Publications

Here is a link to my Google Scholar profile

And below is a list of papers:

2025

Reconstruction of ancestral protein sequences using autoregressive generative models
Matteo De Leonardis, Andrea Pagnani, Pierre Barrat-Charlaix
bioRXiv, February 2025, https://www.biorxiv.org/content/10.1101/2024.09.17.613387v1

2024

Eco-evolutionary dynamics of adapting pathogens and host immunity
Pierre Barrat-Charlaix, Richard A Neher
eLife, December 2024, https://elifesciences.org/articles/97350

2022

TreeKnit: Inferring Ancestral Reassortment Graphs of influenza viruses
Pierre Barrat-Charlaix, Timothy G. Vaughan, Richard A Neher
PLoS Comput Biol, August 2022, https://doi.org/10.1371/journal.pcbi.1010394

Sparse generative modeling via parameter reduction of Boltzmann machines: Application to protein-sequence families
Pierre Barrat-Charlaix, Anna Paola Muntoni, Kai Shimagaki, Martin Weigt, Francesco Zamponi
Physical Review E 104, August 2021, https://journals.aps.org/pre/abstract/10.1103/PhysRevE.104.024407

2021

Global multivariate model learning from hierarchically correlated data
Edwin Rodríguez Horta, Alejandro Lage-Castellanos, Martin Weigt, Pierre Barrat-Charlaix
Journal of Statistical Mechanics: Theory and Experiment 7, July 2021, https://iopscience.iop.org/article/10.1088/1742-5468/ac06c2/meta

Limited predictability of amino acid substitutions in seasonal influenza viruses
Pierre Barrat-Charlaix, John Huddleston, Trevor Bedford, Richard A Neher
Molecular Biology and Evolution, March 2021, https://doi.org/10.1093/molbev/msab065

2020

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution John Huddleston et.al. eLife, August 2020, https://elifesciences.org/articles/60067

An evolution-based model for designing chorismate mutase enzymes
William P. Russ, Matteo Figliuzzi, Christian Stocker, Pierre Barrat-Charlaix, Michael Socolich, Peter Kast, Donald Hilvert, Remi Monasson, Simona Cocco, Martin Weigt, Rama Ranganathan
Science July 2020: 440-445, https://science.sciencemag.org/content/369/6502/440.full

2019

Toward Inferring Potts Models for Phylogenetically Correlated Sequence Data
Edwin Rodriguez Horta, Pierre Barrat-Charlaix, Martin Weigt
MDPI Entropy 21, November 2019 https://www.mdpi.com/1099-4300/21/11/1090/htm

2018

How pairwise coevolutionary models capture the collective residue variability in proteins?
Matteo Figliuzzi, Pierre Barrat-Charlaix, Martin Weigt
Molecular Biology and Evolution 35 (4), January 2018, https://doi.org/10.1093/molbev/msy007

2016

Improving landscape inference by integrating heterogeneous data in the inverse Ising problem
Pierre Barrat-Charlaix, Matteo Figliuzzi, Martin Weigt
Scientific Reports 6 37812, November 2016, https://doi.org/10.1038/srep37812