Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings PDF
Preview Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings
Aaron Darling Jens Stoye (Eds.) Algorithms 6 2 1 8 I in Bioinformatics B N L 13th International Workshop, WABI 2013 Sophia Antipolis, France, September 2013 Proceedings 123 Lecture Notes in Bioinformatics 8126 EditedbyS.Istrail,P.Pevzner,andM.Waterman EditorialBoard: A.Apostolico S.Brunak M.Gelfand T.Lengauer S.Miyano G.Myers M.-F.Sagot D.Sankoff R.Shamir T.Speed M.Vingron W.Wong Subseries of Lecture Notes in Computer Science Aaron Darling Jens Stoye (Eds.) Algorithms in Bioinformatics 13th International Workshop, WABI 2013 Sophia Antipolis, France, September 2-4, 2013 Proceedings 1 3 VolumeEditors AaronDarling UniversityofTechnologySydney ithreeinstitute Ultimo,NSW2007,Australia E-mail:[email protected] JensStoye BielefeldUniversity FacultyofTechnology Universitätsstraße25 33615Bielefeld,Germany E-mail:[email protected] ISSN0302-9743 e-ISSN1611-3349 ISBN978-3-642-40452-8 e-ISBN978-3-642-40453-5 DOI10.1007/978-3-642-40453-5 SpringerHeidelbergNewYorkDordrechtLondon LibraryofCongressControlNumber:2013945447 CRSubjectClassification(1998):F.2,J.3,G.2.2,F.1,I.2.6,H.2.8,G.1.2 LNCSSublibrary:SL8–Bioinformatics ©Springer-VerlagBerlinHeidelberg2013 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof thematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped.Exemptedfromthislegalreservationarebriefexcerptsinconnection withreviewsorscholarlyanalysisormaterialsuppliedspecificallyforthepurposeofbeingenteredand executedonacomputersystem,forexclusiveusebythepurchaserofthework.Duplicationofthispublication orpartsthereofispermittedonlyundertheprovisionsoftheCopyrightLawofthePublisher’slocation, initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Permissionsforuse maybeobtainedthroughRightsLinkattheCopyrightClearanceCenter.Violationsareliabletoprosecution undertherespectiveCopyrightLaw. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Whiletheadviceandinformationinthisbookarebelievedtobetrueandaccurateatthedateofpublication, neithertheauthorsnortheeditorsnorthepublishercanacceptanylegalresponsibilityforanyerrorsor omissionsthatmaybemade.Thepublishermakesnowarranty,expressorimplied,withrespecttothe materialcontainedherein. Typesetting:Camera-readybyauthor,dataconversionbyScientificPublishingServices,Chennai,India Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface It is our great pleasure to present the proceedings of the 13th Workshop on Algorithms in Bioinformatics (WABI 2013), held at Sophia Antipolis, France, September 2–4, 2013. The WABI 2013 workshop was part of the seven ALGO 2013 conference meetings, which included ESA, IPEC, WAOA, ALGOSEN- SORS,MASSIVE,andATMOS.WABI2013washostedbyINRIAandCampus SophiaTech, and sponsored by the European Association for Theoretical Com- puterScience(EATCS)andtheInternationalSocietyforComputationalBiology (ISCB). See http://algo2013.inria.fr/wabi.shtmlfor more details. The Workshop on Algorithms in Bioinformatics highlights research in algo- rithmicworkforbioinformatics,computationalbiologyandsystemsbiology.The emphasis is mainly on discrete algorithms and machine-learning methods that address important problems in molecular biology, that are founded on sound models,thatarecomputationallyefficient,andthathavebeenimplementedand testedinsimulationsandonrealdatasets.Thegoalis topresentrecentresearch results,including significantwork-in-progress,andto identify andexploredirec- tions of future research. Original research papers (including significant work-in-progress)or state-of- the-art surveys were solicited for WABI 2013 in all aspects of algorithms in bioinformatics, computational biology and systems biology. In response to our call, we received 61 submissions for papers and 27 were accepted. In addition, WABI2013hostedapostersessionandadistinguishedlecturebyBernardMoret, ofE´colePolytechniqueF´ed´eralede Lausanne(EPFL),Switzerland. Prof.Moret founded the WABI series 13 years ago and provided leadership to expand the meeting over the past 13 years. Last year Prof. Moret stepped down from his position of steering the meeting and formed a Steering Committee to facilitate the workshop’s continued success. We would like to sincerely thank the authors of all submitted papers and the conference participants. We also thank the Program Committee and their sub-referees for their hard work in reviewing, discussing, and selecting papers for this year’s workshop. July 2013 Aaron Darling Jens Stoye Organization Steering Committee Bernard Moret EPFL, Switzerland Vincent Moulton University of East Anglia, UK Jens Stoye Bielefeld University, Germany Tandy Warnow The University of Texas at Austin, USA Program Committee Mohamed Abouelhoda Cairo University, Egypt Tatsuya Akutsu Kyoto University, Japan Anne Bergeron University of Quebec at Montreal, Canada Paola Bonizzoni Universita` di Milano-Bicocca, Italy Guillaume Bourque McGill University, Canada Marilia Braga Inmetro - Ditel, Brazil C. Titus Brown Michigan State University, USA Daniel Brown University of Waterloo, Canada David Bryant University of Otago, New Zealand Philipp Bucher Swiss Institute for Experimental Cancer Research, Switzerland Sebastian B¨ocker Friedrich Schiller University Jena, Germany Rita Casadio UNIBO, Italy Cedric Chauve Simon Fraser University, Canada Benny Chor Tel Aviv University, Israel Lachlan Coin The University of Queensland, Australia Lenore Cowen Tufts University, USA Keith Crandall George Washington University, USA Aaron Darling University of Technology Sydney, Australia Nadia El-Mabrouk University of Montreal, Canada Eleazar Eskin University of California, Los Angeles, USA Liliana Florea Johns Hopkins University, USA Martin Frith CBRC, AIST, Japan Anna Gambin Warsaw University, Poland Olivier Gascuel LIRMM, CNRS - University of Montpellier 2, France Nicholas Hamilton The University of Queensland, Australia Barbara Holland University of Tasmania, Australia Katharina Huber University of East Anglia, UK Carl Kingsford Carnegie Mellon University, USA Jinyan Li University of Technology Sydney, Australia VIII Organization Zsuzsanna Lipta´k University of Verona, Italy Stefano Lonardi UC Riverside, USA Ion Mandoiu University of Connecticut, USA Giovanni Manzini University of Eastern Piedmont, Italy Paul Medvedev Pennsylvania State University, USA Joao Meidanis UniversityofCampinas/ScyllaBioinformatics, Brazil Istvan Miklos Renyi Institute, Hungary Satoru Miyano University of Tokyo, Japan Bernard Moret EPFL, Switzerland Burkhard Morgenstern University of G¨ottingen, Germany Vincent Moulton University of East Anglia, UK Gene Myers MPI Cell Biology and Genetics, Germany Veli M¨akinen University of Helsinki, Finland Luay Nakhleh Rice University, USA Nadia Pisanti UniversityofPisa, Italyand LeidenUniversity, The Netherlands Teresa Przytycka NIH, USA Sven Rahmann University of Duisburg-Essen, Germany Ben Raphael Brown University, USA Knut Reinert FU Berlin, Germany Marie-France Sagot INRIA Grenoble Rhoˆne-Alpes and Universit´e de Lyon 1, Villeurbanne, France S. Cenk Sahinalp Simon Fraser University, Canada David Sankoff University of Ottawa, Canada Russell Schwartz Carnegie Mellon University, USA Joao Setubal University of Sa˜o Paulo, Brazil Saurabh Sinha University of Illinois, USA Jens Stoye Bielefeld University, Germany Krister Swenson Universit´e de Montr´eal / McGill University, Canada Jijun Tang University of South Carolina, USA Eric Tannier INRIA, France Glenn Tesler University of California, San Diego, USA Lusheng Wang City University of Hong Kong, China Yuzhen Ye Indiana University, USA Louxin Zhang National University of Singapore, Singapore Michal Ziv-Ukelson Ben-Gurion University of the Negev, Israel Additional Reviewers Aiche, Stephan Cicalese, Ferdinando Badr, Ghada Conrad, Tim Biller, Priscila D’Addario, Marianna Chateau, Annie Dao, Phuong Organization IX Dittwald, Piotr Pinhas, Tamar Donmez, Nilgun Pizzi, Cinzia Drori, Hagai Polishko, Anton Duggal, Geet Rizzi, Raffaella Duma, Denisa Sadakane, Kunihiko Goldberg, Tatyana Scheubert, Kerstin Gorecki, Pawel Scornavacca, Celine Hazelhurst, Scott Sheridan, Paul Higashi, Susan Sinaimeri, Blerina Hormozdiari, Farhad Snir, Sagi Hufsky, Franziska Startek, Micha(cid:4)l Kluge, Bogusl(cid:4)aw Tomescu, Alexandru Kocsis, Levente Wang, Zhanyong Lacroix, Vincent White, Walton Timothy James Leoncini, Mauro Wohlers, Inken Marino, Andrea Yakhini, Zohar McPherson, Andrew Yasuda, Tomohiro Mirebrahim, Seyed Yue, Feng Oesper, Layla Zakov, Shay Pardi, Fabio Zanetti, Jo˜ao Paulo Pereira Pardini, Giovanni L(cid:4) acki, Mateusz (cid:2) Patterson, Murray Table of Contents Extending the Reach of Phylogenetic Inference....................... 1 Bernard M.E. Moret Protein(Multi-)LocationPrediction:UsingLocationInter-dependencies in a Probabilistic Framework ...................................... 3 Ramanuja Simha and Hagit Shatkay Towards Reliable Automatic Protein Structure Alignment............. 18 Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, and Ming Li A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions ........................................ 33 Arnon Mazza, Irit Gat-Viks, Hesso Farhan, and Roded Sharan Faster Mass Decomposition ....................................... 45 Kai Du¨hrkop, Marcus Ludwig, Marvin Meusel, and Sebastian B¨ocker On NP-Hardness of the Paired de Bruijn Sound Cycle Problem ........ 59 Evgeny Kapun and Fedor Tsarev Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing ......................................................... 70 Denisa Duma, Mary Wootters, Anna C. Gilbert, Hung Q. Ngo, Atri Rudra, Matthew Alpert, Timothy J. Close, Gianfranco Ciardo, and Stefano Lonardi A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths ...................... 85 Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, and Veli M¨akinen A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data ................... 99 Gustavo Sacomoto, Vincent Lacroix, and Marie-France Sagot Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures............................................. 112 Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, and Peter F. Stadler XII Table of Contents Faster Algorithms for RNA-Folding Using the Four-Russians Method ... 126 Balaji Venkatachalam, Dan Gusfield, and Yelena Frid Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree ............................... 141 Jesper Jansson, Chuanqi Shen, and Wing-Kin Sung The Generalized Robinson-Foulds Metric............................ 156 Sebastian B¨ocker, Stefan Canzar, and Gunnar W. Klau Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time .................................................. 170 Constantinos Tsirogiannis and Brody Sandel Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs .................................................. 185 Sudheer Vakati and David Fern´andez-Baca Unifying ParsimoniousTree Reconciliation .......................... 200 Nicolas Wieseke, Matthias Bernt, and Martin Middendorf Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes ............................. 215 Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, and Son Pham On the Matrix Median Problem.................................... 230 Jo˜ao Paulo Pereira Zanetti, Priscila Biller, and Jo˜ao Meidanis A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications............................................ 244 Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz, and Irena Rusu MSARC: Multiple Sequence Alignment by Residue Clustering ......... 259 Micha(cid:2)l Modzelewski and Norbert Dojer Mutual Enrichment in Ranked Lists and the Statistical Assessment of Position Weight Matrix Motifs..................................... 273 Limor Leibovich and Zohar Yakhini Probabilistic Approaches to Alignment with Tandem Repeats.......... 287 Michal N´an´asi, Toma´ˇs Vinaˇr, and Bronˇa Brejov´a Multiscale Identification of Topological Domains in Chromatin......... 300 Darya Filippova, Rob Patro, Geet Duggal, and Carl Kingsford Modeling Intratumor Gene Copy Number Heterogeneity Using Fluorescence in Situ Hybridization Data ............................ 313 Charalampos E. Tsourakakis
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