TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. - Felipe Borim Corrêa; João Pedro Saraiva; Peter F. Stadler; Ulisses Nunes da Rocha (Nucleic Acids Res., 2020)

Feature Importance Analysis of Non-coding DNA/RNA Sequences Based on Machine Learning Approaches. - Breno Lívio Silva de Almeida; Alvaro Pedroso Queiroz; Anderson Paulo Avila Santos; Robson Parmezan Bonidia; Ulisses Nunes da Rocha; Danilo Sipoli Sanches; André Carlos Ponce de Leon Ferreira de Carvalho (BSB, 2021)

HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. - Jonas Coelho Kasmanas; Alexander Bartholomäus; Felipe Borim Corrêa; Tamara L. Tal; Nico Jehmlich; Gunda Herberth; Martin von Bergen; Peter F. Stadler; André Carlos Ponce de Leon Ferreira de Carvalho; Ulisses Nunes da Rocha (Nucleic Acids Res., 2021)

BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria. - Robson Bonidia; Anderson P. Avila-Santos; Breno Lívio Silva de Almeida; Peter F. Stadler; Ulisses Nunes da Rocha; Danilo Sipoli Sanches; André C. P. L. F. de Carvalho (Briefings Bioinform., 2022)

Information Theory for Biological Sequence Classification: A Novel Feature Extraction Technique Based on Tsallis Entropy. - Robson Parmezan Bonidia; Anderson P. Avila-Santos; Breno Lívio Silva de Almeida; Peter F. Stadler; Ulisses Nunes da Rocha; Danilo Sipoli Sanches; André C. P. L. F. de Carvalho (Entropy, 2022)

Genomic and phylogenetic analysis of plant growth-promoting bacteria. - Marcus Vinicius da Silva Rodrigues; João Paulo de Oliveira; Sandriele Aparecida Noriler; Angelo Barreiro Garcia; Ulisses de Pádua Pereira; Ulisses Nunes da Rocha; Admilton Gonçalves de Oliveira Junior; Glaucia Maria Bressan (BSB, 2024)

Democratising Artificial Intelligence for Pandemic Preparedness and Global Governance in Latin American and Caribbean Countries. - André C. P. L. F. de Carvalho; Robson Bonidia; Jude Dzevela Kong; Mariana Dauhajre; Cláudio José Struchiner; Guilherme Tegoni Goedert; Peter F. Stadler; Maria Emília M. T. Walter; Danilo Sipoli Sanches; Troy Day; Marcia Castro; John Edmunds; et al. (CoRR, 2024)

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery. - Ulisses Nunes da Rocha; Jonas Coelho Kasmanas; Rodolfo Toscan; Danilo Sipoli Sanches; Stefanía Magnúsdóttir; João Pedro Saraiva (PLoS Comput. Biol., 2024)