Advances in Bioinformatics and Computational Biology: 13th Brazilian Symposium on Bioinformatics, BSB 2020, São Paulo, Brazil, November 23–27, 2020, Proceedings PDF
Preview Advances in Bioinformatics and Computational Biology: 13th Brazilian Symposium on Bioinformatics, BSB 2020, São Paulo, Brazil, November 23–27, 2020, Proceedings
João C. Setubal Waldeyr Mendes Silva (Eds.) Advances 8 5 5 in Bioinformatics and 2 1 I B Computational Biology N L 13th Brazilian Symposium on Bioinformatics, BSB 2020 São Paulo, Brazil, November 23–27, 2020 Proceedings 123 Lecture Notes in Bioinformatics 12558 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 subseries at http://www.springer.com/series/5381 ã Jo o C. Setubal Waldeyr Mendes Silva (Eds.) (cid:129) Advances in Bioinformatics and Computational Biology 13th Brazilian Symposium on Bioinformatics, BSB 2020 ã – S o Paulo, Brazil, November 23 27, 2020 Proceedings 123 Editors João C. Setubal WaldeyrMendesSilva University of SãoPaulo Instituto Federal deGoiás São Paulo, Brazil Formosa, Goiás, Brazil ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notesin Bioinformatics ISBN 978-3-030-65774-1 ISBN978-3-030-65775-8 (eBook) https://doi.org/10.1007/978-3-030-65775-8 LNCSSublibrary:SL8–Bioinformatics ©SpringerNatureSwitzerlandAG2020 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 TheBrazilianSymposiumonBioinformatics (BSB)isaninternational conferencethat covers all aspects of bioinformatics and computational biology. This volume contains the accepted papers for BSB 2020, held virtually during November 23–27, 2020. Asinpastyears,thespecialinterest groupinComputationalBiology(CEbiocomp) of the Brazilian Computer Society (SBC) organized the event. A Program Committee (PC) was incharge ofreviewingsubmitted papers;this year, thePC had46 members. Each submission was reviewed by three PC members. There were two submission tracks:fullpapersandshortpapers.Oneofus(Setubal)supervisedthefullpapertrack, andtheother(MendesdaSilva)supervisedtheshortpapertrack.Inthefullpapertrack, 20 papers were accepted; 5 papers were accepted in theshort paper track. All of them are printed in this volume and were presented orally at the event. In addition to the technical presentations, BSB 2020 featured the following invited speakers, with the respective talk titles: David Roos (University of Pennsylvania, USA), “Cross-silo integration and interrogation of complex biomedical datasets: from genomics to epi- demiology and back again”; Bas E. Dutilh (Utrecht University, The Netherlands), “Metagenomics: from illuminating “dark matter” to modeling the microbiome”; and Jens Stoye (Bielefeld University, Germany), “Searching for Genomic Variants in Multiple Genomes at Once”. Based on PC reviews, we chose the authors of the paper by Gabriel Oliveira et al., “COVID-19 X-ray Image Diagnostic with Deep Neural Networks”, as the recipients oftheBSB2020BestPaperAward.Althoughnotpartoftheselectioncriteria,wewere happytoseethatit turned outthat thispaper addressesoneofthemanytopicsarising from the current COVID-19 pandemic. BSB 2020 was made possible by the dedication and work of many people and organizations.WewouldliketoexpressourthankstoallPCmembers,aswellastothe externalad-hocreviewers.Theirnamesarelistedinthepagesthatfollow.Wearealso grateful to the local organizers and volunteers for their valuable help; to Raquel Minardi for helping out with social media; to the sponsors for making the event financially viable; to the developers of EasyChair (full papers) and JEMS (short papers), which were the systems we used to handle submissions; and Springer for agreeing to publish this volume and their stafffor working with us on its production. 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. November 2020 João C. Setubal Waldeyr Mendes Silva Organization Conference Chair Daniel Cardoso Moraes de Fluminense Federal University, Brazil Oliveira Program Committee Chairs João Carlos Setubal University of São Paulo, Brazil Waldeyr C. Mendes da Instituto Federal de Goiás, Brazil Silva Steering Committee Daniel Cardoso Moraes de Fluminense Federal University, Brazil Oliveira João Carlos Setubal University of São Paulo, Brazil Luis Antonio Kowada Fluminense Federal University, Brazil Natália Florencio Martins Empresa Brasileira de Pesquisa Agropecuária, Brazil Ronnie Alves Instituto Tecnológico Vale, Brazil Sérgio Lifschitz Pontifícia Universidade Católica do Rio de Janeiro, Brazil Sérgio Vale Aguiar Campos Federal University of Minas Gerais, Brazil Tainá Raiol Fundação Oswaldo Cruz, Brazil Waldeyr Mendes Instituto Federal de Goiás, Brazil Program Committee Said Sadique Adi Federal University of Mato Grosso do Sul, Brazil Nalvo Almeida Federal University of Mato Grosso do Sul, Brazil Ronnie Alves ITV Sustainable Development, Brazil Deyvid Amgarten University of São Paulo, Brazil Marilia Braga Bielefeld University, Germany Laurent Brehelin Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, France Marcelo Brigido University of Brasília, Brazil Sérgio Campos Federal University of Minas Gerais, Brazil Andre Carvalho University of São Paulo, Brazil Ricardo Cerri Federal University of Sao Carlos, Brazil Luís Cunha Fluminense Federal University, Brazil Alberto Davila FIOCRUZ-RJ, Brazil Ulisses Dias University of Campinas, Brazil viii Organization Zanoni Dias University of Campinas, Brazil Luciano Antonio University of São Paulo, Brazil Digiampietri Bas E. Dutilh Utrecht University, The Netherlands Andre Fujita University of São Paulo, Brazil Ronaldo Fumio Hashimoto University of São Paulo, Brazil Luis Kowada Fluminense Federal University, Brazil Sergio Lifschitz PUC-RJ, Brazil Felipe Prata Lima Federal Institute of Alagoas, Brazil Fabrício Martins Lopes Federal University of Technology of Paraná, Brazil Felipe A. Louza Federal University of Uberlândia, Brazil Fábio Henrique Viduani Federal University of Mato Grosso do Sul, Brazil Martinez Natalia Martins Embrapa Genetic Research and Biotechnology, Brazil João Meidanis University of Campinas, Brazil Raquel Melo-Minardi Federal University of Minas Gerais, Brazil Jhonatas Monteiro University of São Paulo, Brazil Jefferson Morais Federal University of Pará, Brazil Daniel de Oliveira Fluminense Federal University, Brazil Sergio Pantano Institut Pasteur de Montevideo, Uruguay Alexandre Rossi Paschoal Federal University of Technology of Paraná, Brazil José Patané Butantan Institute, Brazil Daniel Pinheiro University of São Paulo, Brazil David Pires Butantan Institute, Brazil Rommel Ramos Federal University of Pará, Brazil Mariana Federal University of Rio Grande do Sul, Brazil Recamonde-Mendoza Marcel da Câmara Institut Curie, France Ribeiro-Dantas Fernando Luís Barroso Da University of São Paulo, Brazil Silva Thais Amaral e Sousa Instituto Federal de Goiás, Brazil Marcilio de Souto University of Orleans, France Kleber Padovani De Souza Federal University of Pará, Brazil Sadegh Sulaimany University of Kurdistan, Iran Guilherme Telles University of Campinas, Brazil Alessandro Varani São Paulo State University, Brazil Maria Emília Machado University of Brasília, Brazil Telles Walter Additional Reviewers Eloi Araújo Daniel Saad Nogueira Nunes Lucas Oliveira Organization ix Funding Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Brazil Sponsor Sociedade Brasileira de Computação (SBC), Brazil Contents A Classification of de Bruijn Graph Approaches for De Novo Fragment Assembly. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Elvismary Molina de Armas, Maristela Holanda, Daniel de Oliveira, Nalvo F. Almeida, and Sérgio Lifschitz Redundancy Treatment of NGS Contigs in Microbial Genome Finishing with Hashing-Based Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Marcus Braga, Kenny Pinheiro, Fabrício Araújo, Fábio Miranda, Artur Silva, and Rommel Ramos Efficient Out-of-Core Contig Generation . . . . . . . . . . . . . . . . . . . . . . . . . . 25 Julio Omar Prieto Entenza, Edward Hermann Haeusler, and Sérgio Lifschitz In silico Pathogenomic Analysis of Corynebacterium Pseudotuberculosis Biovar Ovis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 Iago Rodrigues Blanco, Carlos Leonardo Araújo, and Adriana Carneiro Folador Assessing the Sex-Related Genomic Composition Difference Using a k-mer-Based Approach: A Case of Study in Arapaima gigas (Pirarucu) . . . 50 Renata Lilian Dantas Cavalcante, Jose Miguel Ortega, Jorge Estefano Santana de Souza, and Tetsu Sakamoto COVID-19 X-ray Image Diagnostic with Deep Neural Networks . . . . . . . . . 57 Gabriel Oliveira, Rafael Padilha, André Dorte, Luis Cereda, Luiz Miyazaki, Maurício Lopes, and Zanoni Dias Classification of Musculoskeletal Abnormalities with Convolutional Neural Networks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Guilherme Tiaki Sassai Sato, Leodécio Braz da Silva Segundo, and Zanoni Dias Combining Mutation and Gene Network Data in a Machine Learning Approach for False-Positive Cancer Driver Gene Discovery. . . . . . . . . . . . . 81 Jorge Francisco Cutigi, Renato Feijo Evangelista, Rodrigo Henrique Ramos, Cynthia de Oliveira Lage Ferreira, Adriane Feijo Evangelista, Andre C. P. L. F. de Carvalho, and Adenilso Simao
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