese University of Hong Kong
  • Nadia Tahiri, University of Sherbrooke
  • Sharma Thankachan, North Carolina State University, Raleigh
  • Simone Zaccaria, UCL Cancer Institute
  • Meirav Zehavi, Ben-Gurion University
  • Jie Zheng, ShanghaiTech University