Publications

Publications in reversed chronological order.

2026

  1. Biorxiv
    Origin-1: a generative AI platform for de novo antibody design against novel epitopes
    Biorxiv, 2026
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2025

  1. Bioinformatics
    DiffPaSS—high-performance differentiable pairing of protein sequences using soft scores
    Umberto Lupo, Damiano Sgarbossa, Martina Milighetti, and 1 more author
    Bioinformatics, 2025
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2024

  1. PNAS
    Pairing interacting protein sequences using masked language modeling
    Umberto Lupo, Damiano Sgarbossa, and Anne-Florence Bitbol
    Proceedings of the National Academy of Sciences of the United States of America, 2024
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2023

  1. eLife
    Generative power of a protein language model trained on multiple sequence alignments
    Damiano Sgarbossa, Umberto Lupo, and Anne-Florence Bitbol
    eLife, 2023
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  2. J. R. Soc. Interface
    Impact of phylogeny on structural contact inference from protein sequence data
    Nicola Dietler, Umberto Lupo, and Anne-Florence Bitbol
    Journal of the Royal Society Interface, 2023
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2022

  1. Nat Commun
    Protein language models trained on multiple sequence alignments learn phylogenetic relationships
    Umberto Lupo, Damiano Sgarbossa, and Anne-Florence Bitbol
    Nature Communications, 2022
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  2. PMLR
    ICLR 2022 Challenge for Computational Geometry & Topology: Design and Results
    Adele Myers, Saiteja Utpala, Shubham Talbar, and 8 more authors
    In Topological, Algebraic and Geometric Learning Workshops 2022, 2022
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  3. JACT
    Persistence Steenrod modules
    Umberto Lupo, Anibal M Medina-Mardones, and Guillaume Tauzin
    Journal of Applied and Computational Topology, 2022
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2021

  1. ICLR 2021 Challenge for Computational Geometry & Topology: Design and Results
    Nina Miolane, Matteo Caorsi, Umberto Lupo, and 8 more authors
    arXiv preprint arXiv:2108.09810, 2021
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  2. giotto-ph: A Python Library for High-Performance Computation of Persistent Homology of Vietoris-Rips Filtrations
    Julián Burella Pérez, Sydney Hauke, Umberto Lupo, and 2 more authors
    arXiv preprint arXiv:2107.05412, 2021
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  3. JMLR
    giotto-tda: A Topological Data Analysis Toolkit for Machine Learning and Data Exploration
    Guillaume Tauzin, Umberto Lupo, Lewis Tunstall, and 5 more authors
    J. Mach. Learn. Res., 2021
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2018

  1. LMP
    On the global "two-sided" characteristic Cauchy problem for linear wave equations on manifolds
    Umberto Lupo
    Letters in Mathematical Physics, 2018
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2016

  1. Class. Quantum Grav.
    Non-existence of isometry-invariant Hadamard states for a Kruskal black hole in a box and for massless fields on 1+ 1 Minkowski spacetime with a uniformly accelerating mirror
    Bernard S Kay, and Umberto Lupo
    Classical and Quantum Gravity, 2016
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2010

  1. New J. Phys.
    On the structure and topography of free-standing chemically modified graphene
    NR Wilson, PA Pandey, R Beanland, and 4 more authors
    New Journal of Physics, 2010
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