2023
51 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
2023 - eLife
Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benny Chain, Thierry Mora, Aleksandra Walczak, Nir Friedman
2023 - eLife
52 Inferring the T cell repertoire dynamics of healthy individuals
Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra Walczak, Thierry Mora
2023 - Proceedings of the National Academy of Sciences of the United States of America
Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra Walczak, Thierry Mora
2023 - Proceedings of the National Academy of Sciences of the United States of America
53 Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment
Cyril Malbranke, William Rostain, Florence Depardieu, Simona Cocco, Rémi Monasson, David Bikard
2023 - PLoS Computational Biology
Cyril Malbranke, William Rostain, Florence Depardieu, Simona Cocco, Rémi Monasson, David Bikard
2023 - PLoS Computational Biology
54 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
2023 - 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
2023 - Nature Communications
55 Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data
Lorenzo Posani, Francesca Rizzato, Rémi Monasson, Simona Cocco
2023 - PLoS Computational Biology
Lorenzo Posani, Francesca Rizzato, Rémi Monasson, Simona Cocco
2023 - PLoS Computational Biology
56 Generalized Glauber dynamics for inference in biology
Xiaowen Chen, Maciej Winiarski, Alicja Puscian, Ewelina Knapska, Aleksandra M. Walczak, Thierry Mora
2023 - Physical Review X
Xiaowen Chen, Maciej Winiarski, Alicja Puscian, Ewelina Knapska, Aleksandra M. Walczak, Thierry Mora
2023 - Physical Review X
2022
57 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
2022 - iScience
José Antonio Pereiro-Morejon, Jorge Fernandez-De-Cossio-Diaz, Roberto Mulet
2022 - iScience
58 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
2022 - Nature Communications
Matías Goldin, Baptiste Lefebvre, Samuele Virgili, Mathieu Kim Pham van Cang, Alexander Ecker, Thierry Mora, Ulisse Ferrari, Olivier Marre
2022 - Nature Communications
59 Nonequilibrium dynamics of adaptation in sensory systems
Daniele Conti, Thierry Mora
2022 - Physical Review E
Daniele Conti, Thierry Mora
2022 - Physical Review E
60 NoisET: Noise learning and Expansion detection of T-cell receptors with Python
Meriem Bensouda Koraichi, Maximilian Puelma Touzel, Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
2022 - Journal of Physical Chemistry A
Meriem Bensouda Koraichi, Maximilian Puelma Touzel, Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
2022 - Journal of Physical Chemistry A
61 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
2022 - PLoS Computational Biology
Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Šulc
2022 - PLoS Computational Biology
62 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
2022 - Cell Systems
Victor Greiff, Eline Luning Prak, Tim O’donnell, Francesca Finotello, Sai Reddy, Walczak Aleksandra, Thierry Mora
2022 - Cell Systems
63 Signatures of irreversibility in microscopic models of flocking
Federica Ferretti, Simon Grosse-Holz, Caroline Holmes, Jordan Shivers, Irene Giardina, Thierry Mora, Aleksandra Walczak
2022 - Physical Review E
Federica Ferretti, Simon Grosse-Holz, Caroline Holmes, Jordan Shivers, Irene Giardina, Thierry Mora, Aleksandra Walczak
2022 - Physical Review E
64 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
2022 - Nature Communications
Ruy Gómez-Ocádiz, Massimiliano Trippa, Chun-Lei Zhang, Lorenzo Posani, Simona Cocco, Rémi Monasson, Christoph Schmidt-Hieber
2022 - Nature Communications
65 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
2022 - 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
2022 - Nature
66 Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
Cosimo Lupo, Natanael Spisak, Aleksandra M Walczak, Thierry Mora
2022 - PLoS Computational Biology
Cosimo Lupo, Natanael Spisak, Aleksandra M Walczak, Thierry Mora
2022 - PLoS Computational Biology
67 Heat flux in chains of nonlocally coupled harmonic oscillators: Mean-field limit
Lucianno Defaveri, Carlos Olivares, Celia Anteneodo
2022 - Physical Review E
Lucianno Defaveri, Carlos Olivares, Celia Anteneodo
2022 - Physical Review E
68 Optimal regularizations for data generation with probabilistic graphical models
A Fanthomme, F Rizzato, S Cocco, R Monasson
2022 - Journal of Statistical Mechanics: Theory and Experiment
A Fanthomme, F Rizzato, S Cocco, R Monasson
2022 - Journal of Statistical Mechanics: Theory and Experiment
69 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
2022 - eLife
Gonçalo Fernandes, Huy Tran, Maxime Andrieu, Youssoupha Diaw, Carmina Perez Romero, Cécile Fradin, Mathieu Coppey, Aleksandra Walczak, Nathalie Dostatni
2022 - eLife
70 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
2022 - eNeuro
Mathias Heltberg, Hussein N Awada, Alessandra Lucchetti, Mogens H Jensen, Jakob K Dreyer, Rune N Rasmussen
2022 - eNeuro
71 Fast optical recording of neuronal activity by three-dimensional custom-access serial holography
Walther Akemann, Sébastien Wolf, Vincent Villette, Benjamin Mathieu, Astou Tangara, Jozsua Fodor, Cathie Ventalon, Jean-François Léger, Stéphane Dieudonné, Laurent Bourdieu
2022 - Nature Methods
Walther Akemann, Sébastien Wolf, Vincent Villette, Benjamin Mathieu, Astou Tangara, Jozsua Fodor, Cathie Ventalon, Jean-François Léger, Stéphane Dieudonné, Laurent Bourdieu
2022 - Nature Methods
72 Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints
Victor Chardès, Massimo Vergassola, Aleksandra Walczak, Thierry Mora
2022 - Proceedings of the National Academy of Sciences of the United States of America
Victor Chardès, Massimo Vergassola, Aleksandra Walczak, Thierry Mora
2022 - Proceedings of the National Academy of Sciences of the United States of America
73 Renormalization group approach to connect discrete- and continuous-time descriptions of Gaussian processes
Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
2022 - Physical Review E
Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
2022 - Physical Review E
74 Gell-Mann–Low Criticality in Neural Networks
Lorenzo Tiberi, Jonas Stapmanns, Tobias Kühn, Thomas Luu, David Dahmen, Moritz Helias
2022 - Physical Review Letters
Lorenzo Tiberi, Jonas Stapmanns, Tobias Kühn, Thomas Luu, David Dahmen, Moritz Helias
2022 - Physical Review Letters
75 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
2022 - 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
2022 - Nucleic Acids Research
76 Mutual information maximization for amortized likelihood inference from sampled trajectories: MINIMALIST
Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra Walczak
2022 - Physical Review E
Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra Walczak
2022 - Physical Review E
77 Evolution and folding of repeat proteins
Ezequiel Galpern, Jacopo Marchi, Thierry Mora, Aleksandra Walczak, Diego Ferreiro
2022 - Proceedings of the National Academy of Sciences of the United States of America
Ezequiel Galpern, Jacopo Marchi, Thierry Mora, Aleksandra Walczak, Diego Ferreiro
2022 - Proceedings of the National Academy of Sciences of the United States of America
2021
78 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
2021 - RNA
Andrea Di Gioacchino, Rachel Legendre, Yannis Rahou, Valérie Najburg, Pierre Charneau, Benjamin Greenbaum, Frédéric Tangy, Sylvie van Der Werf, Simona Cocco, Anastassia Komarova
2021 - RNA
79 AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape
Luca Sesta, Guido Uguzzoni, Jorge Fernandez-De-Cossio-Diaz, Andrea Pagnani
2021 - International Journal of Molecular Sciences
Luca Sesta, Guido Uguzzoni, Jorge Fernandez-De-Cossio-Diaz, Andrea Pagnani
2021 - International Journal of Molecular Sciences
80 Barriers and Dynamical Paths in Alternating Gibbs Sampling of Restricted Boltzmann Machines
Clément Roussel, Simona Cocco, Rémi Monasson
2021 - Physical Review E
Clément Roussel, Simona Cocco, Rémi Monasson
2021 - Physical Review E
81 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
2021 - eLife
Angela Phillips, Katherine Lawrence, Alief Moulana, Thomas Dupic, Jeffrey Chang, Milo Johnson, Ivana Cvijovic, Thierry Mora, Aleksandra Walczak, Michael Desai
2021 - eLife
82 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
2021 - PLoS Computational Biology
Barbara Bravi, Vinod P Balachandran, Benjamin D Greenbaum, Aleksandra M Walczak, Thierry Mora, Rémi Monasson, Simona Cocco
2021 - PLoS Computational Biology
83 Inferring epistasis from genomic data with comparable mutation and outcrossing rate
Hong-Li Zeng, Eugenio Mauri, Vito Dichio, Simona Cocco, Rémi Monasson, Erik Aurell
2021 - Journal of Statistical Mechanics: Theory and Experiment
Hong-Li Zeng, Eugenio Mauri, Vito Dichio, Simona Cocco, Rémi Monasson, Erik Aurell
2021 - Journal of Statistical Mechanics: Theory and Experiment
84 Antigenic waves of virus–immune coevolution
Jacopo Marchi, Michael Lässig, Aleksandra M Walczak, Thierry Mora
2021 - Proceedings of the National Academy of Sciences of the United States of America
Jacopo Marchi, Michael Lässig, Aleksandra M Walczak, Thierry Mora
2021 - Proceedings of the National Academy of Sciences of the United States of America
85 Emergent Statistical Laws in Single-Cell Transcriptomic Data
Silvia Lazzardi, Filippo Valle, Andrea Mazzolini, Antonio Scialdone, Michele Caselle, Matteo Osella
2021 - Physical Review E
Silvia Lazzardi, Filippo Valle, Andrea Mazzolini, Antonio Scialdone, Michele Caselle, Matteo Osella
2021 - Physical Review E
86 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
2021 - Molecular Biology and Evolution
Andrea Di Gioacchino, Petr Sulc, Anastassia V Komarova, Benjamin D Greenbaum, Remi Monasson, Simona Cocco
2021 - Molecular Biology and Evolution
87 Transient Chaotic Dimensionality Expansion by Recurrent Networks
Christian Keup, Tobias Kühn, David Dahmen, Moritz Helias
2021 - Physical Review X
Christian Keup, Tobias Kühn, David Dahmen, Moritz Helias
2021 - Physical Review X
88 Roadmap on biology in time varying environments
Arvind Murugan, Kabir Husain, Michael Rust, Chelsea Hepler, Joseph Bass, Julian Pietsch, Peter Swain, Siddhartha Jena, Jared Toettcher, Arup Chakraborty, Kayla Sprenger, T Mora, A Walczak, Olivier Rivoire, Shenshen Wang, Kevin Wood, Antun Skanata, Edo Kussell, Rama Ranganathan, Hong-Yan Shih, Nigel Goldenfeld
2021 - Physical Biology
Arvind Murugan, Kabir Husain, Michael Rust, Chelsea Hepler, Joseph Bass, Julian Pietsch, Peter Swain, Siddhartha Jena, Jared Toettcher, Arup Chakraborty, Kayla Sprenger, T Mora, A Walczak, Olivier Rivoire, Shenshen Wang, Kevin Wood, Antun Skanata, Edo Kussell, Rama Ranganathan, Hong-Yan Shih, Nigel Goldenfeld
2021 - Physical Biology
89 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
2021 - 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
2021 - Cell Reports
90 Deep generative selection models of T and B cell receptor repertoires with soNNia
Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
2021 - Proceedings of the National Academy of Sciences of the United States of America
Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
2021 - Proceedings of the National Academy of Sciences of the United States of America
91 Optimal prediction with resource constraints using the information bottleneck
Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie Palmer
2021 - PLoS Computational Biology
Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie Palmer
2021 - PLoS Computational Biology
92 In‐silico media optimization for continuous cultures using genome scale metabolic networks: The case of CHO‐K1
Bárbara Pérez-Fernández, Jorge Fernandez-De-Cossio-Diaz, Tammy Boggiano, Kalet León, Roberto Mulet
2021 - Biotechnology and Bioengineering
Bárbara Pérez-Fernández, Jorge Fernandez-De-Cossio-Diaz, Tammy Boggiano, Kalet León, Roberto Mulet
2021 - Biotechnology and Bioengineering
93 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
2021 - Cell Systems
Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora, Aleksandra M Walczak
2021 - Cell Systems
94 Single molecule microscopy reveals key physical features of repair foci in living cells
Judith Miné-Hattab, Mathias Heltberg, Marie Villemeur, Chloé Guedj, Thierry Mora, Aleksandra Walczak, Maxime Dahan, Angela Taddei
2021 - eLife
Judith Miné-Hattab, Mathias Heltberg, Marie Villemeur, Chloé Guedj, Thierry Mora, Aleksandra Walczak, Maxime Dahan, Angela Taddei
2021 - eLife
95 Chapter 22. Connections to Statistical Physics
Fabrizio Altarelli, Rémi Monasson, Guilhem Semerjian, Francesco Zamponi
2021 -
Fabrizio Altarelli, Rémi Monasson, Guilhem Semerjian, Francesco Zamponi
2021 -
96 Contribution of resident and circulating precursors to tumor-infiltrating CD8 + T cell populations in lung cancer
Paul Gueguen, Christina Metoikidou, Thomas Dupic, Myriam Lawand, Christel Goudot, Sylvain Baulande, Sonia Lameiras, Olivier Lantz, Nicolas Girard, Agathe Seguin-Givelet, Marine Lefevre, Thierry Mora, Aleksandra Walczak, Joshua Waterfall, Sebastian Amigorena
2021 - Science Immunology
Paul Gueguen, Christina Metoikidou, Thomas Dupic, Myriam Lawand, Christel Goudot, Sylvain Baulande, Sonia Lameiras, Olivier Lantz, Nicolas Girard, Agathe Seguin-Givelet, Marine Lefevre, Thierry Mora, Aleksandra Walczak, Joshua Waterfall, Sebastian Amigorena
2021 - Science Immunology
97 Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection
Anastasia Minervina, Ekaterina Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Mamedov, Andre Franke, Grigory Efimov, Dmitriy Chudakov, Thierry Mora, Aleksandra Walczak, Yuri Lebedev, Mikhail Pogorelyy
2021 - eLife
Anastasia Minervina, Ekaterina Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Mamedov, Andre Franke, Grigory Efimov, Dmitriy Chudakov, Thierry Mora, Aleksandra Walczak, Yuri Lebedev, Mikhail Pogorelyy
2021 - eLife
98 Gaussian Closure Scheme in the Quasi--Linkage Equilibrium Regime of Evolving Genome Populations
Eugenio Mauri, Simona Cocco, Rémi Monasson
2021 - EPL - Europhysics Letters
Eugenio Mauri, Simona Cocco, Rémi Monasson
2021 - EPL - Europhysics Letters
99 Survival probability and size of lineages in antibody affinity maturation
Marco Molari, Rémi Monasson, Simona Cocco
2021 - Physical Review E
Marco Molari, Rémi Monasson, Simona Cocco
2021 - Physical Review E
100 Parameters and determinants of responses to selection in antibody libraries
Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire
2021 - PLoS Computational Biology
Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire
2021 - PLoS Computational Biology
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