265 citations · 2.3k across the 48 of their papers we have counts for
49 papers
Transition paths in Potts-like energy landscapes: general properties and application to protein sequence models
Eugenio Mauri, Simona Cocco, Rémi Monasson
We study transition paths in energy landscapes over multi-categorical Potts configurations using the mean-field approach introduced by Mauri et al., {\em Phys Rev Lett 130, 158402…
Evolutionary Dynamics of a Lattice Dimer: a Toy Model for Stability vs. Affinity Trade-offs in Proteins
Emanuele Loffredo, Elisabetta Vesconi, Rostam Razban +4
Understanding how a stressor applied on a biological system shapes its evolution is key to achieving targeted evolutionary control. Here we present a toy model of two interacting l…
Computational protein design with evolutionary-based and physics-inspired modeling: current and future synergies
Cyril Malbranke, David Bikard, Simona Cocco +2
Computational protein design facilitates discovery of novel proteins with prescribed structure and functionality. Exciting designs were recently reported using novel data-driven me…
Statistical-physics approaches to RNA molecules, families and networks
Simona Cocco, Andrea De Martino, Andrea Pagnani +1
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural…
Disentangling representations in Restricted Boltzmann Machines without adversaries
Jorge Fernandez-de-Cossio-Diaz, Simona Cocco, Remi Monasson
A goal of unsupervised machine learning is to build representations of complex high-dimensional data, with simple relations to their properties. Such disentangled representations m…
Mutational paths with sequence-based models of proteins: from sampling to mean-field characterisation
Eugenio Mauri, Simona Cocco, Rémi Monasson
Identifying and characterizing mutational paths is an important issue in evolutionary biology and in bioengineering. We here introduce a generic description of mutational paths in…