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Umberto Lupo

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Prof. Bitbol Group

EPFL
SV
IBI-SV
UPBITBOL

Related publications (5)

Please note that this is not a complete list of this person’s publications. It includes only semantically relevant works. For a full list, please refer to Infoscience.

Pairing interacting protein sequences using masked language modeling

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

Predicting which proteins interact together from amino acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments (MSAs), such ...

National Academy of Sciences2024

DiffPaSS-high-performance differentiable pairing of protein sequences using soft scores

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

MOTIVATION: Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature correlations i ...

2024

Impact of phylogeny on structural contact inference from protein sequence data

Nicola Dietler, Umberto Lupo, Anne-Florence Raphaëlle Bitbol

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023