2023

1   A statistical mechanics framework for Bayesian deep neural networks beyond the infinite-width limit
 R. Pacelli, S. Ariosto, M. Pastore, F. Ginelli, M. Gherardi, P. Rotondo
Nature Machine Intelligence
DOI PDF HAL
2   Evolutionary stability of antigenically escaping viruses
 Victor Chardès, Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
Proceedings of the National Academy of Sciences of the United States of America
DOI PDF HAL
3   Evolutionary dynamics of a lattice dimer: a toy model for stability vs. affinity trade-offs in proteins
 E Loffredo, E Vesconi, R Razban, O Peleg, E Shakhnovich, S Cocco, R Monasson
Journal of Physics A: Mathematical and Theoretical
DOI PDF HAL
4   Dynamical Information Synergy in Biochemical Signaling Networks
 Lauritz Hahn, Walczak Aleksandra, Thierry Mora
Physical Review Letters
DOI PDF HAL
5   A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity
 Barbara Bravi, Andrea Di Gioacchino, Jorge Fernandez-De-Cossio-Diaz, Aleksandra Walczak, Thierry Mora, Simona Cocco, Rémi Monasson
eLife
DOI PDF HAL
6   Transition paths in Potts-like energy landscapes: General properties and application to protein sequence models
 Eugenio Mauri, Simona Cocco, Rémi Monasson
Physical Review E
DOI PDF HAL
7   Small-correlation expansion to quantify information in noisy sensory systems
 Gabriel Mahuas, Olivier Marre, Thierry Mora, Ulisse Ferrari
Physical Review E
DOI PDF HAL
8   Quantitative Theory of Viral-Immune Coevolution May Be within Reach
 Thierry Mora, Aleksandra Walczak
PRX Life
DOI PDF HAL
9   Towards a quantitative theory of tolerance
 Thierry Mora, Aleksandra Walczak
Trends in Immunology
DOI PDF HAL
10   Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies
 Cyril Malbranke, David Bikard, Simona Cocco, Rémi Monasson, Jérôme Tubiana
Current Opinion in Structural Biology
DOI PDF HAL
11   Inspecting the interaction between human immunodeficiency virus and the immune system through genetic turnover
 Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
Philosophical Transactions of the Royal Society B: Biological Sciences
DOI PDF HAL
12   Emergence of time persistence in an interpretable data-driven neural network model
 Sebastien Wolf, Guillaume Le Goc, Simona Cocco, Georges Debrégeas, Rémi Monasson
eLife
DOI PDF HAL
13   Mutational Paths with Sequence-Based Models of Proteins: From Sampling to Mean-Field Characterization
 Eugenio Mauri, Simona Cocco, Rémi Monasson
Physical Review Letters
DOI PDF HAL
14   Disentangling Representations in Restricted Boltzmann Machines without Adversaries
 Jorge Fernandez-De-Cossio-Diaz, Simona Cocco, Rémi Monasson
Physical Review X
DOI PDF HAL
15   Granger causality analysis for calcium transients in neuronal networks, challenges and improvements
 Xiaowen Chen, Faustine Ginoux, Martin Carbo-Tano, Thierry Mora, Aleksandra Walczak, Claire Wyart
eLife
DOI PDF HAL
16   Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report
 Pieter Meysman, Justin Barton, Barbara Bravi, Liel Cohen-Lavi, Vadim Karnaukhov, Elias Lilleskov, Alessandro Montemurro, Morten Nielsen, Thierry Mora, Paul Pereira, Anna Postovskaya, María Rodríguez Martínez, Jorge Fernandez-De-Cossio-Diaz, Alexandra Vujkovic, Aleksandra Walczak, Anna Weber, Rose Yin, Anne Eugster, Virag Sharma
ImmunoInformatics
DOI PDF HAL
17   Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals
 María Ruiz Ortega, Natanael Spisak, Thierry Mora, Aleksandra Walczak
PLoS Genetics
DOI PDF HAL
18   Quantifying changes in the T cell receptor repertoire during thymic development
 Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benny Chain, Thierry Mora, Aleksandra Walczak, Nir Friedman
eLife
DOI PDF HAL
19   Inferring the T cell repertoire dynamics of healthy individuals
 Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
DOI PDF HAL
20   DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age
 Jos Urbanus, Jason Cosgrove, Joost Beltman, Yuval Elhanati, Rafael Moral, Cecile Conrad, Jeroen van Heijst, Emilie Tubeuf, Arno Velds, Lianne Kok, Candice Merle, Jens Magnusson, Léa Guyonnet, Jonas Frisén, Silvia Fre, Aleksandra Walczak, Thierry Mora, Heinz Jacobs, Ton Schumacher, Leïla Perié
Nature Communications
DOI PDF HAL
21   Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data
 Lorenzo Posani, Francesca Rizzato, Rémi Monasson, Simona Cocco
PLoS Computational Biology
DOI PDF HAL
22   Generalized Glauber dynamics for inference in biology
 Xiaowen Chen, Maciej Winiarski, Alicja Puscian, Ewelina Knapska, Aleksandra M. Walczak, Thierry Mora
Physical Review X
DOI PDF HAL

2022

23   Inference of metabolic fluxes in nutrient-limited continuous cultures: A Maximum Entropy approach with the minimum information
 José Antonio Pereiro-Morejon, Jorge Fernandez-De-Cossio-Diaz, Roberto Mulet
iScience
DOI HAL
24   Context-dependent selectivity to natural images in the retina
 Matías Goldin, Baptiste Lefebvre, Samuele Virgili, Mathieu Kim Pham van Cang, Alexander Ecker, Thierry Mora, Ulisse Ferrari, Olivier Marre
Nature Communications
DOI PDF HAL
25   Nonequilibrium dynamics of adaptation in sensory systems
 Daniele Conti, Thierry Mora
Physical Review E
DOI PDF HAL
26   NoisET: Noise learning and Expansion detection of T-cell receptors with Python
 Meriem Bensouda Koraichi, Maximilian Puelma Touzel, Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
Journal of Physical Chemistry A
DOI PDF HAL
27   Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection
 Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Šulc
PLoS Computational Biology
DOI PDF HAL
28   Signatures of irreversibility in microscopic models of flocking
 Federica Ferretti, Simon Grosse-Holz, Caroline Holmes, Jordan Shivers, Irene Giardina, Thierry Mora, Aleksandra Walczak
Physical Review E
DOI PDF HAL
29   What are the current driving questions in immune repertoire research?
 Victor Greiff, Eline Luning Prak, Tim O’donnell, Francesca Finotello, Sai Reddy, Walczak Aleksandra, Thierry Mora
Cell Systems
DOI PDF HAL
30   Evolution and folding of repeat proteins
 Ezequiel Galpern, Jacopo Marchi, Thierry Mora, Aleksandra Walczak, Diego Ferreiro
Proceedings of the National Academy of Sciences of the United States of America
DOI PDF HAL
31   A synaptic signal for novelty processing in the hippocampus
 Ruy Gómez-Ocádiz, Massimiliano Trippa, Chun-Lei Zhang, Lorenzo Posani, Simona Cocco, Rémi Monasson, Christoph Schmidt-Hieber
Nature Communications
DOI PDF HAL
32   Neoantigen quality predicts immunoediting in survivors of pancreatic cancer
 Marta Łuksza, Zachary Sethna, Luis Rojas, Jayon Lihm, Barbara Bravi, Yuval Elhanati, Kevin Soares, Masataka Amisaki, Anton Dobrin, David Hoyos, Pablo Guasp, Abderezak Zebboudj, Rebecca Yu, Adrienne Kaya Chandra, Theresa Waters, Zagaa Odgerel, Joanne Leung, Rajya Kappagantula, Alvin Makohon-Moore, Amber Johns, Anthony Gill, Mathieu Gigoux, Jedd Wolchok, Taha Merghoub, Michel Sadelain, Erin Patterson, Remi Monasson, Thierry Mora, Aleksandra Walczak, Simona Cocco, Christine Iacobuzio-Donahue, Benjamin Greenbaum, Vinod Balachandran
Nature
DOI PDF HAL
33   Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
 Cosimo Lupo, Natanael Spisak, Aleksandra M Walczak, Thierry Mora
PLoS Computational Biology
DOI HAL
34   Optimal regularizations for data generation with probabilistic graphical models
 A Fanthomme, F Rizzato, S Cocco, R Monasson
Journal of Statistical Mechanics: Theory and Experiment
DOI PDF HAL
35   Mutual information maximization for amortized likelihood inference from sampled trajectories: MINIMALIST
 Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra Walczak
Physical Review E
DOI PDF HAL
36   Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription
 Gonçalo Fernandes, Huy Tran, Maxime Andrieu, Youssoupha Diaw, Carmina Perez Romero, Cécile Fradin, Mathieu Coppey, Aleksandra Walczak, Nathalie Dostatni
eLife
DOI HAL
37   Renormalization group approach to connect discrete- and continuous-time descriptions of Gaussian processes
 Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review E
DOI PDF HAL
38   Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints
 Victor Chardès, Massimo Vergassola, Aleksandra Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
DOI PDF HAL
39   Biophysical Modeling of Dopaminergic Denervation Landscapes in the Striatum Reveals New Therapeutic Strategy
 Mathias Heltberg, Hussein N Awada, Alessandra Lucchetti, Mogens H Jensen, Jakob K Dreyer, Rune N Rasmussen
eNeuro
DOI HAL
40   Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain
 Fangyuan Ding, Simona Cocco, Saurabh Raj, Maria Manosas, Thao Thi Thu Nguyen, Michelle M Spiering, David Bensimon, Jean-François Allemand, V. Croquette
Nucleic Acids Research
DOI PDF HAL

2021

41   sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs
 Andrea Di Gioacchino, Rachel Legendre, Yannis Rahou, Valérie Najburg, Pierre Charneau, Benjamin Greenbaum, Frédéric Tangy, Sylvie van Der Werf, Simona Cocco, Anastassia Komarova
RNA
DOI PDF HAL
42   AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape
 Luca Sesta, Guido Uguzzoni, Jorge Fernandez-De-Cossio-Diaz, Andrea Pagnani
International Journal of Molecular Sciences
DOI PDF HAL
43   Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies
 Angela Phillips, Katherine Lawrence, Alief Moulana, Thomas Dupic, Jeffrey Chang, Milo Johnson, Ivana Cvijovic, Thierry Mora, Aleksandra Walczak, Michael Desai
eLife
DOI PDF HAL
44   Barriers and Dynamical Paths in Alternating Gibbs Sampling of Restricted Boltzmann Machines
 Clément Roussel, Simona Cocco, Rémi Monasson
Physical Review E : Statistical, Nonlinear, and Soft Matter Physics
DOI PDF HAL
45   Probing T-cell response by sequence-based probabilistic modeling
 Barbara Bravi, Vinod P Balachandran, Benjamin D Greenbaum, Aleksandra M Walczak, Thierry Mora, Rémi Monasson, Simona Cocco
PLoS Computational Biology
DOI PDF HAL
46   Antigenic waves of virus–immune coevolution
 Jacopo Marchi, Michael Lässig, Aleksandra M Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
DOI PDF HAL
47   The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2
 Andrea Di Gioacchino, Petr Sulc, Anastassia V Komarova, Benjamin D Greenbaum, Remi Monasson, Simona Cocco
Molecular Biology and Evolution
DOI PDF HAL
48   Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19
 Zachary Montague, Huibin Lv, Jakub Otwinowski, William S Dewitt, Giulio Isacchini, Garrick K Yip, Wilson W Ng, Owen Tak-Yin Tsang, Meng Yuan, Hejun Liu, Ian A Wilson, J.S. Malik S Malik Peiris, Nicholas C Wu, Armita Nourmohammad, Chris Ka Pun Mok
Cell Reports
DOI PDF HAL
49   Deep generative selection models of T and B cell receptor repertoires with soNNia
 Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
Proceedings of the National Academy of Sciences of the United States of America
DOI PDF HAL
50   Optimal prediction with resource constraints using the information bottleneck
 Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie Palmer
PLoS Computational Biology
DOI PDF HAL
99
Publications
5
Années

2020
24
2023
22
2022
18

Documents récupérés de l'archive ouverte HAL logo