Publications by authors named "Simona Cocco"

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Repeats mimic pathogen-associated patterns across a vast evolutionary landscape.
Petr Šulc, Andrea Di Gioacchino, Alexander Solovyov, Siyu Sun, Stephen Martis, Simona Cocco

Cell Genom· December 2025

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Designing molecular RNA switches with Restricted Boltzmann machines.
Jorge Fernandez-de-Cossio-Diaz, Pierre Hardouin, Francois-Xavier Lyonnet du Moutier, Andrea Di Gioacchino, Bertrand Marchand, Simona Cocco

Nat Commun· December 2025

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Constrained Evolutionary Funnels Shape Viral Immune Escape.
Marian Huot, Dianzhuo Wang, Eugene Shakhnovich, Rémi Monasson, Simona Cocco

bioRxiv· October 2025

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A High-Order Cumulant Extension of Quasi-Linkage Equilibrium.
Kai S Shimagaki, Jorge Fernandez-de-Cossio-Diaz, Mauro Pastore, Rémi Monasson, Simona Cocco

ArXiv· September 2025

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Deciphering the Code of Viral-Host Adaptation Through Maximum-Entropy Nucleotide Bias Models.
Andrea Di Gioacchino, Ivan Lecce, Benjamin D Greenbaum, Rémi Monasson, Simona Cocco

Mol Biol Evol· June 2025

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Functional effects of mutations in proteins can be predicted and interpreted by guided selection of sequence covariation information.
Simona Cocco, Lorenzo Posani, Rémi Monasson

Proc Natl Acad Sci U S A· June 2024

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Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment.
Cyril Malbranke, William Rostain, Florence Depardieu, Simona Cocco, Rémi Monasson

PLoS Comput Biol· November 2023

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Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data.
Lorenzo Posani, Francesca Rizzato, Rémi Monasson, Simona Cocco

PLoS Comput Biol· October 2023

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A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity.
Barbara Bravi, Andrea Di Gioacchino, Jorge Fernandez-de-Cossio-Diaz, Aleksandra M Walczak, Thierry Mora, Simona Cocco

Elife· September 2023

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Transition paths in Potts-like energy landscapes: General properties and application to protein sequence models.
Eugenio Mauri, Simona Cocco, Rémi Monasson

Phys Rev E· August 2023

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Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies.
Cyril Malbranke, David Bikard, Simona Cocco, Rémi Monasson, Jérôme Tubiana

Curr Opin Struct Biol· June 2023

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Mutational Paths with Sequence-Based Models of Proteins: From Sampling to Mean-Field Characterization.
Eugenio Mauri, Simona Cocco, Rémi Monasson

Phys Rev Lett· April 2023

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Emergence of time persistence in a data-driven neural network model.
Sebastien Wolf, Guillaume Le Goc, Georges Debrégeas, Simona Cocco, Rémi Monasson

Elife· March 2023

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Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain.
Fangyuan Ding, Simona Cocco, Saurabh Raj, Maria Manosas, Thao Thi Thu Nguyen

Nucleic Acids Res· November 2022

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Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection.
Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S Schreck, Yu Zhou, Simona Cocco

PLoS Comput Biol· September 2022

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A synaptic signal for novelty processing in the hippocampus.
Ruy Gómez-Ocádiz, Massimiliano Trippa, Chun-Lei Zhang, Lorenzo Posani, Simona Cocco

Nat Commun· July 2022

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Neoantigen quality predicts immunoediting in survivors of pancreatic cancer.
Marta Łuksza, Zachary M Sethna, Luis A Rojas, Jayon Lihm, Barbara Bravi, Simona Cocco

Nature· June 2022

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sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs.
Andrea Di Gioacchino, Rachel Legendre, Yannis Rahou, Valérie Najburg, Pierre Charneau, Simona Cocco

RNA· March 2022

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Improving sequence-based modeling of protein families using secondary-structure quality assessment.
Cyril Malbranke, David Bikard, Simona Cocco, Rémi Monasson

Bioinformatics· November 2021

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Probing T-cell response by sequence-based probabilistic modeling.
Barbara Bravi, Vinod P Balachandran, Benjamin D Greenbaum, Aleksandra M Walczak, Thierry Mora, Simona Cocco

PLoS Comput Biol· September 2021

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Barriers and dynamical paths in alternating Gibbs sampling of restricted Boltzmann machines.
Clément Roussel, Simona Cocco, Rémi Monasson

Phys Rev E· September 2021

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The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2.
Andrea Di Gioacchino, Petr Šulc, Anastassia V Komarova, Benjamin D Greenbaum, Rémi Monasson, Simona Cocco

Mol Biol Evol· May 2021

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Survival probability and size of lineages in antibody affinity maturation.
Marco Molari, Rémi Monasson, Simona Cocco

Phys Rev E· May 2021

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Parameters and determinants of responses to selection in antibody libraries.
Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson

PLoS Comput Biol· March 2021

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RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles.
Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora

Cell Syst· February 2021

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