publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2024

  1. Inference and design of antibody specificity: from experiments to models and back
    Jorge Fernandez-de-Cossio-Diaz, Guido Uguzzoni, Kévin Ricard, and 4 more authors
    PLOS Computational Biology, 2024
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  2. Unsupervised modeling of mutational landscapes of adeno-associated viruses viability
    Matteo De Leonardis, Jorge Fernandez-de-Cossio-Diaz, Guido Uguzzoni, and 1 more author
    BMC bioinformatics, 2024
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2023

  1. Inference of annealed protein fitness landscapes with AnnealDCA
    Luca Sesta, Andrea Pagnani, Jorge Fernandez-de-Cossio-Diaz, and 1 more author
    bioRxiv, Feb 2023
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2022

  1. Computer implemented method to optimize physical-chemical properties of biological sequences
    Guido Uguzzoni, Andrea Pagnani, and Jorge Fernandez-de-Cossio-Diaz
    Oct 2022
    US Patent App. 17/620,768

2021

  1. Unsupervised inference of protein fitness landscape from deep mutational scan
    Jorge Fernandez-de-Cossio-Diaz, Guido Uguzzoni, and Andrea Pagnani
    Molecular Biology and Evolution, Oct 2021
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  2. Efficient generative modeling of protein sequences using simple autoregressive models
    Jeanne Trinquier, Guido Uguzzoni, Andrea Pagnani, and 2 more authors
    Nature communications, Oct 2021
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  3. Amala: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape
    Luca Sesta, Guido Uguzzoni, Jorge Fernandez-de-Cossio-Diaz, and 1 more author
    International Journal of Molecular Sciences, Oct 2021
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2020

  1. Learning clinical networks from medical records based on information estimates in mixed-type data
    Vincent Cabeli, Louis Verny, Nadir Sella, and 3 more authors
    PLoS computational biology, Oct 2020

2018

  1. MIIC online: a web server to reconstruct causal or non-causal networks from non-perturbative data
    Nadir Sella, Louis Verny, Guido Uguzzoni, and 2 more authors
    Bioinformatics, Oct 2018

2017

  1. Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis
    Guido Uguzzoni, Shalini John Lovis, Francesco Oteri, and 3 more authors
    Proceedings of the National Academy of Sciences, Oct 2017
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2016

  1. Maximum-entropy models of sequenced immune repertoires predict antigen-antibody affinity
    Lorenzo Asti, Guido Uguzzoni, Paolo Marcatili, and 1 more author
    PLoS computational biology, Oct 2016
  2. Direct coevolutionary couplings reflect biophysical residue interactions in proteins
    Alice Coucke, Guido Uguzzoni, Francesco Oteri, and 3 more authors
    The Journal of chemical physics, Oct 2016

2013

  1. Collective behaviours: from biochemical kinetics to electronic circuits
    Elena Agliari, Adriano Barra, Raffaella Burioni, and 2 more authors
    Scientific Reports, Oct 2013
  2. CORRIGENDUM: Collective behaviours: from biochemical kinetics to electronic circuits
    Elena Agliari, Adriano Barra, Raffaella Burioni, and 2 more authors
    Scientific Reports, Oct 2013

2012

  1. Analogue neural networks on correlated random graphs
    Elena Agliari, Lorenzo Asti, Adriano Barra, and 2 more authors
    Journal of Physics A: Mathematical and Theoretical, Oct 2012
  2. Reaction networks as systems for resource allocation: A variational principle for their non-equilibrium steady states
    Andrea De Martino, Daniele De Martino, Roberto Mulet, and 1 more author
    PloS one, Oct 2012
  3. The true reinforced random walk with bias
    Elena Agliari, Raffaella Burioni, and Guido Uguzzoni
    New Journal of Physics, Oct 2012
  4. Reaction Networks as Systems for Resource Allocation: A Variational Principle for Their Non
    A De Martino, D De Martino, R Mulet, and 1 more author
    Oct 2012