Goldberg's Algorithm for Maximum Flow in Perspective: A Computational Study. - Richard J. Anderson 001; João Carlos Setubal (Network Flows And Matching, 1991)

On the Parallel Implementation of Goldberg's Maximum Flow Algorithm. - Richard J. Anderson 001; João C. Setubal (SPAA, 1992)

Multiple Alignment of Biological Sequences with Gap Flexibility. - Joao Meidanis; João C. Setubal (LATIN, 1995)

A Parallel Implementation of the Push-Relabel Algorithm for the Maximum Flow Problem. - Richard J. Anderson 001; João C. Setubal (J. Parallel Distributed Comput., 1995)

Introduction to computational molecular biology. - João Carlos Setubal; João Meidanis (PWS Publishing Company, 1997)

Augment or Push? A computational study of Bipartite Matching and Unit Capacity Flow Algorithms. - Boris V. Cherkassky; Andrew V. Goldberg; Paul Martin 006; João C. Setubal; Jorge Stolfi (WAE, 1997)

Finding Minimum Congestion Spanning Trees. - Renato Fonseca F. Werneck; João C. Setubal; Arlindo Flávio da Conceição (WAE, 1999)

Finding Minimum Congestion Spanning Trees. - Renato Fonseca F. Werneck; João C. Setubal (ACM J. Exp. Algorithmics, 2000)

A data model for comparative genomics. - Luciano A. Digiampietri; Claudia Bauzer Medeiros; João C. Setubal (WOB, 2003)

A relational database for COG data. - Marcelo Perez; Patrícia Carrião; João C. Setubal (WOB, 2003)

New ways for automatic detection of contaminats in EST projects. - João Piazza; João C. Setubal (WOB, 2003)

A method to determine homologous protein families based on graph cliques and profiles. - Nalvo F. de Almeida Jr.; João C. Setubal; Marcelo de Carvalho; Carlos Juliano M. Viana (WOB, 2004)

Parsing BLAST results to find pseudogenes in bacterial genomes. - Patrícia Carrião; Marcelo Perez; João C. Setubal (WOB, 2004)

A framewok based in Web services orchestration for bioinformatics workflow management. - Luciano A. Digiampietri; Claudia Bauzer Medeiros; João C. Setubal (WOB, 2004)

Brazilian Symposium on Bioinformatics. - João Carlos Setubal; Sergio Verjovski-Almeida (Comput. Biol. Medicine, 2007)

PATRIC: The VBI PathoSystems Resource Integration Center. - E. E. Snyder; N. Kampanya; J. Lu; Eric K. Nordberg; H. R. Karur; Maulik Shukla; Jeetendra Soneja; Y. Tian; Tian Xue; Hyun Seung Yoo; Fengkai Zhang; C. Dharmanolla; et al. (Nucleic Acids Res., 2007)

The Genome Reverse Compiler: an explorative annotation tool. - Andrew S. Warren; João Carlos Setubal (BMC Bioinform., 2009)

Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes. - Kuan Yang; João C. Setubal (BCB, 2010)

The Complexity and Application of Syntactic Pattern Recognition Using Finite Inductive Strings. - Elijah Myers; Paul S. Fisher; Keith Irwin; Jinsuk Baek; João C. Setubal (PRIB, 2010)

A Simulation Tool for the Study of Symmetric Inversions in Bacterial Genomes. - Ulisses Dias; Zanoni Dias; João C. Setubal (RECOMB-CG, 2010)

Missing genes in the annotation of prokaryotic genomes. - Andrew S. Warren; Jeremy S. Archuleta; Wu-chun Feng; João Carlos Setubal (BMC Bioinform., 2010)

Global-scale distributed I/O with ParaMEDIC. - Pavan Balaji; Wu-chun Feng; Heshan Lin; Jeremy S. Archuleta; Satoshi Matsuoka; Andrew S. Warren; João Carlos Setubal; Ewing L. Lusk; Rajeev Thakur; Ian T. Foster; Daniel S. Katz; Shantenu Jha; et al. (Concurr. Comput. Pract. Exp., 2010)

Using inversion signatures to generate draft genome sequence scaffolds. - Zanoni Dias; Ulisses Dias; João C. Setubal (BCB, 2011)

A whole genome simulator of prokaryote genome evolution. - Kuan Yang; João Carlos Setubal (BCB, 2011)

A Cloud Architecture for Bioinformatics Workflows. - Hugo Saldanha; Edward de Oliveira Ribeiro; Maristela Holanda; Aletéia P. F. Araújo; Genaína Nunes Rodrigues; Maria Emília Telles Walter; João Carlos Setubal; Alberto M. R. Dávila (CLOSER, 2011)

Sorting genomes using almost-symmetric inversions. - Zanoni Dias; Ulisses Dias; Lenwood S. Heath; João C. Setubal (SAC, 2012)

SIS: a program to generate draft genome sequence scaffolds for prokaryotes. - Zanoni Dias; Ulisses Dias; João C. Setubal (BMC Bioinform., 2012)

Using Entropy Estimates for DAG-Based Ontologies. - Andrew S. Warren; João C. Setubal (CoRR, 2014)

TCBB Special Section on the Brazilian Symposium on Bioinformatics 2013. - João C. Setubal; Nalvo F. Almeida (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. - David Páez-Espino; I-Min A. Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; Ernest Szeto; Manoj Pillay; Jinghua Huang; Victor M. Markowitz; Torben Nielsen; Marcel Huntemann; T. B. K. Reddy; et al. (Nucleic Acids Res., 2017)

TabPath: interactive tables for metabolic pathway analysis. - Lauro Ângelo Gonçalves de Moraes; Érica Barbosa Felestrino; Renata de Almeida Barbosa Assis; Diogo Matos; Joubert de Castro Lima; Leandro de Araújo Lima; Nalvo F. de Almeida Jr.; João Carlos Setubal; Camila Carrião Machado Garcia; Leandro Márcio Moreira (Bioinform., 2018)

Machine learning meets genome assembly. - Kleber Padovani de Souza; João Carlos Setubal; André Carlos Ponce de Leon Ferreira de Carvalho; Guilherme Oliveira; Annie Chateau; Ronnie Alves (Briefings Bioinform., 2019)

PlantSimLab - a modeling and simulation web tool for plant biologists. - S. Ha; Elena S. Dimitrova; Stefan Hoops; Doaa Altarawy; Mitra Ansariola; D. Deb; Jane Glazebrook; R. Hillmer; Hossameldin Shahin; Fumiaki Katagiri; J. McDowell; Molly Megraw; et al. (BMC Bioinform., 2019)

A computational pipeline for species- and strain-level classification of metagenomic sequences. - Arthur Henrique Barrios Solano; João Carlos Setubal (BSB, 2024)