[PAPER REGISTRATION HERE]

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.

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 ALGO 2020.

Important Dates

  • Paper submission deadline: May 18, 2020
  • Notification: June 29, 2020
  • Camera ready: July 10, 2020
  • Conference: September 7 - 9, 2020, in Pisa, Italy

Call For Papers

Paper Submission

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:

https://easychair.org/conferences/?conf=wabi2020

For scientific information, please contact one of the WABI program committee co-chairs, Nadia Pisanti (pisanti@di.unipi.it) or Carl Kingsford (carlk@cs.cmu.edu). 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.

Proceedings

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).

Programme Committee

  • Tatsuya Akutsu, Kyoto University, Japan
  • Carl Barton, EBI, UK
  • Anne Bergeron, Universite du Quebec a Montreal, Canada
  • Paola Bonizzoni, Università di Milano-Bicocca, Italy
  • Christina Boucher, University of Florida, USA
  • Alessandra Carbone, Université Pierre et Marie Curie, France
  • Rayan Chikhi, Pasteur Institute, France
  • Lenore Cowen, Tufts University, USA
  • Gianluca Della Vedova, University of Milano-Bicocca, Italy
  • Nadia El-Mabrouk, University of Montreal, Canada
  • Anna Gambin, Warsaw University, Poland
  • Raffaele Giancarlo, University of Palermo, Italy
  • Dan Gusfield, UC Davis, USA
  • Bjarni Halldorsson, deCODE genetics and Reykjavik University, Iceland
  • Katharina Huber, University of East Anglia, UK
  • Carl Kingsford, Carnegie Mellon University, USA (co-chair)
  • Gunnar Klau, Heinrich Heine University Düsseldorf, Germany
  • Gregory Kucherov, University of Paris Est, France
  • Ritu Kundu, National University of Singapore, Singapore
  • Manuel Lafond, Université de Sherbrooke, Canada
  • Stefano Lonardi, University of California Riverside, USA
  • Veli Makinen, University of Helsinki, Finland
  • Guillaume Marçais, Carnegie Mellon University, USA
  • Tobias Marschall, Heinrich Heine University, Düsseldorf, Germany
  • Bernard Moret, Ecole Polytechnique Fédérale de Lausanne, Switzerland
  • Vincent Moulton, University of East Anglia, UK
  • Luay Nakhleh, Rice University, USA
  • William Stafford, Noble University of Washington, USA
  • Nadia Pisanti, University of Pisa, Italy (co-chair)
  • Solon Pissis, CWI Amsterdam, the Netherlands
  • Alberto Policriti, University of Udine, Italy
  • Mihai Pop, University of Maryland, USA
  • Teresa Przytycka NCBI, NIH, USA
  • Sven Rahmann, University of Duisburg-Essen, Germany
  • Knut Reinert, FU Berlin, Germany
  • Eric Rivals, LIRMM - Université de Montpellier, France
  • Giovanna Rosone, University of Pisa, Italy
  • Marie-France Sagot, INRIA Rhône-Alpes, France
  • Alexander Schoenhuth, Bielefeld University, Germany
  • Jens Stoye, Bielefeld University, Germany
  • Krister Swenson, CNRS & Université de Montpellier, France
  • Sharma Thankachan, University of Central Florida, USA
  • Alexandru Tomescu, University of Helsinki, Finland
  • Hélène Touzet, CNRS, CRIStAL Lille, France
  • Esko Ukkonen, University of Helsinki, Finland
  • Tomas Vinar, Comenius University, Slovakia
  • Tandy Warnow, University of Illinois at Urbana-Champaign, USA
  • Prudence W.H.Wong, University of Liverpool, UK
  • Louxin Zhang, National University of Singapore, Singapore
  • Michal Ziv-Ukelson, Ben Gurion University of the Negev, Israel

Accepted papers

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.

ALGO PLENARY KEYNOTE SPEAKER

Dan Gusfield

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.

WABI INVITED SPEAKERS

Valentina Boeva

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.

Erik Garrison

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.