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Algorithms in Bioinformatics 15Th International Workshop, WABI 2015 Atlanta, GA, USA, September 10–12, 2015 Proceedings Mihai Pop Hélène Touzet (Eds.) Algorithms LNBI 9289 in Bioinformatics 15th International Workshop, WABI 2015 Atlanta, GA, USA, September 10–12, 2015 Proceedings 123 Lecture Notes in Bioinformatics 9289 Subseries of Lecture Notes in Computer Science LNBI 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 LNBI Editorial Board Alberto Apostolico Georgia Institute of Technology, Atlanta, GA, USA 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, 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, Canada Ron Shamir Tel Aviv University, Ramat Aviv, Tel Aviv, Israel Terry Speed Walter and Eliza Hall Institute of Medical Research 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 Mihai Pop • Hélène Touzet (Eds.) Algorithms in Bioinformatics 15th International Workshop, WABI 2015 Atlanta, GA, USA, September 10–12, 2015 Proceedings 123 Editors Mihai Pop Hélène Touzet University of Maryland University of Lille College Park, MD Lille USA France ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notes in Bioinformatics ISBN 978-3-662-48220-9 ISBN 978-3-662-48221-6 (eBook) DOI 10.1007/978-3-662-48221-6 Library of Congress Control Number: 2015946588 LNCS Sublibrary: SL8 – Bioinformatics Springer Heidelberg New York Dordrecht London © Springer-Verlag Berlin Heidelberg 2015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the 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 storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper Springer-Verlag GmbH Berlin Heidelberg is part of Springer Science+Business Media (www.springer.com) Preface This proceedings volume contains papers presented at the Workshop on Algorithms in Bioinformatics 2015 (WABI 2015) that was held at Georgia Technological Institute, Atlanta, Georgia, USA, during September 10–12, 2015. WABI was held in conjunction with the ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). WABI is an annual conference series on all aspects of algorithms and data structures in molecular biology, genomics, and phylogeny data analysis that was first held in 2001. WABI 2015 was sponsored by the ACM Special Interest Group in Bioinformatics (ACM SIGBio), the European Association for The- oretical Computer Science (EATCS), and the International Society for Computational Biology (ISCB). In 2015, a total of 57 manuscripts were submitted to WABI from which 26 were selected for presentation at the conference. Among them 23 were full papers not previously published in journals, and three were short abstracts for papers published simultaneously in journals. The papers were selected based on a thorough review from at least three independent reviewers as well as active discussions between members of the Program Committee. The selected papers cover a wide range of topics from networks, to phylogenetic studies, sequence and genome analysis, comparative genomics, and RNA structure. Extended versions of selected papers will be published in a thematic series in the journal Algorithms for Molecular Biology (AMB), published by BioMed Central. We thank all the authors of submitted papers and the members of the Program Committee for their efforts that made this conference possible and the WABI Steering Committee for help and advice. In particular, we are indebted to the keynote speaker of the conference, Paola Bonizzoni, for her presentation. We are also grateful to Srinivas Aluru and the local Organizing Committee for their help in making WABI a success. September 2015 Mihai Pop Hélène Touzet Organization General Chair Srinivas Aluru Georgia Tech, USA Program Chairs Mihai Pop University of Maryland, USA Hélène Touzet University of Lille, France Program Committee Tatsuya Akutsu Kyoto University, Japan Vikas Bansal University of California San Diego, USA Anne Bergeron Université du Québec à Montreal, Canada Daniel Brown University of Waterloo, Canada Rita Casadio University of Bologna, Italy Kun-Mao Chao National Taiwan University, Taiwan Ting Chen University of Southern California, USA Rayan Chikhi University of Lille, France Nadia El-Mabrouk University of Montreal, Canada Gang Fang Mount Sinai School of Medicine, USA Liliana Florea Johns Hopkins University, USA Anna Gambin Warsaw University, Poland Katharina Huber University of East Anglia, UK Rui Jiang Tsinghua University, China Carl Kingsford Carnegie Mellon University, USA Sergey Koren BNBI/NBACC, USA Vincent Lacroix Université Lyon 1, France Dominique Lavenier CNRS/IRISA, France Ming Li University of Waterloo, Canada Stefano Lonardi UC Riverside, USA Veli Mäkinen University of Helsinki, Finland Paul Medvedev Pennsylvania State University, USA Bernard Moret EPFL, Lausanne, Switzerland Burkhard Morgenstern University of Göttingen, Germany Vincent Moulton University of East Anglia, UK Niranjan Nagarajan Genome Institute of Singapore, Singapore William Stafford Noble University of Washington, USA Laurent Noé University of Lille, France Aïda Ouangraoua University of Sherbrooke, Canada VIII Organization Pierre Peterlongo Inria Rennes-Bretagne-Atlantique, France Adam Phillippy BNBI/NBACC, USA Nadia Pisanti Università di Pisa, Italy Yann Ponty CNRS/LIX, École Polytechnique, France Teresa Przytycka NIH, USA Ben Raphael Brown University, USA Marie-France Sagot Inria Grenoble Rhône-Alpes and Université de Lyon 1, France Cenk Sahinalp Indiana University, USA David Sankoff University of Ottawa, Canada Michael Schatz Cold Spring Harbor Laboratory, USA Russell Schwartz Carnegie Mellon University, USA Jared Simpson Ontario Institute for Cancer Research, Canada Mona Singh Princeton University, USA Andrew Smith University of Southern California, USA Jens Stoye Bielefeld University, Germany Krister Swenson LIRMM, CNRS, Université de Montpellier, France Haixu Tang Indiana University, USA Todd Treangen BNBI/NBACC, USA Jérôme Waldispühl McGill University, Canada Tandy Warnow The University of Illinois at Urbana-Champaign, USA Sebastian Will University of Leipzig, Germany Xiaohui Xie University of California Irvine, USA Dong Xu University of Missouri-Columbia, USA Yuzhen Ye Indiana University, USA Louxin Zhang National University of Singapore, Singapore Xuegong Zhang Tsinghua University, China Michal Ziv-Ukelson Ben-Gurion University of the Negev, Israel WABI Steering Committee Bernard Moret EPFL, Switzerland Vincent Moulton University of East Anglia, UK Jens Stoye Bielefeld University, Germany Tandy Warnow University of Illinois, USA ACM BCB Organizing Committee Srinivas Aluru May D. Wang (Co-chair) Mark Borodovski Ying Xu T.M. Murali Christopher C. Yang Yi Pan Aidong Zhang (Co-chair) Organization IX Additional Reviewers Hind Alhakami Seyed Hamid Mirebrahim Rumen Andonov Brian Ondov Djamal Belazzougui Weihua Pan Xin Chen Solon Pissis Dongyeon Cho Jianghan Qu Matei David Sohini Ramachandran Benjamin Decato Sebastien Roch Piero Fariselli Kristoffer Sahlin Darya Filippova Leena Salmela Alexander Gawronski Alexander Schoenhuth Jean-Pierre Glouzon Jacob Schreiber John Halloran Raunak Shrestha Md Abid Hasan Blerina Sinaimeri Ermin Hodzic Ilan Smoly Jan Hoinka Brad Solomon Guillaume Holley Li Song Yoo-Ah Kim Michał Startek Gunnar W. Klau Linda Sundermann Mateusz Krzysztof Łącki Ramesh Krishnan Pallavoor Suresh Manuel Lafond Haixu Tang Thierry Lecroq Om Thakkar Heewook Lee Philip Uren Mark Leiserson Gabriel Valiente Claire Lemaitre Juexin Wang Yi Li Mathias Weller Jie Liu Bartek Wilczynski Wenxiu Ma Damian Wójtowicz Salem Malikic Yun Wu Pier Luigi Martelli Qiuming Yao Blazej Miasojedow Zhaoxia Yu Paolo Milazzo Meng Zhou Ilia Minkin Abstracts Reference-free Compression of High Throughput Sequencing Data with a Probabilistic de Bruijn Graph Gaëtan Benoit1, Claire Lemaitre1, Dominique Lavenier1, Erwan Drezen1, Thibault Dayris2, Raluca Uricaru2, and Guillaume Rizk1 1 INRIA/IRISA/GenScale, Campus de Beaulieu, 35042 Rennes, France 2 University of Bordeaux, CNRS/LaBRI, 33405, Talence Abstract. Data volumes generated by
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