de Almeida, Bernardo P.

Nucleotide Transformer: building and evaluating robust foundation models for human genomics

Dalla-Torre, H., Gonzalez, L., Mendoza-Revilla, J., Lopez Carranza, N., Grzywaczewski, A. H., Oteri, F., Dallago, C., Trop, E., de Almeida, B. P., Sirelkhatim, H., et al. (2025) · Nature Methods

Machine Learning in BioinformaticsGenetic Associations and Epidemiology

Cited by 772

The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Dalla-Torre, H., Gonzalez, L., Mendoza Revilla, J., Lopez Carranza, N., Henryk Grywaczewski, A., Oteri, F., Dallago, C., Trop, E., De Almeida, B. P., Sirelkhatim, H., et al. (2023) · Nature Methods

Machine Learning in BioinformaticsGenomics and Phylogenetic Studies

Cited by 680

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers

de Almeida, B. P., Reiter, F., Pagani, M., & Stark, A. (2021) · Nature Genetics

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 284

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

de Almeida, B. P., Reiter, F., Pagani, M., & Stark, A. (2022) · Nature Genetics

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 283

Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo

de Almeida, B. P., Schaub, C., Pagani, M., Secchia, S., Furlong, E. E. M., & Stark, A. (2024) · Nature

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 87

Are genomic language models all you need? Exploring genomic language models on protein downstream tasks

Boshar, S., Trop, E., de Almeida, B. P., Copoiu, L., & Pierrot, T. (2024) · Bioinformatics

Machine Learning in BioinformaticsGenomics and Phylogenetic Studies

Cited by 16

Are Genomic Language Models All You Need? Exploring Genomic Language Models on Protein Downstream Tasks

Boshar, S., Trop, E., de Almeida, B. P., Copoiu, L., & Pierrot, T. (2024) · Bioinformatics

Machine Learning in BioinformaticsGenomics and Phylogenetic Studies

Cited by 16