Publications and Presentations

Preprints and Publications in Peer-Reviewed Journals

† The authors contributed equally to the work.

  • de Almeida, B. L., Bonidia, R. P., Bole, M., Avila-Santos, A. P., Stadler, P. F., Nunes da Rocha, U., & de Carvalho, A. C. P. L. F. (2026). BioAutoML-FAST: an automated machine-learning platform for reusable and benchmarked biological sequence models. bioRxiv. DOI: 10.64898/2026.04.18.719383. Manuscript under revision at Bioinformatics following a major revision decision.
  • Duan, Y., Santos-Júnior, C. D., Schmidt, T. S., Fullam, A., de Almeida, B. L., Zhu, C., ... & Coelho, L. P. (2024). A catalog of small proteins from the global microbiome. Nature Communications, 15(1), 7563. DOI: 10.1038/s41467-024-51894-6.
  • de Almeida, B. L.†, Avila Santos, A. P.†, Bonidia, R. P., Stadler, P. F., Stefanic, P., Mandic-Mulec, I., ... & de Carvalho, A. C. (2024). BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification. RNA Biology, 21(1), 410-421. DOI: 10.1080/15476286.2024.2329451.
  • Bonidia, R. P., Avila Santos, A. P., de Almeida, B. L., Stadler, P. F., Nunes da Rocha, U., Sanches, D. S., & De Carvalho, A. C. (2022). Information theory for biological sequence classification: A novel feature extraction technique based on Tsallis entropy. Entropy, 24(10), 1398. DOI: 10.3390/e24101398.
  • Bonidia, R. P., Santos, A. P. A., de Almeida, B. L., Stadler, P. F., da Rocha, U. N., Sanches, D. S., & de Carvalho, A. C. (2022). BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria. Briefings in Bioinformatics, 23(4), bbac218. DOI: 10.1093/bib/bbac218.
  • Tavares, D., Barreto, M. C. A., de Almeida, B. L. S., Florentino, B. R., Tetzner, F., Goedert, G., Struchiner, C., Bonidia, R., & de Carvalho, A. Dominique: An AI-powered fact-checking chatbot for democratizing access to reliable information. Oxford Open Digital Health. Accepted for publication.
  • de Almeida, B. L. S.†, Bonidia, R.†, Florentino, B.†, Barreto, M. C. A.†, Constantino, J. L. R.†, Tavares da Silva, D.†, Zwicker, G. G., Rocha, U., Goedert, G., Struchiner, C., & de Carvalho, A. AutoAI Hub: From data to society, democratizing machine learning for everyone. Oxford Open Digital Health. Accepted for publication.

Conference Proceedings

  • de Almeida, B. L. S.†, Queiroz, A. P.†, Santos, A. P. A.†, Bonidia, R. P., da Rocha, U. N., Sanches, D. S., & de Carvalho, A. C. P. D. L. F. (2021, November). Feature importance analysis of non-coding DNA/RNA sequences based on machine learning approaches. In Brazilian Symposium on Bioinformatics (pp. 81-92). Cham: Springer International Publishing. DOI: 10.1007/978-3-030-91814-9_8.

Abstract Presentations

  • Santos, A. P. A., de Almeida, B. L. S., Bole, M., Kamath, S., & Rocha, U. N. A FAIR-by-Design and Standard-Compliant System for Automated Submission of Microbial Genomes to the European Nucleotide Archive. In: VAAM Annual Conference, 2026, Berlin. VAAM Annual Conference, 2026.
  • Borchert, E., Tualla, I. P. B., Ngugi, D. K., de Almeida, B. L. S., Carvalho, A. C. P. L. F., Thies, S., Böhnke-Brandt, S., & Rocha, U. N. From sponges to the sea? Creating functional understanding and sustainable utilization of marine microbiomes in the age of AI. In: VAAM Annual Conference, 2026, Berlin. VAAM Annual Conference, 2026.
  • Bonidia, R. P., Florentino, B. R., Barreto, M. C. A., de Almeida, B. L. S., Constantino, J. L. R., Silva, D. T., Rocha, U. N., Goedert, G. T., Struchiner, C. J., & Carvalho, A. C. P. L. F. AutoAI Hub: From Data to Society, Democratizing Machine Learning for Everyone. In: Human Genome Meeting 2026, 2026, Athens. Human Genome Meeting 2026, 2026.
  • de Almeida, B. L. S., Kamath, S., Santos, A. P. A., Bonidia, R. P., Espindola Hernandez, P., Stadler, P. F., Wierckx, N., Borchert, E., Rother, D., Oliveira, A., Carvalho, A. C. P. L. F., & Rocha, U. N. Combining protein language models with different architectures expands protein family annotation 14.2-fold across 16 million open reading frames from 3,802 environmental metagenomes. In: 20th International Symposium on Microbial Ecology (ISME20), 2026, Auckland. 20th International Symposium on Microbial Ecology (ISME20), 2026.
  • de Almeida, B. L. S., Bonidia, R. P., Bole, M., Santos, A. P. A., Stadler, P. F., Rocha, U. N., & Carvalho, A. C. P. L. F. From sequences to traits: An AI-driven AutoML framework for genome-resolved microbial ecology. In: 20th International Symposium on Microbial Ecology (ISME20), 2026, Auckland. 20th International Symposium on Microbial Ecology (ISME20), 2026.
  • de Almeida, B. L. S., Kamath, S., Santos, A. P. A., Bonidia, R. P., Espindola Hernandez, P., Stadler, P. F., Wierckx, N., Borchert, E., Rother, D., Oliveira, A., Carvalho, A. C. P. L. F., & Rocha, U. N. Different protein language models uncover 23.21% of the functional dark matter across 16 million open reading frames recovered from thousands of environmental metagenomes. In: VAAM Annual Conference, 2026, Berlin. VAAM Annual Conference, 2026.
  • de Almeida, B. L. S., Kamath, S., Santos, A. P. A., Bonidia, R. P., Espindola Hernandez, P., Stadler, P. F., Oliveira, A., Carvalho, A. C. P. L. F., & Rocha, U. N. Unveiling protein domains and families in 183,044 novel orthologs exploring multiple protein language models and over 16 million open reading frames recovered from thousands of terrestrial metagenomes. In: Helmholtz AI Conference, 2025, Messe Karlsruhe. Helmholtz AI Conference, 2025.
  • de Almeida, B. L. S., Kamath, S., Santos, A. P. A., Bonidia, R. P., Espindola Hernandez, P., Stadler, P. F., Oliveira, A., Carvalho, A. C. P. L. F., & Rocha, U. N. Exploration of multiple protein language models and over 16 million open reading frames recovered from thousands of terrestrial metagenomes uncover protein domains and families in 13,486 previously unknown orthologs. In: 17th Symposium on Genetics and Bacterial Ecology, 2025, Graz. 17th Symposium on Genetics and Bacterial Ecology, 2025.
  • Bonidia, R. P., de Almeida, B. L. S., Santos, A. P. A., Goedert, G. T., Rocha, U. N., Struchiner, C. J., Kong, J., & Carvalho, A. C. P. L. F. AutoAI-Pandemics: Democratizing Machine Learning for Analysis, Study, and Control of Epidemics and Pandemics. In: Helmholtz AI Conference, 2024, Düsseldorf. Helmholtz AI Conference 2024, 2024.
  • de Almeida, B. L. S., Kamath, S., Santos, A. P. A., Bonidia, R. P., Stadler, P. F., Wierckx, N., Borchert, E., Rother, D., Oliveira, A., Sanches, D. S., Carvalho, A. C. P. L. F., & Rocha, U. N. HiPfam: Expanding the universe of known protein using large language models. In: Helmholtz AI Conference, 2024, Düsseldorf. Helmholtz AI Conference 2024, 2024.
  • Santos, A. P. A., de Almeida, B. L. S., Bonidia, R. P., Stadler, P. F., Stefanic, P., Mandic-Mulec, I., Rocha, U. N., Sanches, D. S., & Carvalho, A. C. P. L. F. Democratizing Life Sciences Research: How BioDeepFuse May Stimulate Non-computer Scientists to Use Deep Learning. In: Helmholtz AI Conference, 2024, Düsseldorf. Helmholtz AI Conference 2024, 2024.
  • Santos, A. P. A., de Almeida, B. L. S., Bonidia, R. P., Stadler, P. F., Sanches, D. S., Carvalho, A. C. P. L. F., & Rocha, U. N. BioMetaExplorer: democratizing the analysis of non-Coding RNA with multi-omics and data-centric AI. In: Helmholtz AI Conference, 2024, Düsseldorf. Helmholtz AI Conference 2024, 2024.
  • Bonidia, R. P., de Almeida, B. L. S., Santos, A. P. A., Goedert, G. T., Rocha, U. N., Struchiner, C. J., Kong, J., & Carvalho, A. C. P. L. F. AutoAI-Pandemics: Democratizing Machine Learning for Analysis, Study, and Control of Epidemics and Pandemics. In: 8th Global Symposium on Health Systems Research, 2024, Nagasaki. 8th Global Symposium on Health Systems Research, 2024.
  • Santos, A. P. A., de Almeida, B. L. S., Bonidia, R. P., Stadler, P. F., Rocha, U. N., Sanches, D. S., & Carvalho, A. C. P. L. F. Feature Extraction Techniques based on Deep Learning Framework for Enhanced Classification of Non-coding RNA. In: 16th Symposium on Genetics and Bacterial Ecology 2023 (BAGECO 2023), 2023, Copenhagen. New approaches/technologies in microbial ecology, 2023.
  • Bonidia, R. P., Santos, A. P. A., de Almeida, B. L. S., Stadler, P. F., Rocha, U. N., Sanches, D. S., & Carvalho, A. C. P. L. F. BioAutoML: End-to-End Machine Learning Package for Life Sciences. In: 10th FEMS Congress of European Microbiologists, 2023, Hamburg. 10th FEMS Congress of European Microbiologists, 2023.