Zobrazeno 1 - 10
of 236
pro vyhledávání: '"Simona Cocco"'
Autor:
Cyril Malbranke, William Rostain, Florence Depardieu, Simona Cocco, Rémi Monasson, David Bikard
Publikováno v:
PLoS Computational Biology, Vol 19, Iss 11, p e1011621 (2023)
We present here an approach to protein design that combines (i) scarce functional information such as experimental data (ii) evolutionary information learned from a natural sequence variants and (iii) physics-grounded modeling. Using a Restricted Bol
Externí odkaz:
https://doaj.org/article/05b943bf0d4e4bd9be8e836d8265bc37
Publikováno v:
PLoS Computational Biology, Vol 19, Iss 10, p e1011521 (2023)
Predicting the effects of mutations on protein function is an important issue in evolutionary biology and biomedical applications. Computational approaches, ranging from graphical models to deep-learning architectures, can capture the statistical pro
Externí odkaz:
https://doaj.org/article/93d74210f67a445588adcc33de68db4f
Autor:
Barbara Bravi, Andrea Di Gioacchino, Jorge Fernandez-de-Cossio-Diaz, Aleksandra M Walczak, Thierry Mora, Simona Cocco, Rémi Monasson
Publikováno v:
eLife, Vol 12 (2023)
Antigen immunogenicity and the specificity of binding of T-cell receptors to antigens are key properties underlying effective immune responses. Here we propose diffRBM, an approach based on transfer learning and Restricted Boltzmann Machines, to buil
Externí odkaz:
https://doaj.org/article/3aa7f87a1a4c4800a52f77d2f9c090cd
Publikováno v:
Machine Learning: Science and Technology, Vol 5, Iss 2, p 025078 (2024)
Boltzmann machines (BMs) are graphical models with interconnected binary units, employed for the unsupervised modeling of data distributions. When trained on real data, BMs show the tendency to behave like critical systems, displaying a high suscepti
Externí odkaz:
https://doaj.org/article/ea1cbbeda81c4921bd183507c8781d45
Autor:
Ruy Gómez-Ocádiz, Massimiliano Trippa, Chun-Lei Zhang, Lorenzo Posani, Simona Cocco, Rémi Monasson, Christoph Schmidt-Hieber
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-15 (2022)
Memory formation and recall are complementary processes within the hippocampus. Here the authors demonstrate a synaptic signal of novelty in the hippocampus and provide a computational framework for how such a novelty-driven switch may enable flexibl
Externí odkaz:
https://doaj.org/article/6fb149d6d7df4f85895b7ddd27e1ac86
Publikováno v:
eLife, Vol 12 (2023)
Establishing accurate as well as interpretable models of network activity is an open challenge in systems neuroscience. Here, we infer an energy-based model of the anterior rhombencephalic turning region (ARTR), a circuit that controls zebrafish swim
Externí odkaz:
https://doaj.org/article/144b55d93cf5414582199b06892631a7
Autor:
Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Šulc
Publikováno v:
PLoS Computational Biology, Vol 18, Iss 9, p e1010561 (2022)
Selection protocols such as SELEX, where molecules are selected over multiple rounds for their ability to bind to a target of interest, are popular methods for obtaining binders for diagnostic and therapeutic purposes. We show that Restricted Boltzma
Externí odkaz:
https://doaj.org/article/c65fb6b19df0481c89893421f10045c6
Publikováno v:
Physical Review X, Vol 13, Iss 2, p 021003 (2023)
A goal of unsupervised machine learning is to build representations of complex high-dimensional data, with simple relations to their properties. Such disentangled representations make it easier to interpret the significant latent factors of variation
Externí odkaz:
https://doaj.org/article/b76a351ce38b4ae8a8779680705032d1
Autor:
Barbara Bravi, Vinod P Balachandran, Benjamin D Greenbaum, Aleksandra M Walczak, Thierry Mora, Rémi Monasson, Simona Cocco
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 9, p e1009297 (2021)
With the increasing ability to use high-throughput next-generation sequencing to quantify the diversity of the human T cell receptor (TCR) repertoire, the ability to use TCR sequences to infer antigen-specificity could greatly aid potential diagnosti
Externí odkaz:
https://doaj.org/article/1b09e79bd3cc42a9a6d184af909b44d9
Autor:
Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 3, p e1008751 (2021)
The sequences of antibodies from a given repertoire are highly diverse at few sites located on the surface of a genome-encoded larger scaffold. The scaffold is often considered to play a lesser role than highly diverse, non-genome-encoded sites in co
Externí odkaz:
https://doaj.org/article/2f943f4dac2f40de917396f4af72eb04