BioDeepfuse a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification
Anderson Paulo Avila Santos Breno Lívio Silva de Almeida; Robson Parmezan Bonidia; Peter F Stadler; Polonca Štefanič; Ines Mandic-Mulec; Ulisses Nunes da Rocha; Danilo Sipoli Sanches; Andre Carlos Ponce de Leon Ferreira de Carvalho
RNA Biology Philadelphia v. 21, n. 1, p. 1-12, 2024
MuDoGeR multi-domain genome recovery from metagenomes made easy
Ulisses Nunes da Rocha Jonas Coelho Kasmanas; René Kallies; João Pedro Saraiva; Rodolfo Brizola Toscan; Polonca Štefanič; Marcos Fleming Bicalho; Felipe Borim Corrêa; Merve Nida Baştürk; Efthymios Fousekis; Luiz Miguel Viana Barbosa; Julia Plewka; Alexander J Probst; Petr Baldrian; Peter F Stadler; CLUE-TERRA Consortium
Molecular Ecology Resources Hoboken v. 24, n. 2, p. 1-12, Feb. 2024
HumanMetagenomeDB a public repository of curated and standardized metadata for human metagenomes
Jonas Coelho Kasmanas Alexander Bartholomäus; Felipe Borim Corrêa; Tamara 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 Research Oxford : Oxford University Press v. 49, n. D1, p. D743–D750, Jan. 2021
OrtSuite from genomes to prediction of microbial interactions within targeted ecosystem processes
João Pedro Saraiva Alexander Bartholomäus; René Kallies; Marta Gomes; Marcos Bicalho; Jonas Coelho Kasmanas; Carsten Vogt; Antonis Chatzinotas; Peter F Stadler; Oscar Dias; Ulisses Nunes da Rocha
Life Science Alliance Cold Spring Harbor v. 4, n. 12, p. 1-14, 2021
BioAutoML automated feature engineering and metalearning to predict noncoding RNAs in bacteria
Robson Parmezan Bonidia Anderson Paulo Avila Santos; Breno Lívio Silva de Almeida; Peter F Stadler; Ulisses Nunes da Rocha; Danilo Sipoli Sanches; André Carlos Ponce de Leon Ferreira de Carvalho
Briefings in Bioinformatics Oxford v. 23, n. 4, p. 1-13, 2022
Information theory for biological sequence classification a novel feature extraction technique based on Tsallis entropy
Robson Parmezan Bonidia Anderson Paulo Avila Santos; Breno Lívio Silva de Almeida; Peter F Stadler; Ulisses Nunes da Rocha; Danilo Sipoli Sanches; André Carlos Ponce de Leon Ferreira de Carvalho
MarineMetagenomeDB a public repository for curated and standardized metadata for marine metagenomes
Muhammad Kabiru Nata'ala Anderson Paulo Avila Santos; Jonas Coelho Kasmanas; Alexander Bartholomäus; João Pedro Saraiva; Sandra Godinho Silva; Tina Keller-Costa; Rodrigo Costa; Newton Carlos Marcial Gomes; André Carlos Ponce de Leon Ferreira de Carvalho; Peter F Stadler; Danilo Sipoli Sanches; Ulisses Nunes da Rocha
Environmental Microbiome London v. 17, p. 1-10, 2022
The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes
Anderson Paulo Avila Santos Muhammad Kabiru Nata'ala; Jonas Coelho Kasmanas; Alexander Bartholomäus; Tina Keller-Costa; Stephanie D Jurburg; Tamara Tal; Amélia Camarinha-Silva; João Pedro Saraiva; André Carlos Ponce de Leon Ferreira de Carvalho; Peter F Stadler; Danilo Sipoli Sanches; Ulisses Nunes da Rocha