Výsledky vyhľadávania - "Monasson, Remi"

Learning protein constitutive motifs from sequence data Autor Tubiana, Jérôme, Cocco, Simona, Monasson, Rémi

“…Statistical analysis of evolutionary-related protein sequences provides information about their structure, function, and history. We show that Restricted…”
Získať plný text

An evolution-based model for designing chorismate mutase enzymes Autor Russ, William P, Figliuzzi, Matteo, Stocker, Christian, Barrat-Charlaix, Pierre, Socolich, Michael, Kast, Peter, Hilvert, Donald, Monasson, Remi, Cocco, Simona, Weigt, Martin, Ranganathan, Rama

“…The rational design of enzymes is an important goal for both fundamental and practical reasons. Here, we describe a process to learn the constraints for…”
Zistit podrobnosti o prístupe

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction Autor Cocco, Simona, Monasson, Remi, Weigt, Martin

“…Various approaches have explored the covariation of residues in multiple-sequence alignments of homologous proteins to extract functional and structural…”
Získať plný text

Direct coevolutionary couplings reflect biophysical residue interactions in proteins Autor Coucke, Alice, Uguzzoni, Guido, Oteri, Francesco, Cocco, Simona, Monasson, Remi, Weigt, Martin

“…Coevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis…”
Zistit podrobnosti o prístupe

Capacity-Resolution Trade-Off in the Optimal Learning of Multiple Low-Dimensional Manifolds by Attractor Neural Networks Autor Battista, Aldo, Monasson, Rémi

“…Recurrent neural networks (RNN) are powerful tools to explain how attractors may emerge from noisy, high-dimensional dynamics. We study here how to learn the…”
Získať plný text

Inverse statistical physics of protein sequences: a key issues review Autor Cocco, Simona, Feinauer, Christoph, Figliuzzi, Matteo, Monasson, Rémi, Weigt, Martin

“…In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their…”
Zistit podrobnosti o prístupe

Collective Phase in Resource Competition in a Highly Diverse Ecosystem Autor Tikhonov, Mikhail, Monasson, Remi

“…Organisms shape their own environment, which in turn affects their survival. This feedback becomes especially important for communities containing a large…”
Získať plný text

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

“…Predicting the effects of one or more mutations to the in vivo or in vitro properties of a wild-type protein is a major computational challenge, due to the…”
Zistit podrobnosti o prístupe

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

“…Identifying and characterizing mutational paths is an important issue in evolutionary biology, with potential applications to bioengineering. We here propose…”
Získať plný text

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

“…Computational protein design facilitates the discovery of novel proteins with prescribed structure and functionality. Exciting designs were recently reported…”
Získať plný text

Low-Dimensional Manifolds Support Multiplexed Integrations in Recurrent Neural Networks Autor Fanthomme, Arnaud, Monasson, Rémi

“…We study the learning dynamics and the representations emerging in recurrent neural networks (RNNs) trained to integrate one or multiple temporal signals…”
Zistit podrobnosti o prístupe

Disentangling Representations in Restricted Boltzmann Machines without Adversaries Autor Fernandez-de-Cossio-Diaz, Jorge, Cocco, Simona, Monasson, Rémi

“…A goal of unsupervised machine learning is to build representations of complex high-dimensional data, with simple relations to their properties. Such…”
Získať plný text

Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice Proteins Autor Tubiana, Jérôme, Cocco, Simona, Monasson, Rémi

“…A restricted Boltzmann machine (RBM) is an unsupervised machine learning bipartite graphical model that jointly learns a probability distribution over data and…”
Zistit podrobnosti o prístupe

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

“…We present here an approach to protein design that combines (i) scarce functional information such as experimental data (ii) evolutionary information learned…”
Získať plný text

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

“…Abstract Motivation Modeling of protein family sequence distribution from homologous sequence data recently received considerable attention, in particular for…”
Získať plný text

Quantitative modeling of the effect of antigen dosage on B-cell affinity distributions in maturating germinal centers Autor Molari, Marco, Eyer, Klaus, Baudry, Jean, Cocco, Simona, Monasson, Rémi

“…Affinity maturation is a complex dynamical process allowing the immune system to generate antibodies capable of recognizing antigens. We introduce a model for…”
Získať plný text

Adaptation of olfactory receptor abundances for efficient coding Autor Teşileanu, Tiberiu, Cocco, Simona, Monasson, Rémi, Balasubramanian, Vijay

“…Olfactory receptor usage is highly heterogeneous, with some receptor types being orders of magnitude more abundant than others. We propose an explanation for…”
Získať plný text

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction Autor De Leonardis, Eleonora, Lutz, Benjamin, Ratz, Sebastian, Cocco, Simona, Monasson, Rémi, Schug, Alexander, Weigt, Martin

“…Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence…”
Získať plný text

Integration and multiplexing of positional and contextual information by the hippocampal network Autor Posani, Lorenzo, Cocco, Simona, Monasson, Rémi

“…The hippocampus is known to store cognitive representations, or maps, that encode both positional and contextual information, critical for episodic memories…”
Získať plný text

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

“…Antigen immunogenicity and the specificity of binding of T-cell receptors to antigens are key properties underlying effective immune responses. Here we propose…”
Získať plný text