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The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes

A. Avila Santos, M. Kabiru Nata’ala, J. Kasmanas, A. Bartholomäus, T. Keller-Costa, S. Jurburg, T. Tal, A. Camarinha-Silva, J. Saraiva, A. Ponce de Leon Ferreira de Carvalho, P. Stadler, D. Sipoli Sanches, and U. Rocha. Animal Microbiome, (October 2023)
DOI: 10.1186/s42523-023-00267-3

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BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classificationA. Avila Santos, B. de Almeida, R. Bonidia, P. Stadler, P. Stefanic, I. Mandic-Mulec, U. Rocha, D. Sanches, and A. de Carvalho. RNA Biology, 21 (1): 410–421 (March 2024)The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomesA. Avila Santos, M. Kabiru Nata’ala, J. Kasmanas, A. Bartholomäus, T. Keller-Costa, S. Jurburg, T. Tal, A. Camarinha-Silva, J. Saraiva, A. Ponce de Leon Ferreira de Carvalho and 3 other author(s). Animal Microbiome, (October 2023)MuDoGeR: Multi-Domain Genome recovery from metagenomes made easyU. Rocha, J. Coelho Kasmanas, R. Kallies, J. Saraiva, R. Toscan, P. Stefanic, M. Bicalho, F. Borim Correa, M. Bastürk, E. Fousekis and 1 other author(s). Molecular Ecology Resources, 24 (2): e13904 (2024)Democratising Artificial Intelligence for Pandemic Preparedness and Global Governance in Latin American and Caribbean CountriesA. de Carvalho, R. Bonidia, J. Kong, M. Dauhajre, C. Struchiner, G. Goedert, P. Stadler, M. Walter, D. Sanches, T. Day and 9 other author(s). (2024)PredicTF: a tool to predict bacterial transcription factors in complex microbial communitiesL. Oliveira Monteiro, J. Saraiva, R. Toscan, P. Stadler, R. Silva-Rocha, and U. da Rocha. (January 2021)StandEnA: a customizable workflow for standardized annotation and generating a presence–absence matrix of proteinsF. Chafra, F. Borim Correa, F. Oni, \. Konu Karakayalı, P. Stadler, and U. Nunes da Rocha. Bioinformatics Advances, (January 2023)Information theory for biological sequence classification: a novel feature extraction technique based on Tsallis entropyR. Bonidia, A. Avila Santos, B. de Almeida, P. Stadler, U. Nunes da Rocha, D. Sanches, and A. De Carvalho. Entropy, 24 (10): 1398 (2022)StandEnA: a customizable workflow for standardized annotation and generating a presence--absence matrix of proteinsF. Chafra, F. Borim Correa, F. Oni, {. Konu Karakayalı, P. Stadler, and U. Nunes da Rocha. Bioinformatics Advances, 3 (1): vbad069 (2023)BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteriaR. Bonidia, A. Santos, B. de Almeida, P. Stadler, U. da Rocha, D. Sanches, and A. de Carvalho. Briefings in Bioinformatics, (June 2022)MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomesM. Nata'ala, A. Avila Santos, J. Coelho Kasmanas, A. Bartholomäus, J. Saraiva, S. Godinho Silva, T. Keller-Costa, R. Costa, N. Gomes, A. Ponce de Leon Ferreira de Carvalho and 3 other author(s). Environ. Microbiome, 17 (1): 57 (November 2022)

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