Thierry Mora, PhD - Publications


88 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Isacchini G, Walczak AM, Mora T, Nourmohammad A. Deep generative selection models of T and B cell receptor repertoires with soNNia. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33795515 DOI: 10.1073/pnas.2023141118  1
2021 Sachdeva V, Mora T, Walczak AM, Palmer SE. Optimal prediction with resource constraints using the information bottleneck. Plos Computational Biology. 17: e1008743. PMID 33684112 DOI: 10.1371/journal.pcbi.1008743  1
2021 Miné-Hattab J, Heltberg M, Villemeur M, Guedj C, Mora T, Walczak AM, Dahan M, Taddei A. Single molecule microscopy reveals key physical features of repair foci in living cells. Elife. 10. PMID 33543712 DOI: 10.7554/eLife.60577  1
2021 Gueguen P, Metoikidou C, Dupic T, Lawand M, Goudot C, Baulande S, Lameiras S, Lantz O, Girard N, Seguin-Givelet A, Lefevre M, Mora T, Walczak AM, Waterfall JJ, Amigorena S. Contribution of resident and circulating precursors to tumor-infiltrating CD8 T cell populations in lung cancer. Science Immunology. 6. PMID 33514641 DOI: 10.1126/sciimmunol.abd5778  1
2021 Murugan A, Husain K, Rust M, Bass JT, Hepler C, Pietsch JMJ, Swain PS, Toettcher JE, Jena S, Chakraborty AK, Sprenger KG, Mora T, Walczak A, Rivoire O, Wang S, et al. Roadmap on biology in time varying environments. Physical Biology. PMID 33477124 DOI: 10.1088/1478-3975/abde8d  1
2021 Minervina AA, Komech EA, Titov A, Bensouda Koraichi M, Rosati E, Mamedov IZ, Franke A, Efimov GA, Chudakov DM, Mora T, Walczak AM, Lebedev YB, Pogorelyy MV. Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection. Elife. 10. PMID 33399535 DOI: 10.7554/eLife.63502  1
2021 Dupic T, Bensouda Koraichi M, Minervina AA, Pogorelyy MV, Mora T, Walczak AM. Immune fingerprinting through repertoire similarity. Plos Genetics. 17: e1009301. PMID 33395405 DOI: 10.1371/journal.pgen.1009301  1
2020 Bravi B, Tubiana J, Cocco S, Monasson R, Mora T, Walczak AM. RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles. Cell Systems. PMID 33338400 DOI: 10.1016/j.cels.2020.11.005  1
2020 Sethna Z, Isacchini G, Dupic T, Mora T, Walczak AM, Elhanati Y. Population variability in the generation and selection of T-cell repertoires. Plos Computational Biology. 16: e1008394. PMID 33296360 DOI: 10.1371/journal.pcbi.1008394  1
2020 Spisak N, Walczak AM, Mora T. Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data. Nucleic Acids Research. PMID 33035336 DOI: 10.1093/nar/gkaa825  1
2020 Isacchini G, Olivares C, Nourmohammad A, Walczak AM, Mora T. SOS: online probability estimation and generation of T-and B-cell receptors. Bioinformatics (Oxford, England). PMID 32814974 DOI: 10.1093/Bioinformatics/Btaa574  1
2020 Isacchini G, Sethna Z, Elhanati Y, Nourmohammad A, Walczak AM, Mora T. Generative models of T-cell receptor sequences. Physical Review. E. 101: 062414. PMID 32688532 DOI: 10.1103/Physreve.101.062414  1
2020 Puelma Touzel M, Walczak AM, Mora T. Inferring the immune response from repertoire sequencing. Plos Computational Biology. 16: e1007873. PMID 32348312 DOI: 10.1371/Journal.Pcbi.1007873  1
2020 Minervina AA, Pogorelyy MV, Komech EA, Karnaukhov VK, Bacher P, Rosati E, Franke A, Chudakov D, Mamedov IZ, Lebedev YB, Mora T, Walczak AM. Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones. Elife. 9. PMID 32081129 DOI: 10.7554/Elife.53704  1
2020 Kreer C, Gruell H, Mora T, Walczak AM, Klein F. Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies. Vaccines. 8. PMID 31906351 DOI: 10.3390/Vaccines8010013  1
2019 Marchi J, Galpern EA, Espada R, Ferreiro DU, Walczak AM, Mora T. Size and structure of the sequence space of repeat proteins. Plos Computational Biology. 15: e1007282. PMID 31415557 DOI: 10.1371/Journal.Pcbi.1007282  1
2019 Marchi J, Lässig M, Mora T, Walczak AM. Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems. Pathogens (Basel, Switzerland). 8. PMID 31362404 DOI: 10.3390/Pathogens8030115  1
2019 Nourmohammad A, Otwinowski J, Łuksza M, Mora T, Walczak AM. Fierce selection and interference in B-cell repertoire response to chronic HIV-1. Molecular Biology and Evolution. PMID 31209469 DOI: 10.1093/Molbev/Msz143  1
2019 Pogorelyy MV, Minervina AA, Shugay M, Chudakov DM, Lebedev YB, Mora T, Walczak AM. Detecting T cell receptors involved in immune responses from single repertoire snapshots. Plos Biology. 17: e3000314. PMID 31194732 DOI: 10.1371/Journal.Pbio.3000314  1
2019 Mayer A, Balasubramanian V, Walczak AM, Mora T. How a well-adapting immune system remembers. Proceedings of the National Academy of Sciences of the United States of America. PMID 30988203 DOI: 10.1073/Pnas.1812810116  1
2019 Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review. E. 99: 022423. PMID 30934315 DOI: 10.1103/Physreve.99.022423  0.72
2019 Bradde S, Mora T, Walczak AM. Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 374: 20180095. PMID 30905281 DOI: 10.1098/Rstb.2018.0095  1
2019 Dupic T, Marcou Q, Walczak AM, Mora T. Genesis of the αβ T-cell receptor. Plos Computational Biology. 15: e1006874. PMID 30830899 DOI: 10.1371/Journal.Pcbi.1006874  1
2019 Sethna Z, Elhanati Y, Callan CG, Walczak AM, Mora T. OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs. Bioinformatics (Oxford, England). PMID 30657870 DOI: 10.1093/Bioinformatics/Btz035  1
2019 Gardella C, Marre O, Mora T. Modeling the Correlated Activity of Neural Populations: A Review. Neural Computation. 31: 233-269. PMID 30576613 DOI: 10.1162/Neco_A_01154  0.72
2018 Adams RM, Kinney JB, Walczak AM, Mora T. Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy. Cell Systems. PMID 30611676 DOI: 10.1016/J.Cels.2018.12.004  1
2018 Rossi NA, Mora T, Walczak AM, Dunlop MJ. Active degradation of MarA controls coordination of its downstream targets. Plos Computational Biology. 14: e1006634. PMID 30589845 DOI: 10.1371/Journal.Pcbi.1006634  1
2018 Pogorelyy MV, Minervina AA, Touzel MP, Sycheva AL, Komech EA, Kovalenko EI, Karganova GG, Egorov ES, Komkov AY, Chudakov DM, Mamedov IZ, Mora T, Walczak AM, Lebedev YB. Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins. Proceedings of the National Academy of Sciences of the United States of America. PMID 30459272 DOI: 10.1073/Pnas.1809642115  1
2018 Magadan S, Jouneau L, Puelma Touzel M, Marillet S, Chara W, Six A, Quillet E, Mora T, Walczak AM, Cazals F, Sunyer O, Fillatreau S, Boudinot P. Origin of Public Memory B Cell Clones in Fish After Antiviral Vaccination. Frontiers in Immunology. 9: 2115. PMID 30319606 DOI: 10.3389/Fimmu.2018.02115  1
2018 Ferrari U, Deny S, Marre O, Mora T. A Simple Model for Low Variability in Neural Spike Trains. Neural Computation. 1-28. PMID 30148708 DOI: 10.1162/Neco_A_01125  0.72
2018 Toledano A, Elhanati Y, Benichou JIC, Walczak AM, Mora T, Louzoun Y. Evidence for Shaping of Light Chain Repertoire by Structural Selection. Frontiers in Immunology. 9: 1307. PMID 29988361 DOI: 10.3389/Fimmu.2018.01307  1
2018 Elhanati Y, Sethna Z, Callan CG, Mora T, Walczak AM. Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination. Immunological Reviews. 284: 167-179. PMID 29944757 DOI: 10.1111/Imr.12665  1
2018 Pogorelyy MV, Minervina AA, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM. Method for identification of condition-associated public antigen receptor sequences. Elife. 7. PMID 29533178 DOI: 10.7554/Elife.33050  1
2018 Gardella C, Marre O, Mora T. Blindfold learning of an accurate neural metric. Proceedings of the National Academy of Sciences of the United States of America. PMID 29531065 DOI: 10.1073/Pnas.1718710115  0.72
2018 Marcou Q, Mora T, Walczak AM. High-throughput immune repertoire analysis with IGoR. Nature Communications. 9: 561. PMID 29422654 DOI: 10.1038/S41467-018-02832-W  1
2018 Marcou Q, Carmi-Levy I, Trichot C, Soumelis V, Mora T, Walczak A. A model for the integration of conflicting exogenous and endogenous signals by dendritic cells. Physical Biology. PMID 29360100 DOI: 10.1088/1478-3975/Aaaa0A  1
2017 Ferrari U, Gardella C, Marre O, Mora T. Closed-Loop Estimation of Retinal Network Sensitivity by Local Empirical Linearization. Eneuro. 4. PMID 29379871 DOI: 10.1523/Eneuro.0166-17.2017  0.72
2017 Mayer A, Mora T, Rivoire O, Walczak AM. Transitions in optimal adaptive strategies for populations in fluctuating environments. Physical Review. E. 96: 032412. PMID 29346942 DOI: 10.1103/Physreve.96.032412  1
2017 Mayer A, Rivoire O, Mora T, Walczak A. [Evolutionary explanation of the diversity of immune strategies]. Medecine Sciences : M/S. 33: 593-595. PMID 28990557 DOI: 10.1051/Medsci/20173306012  1
2017 Pogorelyy MV, Elhanati Y, Marcou Q, Sycheva AL, Komech EA, Nazarov VI, Britanova OV, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM. Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires. Plos Computational Biology. 13: e1005572. PMID 28683116 DOI: 10.1371/Journal.Pcbi.1005572  1
2017 Ren Z, Ma S, Jin L, Liu Z, Liu D, Zhang X, Cai Q, Yang X. Repairing a bone defect with a three-dimensional cellular construct composed of a multi-layered cell sheet on electrospun mesh. Biofabrication. 9: 025036. PMID 28631613 DOI: 10.1088/1758-5090/aa747f  0.32
2017 Espada R, Parra RG, Mora T, Walczak AM, Ferreiro DU. Inferring repeat-protein energetics from evolutionary information. Plos Computational Biology. 13: e1005584. PMID 28617812 DOI: 10.1371/Journal.Pcbi.1005584  1
2017 Fisher CK, Mora T, Walczak AM. Variable habitat conditions drive species covariation in the human microbiota. Plos Computational Biology. 13: e1005435. PMID 28448493 DOI: 10.1371/Journal.Pcbi.1005435  1
2017 Sethna Z, Elhanati Y, Dudgeon CS, Callan CG, Levine AJ, Mora T, Walczak AM. Insights into immune system development and function from mouse T-cell repertoires. Proceedings of the National Academy of Sciences of the United States of America. PMID 28196891 DOI: 10.1073/Pnas.1700241114  1
2016 Adams RM, Mora T, Walczak AM, Kinney JB. Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. Elife. 5. PMID 28035901 DOI: 10.7554/Elife.23156  1
2016 Mora T, Walczak AM, Castello LD, Ginelli F, Melillo S, Parisi L, Viale M, Cavagna A, Giardina I. Local equilibrium in bird flocks. Nature Physics. 12: 1153-1157. PMID 27917230 DOI: 10.1038/Nphys3846  1
2016 Gardella C, Marre O, Mora T. A Tractable Method for Describing Complex Couplings between Neurons and Population Rate. Eneuro. 3. PMID 27570827 DOI: 10.1523/Eneuro.0160-15.2016  0.72
2016 Mayer A, Mora T, Rivoire O, Walczak AM. Diversity of immune strategies explained by adaptation to pathogen statistics. Proceedings of the National Academy of Sciences of the United States of America. PMID 27432970 DOI: 10.1073/Pnas.1600663113  1
2016 Mora T, Walczak AM. Rényi entropy, abundance distribution, and the equivalence of ensembles. Physical Review. E. 93: 052418. PMID 27300934 DOI: 10.1103/Physreve.93.052418  1
2016 Elhanati Y, Marcou Q, Mora T, Walczak AM. repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data. Bioinformatics (Oxford, England). PMID 27153709 DOI: 10.1093/Bioinformatics/Btw112  1
2016 Mora T, Peliti L, Rivoire O. JSP Special Issue on Information Processing in Living Systems Journal of Statistical Physics. 1-3. DOI: 10.1007/S10955-016-1459-2  1
2015 Desponds J, Mora T, Walczak AM. Fluctuating fitness shapes the clone-size distribution of immune repertoires. Proceedings of the National Academy of Sciences of the United States of America. PMID 26711994 DOI: 10.1073/Pnas.1512977112  1
2015 Espada R, Parra RG, Sippl MJ, Mora T, Walczak AM, Ferreiro DU. Repeat proteins challenge the concept of structural domains. Biochemical Society Transactions. 43: 844-9. PMID 26517892 DOI: 10.1042/Bst20150083  1
2015 Bagnara D, Squillario M, Kipling D, Mora T, Walczak AM, Da Silva L, Weller S, Dunn-Walters DK, Weill JC, Reynaud CA. A Reassessment of IgM Memory Subsets in Humans. Journal of Immunology (Baltimore, Md. : 1950). 195: 3716-24. PMID 26355154 DOI: 10.4049/Jimmunol.1500753  1
2015 Tkačik G, Mora T, Marre O, Amodei D, Palmer SE, Berry MJ, Bialek W. Thermodynamics and signatures of criticality in a network of neurons. Proceedings of the National Academy of Sciences of the United States of America. 112: 11508-13. PMID 26330611 DOI: 10.1073/Pnas.1514188112  1
2015 Mora T. Physical Limit to Concentration Sensing Amid Spurious Ligands. Physical Review Letters. 115: 038102. PMID 26230828 DOI: 10.1103/Physrevlett.115.038102  1
2015 Elhanati Y, Sethna Z, Marcou Q, Callan CG, Mora T, Walczak AM. Inferring processes underlying B-cell repertoire diversity. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370. PMID 26194757 DOI: 10.1098/Rstb.2014.0243  1
2015 Espada R, Parra RG, Mora T, Walczak AM, Ferreiro DU. Capturing coevolutionary signals inrepeat proteins. Bmc Bioinformatics. 16: 207. PMID 26134293 DOI: 10.1186/S12859-015-0648-3  1
2015 Mayer A, Balasubramanian V, Mora T, Walczak AM. How a well-adapted immune system is organized. Proceedings of the National Academy of Sciences of the United States of America. 112: 5950-5. PMID 25918407 DOI: 10.1073/Pnas.1421827112  1
2015 Mora T, Deny S, Marre O. Dynamical criticality in the collective activity of a population of retinal neurons. Physical Review Letters. 114: 078105. PMID 25763977 DOI: 10.1103/Physrevlett.114.078105  1
2015 Marre O, Botella-Soler V, Simmons KD, Mora T, Tkačik G, Berry MJ. High Accuracy Decoding of Dynamical Motion from a Large Retinal Population Plos Computational Biology. 11. DOI: 10.1371/journal.pcbi.1004304  1
2014 Lang AH, Fisher CK, Mora T, Mehta P. Thermodynamics of statistical inference by cells. Physical Review Letters. 113: 148103. PMID 25325665 DOI: 10.1103/Physrevlett.113.148103  1
2014 Elhanati Y, Murugan A, Callan CG, Mora T, Walczak AM. Quantifying selection in immune receptor repertoires. Proceedings of the National Academy of Sciences of the United States of America. 111: 9875-80. PMID 24941953 DOI: 10.1073/Pnas.1409572111  1
2014 Santolini M, Mora T, Hakim V. A general pairwise interaction model provides an accurate description of in vivo transcription factor binding sites. Plos One. 9: e99015. PMID 24926895 DOI: 10.1371/Journal.Pone.0099015  1
2014 Cavagna A, Giardina I, Ginelli F, Mora T, Piovani D, Tavarone R, Walczak AM. Dynamical maximum entropy approach to flocking. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 89: 042707. PMID 24827278 DOI: 10.1103/Physreve.89.042707  1
2014 Bialek W, Cavagna A, Giardina I, Mora T, Pohl O, Silvestri E, Viale M, Walczak AM. Social interactions dominate speed control in poising natural flocks near criticality. Proceedings of the National Academy of Sciences of the United States of America. 111: 7212-7. PMID 24785504 DOI: 10.1073/Pnas.1324045111  1
2014 Cavagna A, Del Castello L, Giardina I, Grigera T, Jelic A, Melillo S, Mora T, Parisi L, Silvestri E, Viale M, Walczak AM. Flocking and Turning: a New Model for Self-organized Collective Motion Journal of Statistical Physics. 158: 601-627. DOI: 10.1007/S10955-014-1119-3  1
2013 Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P. The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis. Frontiers in Immunology. 4: 413. PMID 24348479 DOI: 10.3389/Fimmu.2013.00413  1
2013 Julou T, Mora T, Guillon L, Croquette V, Schalk IJ, Bensimon D, Desprat N. Cell-cell contacts confine public goods diffusion inside Pseudomonas aeruginosa clonal microcolonies. Proceedings of the National Academy of Sciences of the United States of America. 110: 12577-82. PMID 23858453 DOI: 10.1073/Pnas.1301428110  1
2013 Mora T, Walczak AM. Effect of phenotypic selection on stochastic gene expression. The Journal of Physical Chemistry. B. 117: 13194-205. PMID 23795617 DOI: 10.1021/Jp403231F  1
2013 Stephens GJ, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural images. Physical Review Letters. 110: 018701. PMID 23383852 DOI: 10.1103/Physrevlett.110.018701  1
2013 Tka?ik G, Marre O, Mora T, Amodei D, Berry MJ, Bialek W. The simplest maximum entropy model for collective behavior in a neural network Journal of Statistical Mechanics: Theory and Experiment. 2013. DOI: 10.1088/1742-5468/2013/03/P03011  1
2012 Murugan A, Mora T, Walczak AM, Callan CG. Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proceedings of the National Academy of Sciences of the United States of America. 109: 16161-6. PMID 22988065 DOI: 10.1073/Pnas.1212755109  1
2012 Mora T, Walczak AM, Zamponi F. Transition path sampling algorithm for discrete many-body systems. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 85: 036710. PMID 22587212 DOI: 10.1103/Physreve.85.036710  1
2012 Bialek W, Cavagna A, Giardina I, Mora T, Silvestri E, Viale M, Walczak AM. Statistical mechanics for natural flocks of birds. Proceedings of the National Academy of Sciences of the United States of America. 109: 4786-91. PMID 22427355 DOI: 10.1073/Pnas.1118633109  1
2011 Mora T, Bai F, Che YS, Minamino T, Namba K, Wingreen NS. Non-genetic individuality in Escherichia coli motor switching. Physical Biology. 8: 024001. PMID 21422514 DOI: 10.1088/1478-3975/8/2/024001  1
2011 Mora T, Bialek W. Are Biological Systems Poised at Criticality? Journal of Statistical Physics. 144: 268-302. DOI: 10.1007/S10955-011-0229-4  1
2010 Mora T, Wingreen NS. Limits of sensing temporal concentration changes by single cells. Physical Review Letters. 104: 248101. PMID 20867338 DOI: 10.1103/Physrevlett.104.248101  1
2010 Mora T, Walczak AM, Bialek W, Callan CG. Maximum entropy models for antibody diversity. Proceedings of the National Academy of Sciences of the United States of America. 107: 5405-10. PMID 20212159 DOI: 10.1073/Pnas.1001705107  1
2009 Mora T, Yu H, Wingreen NS. Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor. Physical Review Letters. 103: 248102. PMID 20366231 DOI: 10.1103/Physrevlett.103.248102  1
2009 Mora T, Yu H, Sowa Y, Wingreen NS. Steps in the bacterial flagellar motor. Plos Computational Biology. 5: e1000540. PMID 19851449 DOI: 10.1371/Journal.Pcbi.1000540  1
2009 Mézard M, Mora T. Constraint satisfaction problems and neural networks: A statistical physics perspective. Journal of Physiology, Paris. 103: 107-13. PMID 19616623 DOI: 10.1016/J.Jphysparis.2009.05.013  1
2008 Daudé H, Mézard M, Mora T, Zecchina R. Pairs of SAT-assignments in random Boolean formulæ Theoretical Computer Science. 393: 260-279. DOI: 10.1016/J.Tcs.2008.01.005  1
2008 Mora T, Zdeborová L. Random subcubes as a toy model for constraint satisfaction problems Journal of Statistical Physics. 131: 1121-1138. DOI: 10.1007/S10955-008-9543-X  1
2006 Mora T, Rivoire O. Statistical mechanics of error exponents for error-correcting codes. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 74: 056110. PMID 17279971 DOI: 10.1103/Physreve.74.056110  1
2006 Mora T, Boudaoud A. Buckling of swelling gels. The European Physical Journal. E, Soft Matter. 20: 119-24. PMID 16779528 DOI: 10.1140/Epje/I2005-10124-5  1
2006 Mora T, Mézard M. Geometrical organization of solutions to random linear Boolean equations Journal of Statistical Mechanics: Theory and Experiment. DOI: 10.1088/1742-5468/2006/10/P10007  1
2005 Mézard M, Mora T, Zecchina R. Clustering of solutions in the random satisfiability problem. Physical Review Letters. 94: 197205. PMID 16090207 DOI: 10.1103/Physrevlett.94.197205  1
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