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.
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. 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
Schedule
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.
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
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:
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