Advances in Bioinformatics and Computational Biology: 8th Brazilian Symposium on Bioinformatics, BSB 2013, Recife, Brazil, November 3-7, 2013, Proceedings PDF
Preview Advances in Bioinformatics and Computational Biology: 8th Brazilian Symposium on Bioinformatics, BSB 2013, Recife, Brazil, November 3-7, 2013, Proceedings
João C. Setubal Nalvo F. Almeida (Eds.) Advances 3 in Bioinformatics and 1 2 8 I B Computational Biology N L 8th Brazilian Symposium on Bioinformatics, BSB 2013 Recife, Brazil, November 2013 Proceedings 123 Lecture Notes in Bioinformatics 8213 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 João C. Setubal Nalvo F. Almeida (Eds.) Advances in Bioinformatics and Computational Biology 8thBrazilianSymposiumonBioinformatics,BSB2013 Recife, Brazil, November 3-7, 2013 Proceedings 1 3 VolumeEditors JoãoC.Setubal UniversityofSãoPaulo,InstituteofChemistry AvenidaProf.LineuPrestes,748sala911,05508-000SãoPaulo,SP,Brazil E-mail:[email protected] NalvoF.Almeida FederalUniversityofMatoGrossodoSul,SchoolofComputing Facom-UFMS,CP549,79070-900CampoGrande,MS,Brazil E-mail:[email protected] ISSN0302-9743 e-ISSN1611-3349 ISBN978-3-319-02623-7 e-ISBN978-3-319-02624-4 DOI10.1007/978-3-319-02624-4 SpringerChamHeidelbergNewYorkDordrechtLondon LibraryofCongressControlNumber:2013949541 CRSubjectClassification(1998):J.3,F.2,H.2,I.5,I.2,F.1,I.5 LNCSSublibrary:SL8–Bioinformatics ©SpringerInternationalPublishingSwitzerland2013 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 This volume contains the papers selected for presentation at the 8th Brazilian Symposium on Bioinformatics (BSB 2013), held during November 3–6, 2013, in Recife,Brazil.BSBisaninternationalconferencethatcoversallaspectsofbioin- formatics and computational biology. This year the event was jointly organized by the special interest group in Computational Biology of the Brazilian Com- puter Society (SBC), which has been the organizer of BSB for the past several years, and by the Brazilian Association for Bioinformatics and Computational Biology(AB3C),whichhasbeentheorganizerofanotherevent,theX-Meeeting, also for the past several years. This year for the first time the two events were co-located. As in previous editions, BSB 2013had aninternational ProgramCommittee (PC) of46 members. After a rigorousreview process by the PC, 18 papers were accepted to be orally presented at the event, and are printed in this volume. In addition to the technical presentations, BSB 2013 featured keynote talks from David Roos (University of Pennsylvania), Peter Stadler (University of Leipzig), and Martin Tompa (University of Washington). Peter Stadler graciously con- tributed an invited paper to these proceedings (“The Trouble with Long-Range Base Pairs in RNA Folding”). BSB2013wasmadepossiblebythededicationandworkofmanypeopleand organizations.WewouldliketoexpressoursincerethankstoallPCmembers,as wellastotheexternalreviewers.Theirnamesarelistedinthepagesthatfollow. Wearealsogratefultothelocalorganizersandvolunteersfortheirvaluablehelp; the sponsors for making the event financially viable; Guilherme P. Telles and Peter Stadler for assisting in the preparation of the proceedings; and Springer for agreeing to publish this volume. Finally, we would like to thank all authors for their time and effort in submitting their work and the invited speakers for having accepted our invitation. This yearselected BSB 2013paperswere invitedfor submissionin expanded format to a special issue of the IEEE/ACM Transactions on Computational Biology and Bioinformatics. We thank Ying Xu (Editor-in-Chief) and Dong Xu (Associate Editor-in-Chief) for this opportunity. November 2013 Jo˜ao C. Setubal Nalvo F. Almeida Organization BSB 2013 was organizedby Universidade Federal de Pernambuco. Conference Chairs Katia S. Guimar˜aes Universidade Federal de Pernambuco, Brazil Paulo Gustavo S. Fonseca Universidade Federal de Pernambuco, Brazil Ana Benko Iseppon Universidade Federal de Pernambuco, Brazil Valdir Balbino Universidade Federal de Pernambuco, Brazil Program Chairs Joa˜o C. Setubal Universidade de Sa˜o Paulo, Brazil Nalvo F. Almeida Universidade Federal de Mato Grosso do Sul, Brazil Steering Comittee Guilherme P. Telles (President) Universidade Estadual de Campinas, Brazil Ivan G. Costa Filho Universidade Federal de Pernambuco, Brazil Luis Antonio Kowada Universidade Federal Fluminense, Brazil Marcelo de Macedo Br´ıgido Universidade de Bras´ılia, Brazil Marcilio C.P. de Souto Universit´e d’Orl´eans, France Osmar Norberto de Souza PUC Rio Grande do Sul, Brazil S´ergio Vale Aguiar Campos Universidade Federal de Minas Gerais, Brazil Sponsors Sociedade Brasileira de Computa¸c˜ao (SBC) Associac¸a˜o Brasileira de Bioinform´atica e Biologia Computacional (AB3C) Funding Conselho Nacional de Desenvolvimento Cient´ıfico e Tecnolo´gico (CNPq) Coordena¸c˜ao de Aperfeic¸oamento de Pessoal de N´ıvel Superior (CAPES) Fundac¸a˜o de Amparo a` Ciˆencia e Tecnologia de Pernambuco (FACEPE) VIII Organization Program Committee Said S. Adi Universidade Federal de Mato Grosso do Sul, Brazil Nalvo F. Almeida Universidade Federal de Mato Grosso do Sul, Brazil Fernando A´lvarez-Val´ın Universidad de la Republica, Uruguay Ana L.C. Bazzan Universidade Federal do Rio Grande do Sul, Brazil Ana M. Benko-Iseppon Universidade Federal de Pernambuco, Brazil Mar´ılia D.V. Braga Inmetro, Brazil Marcelo de Macedo Br´ıgido Universidade de Bras´ılia, Brazil Sergio Campos Universidade Federal de Minas Gerais, Brazil Alessandra Carbone Pierre and Marie Curie University, France Ivan Gesteira Costa Universidade Federal de Pernambuco, Brazil Andr´e C.P.L.F. de Carvalho Universidade de Sa˜o Paulo/Sa˜o Carlos, Brazil Marcilio de Souto Universit´e d’Orl´eans, France Emanuel Maltempi de Souza Universidade Federal do Paran´a, Brazil Osmar Norberto de Souza PUC Rio Grande do Sul, Brazil Luciano Digiampietri Universidade de S˜ao Paulo, Brazil Alan Durham Universidade de Sa˜o Paulo, Brazil Carlos E. Ferreira Universidade de Sa˜o Paulo, Brazil Andr´e Fujita Universidade de S˜ao Paulo, Brazil Katia S. Guimar˜aes Universidade Federal de Pernambuco, Brazil Lenny Heath Virginia Tech, USA Dirk Husmeier University of Glasgow, UK Andre Kashiwabara Universidade Tecnol´ogica Federal do Paran´a, Brazil Ney Lemke Universidade Est. Paulista Ju´lio Mesquita Filho, Brazil Sergio Lifschitz PUC Rio de Janeiro, Brazil Ana Carolina Lorena Universidade Federal do ABC, Brazil Wellington Martins Universidade Federal de Goia´s, Brazil Marta Mattoso Universidade Federal do Rio de Janeiro, Brazil Satoru Miyano University of Tokyo, Japan Houtan Noushmehr Universidade de S˜ao Paulo, Brazil Guilherme Oliveira Funda¸c˜ao Oswaldo Cruz, Minas Gerais, Brazil Alexey Onufriev Virginia Tech, USA Miguel Ortega Universidade Federal de Minas Gerais, Brazil Sergio Pantano Instituto Pasteur de Montevideo, Uruguay Alexandre Rossi Paschoal Universidade Tecnolo´gica Federal do Paran´a, Brazil Duncan Ruiz PUC Rio Grande do Sul, Brazil Marie-France Sagot Inria, France Alexander Schliep Rutgers University, USA Organization IX Joa˜o Setubal Universidade de Sa˜o Paulo, Brazil Peter F. Stadler University of Leipzig, Germany Jens Stoye University of Bielefeld, Germany Guilherme P. Telles Universidade Estadual de Campinas, Brazil Thiago Venancio Universidade Federal Fluminense, Brazil Maria Emilia T. Walter Universidade de Bras´ılia, Brazil Additional Reviewers Poly Hannah Da Silva Universidade Federal Fluminense, Brazil Marcelo Henriques de Carvalho Universidade Federal de Mato Grosso do Sul, Brazil Zanoni Dias Universidade Estadual de Campinas, Brazil Marcio Dorn Universidade Federal do Rio Grande do Sul, Brazil Alessandra Faria-Campos Universidade Federal de Minas Gerais, Brazil Sonja Ha¨nzelmann Universitat Pompeu Fabra, Spain Tobias Jakobi University of Bielefeld, Germany Pablo Jaskowiak Universidade de S˜ao Paulo/Sa˜o Carlos, Brazil Thiago Lipinski Paes PUC Rio Grande do Sul, Brazil Fa´bio Viduani Martinez Universidade Federal de Mato Grosso do Sul, Brazil Mariana Mendoza Universidade Federal do Rio Grande do Sul, Brazil Kary Ocan˜a Universidade Federal do Rio de Janeiro, Brazil Luiz Ot´avio Murta Jr Universidade de Sa˜o Paulo/Ribeir˜ao Preto, Brazil Gethin Norman University of Glasgow, UK Yuri Pirola University of Milano-Bicocca, Italy Tain´a Raiol Universidade de Bras´ılia, Brazil Eric Tannier Inria, France Ian Thorpe University of Maryland, USA Table of Contents The Trouble with Long-Range Base Pairs in RNA Folding ............ 1 Fabian Amman, Stephan H. Bernhart, Gero Doose, Ivo L. Hofacker, Jing Qin, Peter F. Stadler, and Sebastian Will Roles of RORα on Transcriptional Expressions in the Mammalian Circadian Regulatory System...................................... 12 Hiroshi Matsuno and Makoto Akashi HybHap: A Fast and Accurate Hybrid Approach for Haplotype Inference on Large Datasets ....................................... 24 Rog´erio S. Rosa and Katia S. Guimar˜aes Restricted DCJ-Indel Model Revisited .............................. 36 Mar´ılia D.V. Braga and Jens Stoye MSA-GPU: Exact Multiple Sequence Alignment Using GPU .......... 47 Daniel Sundfeld and Alba C.M.A. de Melo MultiSETTER - Multiple RNA Structure Similarity Algorithm ........ 59 David Hoksza, Peter Sz´epe, and Daniel Svozil Assessing the Accuracy of the SIRAH Force Field to Model DNA at Coarse Grain Level............................................... 71 Pablo D. Dans, Leonardo Darr´e, Mat´ıas R. Machado, Ari Zeida, Astrid F. Brandner, and Sergio Pantano How to Multiply Dynamic Programming Algorithms ................. 82 Christian H¨oner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler Influence of Scaffold Stability and Electrostatics on Top7-Based Engineered Helical HIV-1 Epitopes................................. 94 Isabelle F.T. Viana, Rafael Dhalia, Marco A. Krieger, Ernesto T.A. Marques, and Roberto D. Lins Random Forest and Gene Networks for Association of SNPs to Alzheimer’s Disease .............................................. 104 Gilderlanio S. Arau´jo, Manuela R.B. Souza, Jo˜ao Ricardo M. Oliveira, Ivan G. Costa, and for the Alzheimer’s Disease Neuroimaging Initiative XII Table of Contents Multilayer Cluster Heat Map Visualizing Biological Tensor Data ....... 116 Atsushi Niida, Georg Tremmel, Seiya Imoto, and Satoru Miyano On the 1.375-Approximation Algorithm for Sorting by Transpositions in O(nlogn) Time ............................................... 126 Lu´ıs Felipe I. Cunha, Luis Antonio B. Kowada, Rodrigo de A. Hausen, and Celina M.H. de Figueiredo ncRNA-Agents: A Multiagent System for Non-coding RNA Annotation...................................................... 136 Wosley Arruda, C´elia G. Ralha, Tain´a Raiol, Marcelo M. Br´ıgido, Maria Em´ılia M.T. Walter, and Peter F. Stadler Inference of Genetic Regulatory Networks Using an Estimation of Distribution Algorithm ........................................... 148 Thyago Salva´, Leonardo R. Emmendorfer, and Adriano V. Werhli A Network-Based Meta-analysis Strategy for the Selection of Potential Gene Modules in Type 2 Diabetes.................................. 160 Ronnie Alves, Marcus Mendes, and Diego Bonnato RAIDER: Rapid Ab Initio Detection of Elementary Repeats........... 170 Nathaniel Figueroa, Xiaolin Liu, Jiajun Wang, and John Karro A Probabilistic Model Checking Analysis of the Potassium Reactions with the Palytoxin and Na+/K+-ATPase Complex ................... 181 Fernando Braz, Jo˜ao Amaral, Bruno Ferreira, Jader Cruz, Alessandra Faria-Campos, and S´ergio Campos False Discovery Rate for Homology Searches......................... 194 Hyrum D. Carroll, Alex C. Williams, Anthony G. Davis, and John L. Spouge A Pipeline to Characterize Virulence Factors in Mycobacterium Massiliense Genome.............................................. 202 Guilherme Meneg´oi, Taina´ Raiol, Jo˜ao Victor de Arau´jo Oliveira, Edans Fla´vius de Oliveira Sandes, Alba Cristina Magalh˜aes Alves de Melo, Andr´ea Queiroz Maranh˜ao, Ildinete Silva-Pereira, Anam´elia Lorenzetti Bocca, Ana Paula Junqueira-Kipnis, Maria Em´ılia M.T. Walter, Andr´e Kipnis, and Marcelo de Macedo Br´ıgido Author Index.................................................. 215
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