Structure modeling of a metalloendopeptidase from Corynebacterium pseudotuberculosis. - Luis Guimarães; Natália F. Silva; Anderson Miyoshi; Maria P. C. Schneider; Artur Silva; Vasco Ariston de Carvalho Azevedo; Davi S. B. Brasil; Jerônimo Lameira; Cláudio Nahum Alves (Comput. Biol. Medicine, 2012)

KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa. - Francisco Pereira Lobo; Maíra R. Rodrigues; Gisele O. L. Rodrigues; Heron O. Hilário; Raoni A. Souza; Andreas Tauch; Anderson Miyoshi; Glaura C. Franco; Vasco Ariston de Carvalho Azevedo; Glória R. Franco (Nucleic Acids Res., 2012)

CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands. - Josch Pauling; Richard Röttger; Andreas Tauch; Vasco Ariston de Carvalho Azevedo; Jan Baumbach (Nucleic Acids Res., 2012)

Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles. - Richard Röttger; Prabhav Kalaghatgi; Peng Sun 008; Siomar de Castro Soares; Vasco Ariston de Carvalho Azevedo; Tobias Wittkop; Jan Baumbach (Bioinform., 2013)

On the limits of computational functional genomics for bacterial lifestyle prediction. - Eudes Barbosa; Richard Röttger; Anne-Christin Hauschild; Vasco Ariston de Carvalho Azevedo; Jan Baumbach (GCB, 2014)

The impact of the quality filter for RNA-Seq data over differential expression profile. - Pablo C. Gomes de Sa; Siomar de Castro Soares; Adonney A. de Oliveira Veras; Anne C. Pinto; Luis Guimarães; Vasco Ariston de Carvalho Azevedo; Artur Silva; Rommel Ramos (IWBBIO, 2014)

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. - Nicolas Alcaraz; Josch Pauling; Richa Batra; Eudes Barbosa; Alexander Junge; Anne Christensen; Vasco Ariston de Carvalho Azevedo; Henrik J. Ditzel; Jan Baumbach (BMC Syst. Biol., 2014)

Determining influential miRNA targets in diseases using influence diffusion model. - Joseph Nalluri; Pratip Rana; Vasco Ariston de Carvalho Azevedo; Debmalya Barh; Preetam Ghosh (BCB, 2015)

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology. - Diego C. B. Mariano; Felipe L. Pereira; Edgar L. Aguiar; Letícia de Castro Oliveira; Leandro Benevides; Luis Guimarães; Edson Luiz Folador; Thiago J. Sousa; Preetam Ghosh; Debmalya Barh; Henrique C. P. Figueiredo; Artur Silva; et al. (BMC Bioinform., 2016)

In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. - Edson Luiz Folador; Paulo Vinícius Sanches Daltro de Carvalho; Wanderson Marques Silva; Rafaela Salgado Ferreira; Artur Silva; M. Michael Gromiha; Preetam Ghosh; Debmalya Barh; Vasco Ariston de Carvalho Azevedo; Richard Röttger (BMC Syst. Biol., 2016)

PetriScape - A plugin for discrete Petri net simulations in Cytoscape. - Diogo Almeida; Vasco Ariston de Carvalho Azevedo; Artur Silva; Jan Baumbach (J. Integr. Bioinform., 2016)

Genomic Islands: an overview of current software and future improvements. - Siomar de Castro Soares; Letícia de Castro Oliveira; Arun Kumar Jaiswal; Vasco Ariston de Carvalho Azevedo (J. Integr. Bioinform., 2016)

LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. - Eudes Barbosa; Richard Röttger; Anne-Christin Hauschild; Siomar de Castro Soares; Sebastian Böcker; Vasco Ariston de Carvalho Azevedo; Jan Baumbach (J. Integr. Bioinform., 2017)

A Clustering Approach to Identify Candidates to Housekeeping Genes Based on RNA-seq Data. - Edian F. Franco; Dener Maués; Ronnie Alves; Luis Guimarães; Vasco Ariston de Carvalho Azevedo; Artur Silva; Preetam Ghosh; Jefferson Morais; Rommel Thiago Juca Ramos (BSB, 2019)

Protein-Protein Interactions: An Overview. - Edson Luiz Folador; Sandeep Tiwari; Camila E. Da Paz Barbosa; Syed B. Jamal; Marco Da Costa Schulze; Debmalya Barh; Vasco Ariston de Carvalho Azevedo (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19. - Debmalya Barh; Sandeep Tiwari; Marianna E. Weener; Vasco Ariston de Carvalho Azevedo; Aristóteles Góes-Neto; M. Michael Gromiha; Preetam Ghosh (Comput. Biol. Medicine, 2020)

An immunoinformatics-based designed multi-epitope candidate vaccine (mpme-VAC/STV-1) against Mycoplasma pneumoniae. - Thaís Cristina Vilela Rodrigues; Arun Kumar Jaiswal; Marcela Rezende Lemes; Marcos Vinícius da Silva; Helioswilton Sales-Campos; Luiz Carlos Júnior Alcântara; Sthephane Fraga de Oliveira Tosta; Rodrigo Bentes Kato; Khalid J. Alzahrani; Debmalya Barh; Vasco Ariston de Carvalho Azevedo; Sandeep Tiwari; et al. (Comput. Biol. Medicine, 2022)

Genomic Characterization of Lactobacillus delbrueckii Strains with Probiotics Properties. - Luís Cláudio Lima De Jesus; Flávia Figueira Aburjaile; Thiago De Jesus Sousa; Andrei Giacchetto Felice; Siomar de Castro Soares; Luiz Carlos Júnior Alcântara; Vasco Ariston de Carvalho Azevedo (Frontiers Bioinform., 2022)

PanViTa: Pan Virulence and resisTance analysis. - Diego Lucas Neres Rodrigues; Juan Carlos Ariute; Francielly Morais Rodrigues da Costa; Ana Maria Benko-Iseppon; Debmalya Barh; Vasco Ariston de Carvalho Azevedo; Flávia Figueira Aburjaile (Frontiers Bioinform., 2023)

Immunoinformatics-guided design of a multi-valent vaccine against Rotavirus and Norovirus (ChRNV22). - Amanda de Oliveira Matos; Thaís Cristina Vilela Rodrigues; Sandeep Tiwari; Pedro Henrique dos Santos Dantas; Geraldo Rodrigues Sartori; Vasco Ariston de Carvalho Azevedo; João Herminio Martins Da Silva; Siomar de Castro Soares; Marcelle Silva-Sales; Helioswilton Sales-Campos (Comput. Biol. Medicine, 2023)

Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2. - Fábio Malcher Miranda; Vasco Ariston de Carvalho Azevedo; Rommel Thiago Juca Ramos; Bernhard Y. Renard; Vitor Piro (BMC Bioinform., 2024)