Table Of ContentJoão C. Setubal
Waldeyr Mendes Silva (Eds.)
Advances
8
5
5
in Bioinformatics and
2
1
I
B
Computational Biology
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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
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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
