Publications

Selected

27.

A multimodal conversational agent for DNA, RNA and protein tasks

B.P. de Almeida*, G. Richard*, H. Dalla-Torre, C. Blum, L. Hexemer, P. Pandey, S. Laurent, M. Lopez, A. Laterre, M. Lang, U. Şahin, K. Beguir, T. Pierrot

Nature Machine Intelligence 2025

CODE MODEL DATA Preprint

Twitter thread

Blog post

26.

SegmentNT: annotating the genome at single-nucleotide resolution with DNA foundation models

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

Nature Methods 2025

CODE MODEL HUGGINGFACE COLLECTION Preprint

Twitter thread

Blog post

25.

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

B.P. de Almeida, C. Schaub, M. Pagani, S. Secchia, E.E.M. Furlong, A. Stark

Nature 2024

CODE

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.

Enhancers display constrained sequence flexibility and context-specific modulation of motif function

F. Reiter*, B.P. de Almeida*, A. Stark

Genome Research 2023

CODE Preprint

Decoding the grammar of gene regulation

Poster at EMBL Conference: Transcription and Chromatin (August 2022)

23.

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

B.P. de Almeida, F. Reiter, M. Pagani, A. Stark

Nature Genetics 2022

CODE MODEL DATA GEO Preprint

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.

Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome

B.P. de Almeida, A.F. Vieira, J. Paredes, M. Bettencourt-Dias, N.L. Barbosa-Morais

PLoS Computational Biology 2019

CODE

International media coverage: When a cell's 'fingerprint' can be a weapon against cancer (Science Daily)

21.

Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers

B.P. de Almeida*, J.D. Apolonio*, A. Binnie, P. Castelo-Branco

BMC Cancer 2019

Preprints

20.

A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction

S. Boshar, B. Evans, Z. Tang, A. Picard, Y. Adel, F.K. Lorbeer, C. Rajesh, T. Karch, S. Sidbon, D. Emms, J. Mendoza-Revilla, F. Al-Ani, E. Seitz, Y. Schiff, Y. Bornachot, A. Hernandez, M. Lopez, A. Laterre, K. Beguir, P. Koo, V. Kuleshov, A. Stark, B.P. de Almeida§, T. Pierrot§

bioRxiv 2025

CODE SITE HUGGINGFACE

Twitter thread

19.

High prevalence and dependence of centrosome clustering in mesenchymal tumors and leukemia

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

bioRxiv 2023

Others

18.

Simple Guidance Mechanisms for Discrete Diffusion Models

Y. Schiff, S.S. Sahoo, H. Phung, G. Wang, S. Boshar, H. Dalla-Torre, B.P. de Almeida, A. Rush, T. Pierrot, V. Kuleshov

ICLR 2025

CODE

17.

Multi-modal Transfer Learning between Biological Foundation Models

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§

NeurIPS 2024

MODEL Preprint

16.

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

S. Boshar, E. Trop, B.P. de Almeida, L. Copoiu, T. Pierrot

Bioinformatics 2024

CODE MODEL BENCHMARK Preprint

15.

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

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

Nature Methods 2024

CODE MODELS DATA BENCHMARK Preprint

Research Briefing

Blog post

14.

A Foundational Large Language Model for Edible Plant Genomes

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

Communications Biology 2024

CODE MODEL DATA BENCHMARK Preprint

13.

Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila

V. Loubiere, B.P. de Almeida, M. Pagani, A. Stark

Nature Communications 2024

CODE Preprint

12.

Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis

J.M. Xavier, R. Magno, R. Russell, B.P. de Almeida, A. Jacinta-Fernandes, A. Besouro-Duarte, M. Dunning, S. Samarajiwa, M. O'Reilly, A.M. Maia, C.L. Rocha, N. Rosli, B.A.J. Ponder, A.T. Maia

Scientific Reports 2024

CODE Preprint

11.

Identification and characterization of repressive domains in Drosophila transcription factors

L. Klaus, B.P. de Almeida, A. Vlasova, F. Nemčko, A. Schleiffer, K. Bergauer, L. Hofbauer, M. Rath, A. Stark

The EMBO Journal 2023

Preprint

10.

Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

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§

npj Breast Cancer 2022

Preprint

Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression

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§

ACS Central Science 2021

Expression of receptor activator of NFkB (RANK) drives stemness and resistance to therapy in ER+HER2- breast cancer

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

Oncotarget 2020

Dissecting celastrol with machine learning to unveil dark pharmacology

T. Rodrigues, B.P. de Almeida, N.L. Barbosa-Morais, G.J.L. Bernardes

Chemical Communications 2019

Natural product– drug conjugates for modulation of TRPV1-expressing tumors

C. Baker, T. Rodrigues, B.P. de Almeida, N.L. Barbosa-Morais, G.J.L. Bernardes

Bioorganic & Medicinal Chemistry 2019

Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis

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

Nature Communications 2018

Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation

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

Nature Communications 2018