The Organization Committee (OC) and the Chairs of ALGO 2020 decided to run the conferences online in a virtual way. What is most important is that the scientific activity of the Programme Committees of the ALGO conferences is not suspended or stopped: peer review, accepted papers, camera ready and proceedings will be accomplished as usual. Instructions for authors on how to give their talks online in the virtual room will be provided.
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 ALGO 2020.
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, Nadia Pisanti (email@example.com) or Carl Kingsford (firstname.lastname@example.org). For organizational information, please refer to the ALGO 2020 website.
You will need to register on the EasyChair web site before submitting. A standard .pdf file must be received by May 4, 2020 (time zone of your choice) in order for your submission to be considered. Re-submission of already submitted papers will be possible until May 6, 2020 (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 ALGO 2020, 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).
Near-Linear Time Edit Distance for Indel Channels Arun Ganesh and Aaron Sy. GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs Vijini Mallawaarachchi, Anuradha Wickramarachchi and Yu Lin. Economic Genome Assembly from Low Coverage Illumina and Nanopore Data Thomas Gatter, Sarah von Löhneysen, Polina Drozdova, Tom Hartmann and Peter F. Stadler. Linear Time Construction of Indexable Founder Block Graphs Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri and Alexandru I. Tomescu. Fast lightweight accurate xenograft sorting Jens Zentgraf and Sven Rahmann. Advancing Divide-and-Conquer Phylogeny Estimation using Robinson-Foulds Supertrees Xilin Yu, Thien Le, Sarah Christensen, Erin Molloy and Tandy Warnow. Natural family-free genomic distance Diego P. Rubert, Fábio V. Martinez and Marília D. V. Braga. A graph-theoretic barcode ordering model for linked-reads Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cedric Chauve and Rayan Chikhi. Shape decomposition algorithms for laser capture microdissection Leonie Selbach, Tobias Kowalski, Klaus Gerwert, Maike Buchin and Axel Mosig. Disk compression of k-mer sets Amatur Rahman, Rayan Chikhi and Paul Medvedev. The Longest Run Subsequence Problem Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger and Gunnar W. Klau. Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi and Michal Ziv-Ukelson. The Bourque Distances for Mutation Trees of Cancers Katharina Jahn, Niko Beerenwinkel and Louxin Zhang. Sequence Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations Simone Faro, Domenico Cantone and Arianna Pavone. Fast and Efficient Rmap Assembly using the Bi-labelled de Bruijn Graph Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela and Christina Boucher. Fold family-regularized Bayesian Optimization for Directed Protein Evolution Trevor Frisby and Christopher Langmead. Exact Transcript Quantification over Splice Graph Cong Ma, Hongyu Zheng and Carl Kingsford. Phyolin: Identifying a Linear Perfect Phylogeny in Single-cell DNA Sequencing Data of Tumors Leah Weber and Mohammed El-Kebir. An interpretable classification method for predicting drug resistance in M. tuberculosis Hooman Zabeti, Amir Hosein Safari, Nick Dexter, Nafiseh Sedaghat, Maxwell Libbrecht and Leonid Chindelevitch.
University of California, Davis
Dan's primary interests involve the efficiency of algorithms, particularly for problems in combinatorial optimization and graph theory. These algorithms have been applied to study data security, stable matching, network flow, matroid optimization, string/pattern matching problems, molecular sequence analysis, and optimization problems in population-scale genomics. Currently, he is focused on string and combinatorial problems that arise in computational biology and bioinformatics. He served as chair of the computer science department at UCD from July 2000 until August 2004, and was the founding Editor-in-Chief of The IEEE/ACM Transactions of Computational Biology and Bioinformatics until January 2009.
ETH Zurich, Switzerland, and Institute Cochin Paris, France.
Valentina Boeva graduated from the department of Mechanics and Mathematics of the Lomonosov Moscow State University (MSU) in 2003. She holds a PhD in Biophysics from the Department of Bioengineering and Bioinformatics of MSU, defended in January 2007. Between 2007 and 2015, Valentina Boeva worked as postdoc and research scientist at Ecole Polytechnique and the Curie Institute in Paris, France, developing novel approaches to analyze cancer -omics data. In 2016, she started her research group on Computational Cancer Epigenetics at the Cochin Institute in Paris. She moved to Zurich in 2019 to become an assistant professor at the Computer Science Department of ETH Zürich. The focus of Valentina Boeva's team at ETH is extracting novel biological knowledge and improving cancer survival models using machine learning approaches.
UC Santa Cruz, USA
Erik was born and raised in Kentucky, and then studied quantitative social science and open source software communities at Harvard University. He moved into biology after his graduation, first working on the open source "Polonator" sequencing platform, and later developing Bayesian methods for genotyping and variant calling from short read sequencing data in the 1000 Genomes Project. Erik focused his PhD studies at the Wellcome Sanger Institute and Cambridge University on graphical data structures for the representation of pangenomes. Currently a postdoctoral fellow at the University of California, Santa Cruz, he is scaling these methods to the problem of comparing many large whole genome assemblies. In particular, Erik applying them to create unified representations of the genome assemblies produced in the Human Pangenome Project, where he is a co-chair of the Pangenomes group tasked with the generation of the final project data release.
WABI 2020 proceedings will to be available in the Leibniz International Proceedings in Informatics (LIPIcs) series, at the beginning of the conference. Previous proceedings of WABI appeared in LNCS/LNBI volumes 2149 (WABI 2001, Aarhus), 2452 (WABI 2002, Rome), 2812 (WABI 2003, Budapest), 3240 (WABI 2004, Bergen), 3692 (WABI 2005, Mallorca), 4175 (WABI 2006, Zurich), 4645 (WABI 2007, Philadelphia), 5251 (WABI 2008, Karlsruhe), 5724 (WABI 2009, Philadelphia), 6293 (WABI 2010, Liverpool), 6833 (WABI 2011, Saarbrücken), 7534 (WABI 2012, Ljubljana), 8126 (WABI 2013, Sophia Antipolis), 8701 (WABI 2014, Wroclaw), 9289 (WABI 2015, Atlanta), and 9838 (WABI 2016, Aarhus). As of 2016, they appeared in LIPICS volumes 88 (WABI 2017, Boston), 113 (WABI 2018, Helsinki), and 143 (WABI 2019, Boston).