Research in Computational Molecular Biology: 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings PDF
Preview Research in Computational Molecular Biology: 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings
Minghua Deng Rui Jiang Fengzhu Sun Xuegong Zhang (Eds.) Research 1 2 in Computational 8 7 I B Molecular Biology N L 17th Annual International Conference, RECOMB 2013 Beijing, China, April 2013 Proceedings 123 Lecture Notes in Bioinformatics 7821 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 Minghua Deng Rui Jiang Fengzhu Sun Xuegong Zhang (Eds.) Research in Computational Molecular Biology 17thAnnual International Conference, RECOMB 2013 Beijing, China,April 7-10, 2013 Proceedings 1 3 SeriesEditors SorinIstrail,BrownUniversity,Providence,RI,USA PavelPevzner,UniversityofCalifornia,SanDiego,CA,USA MichaelWaterman,UniversityofSouthernCalifornia,LosAngeles,CA,USA VolumeEditors MinghuaDeng PekingUniversity,Beijing,China E-mail:[email protected] RuiJiang TsinghuaUniversity,Beijing,China E-mail:[email protected] FengzhuSun UniversityofSouthernCalifornia LosAngeles,CA,USA E-mail:[email protected] XuegongZhang TsinghuaUniversity,Beijing,China E-mail:[email protected] ISSN0302-9743 e-ISSN1611-3349 ISBN978-3-642-37194-3 e-ISBN978-3-642-37195-0 DOI10.1007/978-3-642-37195-0 SpringerHeidelbergDordrechtLondonNewYork LibraryofCongressControlNumber:2013933233 CRSubjectClassification(1998):J.3,H.2.8,G.3,F.2.2,I.5.2,I.6.3-5 LNCSSublibrary:SL8–Bioinformatics ©Springer-VerlagBerlinHeidelberg2013 Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,re-useofillustrations,recitation,broadcasting, reproductiononmicrofilmsorinanyotherway,andstorageindatabanks.Duplicationofthispublication orpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyrightLawofSeptember9,1965, inistcurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Violationsareliable toprosecutionundertheGermanCopyrightLaw. Theuseofgeneraldescriptivenames,registerednames,trademarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelaws andregulationsandthereforefreeforgeneraluse. Typesetting:Camera-readybyauthor,dataconversionbyScientificPublishingServices,Chennai,India Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface The RECOMB conference series — with its full name the Annual International Conference on Research in Computational Molecular Biology — was started in 1997 by Sorin Istrail, Pavel Pevzner, and Michael Waterman. The 17th Annual International Conference on Research in Computational Molecular Biology or RECOMB 2013 was held at Tsinghua University, Beijing, China, hosted by the Bioinformatics Division of Tsinghua National Laboratory for Information Sci- ence andTechnology(TNLIST), TsinghuaUniversity.This volume containsthe 32 extended abstracts selected for oral presentation at RECOMB 2013, which were selected by the Program Committee (PC) out of 167 submissions. Each submission was assigned to at least three reviewers and 14 papers received two reviews and the rest received at least three reviews from the PC or external reviewers invited by PC members. Accepted papers were also invited for sub- mission of an edited journal version to a special issue of the Journal of Compu- tational Biology. Besides the selected talks, this year’s RECOMB conference also featured six invited keynote talks by leading scientists in life sciences aroundthe world.The keynote speakers were Scott Fraser (University of Southern California, USA), Takashi Gojobori (National Institute of Genetics, Japan), Deborah Nickerson (University of Washington, USA), Nadia A. Rosenthal (Monash University in Melbourne, Australia), Chung-I Wu (Beijing Institute of Genomics, Chinese Academy of Sciences, China), and Xiaoliang Sunney Xie (Harvard University, USA). Following a tradition begun with RECOMB 2010, RECOMB 2013 also fea- tured a special track for highlights presenting work that had been published in journals during the last 15 months. Five such highlight talks were selected for oral presentation this year. The success of RECOMB depends on the efforts, dedication, and devotion of many colleagueswho spent countless of hours on the organizationof the con- ference. We thank the PC members and the external reviewers for the timely reviewoftheassignedpapersdespitetheirbusyschedules.Wealsothankallthe authorsforsubmittingtheirexcellentworktoRECOMB.TheSteeringCommit- tee consisting of Vineet Bafna, Serafim Batzoglou, Bonnie Berger, Sorin Istrail, Michal Linial, and Martin Vingron (Chair) gave many excellent suggestions on theorganizationoftheconference.IwouldliketopersonallythankthelocalOr- ganizingCommitteemembersespeciallytheCo-chairsXuegongZhang,Minghua Deng, and Rui Jiang, and the local secretary Zhuwei Joan Zhang for their ef- fortsthatinsuredsmoothcooperationontheadministrativeandlogisticdetails. VariousorganizationsincludingTsinghuaUniversity,TNLIST,theNationalSci- ence Foundation of China (NSFC), the US National Science Foundation (NSF), theInternationalSocietyofComputationalBiology(ISCB),andalltheindustry VI Preface sponsors for their financial support. Mona Singh (Princeton University) helped with the application for the US NSF student support. Finally, we thank the authors of the papers and posters and all the attendees for their enthusiastic participation of the conference. January 2013 Fengzhu Sun Conference Organizations Steering Committee Vineet Bafna University of California, San Diego, USA Serafim Batzoglou Stanford University, USA Bonnie Berger Massachusetts Institute of Technology, USA Sorin Istrail Brown University, USA Michal Linial The Hebrew University of Jerusalem, Israel Martin Vingron Max Planck Institute for Molecular Genetics, Germany (Chair) Conference Chair Xuegong Zhang Tsinghua University, China Program Chair Fengzhu Sun University of Southern California, USA Program Committee Tatsuya Akutsu Kyoto University, Japan Frank Alber University of Southern California, USA Max Alekseyev University of South Carolina, USA Kiyoshi Asai University of Tokyo, Japan Joel Bader Johns Hopkins University, USA Vineet Bafna University of California, San Diego, USA Ziv Bar-Joseph Carnegie Mellon University, USA Nuno Bandeira University of California, San Diego, USA Serafim Batzoglou Stanford University, USA Bonnie Berger Massachusetts Institute of Technology, USA Sebastian B¨ocker Jena University, Demark Michael Brent Washington University, USA Michael Brudno University of Toronto, Canada Dongbo Bu Chinese Academy of Sciences, China Kun-Mao Chao National Taiwan University, Taiwan VIII Conference Organizations Brian Chen Lehigh University, Canada Luonan Chen Chinese Academy of Sciences, China Phoebe Chen La Trobe University, Australia Ting Chen University of Southern California, USA Francis Chin The University of Hong Kong, Hong Kong Minghua Deng Peking University, China Nadia El-Mabrouk University of Montreal, Canada Mikhail Gelfand Institute for Information Transmission Problems RAS, Russia Eran Halperin Tel Aviv University, Israel Si-Min He Chinese Academy of Sciences, China Wen-Lian Hsu Academia Sinica, Taiwan Heng Huang University of Texas, USA Daniel Huson University of Tu¨bingen, Germany Sorin Istrail Brown University, USA Daniel Huson University of Tu¨bingen, Germany Rui Jiang Tsinghua University, China Simon Kasif Boston University, USA Daniel Huson University of Tu¨bingen, Germany Jens Lagergren Royal Institute of Technology, Sweden Doheon Lee Korea Advanced Institute of Science and Technology, Korea Hyunju Lee Gwangju Institute of Science and Technology, Korea Thomas Lengauer MaxPlanckInstituteforInformatics,Germany Lei M Li Chinese Academy of Sciences, China Ming Li University of Waterloo, Canada Yixue Li Shanghai Center for Bioinformation Technology, China Michal Linial Hebrew University, Israel Jinze Liu University of Kenturky, USA Stefano Lonardi University of California, Riverside, USA Satoru Miyano Tokyo University, Japan Bernard Moret Swiss Federal Institutes of Technology, Switzerland William Noble University of Washington, USA Arlindo Oliveira INESC-ID, Portugal Teresa Przytcka NIH NCBI, USA Ben J Raphael Brown University, USA Knut Reinert Freie Universita¨t Berlin, Germany Marie-France Sagot INRIA, France Cenk Sahinalp Simon Fraiser University, Canada Russell Schwartz Carnegie Mellon University, USA Roded Sharan Tel Aviv University, Israel Mona Singh Princeton University, USA Conference Organizations IX Steven Skiena SUNY, USA Andrew Smith University of Southern California, USA Peter Stadler Universita¨t Leipzig, Germany Yuzhen Ye Indiana University, USA Kai Tan University of Iowa, USA Chao Tang Peking University, China Martin Vingron Max Planck Institute for Molecular Genetics, Germany Jerome Waldispuhl McGill University, Canada Lusheng Wang City University of Hong Kong, China Limsoog Wong National University of Singapore, Singapore Xiaohui Xie UC Irvine, USA Dong Xu University of Missouri, USA Yuzhen Ye Indiana University, USA Sungroh Yoon Seoul National University, Korea Shibu Yooseph JCVI, USA Louxin Zhang National University of Singapore, Singapore Michael Q Zhang UT Dallas, USA and Tsinghua University, China Xuegong Zhang Tsinghua University, China Organizing Committee Xuegong Zhang Tsinghua University, China (Co-chair) Minghua Deng Peking University, China (Co-chair) Rui Jiang Tsinghua University, China (Co-chair) Jin Gu Tsinghua University, China Jingdong Han PICB, CAS, China Ruiqiang Li Peking University, China Xuan Li SIBS, CAS, China Yixue Li Shanghai Bioinformatics Center, China Jingchu Luo Peking University, China Geng Tian Tsinghua University, China Xiujie Wang Institute of Genetics and Development, CAS, China Peiheng Zhang Institute of Computing, CAS, China External Reviewers Aguiar, Derek Antipov, Dmitry Bagherian, Misagh Ahrne, Erik Arndt, Peter Bahrami, Emad Aliphanahi, Babak Askenazi, Manot Bandyopadhyay, Andreotti, Sandro Atias, Nir Nirmalya X Conference Organizations Bankevich, Anton Gao, Xin Sofia Baran, Yael Gautheret, Daniel Lacroix, Vincent Baudet, Christian Gitter, Anthony Lam, Henry Bazykin, Yegor Golan, David Le, Hai-Son Becerra, David Guthals, Adrian Lee, Sael Beglov, Dmitri Hach, Faraz Lee, Sejoon Behnam, Ehsan Hajirasouliha, Iman Lee, Sunjae Bernstein, Laurence Halldorsson, Bjarni Lehmann, Kjong Bienkowska, Jadwiga Halloran, John Leiserson, Mark Blin, Guillaume Han, Buhm Lemaitre, Claire Bozdag, Serdar Hao, Xiaolin Leung, Henry Bryant, David Harris, Elena Li, Ning Buske, Orion He, Danning Li, Shuai Cheng Chang, Chia-Jung He, Xin Li, Wei Chen, Ching-Tai He, Zengyou Li, Weizhong Chen, Tiffany He, Zhiquan Liao, Chung-Shou Chen, Yi-Ching Henry, Henry Libbrecht, Max Cheng, Cheng-Wei Hoffman, Michael Lin, Wei-Yin Cheng, Chia-Ying Holtby, Dan Lin, Yen Yi Chiu, Ka Ho Hosur, Raghavendra Liu, Yan Cho, Dongyeon Howbert, Jeff Liu, Yizhou Choi, Jeong-Hyeon Hu, Jialu Love, Michael Choi, Kwok Pui Hu, Yin Lu, Bingwen Chowdhury, Salim Huang, Yan Lynn, Ke-Shiuan Chu, An-Chiang Hwang, Woochang Ma, Bin Clevert, Djork-Arn´e Irannia, Zohreh Ma, Wenxiu Costello, James Jiang, Shuai Ma, Xiaotu Daley, Timothy Joshi, Trupti Madhusudhan, M.S. Daniels, Noah Kaell, Lukas Mahlab, Shelly Dao, Phuong Kalinina, Olga Makeev, Vsevolod David, Matei Kaplan, Tommy Mammana, Alessandro Dieterich, Christoph Katenka, Natallia Markowetz, Florian Dondi, Riccardo Kehr, Birte Marti-Renom, Marc Donmez, Nilgun Khrameeva, Ekaterina Mazza, Arnon Doose, Gero Kim, Yoo-Ah Medvedev, Paul Duma, Denisa Kim, Younghoon Meusel, Marvin Ermakova,Ekaterina Kirkpatrick, Bonnie Mezlini, Aziz Eskin, Itamar Klau, Gunnar W. Mirebrahim, Seyed Fischer, Martina Kochetov, Alex Mironov, Andrey Fiser, Andras Korkin, Dmitry Misra, Navodit Fleischauer, Markus Korobeynikov,Anton Molla, Michael Fr˚anberg, Mattias Kozakov,Dima Navlakha, Saket Fu, Yan Kulikov, Alexander Ng, Kal Yen Kaow Fuentes, Gloria Kyriazopoulou- Nikolenko, Sergey Gao, Jianjiong Panagiotopoulou, Numanagic, Ibrahim
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