Publications

Selected

25. B.P. de Almeida, C. Schaub, M. Pagani, S. Secchia, E.E.M. Furlong, A. Stark. Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo. Nature 2024

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. Featured commentary: Alexandra Despang. “Designer enhancers for cell-type-specific gene regulation”. Nature Biotechnology 2024
. Artificial Intelligence cracks code of gene regulation
. Twitter thread

24. F. Reiter*, B.P. de Almeida*, A. Stark. Enhancers display constrained sequence flexibility and context-specific modulation of motif function. Genome Research 2023

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. Decoding the grammar of gene regulation
. Poster at EMBL Conference: Transcription and Chromatin (August 2022)

23. B.P. de Almeida, F. Reiter, M. Pagani, A. Stark. DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers. Nature Genetics 2022

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. Featured commentary: Lin Tang. “Predicting and designing enhancers”. Nature Methods 2022
. Awarded the Life Science Research Award Austria 2022, by ÖGMBT
. Harnessing artificial intelligence to predict and control gene regulation

22. B.P. de Almeida, A.F. Vieira, J. Paredes, M. Bettencourt-Dias, N.L. Barbosa-Morais. Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome. PLoS Computational Biology 2019

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. International media coverage: When a cell's 'fingerprint' can be a weapon against cancer (Science Daily) InfoSalus (ES)) ANSA (IT) il Fatto Quotidiano (IT) TuniseSoir - Tunisia Vaaju - Singapore

21. B.P. de Almeida*, J.D. Apolonio*, A. Binnie, P. Castelo-Branco. Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers. BMC Cancer 2019

Preprints

20. G. Richard*, B.P. de Almeida*, H. Dalla-Torre, C. Blum, L. Hexemer, P. Pandey, S. Laurent, M. Lopez, A. Laterre, M. Lang, U. Şahin, K. Beguir, T. Pierrot. ChatNT: A Multimodal Conversational Agent for DNA, RNA and Protein Tasks. bioRxiv 2024

19. B.P. de Almeida*, H. Dalla-Torre*, G. Richard, C. Blum, L. Hexemer, M. Gélard, P. Pandey, S. Laurent, A. Laterre, M. Lang, U. Şahin, K. Beguir, T. Pierrot. SegmentNT: annotating the genome at single-nucleotide resolution with DNA foundation models. bioRxiv 2024

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. Twitter thread

18. E. Trop*, C.-H. Kao*, M. Polen*, Y. Schiff*, B.P. de Almeida, A. Gokaslan, T. Pierrot, V. Kuleshov. Advancing DNA Language Models: The Genomics Long-Range Benchmark. MLGenX ICLR Workshop 2024

17. J. J. Garau-Luis*, P. Bordes*, L. Gonzalez*, M. Roller, B.P. de Almeida, L. Hexemer, C. Blum, S. Laurent, J. Grzegorzewski, M. Lang, T. Pierrot§, G. Richard§. Multi-modal Transfer Learning between Biological Foundation Models. arXiv 2024

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16. V. Loubiere, B.P. de Almeida, M. Pagani, A. Stark. Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila. bioRxiv 2023

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15. N. Moreno-Marin, G. Marteil, N.C. Fresmann, B.P. de Almeida, K. Dores, R. Fragoso, J. Cardoso, J.B. Pereira-Leal, J.T. Barata, S. Godinho, N.L. Barbosa-Morais, M. Bettencourt-Dias. High prevalence and dependence of centrosome clustering in mesenchymal tumors and leukemia. bioRxiv 2023

14. J.M. Xavier, R. Magno, R. Russell, B.P. de Almeida, A. Jacinta-Fernandes, A. Duarte, M. Dunning, S. Samarajiwa, M. O’Reilly, C.L. Rocha, N. Rosli, B.A.J. Ponder, A.T. Maia. Mapping of cis-regulatory variants by differential allelic expression analysis identifies candidate risk variants and target genes of 27 breast cancer risk loci. medRxiv 2022

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Others

13. S. Boshar, E. Trop, B.P. de Almeida, L. Copoiu, T. Pierrot. Are genomic language models all you need? Exploring genomic language models on protein downstream tasks. Bioinformatics 2024

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12. H. Dalla-Torre, L. Gonzalez, J. Mendoza-Revilla, N.L. Carranza, A.H. Grzywaczewski, F. Oteri, C. Dallago, E. Trop, B.P. de Almeida, H. Sirelkhatim, G. Richard, M. Skwark, K. Beguir, M. Lopez, T. Pierrot. The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics. Nat Methods 2024

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11. J. Mendoza-Revilla, E. Trop, L. Gonzalez, M. Roller, H. Dalla-Torre, B.P. de Almeida, G. Richard, J. Caton, N.L. Carranza, M. Skwark, A. Laterre,K. Beguir, T. Pierrot, M. Lopez. A Foundational Large Language Model for Edible Plant Genomes. Commun Biol 2024

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10. L. Klaus, B.P. de Almeida, A. Vlasova, F. Nemčko, A. Schleiffer, K. Bergauer, L. Hofbauer, M. Rath, A. Stark. Identification and characterization of repressive domains in Drosophila transcription factors. The EMBO Journal 2022

Preprint

9. L. Correia, J.M. Xavier, R. Magno, B.P. de Almeida, F. Esteves, I. Duarte, M. Eldridge, C. Sun, A. Bosma, L. Mittempergher, A. Marreiros, R. Bernards, C. Caldas, S.-F. Chin§ and A.-T. Maia§. Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant. npj Breast Cancer 2022

Preprint

8. J. Conde*, R.A. Pumroy*, C. Baker*, T. Rodrigues*, A. Guerreiro, B.B. Sousa, M.C. Marques, B.P. de Almeida, S. Lee, E.P. Leites, D. Picard, A. Samanta, S.H. Vaz, F. Sieglitz, M. Langini, M. Remke, R. Roque, T. Weiss, M. Weller, Y. Liu, S. Han, F. Corzana, V.A. Morais, C.C. Faria, T. Carvalho, P. Filippakopoulos, B. Snijder, N.L. Barbosa-Morais, V.Y. Moiseenkova-Bell§, and G.J.L. Bernardes§. Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression. ACS Cent. Sci. 2021

7. I. Gomes, B.P. de Almeida, S. Dâmaso, A. Mansinho, I. Correia, S. Henriques, R. Cruz-Duarte, G. Vilhais, P. Félix, P. Alves, P. Corredeira, N.L. Barbosa-Morais, L. Costa, S. Casimiro. Expression of receptor activator of NFkB (RANK) drives stemness and resistance to therapy in ER+HER2- breast cancer. Oncotarget 2020

6. T. Rodrigues, B.P. de Almeida, N.L. Barbosa-Morais, G.J.L. Bernardes. Dissecting celastrol with machine learning to unveil dark pharmacology. Chemical Communications 2019

5. C. Baker, T. Rodrigues, B.P. de Almeida, N.L. Barbosa-Morais, G.J.L. Bernardes. Natural product– drug conjugates for modulation of TRPV1-expressing tumors. Bioorganic & Medicinal Chemistry 2019

4. S. Braun*, M. Enculescu*, S.T. Setty*, M. Cortés-López, B.P. de Almeida, F.X.R. Sutandy, L. Schulz, A. Busch, M. Seiler, S. Ebersberger, N.L. Barbosa-Morais, S. Legewie, J. König, K. Zarnack. Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nature Communications 2018

3. G. Marteil, A. Guerrero, A.F. Vieira, B.P. de Almeida, P. Machado, S. Mendonça, M. Mesquita, B. Villarreal, I. Fonseca, M.E. Francia, K. Dores, N.P. Martins, S.S. Jana, E. Tranfield, N.L. Barbosa- Morais, J. Paredes, D. Pellman, S.A. Godinho, M. Bettencourt-Dias. Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation. Nature Communications 2018

Workshop papers

2. E. Trop, C.-H. Kao, M. Polen, Y. Schiff, B.P. de Almeida, A. Gokaslan, T. Pierrot, V. Kuleshov. Advancing DNA language models: The genomics long-range benchmark. AAAI, LLMs4Bio Workshop 2024

1. S. Boshar , E. Trop, B.P. de Almeida, T. Pierrot. Exploring Genomic Language Models on Protein Downstream Tasks. AAAI, LLMs4Bio Workshop 2024

PhD Thesis

B.P. de Almeida. Decoding the cis-regulatory information of enhancer sequences. 2023

For an automatically updated version, check Google Scholar, PubMed or ORCID.

Softwares

B.P. de Almeida*, N. Saraiva-Agostinho*, N.L. Barbosa-Morais. cTRAP: Identification of candidate causal perturbations from differential gene expression data. R package

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* equal contribution, § shared corresponding author