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
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
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
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
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
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
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
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
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
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
Thierry Mora, Aleksandra Walczak
PRX Life
11 Towards a quantitative theory of tolerance
Thierry Mora, Aleksandra Walczak
Trends in Immunology
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
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
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
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
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
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
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
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
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
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
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
Sebastien Wolf, Guillaume Le Goc, Simona Cocco, Georges Debrégeas, Rémi Monasson
eLife
2022
23 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
Matías Goldin, Baptiste Lefebvre, Samuele Virgili, Mathieu Kim Pham van Cang, Alexander Ecker, Thierry Mora, Ulisse Ferrari, Olivier Marre
Nature Communications
24 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
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
25 Nonequilibrium dynamics of adaptation in sensory systems
Daniele Conti, Thierry Mora
Physical Review E
Daniele Conti, Thierry Mora
Physical Review E
26 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
Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Šulc
PLoS Computational Biology
27 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
Federica Ferretti, Simon Grosse-Holz, Caroline Holmes, Jordan Shivers, Irene Giardina, Thierry Mora, Aleksandra Walczak
Physical Review E
28 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
Victor Greiff, Eline Luning Prak, Tim O’donnell, Francesca Finotello, Sai Reddy, Walczak Aleksandra, Thierry Mora
Cell Systems
29 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
Ezequiel Galpern, Jacopo Marchi, Thierry Mora, Aleksandra Walczak, Diego Ferreiro
Proceedings of the National Academy of Sciences of the United States of America
30 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
Ruy Gómez-Ocádiz, Massimiliano Trippa, Chun-Lei Zhang, Lorenzo Posani, Simona Cocco, Rémi Monasson, Christoph Schmidt-Hieber
Nature Communications
31 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
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
32 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
Cosimo Lupo, Natanael Spisak, Aleksandra M Walczak, Thierry Mora
PLoS Computational Biology
33 Optimal regularizations for data generation with probabilistic graphical models
A Fanthomme, F Rizzato, S Cocco, R Monasson
Journal of Statistical Mechanics: Theory and Experiment
A Fanthomme, F Rizzato, S Cocco, R Monasson
Journal of Statistical Mechanics: Theory and Experiment
34 Mutual information maximization for amortized likelihood inference from sampled trajectories: MINIMALIST
Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra Walczak
Physical Review E
Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra Walczak
Physical Review E
35 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
Federica Ferretti, Victor Chardès, Thierry Mora, Walczak Aleksandra, Irene Giardina
Physical Review E
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
Gonçalo Fernandes, Huy Tran, Maxime Andrieu, Youssoupha Diaw, Carmina Perez Romero, Cécile Fradin, Mathieu Coppey, Aleksandra Walczak, Nathalie Dostatni
eLife
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
Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review E
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
Victor Chardès, Massimo Vergassola, Aleksandra Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
2021
39 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
Andrea Di Gioacchino, Rachel Legendre, Yannis Rahou, Valérie Najburg, Pierre Charneau, Benjamin Greenbaum, Frédéric Tangy, Sylvie van Der Werf, Simona Cocco, Anastassia Komarova
RNA
40 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
Luca Sesta, Guido Uguzzoni, Jorge Fernandez-De-Cossio-Diaz, Andrea Pagnani
International Journal of Molecular Sciences
41 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
Clément Roussel, Simona Cocco, Rémi Monasson
Physical Review E : Statistical, Nonlinear, and Soft Matter Physics
42 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
Angela Phillips, Katherine Lawrence, Alief Moulana, Thomas Dupic, Jeffrey Chang, Milo Johnson, Ivana Cvijovic, Thierry Mora, Aleksandra Walczak, Michael Desai
eLife
43 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
Barbara Bravi, Vinod P Balachandran, Benjamin D Greenbaum, Aleksandra M Walczak, Thierry Mora, Rémi Monasson, Simona Cocco
PLoS Computational Biology
44 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
Jacopo Marchi, Michael Lässig, Aleksandra Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
45 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
Jacopo Marchi, Michael Lässig, Aleksandra M Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
46 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
Andrea Di Gioacchino, Petr Sulc, Anastassia V Komarova, Benjamin D Greenbaum, Remi Monasson, Simona Cocco
Molecular Biology and Evolution
47 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
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
48 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
Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
Proceedings of the National Academy of Sciences of the United States of America
49 Optimal prediction with resource constraints using the information bottleneck
Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie Palmer
PLoS Computational Biology
Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie Palmer
PLoS Computational Biology
50 RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles
Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora, Aleksandra M Walczak
Cell Systems
Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora, Aleksandra M Walczak
Cell Systems