Research in Computational Molecular Biology: 23rd Annual International Conference, RECOMB 2019, Washington, DC, USA, May 5-8, 2019, Proceedings PDF
Preview Research in Computational Molecular Biology: 23rd Annual International Conference, RECOMB 2019, Washington, DC, USA, May 5-8, 2019, Proceedings
Lenore J. Cowen (Ed.) 7 6 4 1 Research in Computational 1 I B Molecular Biology N L 23rd Annual International Conference, RECOMB 2019 Washington, DC, USA, May 5–8, 2019 Proceedings 123 Lecture Notes in Bioinformatics 11467 Subseries of Lecture Notes in Computer Science Series Editors Sorin Istrail Brown University, Providence, RI, USA Pavel Pevzner University of California, San Diego, CA, USA Michael Waterman University of Southern California, Los Angeles, CA, USA Editorial Board Members Søren Brunak Technical University of Denmark, Kongens Lyngby, Denmark Mikhail S. Gelfand IITP, Research and Training Center on Bioinformatics, Moscow, Russia Thomas Lengauer Max Planck Institute for Informatics, Saarbrücken, Germany Satoru Miyano University of Tokyo, Tokyo, Japan Eugene Myers Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Marie-France Sagot Université Lyon 1, Villeurbanne, France David Sankoff University of Ottawa, Ottawa, Canada Ron Shamir Tel Aviv University, Ramat Aviv, Tel Aviv, Israel Terry Speed WalterandElizaHallInstituteofMedicalResearch,Melbourne,VIC,Australia Martin Vingron Max Planck Institute for Molecular Genetics, Berlin, Germany W. Eric Wong University of Texas at Dallas, Richardson, TX, USA More information about this series at http://www.springer.com/series/5381 Lenore J. Cowen (Ed.) Research in Computational Molecular Biology 23rd Annual International Conference, RECOMB 2019 – Washington, DC, USA, May 5 8, 2019 Proceedings 123 Editor Lenore J.Cowen TuftsUniversity Cambridge, MA, USA ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notesin Bioinformatics ISBN 978-3-030-17082-0 ISBN978-3-030-17083-7 (eBook) https://doi.org/10.1007/978-3-030-17083-7 LibraryofCongressControlNumber:2019936142 LNCSSublibrary:SL8–Bioinformatics ©SpringerNatureSwitzerlandAG2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodologynow knownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookare believedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictionalclaimsin publishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSwitzerlandAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface This volume contains the 37 extended and short abstracts presented at the 23rd International Conference on Research in Computational Molecular Biology (RECOMB) 2019, which was hosted by the George Washington University in Washington, DC, during May 5–8. These 37 contributions were selected from 175 submissions. There were 204 sub- missions made in total, but after removing submissions that were withdrawn or transferred to other conference tracks at the request of the authors, there were 175 submissions that were ultimately reviewed by the Program Committee (PC). In par- ticular, each of the 175 submissions was assigned to three members of the PC for independent reviews, who in many cases solicited additional advice from external reviewers. Following the initial reviews, final decision were made after an extensive discussionofthesubmissionsamongthemembersofthePC.Reviewsanddiscussions were conducted through the EasyChair Conference Management System. While RECOMB 2019 did not allow parallel submissions, authors of accepted papersweregiventheoptiontopublishshortabstractsintheseproceedingsandsubmit theirfullpaperstoajournal.Inaddition,severalacceptedpaperswereinvitedtosubmit revised manuscripts for consideration for publication in Cell Systems. Papers accepted for oral presentation that were subsequently submitted to a journal are published as short abstracts and were deposited on the preprint server arxiv.org or biorxiv.org. All other papers that appear as long abstracts in the proceedings were invited for sub- missiontotheRECOMB2019specialissueoftheJournalofComputationalBiology. Inadditiontopresentationsofthesecontributedpapers,RECOMB2019featuredsix invitedkeynotetalksgivenbyleadingscientists.ThekeynotespeakerswereCarlosD. Bustamante (Stanford University), Rachel Kolodny (University of Haifa), Franziska Michor(HarvardUniversityandDanaFarberCancerInstitute),MihaiPop(University of Maryland), Eytan Ruppin (US National Cancer Institute), and Alfonso Valencia (Spanish National Bioinformatics Institute, and Barcelona Supercomputing Center). RECOMB 2019 also featured highlight talks of computational biology papers that werepublishedinjournalsduringtheprevious18months.Ofthe43submissionstothe Highlightstrack,10wereselectedfororalpresentationatRECOMB.Therewasalsoa special invited panel session on Genomic Privacy. FourRECOMBSatellitemeetingstookplaceinparalleldirectlyprecedingthemain RECOMB meeting. The RECOMB Genetics Satellite was co-chaired by Itsik Pe’er (Columbia University), Simon Gravel (McGill University), and Seyoung Kim (CarnegieMellonUniversity).TheRECOMBSatelliteWorkshoponMassivelyParallel Sequencing (RECOMB-Seq) was co-chaired by Christina Boucher (University of Florida) and Vikas Bansal (University of California, San Diego). The RECOMB-Computational Cancer Biology Satellite meeting (RECOMB-CCB) was co-chaired by Max Leiserson (University of Maryland) and Rachel Karchin (Johns HopkinsUniversity).TheDREAMmeetingwithRECOMB2019wasco-organizedby vi Preface Laura Heiser (Oregon Health and Science University) and Gustavo Stolovitzky (IBM Research and Icahn School of Medicine at Mount Sinai). The organization of this conference was a dedicated community effort with many colleagues contributing their time and expertise. I thank the Steering Committee for theirinput,especiallythechair,BonnieBerger(MIT), for theirwisdom andguidance, as well as Ben Raphael (Princeton University), the program chair of RECOMB 2018 forhishelp,advice,andsupportthroughouttheprocess.IthankMonaSingh(Princeton University) for chairing the Highlights track, and Rob Patro (Stony Brook University) for chairing the Posters track. I thank co-chairs Max Alekseyev (The George Washington University) and Teresa Przytycka (US National Institutes of Health), and allthemembersoftheirOrganizingCommitteeincludingPavelAvdeyev(TheGeorge Washington University), Rebecca Sarto Basso (University of California, Berkeley), Chanson Benjamin (The George Washington University), Jan Hoinka (US National Institutes of Health), and Damian Wojtowicz (US National Institutes of Health). Damian Wojtowicz also served as chair of the Student Travel Fellowship Award Committee. A very special thanks to Yann Ponty (CNRS/LIX, Ecole Polytechnique) who as chair of the Publications Committee served as proceedings chair for this volume, including chasing down final versions and checking copyright forms and final camera-ready copy. Thanks toall PC members andexternalreviewers who completed their reviews ina very tight timeframedespitetheir busyschedules, theauthors ofthe papers,highlights,andpostersfortheirscientificcontributions,andalltheattendeesfor their enthusiastic participation in the conference. We thank all our conference sponsors for their support, who at press time for this volume included: Akamai Technologies, Computation (MDPI journal), Journal of Computational Biology (Mary Ann Liebert, Inc.), Natera, Springer, and The George Washington University. A very special thanks to our student travel fellowship spon- sors, the US National Science Foundation (NSF) and the International Society for Computational Biology (ISCB). May 2019 Lenore J. Cowen Organization General Chairs Max Alekseyev The George Washington University, USA Teresa Przytycka National Institutes of Health, USA Program Committee Chair Lenore J. Cowen Tufts University, USA Steering Committee Vineet Bafna University of California, San Diego, USA Bonnie Berger (Chair) Massachusetts Institute of Technology, USA Eleazar Eskin University of California, Los Angeles, USA Teresa Przytycka National Institutes of Health, USA Cenk Sahinalp Indiana University, USA Roded Sharan Tel Aviv University, Israel Program Committee Derek Aguiar University of Connecticut, USA Tatsuya Akutsu Kyoto University, Japan Can Alkan Bilkent University, Turkey Rolf Backofen Albert Ludwigs University, Freiburg, Germany Vineet Bafna University of California, San Diego, USA Nuno Bandeira University of California, San Diego, USA Ziv Bar-Joseph Carnegie Mellon University, USA Anastasia Baryshnikova Calico Life Sciences, USA Niko Beerenwinkel ETH Zurich, Switzerland Bonnie Berger Massachusetts Institute of Technology, USA Mathieu Blanchette McGill University, Canada Michael Brudno University of Toronto, Canada Sebastian Böcker Friedrich Schiller University Jena, Germany Tony Capra Vanderbilt University, USA Cedric Chauve Simon Fraser University, Canada Lenore J. Cowen (Chair) Tufts University, USA Nadia El-Mabrouk University of Montreal, Canada Irit Gat-Viks Tel Aviv University, Israel Dario Ghersi University of Nebraska, Omaha, USA Anna Goldenberg Hospital for Sick Kids and University of Toronto, Canada viii Organization Fereydoun Hormozdiari University of California, Davis, USA Sorin Istrail Brown University, USA Tao Jiang University of California, Riverside, USA John Kececioglu University of Arizona, USA Manolis Kellis Massachusetts Institute of Technology, USA Carl Kingsford Carnegie Mellon University, USA Gunnar W. Klau Heinrich Heine University, Düsseldorf, Germany Mehmet Koyuturk Case Western Reserve University, USA Smita Krishnaswamy Yale University, USA Jens Lagergren KTH Royal Institute of Technology, Sweden Mark Leiserson University of Maryland, College Park, USA Ming Li University of Waterloo, Canada Po-Ru Loh Harvard Medical School, USA Paul Medvedev The Pennsylvania State University, USA Bernard Moret EPFL, Switzerland Sara Mostafavi University of British Columbia, Canada Veli Mäkinen University of Helsinki, Finland William Stafford Noble University of Washington, USA Lior Pachter California Institute of Technology, USA Laxmi Parida IBM, USA Robert Patro Stony Brook University, USA Yann Ponty CNRS and École Polytechnique, France Nataša Pržulj University College, London, UK Mireille Régnier CNRS and École Polytechnique, France Knut Reinert Freie Universität Berlin, Germany Cenk Sahinalp Indiana University, USA Michael Schatz Johns Hopkins University, USA Alexander Schönhuth Centrum Wiskunde and Informatica, The Netherlands Russell Schwartz Carnegie Mellon University, USA Roded Sharan Tel Aviv University, Israel Mona Singh Princeton University, USA Donna Slonim Tufts University, USA Sagi Snir University of Haifa, Israel Jens Stoye Bielefeld University, Germany Fengzhu Sun University of Southern California, USA Wing-Kin Sung National University of Singapore, Singapore Ewa Szczurek University of Warsaw, Poland Haixu Tang Indiana University, Bloomington, USA Glen Tesler University of California, San Diego, USA Fabio Vandin University of Padua, Italy Martin Vingron MaxPlanckInstituteforMolecularGenetics,Germany Jérôme Waldispühl McGill University, Canada Tandy Warnow University of Illinois at Urbana-Champaign, USA Sebastian Will University of Vienna, Austria Jinbo Xu Toyota Technological Institute at Chicago, USA Yuzhen Ye Indiana University, Bloomington, USA Organization ix Alex Zelikovsky Georgia State University, USA Jianyang Zeng Tsinghua University, China Louxin Zhang National University of Singapore, Singapore Additional Reviewers Aganezov, Sergey El-Kebir, Mohammed Kockan, Can Alanko, Jarno Ernst, Jason Kovaka, Sam Alkhnbashi, Omer Fischer, Mareike Krug, Joachim Almodaresi, Fatemeh Fleischauer, Markus Kuipers, Jack Altieri, Federico Frishberg, Amit Lafond, Manuel Amodio, Matthew Fröhlich, Holger Lasker, Keren Arvestad, Lars Gambette, Philippe Lee, Heewook Ayati, Marzieh Gaudelet, Thomas Lei, Haoyun Bai, Xin Gervits, Asia Levitan, Anton Balvert, Marleen Gigante, Scott Levovitz, Chaya Ben-Bassat, Ilan Gross, Barak Li, Yue Benner, Philipp Guo, Jun-Tao Lin, Andy Bittremieux, Wout Gursoy, Gamze Lin, Dejun Bruner, Ariel Haiminen, Niina Liu, Jie Budach, Stefan Han, Wontack Liu, Liang Burkhardt, Daniel Harel, Tom Lopez-Rincon, Alejandro Burzykowski, Tomasz Harrison, Robert Lu, Yang Cameron, Christopher He, Liang Ludwig, Marcus Castro, Egbert He, Yuan Lugo-Martinez, Jose Chaisson, Mark Heider, Dominik Ly, Lam-Ha Chen, Yong Heller, David Ma, Cong Cho, Hyunghoon Hescott, Benjamin Maaskola, Jonas Conrad, Tim Hoffmann, Steve Mahmoud, Medhat Costa, Ivan Hormozdiari, Farhad Malcha, Ortal Cowman, Tyler Hou, Lei Malik, Laraib Cristea, Simona Hu, Xiaozhe Malikic, Salem Crovella, Mark Huson, Daniel Malod-Dognin, Noel Csuros, Miklos Huynh, Linh Mandric, Igor Cunial, Fabio Itzhacky, Nitay Marass, Francesco da Silva, Israel Jahn, Katharina Marçais, Guillaume Davila Velderrain, Jose Jain, Siddhartha Mautner, Stefan DeBlasio, Dan Jun, Seong-Hwan Maxwell, Sean Ding, Jun Karpov, Nikolai Mcpherson, Andrew Dirmeier, Simon Kelleher, Jerome Mehringer, Svenja Doerr, Daniel Kim, Jongkyu Mezlini, Aziz Drysdale, Erik Knyazev, Sergey Miladi, Milad Durham, Timothy Kobren, Shilpa Minkin, Ilia Dührkop, Kai Nadimpalli Mohammadi, Shahin
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