2023

1   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
2   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
3   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
4   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
5   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
6   Dynamical Information Synergy in Biochemical Signaling Networks
 Lauritz Hahn, Walczak Aleksandra, Thierry Mora
Physical Review Letters
7   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
8   Transition paths in Potts-like energy landscapes: General properties and application to protein sequence models
 Eugenio Mauri, Simona Cocco, Rémi Monasson
Physical Review E
9   Small-correlation expansion to quantify information in noisy sensory systems
 Gabriel Mahuas, Olivier Marre, Thierry Mora, Ulisse Ferrari
Physical Review E
10   Quantitative Theory of Viral-Immune Coevolution May Be within Reach
 Thierry Mora, Aleksandra Walczak
PRX Life
11   Towards a quantitative theory of tolerance
 Thierry Mora, Aleksandra Walczak
Trends in Immunology
12   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
13   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
14   Mutational Paths with Sequence-Based Models of Proteins: From Sampling to Mean-Field Characterization
 Eugenio Mauri, Simona Cocco, Rémi Monasson
Physical Review Letters
15   Disentangling Representations in Restricted Boltzmann Machines without Adversaries
 Jorge Fernandez-De-Cossio-Diaz, Simona Cocco, Rémi Monasson
Physical Review X
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
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
18   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
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
20   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
21   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
22   Emergence of time persistence in an interpretable data-driven neural network model
 Sebastien Wolf, Guillaume Le Goc, Simona Cocco, Georges Debrégeas, Rémi Monasson
eLife

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
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
25   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
26   Nonequilibrium dynamics of adaptation in sensory systems
 Daniele Conti, Thierry Mora
Physical Review E
27   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
28   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
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
30   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
31   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
32   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
33   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
34   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
35   Optimal regularizations for data generation with probabilistic graphical models
 A Fanthomme, F Rizzato, S Cocco, R Monasson
Journal of Statistical Mechanics: Theory and Experiment
36   Mutual information maximization for amortized likelihood inference from sampled trajectories: MINIMALIST
 Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra Walczak
Physical Review E
37   Renormalization Group Approach to Connect Discrete- and Continuous-Time Descriptions of Gaussian Processes
 Federica Ferretti, Victor Chardès, Thierry Mora, Walczak Aleksandra, Irene Giardina
Physical Review E
38   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
39   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
40   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
41   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

2021

42   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
43   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
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
45   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
46   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
47   Antigenic waves of virus-immune co-evolution
 Jacopo Marchi, Michael Lässig, Aleksandra Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
48   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
49   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
50   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
104
Publications
5
Années