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 2023
F. Reiter*, B.P. de Almeida*, A. Stark. Enhancers display constrained sequence flexibility and context-specific modulation of motif function. Genome Research 2023
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
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
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
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. bioRxiv 2023
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. bioRxiv 2023
B.P. de Almeida*, N. Saraiva-Agostinho*, N.L. Barbosa-Morais. cTRAP: Identification of candidate causal perturbations from differential gene expression data. R package
* equal contribution § shared corresponding author
Reference compendium of non-redundant TF motifs - Clustering of 6,502 TF motif models from multiple species (mostly focused on Drosophila and human) by similarity to remove redundancy
Check my GitHub account for more details.