Author

Hugo Dalla-Torre

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 4

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 3 Organism:human· 3 Assay:whole-genome sequencing· 3 Approach:deep learning· 2 Assay:DNA methylation· 2 Research Focus:gene regulatory network inference· 2 Organism:multiple species· 2 Research Focus:software / tool· 2

Frequent Co-Authors

Bernardo P. de AlmeidaiD· 4 shared Karim BeguiriD· 4 shared Thomas PierrotiD· 4 shared Alexandre Laterre· 3 shared Guillaume RichardiD· 3 shared Javier Mendoza‐RevillaiD· 3 shared Christopher Frederik BlumiD· 2 shared Evan Trop· 2 shared

Activity by Year

2024-2025 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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4 shared papersGenomics

Bernardo P. de AlmeidaORCID

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4 papers

Recent·Most cited

Annotating the genome at single-nucleotide resolution with DNA foundation models

Bernardo P. de Almeida, Hugo Dalla-Torre, Guillaume Richard, Christopher Frederik Blum, Lorenz Hexemer, Maxence Gélard, Javier Mendoza‐Revilla, Ziqi Tang, Frederikke Isa Marin, David Emms, Priyanka Pandey, Stefan Laurent, Marie Lopez, Alexandre Laterre, Maren Lang, , Thomas Pierrot

The paper introduces SegmentNT, a DNA foundation model for genome annotation, achieving state-of-the-art performance in identifying 14 genic and regulatory elements across species.

Nature Methods · Oct 29, 2025Peer-reviewedGenomics

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

Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza‐Revilla, Nicolás López Carranza, Adam Grzywaczewski, Francesco Oteri, Christian Dallago, Evan Trop, Bernardo P. de Almeida, Hassan Sirelkhatim, Guillaume Richard, Marcin J. Skwark, Karim Beguir, M. Lopez, Thomas Pierrot

The paper introduces the Nucleotide Transformer, a foundation model for genomics, showing it can predict molecular phenotypes from DNA sequences with transfer learning across tasks and organisms.

Nature Methods · Nov 28, 2024Peer-reviewedGenomics

A Foundational Large Language Model for Edible Plant Genomes

Javier Mendoza‐Revilla, Evan Trop, Liam Gonzalez, Maša Roller, Hugo Dalla-Torre, Bernardo P. de Almeida, Guillaume Richard, Jonathan Caton, Nicolás López Carranza, Marcin J. Skwark, Alexandre Laterre, Karim Beguir, Thomas Pierrot, Marie Lopez

This paper introduces a large language model for plant genomics that provides state-of-the-art predictions for regulatory annotations and variant prioritization, along with a benchmark dataset for deep learning methods.

Communications Biology · Jul 9, 2024Peer-reviewedGenomics

ChatNT: A Multimodal Conversational Agent for DNA, RNA and Protein Tasks

Guillaume Richard, Bernardo P. de Almeida, Hugo Dalla-Torre, Christopher Frederik Blum, Lorenz Hexemer, Priyanka Pandey, Stefan Laurent, M. Lopez, Alexandre Laterre, Maren Lang, Uğur Şahin, Karim Beguir, Thomas Pierrot

ChatNT is a conversational agent that understands biological sequences and achieves state-of-the-art results on genomics tasks while being accessible to non-coders.

bioRxiv · Apr 30, 2024 · PreprintGenomics