| DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers BP de Almeida, F Reiter, M Pagani, A Stark Nature genetics 54 (5), 613-624, 2022 | 188 | 2022 |
| Nucleotide Transformer: building and evaluating robust foundation models for human genomics H Dalla-Torre, L Gonzalez, J Mendoza-Revilla, N Lopez Carranza, ... Nature Methods, 1-11, 2024 | 168 | 2024 |
| Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers BP de Almeida, JD Apolónio, A Binnie, P Castelo-Branco BMC cancer 19, 1-12, 2019 | 144 | 2019 |
| Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation G Marteil, A Guerrero, AF Vieira, BP De Almeida, P Machado, ... Nature communications 9 (1), 1258, 2018 | 140 | 2018 |
| Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome BP de Almeida, AF Vieira, J Paredes, M Bettencourt-Dias, ... PLoS computational biology 15 (3), e1006832, 2019 | 58 | 2019 |
| Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis S Braun, M Enculescu, ST Setty, M Cortés-López, BP de Almeida, ... Nature communications 9 (1), 3315, 2018 | 54 | 2018 |
| Allosteric antagonist modulation of TRPV2 by piperlongumine impairs glioblastoma progression J Conde, RA Pumroy, C Baker, T Rodrigues, A Guerreiro, BB Sousa, ... ACS Central Science 7 (5), 868-881, 2021 | 50 | 2021 |
| The nucleotide transformer: Building and evaluating robust foundation models for human genomics. bioRxiv H Dalla-Torre, L Gonzalez, J Mendoza-Revilla, NL Carranza, ... | 48 | 2023 |
| Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo BP de Almeida, C Schaub, M Pagani, S Secchia, EEM Furlong, A Stark Nature 626 (7997), 207-211, 2024 | 47 | 2024 |
| Expression of receptor activator of NFkB (RANK) drives stemness and resistance to therapy in ER+ HER2-breast cancer I Gomes, BP de Almeida, S Dâmaso, A Mansinho, I Correia, S Henriques, ... Oncotarget 11 (19), 1714, 2020 | 28 | 2020 |
| A foundational large language model for edible plant genomes J Mendoza-Revilla, E Trop, L Gonzalez, M Roller, H Dalla-Torre, ... Communications Biology 7 (1), 835, 2024 | 22 | 2024 |
| Enhancers display constrained sequence flexibility and context-specific modulation of motif function F Reiter, BP de Almeida, A Stark Genome Research 33 (3), 346-358, 2023 | 12 | 2023 |
| Advancing dna language models: The genomics long-range benchmark CH Kao, E Trop, MK Polen, Y Schiff, BP de Almeida, A Gokaslan, T Pierrot, ... ICLR 2024 Workshop on Machine Learning for Genomics Explorations, 2024 | 10 | 2024 |
| SegmentNT: annotating the genome at single-nucleotide resolution with DNA foundation models BP de Almeida, H Dalla-Torre, G Richard, C Blum, L Hexemer, M Gélard, ... bioRxiv, 2024.03. 14.584712, 2024 | 10 | 2024 |
| Chatnt: A multimodal conversational agent for dna, rna and protein tasks G Richard, BP de Almeida, H Dalla-Torre, C Blum, L Hexemer, P Pandey, ... bioRxiv, 2024.04. 30.591835, 2024 | 9 | 2024 |
| Natural product–drug conjugates for modulation of TRPV1-expressing tumors C Baker, T Rodrigues, BP de Almeida, NL Barbosa-Morais, ... Bioorganic & Medicinal Chemistry 27 (12), 2531-2536, 2019 | 9 | 2019 |
| Dissecting celastrol with machine learning to unveil dark pharmacology T Rodrigues, BP de Almeida, NL Barbosa-Morais, GJL Bernardes Chemical Communications 55 (45), 6369-6372, 2019 | 9 | 2019 |
| Systematic identification and characterization of repressive domains in Drosophila transcription factors L Klaus, BP de Almeida, A Vlasova, F Nemčko, A Schleiffer, K Bergauer, ... The EMBO Journal 42 (3), e112100, 2023 | 8 | 2023 |
| Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant L Correia, R Magno, JM Xavier, BP de Almeida, I Duarte, F Esteves, ... NPJ breast cancer 8 (1), 71, 2022 | 8 | 2022 |
| DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers BP de Almeida, F Reiter, M Pagani, A Stark bioRxiv, 2021.10. 05.463203, 2021 | 5 | 2021 |
