•Statistical physics

Statistical physics and inference for biology

Publications

Statistical physics and inference for biology

1 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

2 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

3 Barriers and Dynamical Paths in Alternating Gibbs Sampling of Restricted Boltzmann Machines
Clément Roussel, Simona Cocco, Rémi Monasson
2021 - Physical Review E

4 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

5 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

6 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

7 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

8 Emergent Statistical Laws in Single-Cell Transcriptomic Data
Silvia Lazzardi, Filippo Valle, Andrea Mazzolini, Antonio Scialdone, Michele Caselle, Matteo Osella
2021 - Physical Review E

9 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

10 Transient Chaotic Dimensionality Expansion by Recurrent Networks
Christian Keup, Tobias Kühn, David Dahmen, Moritz Helias
2021 - Physical Review X

11 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

12 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

13 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

14 Optimal prediction with resource constraints using the information bottleneck
Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie Palmer
2021 - PLoS Computational Biology

15 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

16 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

17 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

18 Chapter 22. Connections to Statistical Physics
Fabrizio Altarelli, Rémi Monasson, Guilhem Semerjian, Francesco Zamponi
2021 -

19 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

20 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

21 Gaussian closure scheme for evolving genomes: application to double-peak fitness landscape with short-range epistasis
Eugenio Mauri, Simona Cocco, Rémi Monasson
2021 - EPL - Europhysics Letters

22 Survival probability and size of lineages in antibody affinity maturation
Marco Molari, Rémi Monasson, Simona Cocco
2021 - Physical Review E

23 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

24 Immune fingerprinting through repertoire similarity
Thomas Dupic, Meriem Bensouda Koraichi, Anastasia Minervina, Mikhail Pogorelyy, Thierry Mora, Aleksandra Walczak
2021 - PLoS Genetics

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Publications

Statistical physics