1. X. Chen, M. Winiarski, A. Puścian, E. Knapska, T. Mora, A. M. Walczak
    Modelling collective behavior in groups of mice housed under semi-naturalistic conditions

    bioRxiv (2023)

  2. G. Isacchini, V. Quiniou, H. Vantomme, P. Stys, E. Mariotti-Ferandiz, D. Klatzmann, A.M. Walczak, T. Mora, A. Nourmohammad
    Variability in the local and global composition of human T-cell receptor repertoires during thymic development across cell types and individuals

    arXiv (2023)

  3. B. Meynard-Piganeau, C. Feinauer, M. Weigt, A. M. Walczak, T. Mora
    TULIP - a Transformer based Unsupervised Language model for Interacting Peptides and T-cell receptors that generalizes to unseen epitopes

    bioRxiv (2023)

  4. F. Camaglia, I. Nemenman, T. Mora, A.M. Walczak
    Bayesian estimation of the Kullback-Leibler divergence for categorical sytems using mixtures of Dirichlet priors

    arXiv (2023)

  5. T. Mora, A.M. Walczak
    Quantitative theory of viral-immune coevolution may be within reach

    PRX Life 1 011001 (2023) [pdf] [arXiv]

  6. V. Chardès, A. Mazzolini, T. Mora, A.M. Walczak
    Evolutionary stability of antigenically escaping viruses

    arXiv (2023)

  7. T. Mora, A.M. Walczak
    Towards a quantitative theory of tolerance

    arXiv (2023)

  8. L. Hahn, A.M. Walczak, T. Mora
    Dynamical information synergy in biochemical signaling networks

    arXiv (2023)

  9. N. Spisak, T. Mora, A.M. Walczak
    Combining mutation and recombination statistics to infer clonal families in antibody repertoires

    arXiv (2022)

  10. J. Urbanus, J. Cosgrove, J. Beltman, Y. Elhanati, R. de Andrade Moral, C. Conrad, J.W. van Heijst, E. Tubeuf, A. Velds, L. Kok, C. Merle, J.P. Magnusson, J. Frisén, S. Fre, A.M. Walczak, T. Mora, H, Jacobs, T.N. Schumacher, Leila Perié
    DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age

    Nature Communications 14 2184 (2023) [pdf] [bioRxiv]

  11. B. Bravi, A. Di Gioacchino, J. Fernandez-de-Cossio-Diaz, A.M. Walczak, T. Mora, S. Cocco, R. Monasson
    Learning the differences: a transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity

    bioRxiv (2022)

  12. G. Mahuas, O. Marre, T. Mora, U. Ferrari
    A small-correlation expansion to quantify information in noisy sensory systems

    Phys. Rev. E 108 024406 (2023) [pdf] [arXiv]

  13. P. Meysman, J. Barton, B. Bravi, L. Cohen-Lavi, V. Karnaukhov, E. Lilleskov, A. Montemurro, M. Nielsen, T. Mora, P. Pereira, A. Postovskaya, M. Rodríguez Martínez, J. Fernandez-de-Cossio-Diaz, A. Vujkovic, A.M. Walczak, A. Weber, R. Yin, A. Eugster, V. Sharma
    Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

    ImmunoInformatics 9:100024 (2023) [pdf] [bioRxiv]

  14. X. Chen, M. Winiarski, A. Puscian, E. Knapska, A. M. Walczak, T. Mora
    Generalized Glauber dynamics for inference in biology

    arXiv (2022)

  15. A. Mazzolini, T. Mora, A.M. Walczak
    Inspecting the interaction between HIV and the immune system through genetic turnover

    Phil. Trans. R. Soc. B 378:20220056 (2023) [pdf] [arXiv]

  16. C. Kreer, C. Lupo, M.S. Ercanoglu, L. Gieselmann, N. Spisak, J. Grossbach, M. Schlotz, P. Schommers, H. Gruell, L. Dold, A. Beyer, A. Nourmohammad, T. Mora, A.M. Walczak, F. Klein
    Determining probabilities of HIV-1 bNAb development in healthy and chronically infected individuals

    bioRxiv (2022)

  17. X. Chen, F. Ginoux, T. Mora, A.M. Walczak, C. Wyart
    Granger causality analysis for calcium transients in neuronal networks: challenges and improvements

    eLife 12:e81279 (2023) [pdf] [bioRxiv]

  18. M. Łuksza, Z.M. Sethna, L.A. Rojas, J. Lihm, B. Bravi, Y. Elhanati, K. Soares, M. Amisaki, A. Dobrin, D. Hoyos, P. Guasp, A. Zebboudj, R. Yu, A. Kaya Chandra, T. Waters, Z. Odgerel, J. Leung, R. Kappagantula, A. Makohon-Moore, A. Johns, A. Gill, M. Gigoux, J. Wolchok, T. Merghoub, M. Sadelain, E. Patterson, R. Monasson, T. Mora, A.M. Walczak, S. Cocco, C. Iacobuzio-Donahue, B.D. Greenbaum & V.P. Balachandran
    Neoantigen quality predicts immunoediting in survivors of pancreatic cancer

    Nature 606389 (2022) [pdf]

  19. F. Ferretti, S. Grosse-Holz, C. Holmes, J.L. Shivers, I. Giardina, T. Mora, A.M. Walczak
    Signatures of irreversibility in microscopic models of flocking

    Phys Rev E 106 034608 (2022) [pdf] [arXiv]

  20. M. Bensouda Koraichi, S. Ferri, A.M. Walczak, T. Mora
    Inferring the T-cells repertoire dynamics of healthy individuals

    Proc Natl Acad Sci 120(4) e2207516120 (2023) [pdf] [bioRxiv]

  21. E.A. Galpern, J. Marchi, T. Mora, A.M. Walczak, D.U. Ferreiro
    Evolution and folding of repeat proteins

    Proc Natl Acad Sci 119(31) e2204131119 (2022) [pdf] [arXiv]

  22. F. Camaglia, A. Ryvkin, E. Greenstein, S. Reich-Zeliger, B. Chain, T. Mora, A. M. Walczak, N. Friedman
    Quantifying changes in the T cell receptor repertoire during thymic development

    eLife 12e81622 (2023) [pdf] [bioRxiv]

  23. M. Ruiz Ortega, N. Spisak, T. Mora, A. M. Walczak
    Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals

    PLoS Genet 19(2):e1010652 (2023) [pdf] [bioRxiv]

  24. C. Lupo, N. Spisak, A. M. Walczak, T. Mora
    Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies

    PLoS Comput Biol 18(6) e1010167 (2022) [pdf] [arXiv]

  25. M.A. Goldin, B. Lefebvre, S. Virgili, A. Ecker, T. Mora, U. Ferrari, O. Marre
    Context-dependent selectivity to natural scenes in the retina

    Nat. Comm. 135556 (2022) [pdf] [bioRxiv]

  26. V. Chardès, M. Vergassola, A.M. Walczak, T. Mora
    Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints

    Proc Natl Acad Sci 119(8) e2113512119 (2021) [pdf] [arXiv]

  27. G. Isacchini, N. Spisak, A. Nourmohammad*, T. Mora*, A.M. Walczak*
    Mutual information maximization for amortized likelihood inference from sampled trajectories: MINIMALIST

    Phys. Rev. E 105 055309 (2022) [pdf] [arXiv]

  28. A.M. Phillips, K.R. Lawrence, A. Moulana, T. Dupic, J. Chang, M. S. Johnson, I. Cvijovic, T. Mora, A.M. Walczak, M.M. Desai
    Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

    eLife 10 e71393 (2021) [pdf] [bioRxiv]

  29. M.L. Heltberg, J. Miné-Hattab, A. Taddei, A.M. Walczak*, T. Mora*
    Physical observables to determine the nature of membrane-less cellular sub-compartments

    eLife 10 e69181 (2021) [pdf] [arXiv]

  30. M. Bensouda Koraichi, M. Puelma Touzel, T. Mora*, A.M. Walczak*
    NoisET: Noise Learning and Expansion Detection of T-Cell Receptors

    J. Phys. Chem. A 126(40) 7407 (2022) [pdf] [arXiv]

  31. J. Marchi, M. Lässig, A.M. Walczak*, T. Mora*
    Antigenic waves of virus-immune co-evolution

    Proc Natl Acad Sci 118(27) e2103398118 (2021) [pdf] [arXiv]

  32. P. Gueguen, C. Metoikidou, T. Dupic, M. Lawand, C. Goudot, S. Baulande, S. Lameiras, O. Lantz, N. Girard, A. Seguin-Givelet, M. Lefevre, T. Mora, A.M. Walczak, J.J. Waterfall, S. Amigorena
    Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer

    Science Immunology 6(55) eabd5778 (2021) [pdf] [bioRxiv]

  33. F. Ferretti, V. Chardès, T. Mora, A.M. Walczak, T. Giardina
    Renormalization group approach to connect discrete-and continuous-time descriptions of Gaussian processes

    Phys. Rev. E 105 044133 (2022) [pdf] [arXiv]

  34. B. Bravi, V.P. Balachandran, B.D. Greenbaum, A.M. Walczak, T. Mora, R. Monasson, S. Cocco
    Probing T-cell response by sequence-based probabilistic modeling

    PLoS Computational Biology 17(9) e1009297 (2021) [pdf] [bioRxiv]

  35. D. Conti, T. Mora
    Non-equilibrium dynamics of adaptation in sensory systems

    Phys. Rev. E 106 054404 (2022) [pdf] [arXiv]

  36. G. Isacchini, A.M Walczak, T. Mora, Armita Nourmohammad
    Deep generative selection models of T and B cell receptor repertoires with soNNia

    Proc Natl Acad Sci 118(14) e2023141118 (2021) [pdf] [arXiv]

  37. Natanael Spisak, A.M. Walczak, T. Mora
    Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data

    Nucleic Acids Research 48 (19) 10702-10712 (2020) [pdf] [arXiv]

  38. T. Dupic, M. Bensouda Koraichi, A. Minervina, M. Pogorelyy, T. Mora, A.M. Walczak
    Immune fingerprinting through repertoire similarity

    PLoS Genetics 17 (1) e1009301 (2021) [pdf] [arXiv]

  39. G. Mahuas, G. Isacchini, O. Marre, U. Ferrari, T. Mora
    A new inference approach for training shallow and deep generalized linear models of noisy interacting neurons

    NeurIPS 2020 [arXiv]

  40. J. Miné-Hattab, M. Heltberg, M. Villemeur, C. Guedj, T. Mora, A. M. Walczak, M. Dahan, A. Taddei
    Single molecule microscopy reveals key physical features of repair foci in living cells

    eLife 10 e60577 (2021) [pdf] [bioRxiv]

  41. A.A. Minervina, E.A. Komech, A. Titov, M. Bensouda Koraichi, E. Rosati, I.Z. Mamedov, A.Franke, G.A. Efimov, D.M. Chudakov, T.Mora, A.M. Walczak, Y.B. Lebedev, M.V. Pogorelyy
    Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection

    eLife 10 e63502 (2020) [pdf] [arXiv]

  42. V. Sachdeva, T. Mora, A.M. Walczak, S. Palmer
    Optimal prediction with resource constraints using the information bottleneck

    PLoS Computational Biology 17(3) e1008743 (2021) [pdf] [bioRxiv]

  43. B. Bravi, J. Tubiana, S. Cocco, R. Monasson, T. Mora, A.M. Walczak
    RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles

    Cell Systems 12 1-8 (2020) [pdf] [bioRxiv]

  44. G. Isacchini, C. Olivares, A. Nourmohammad, A.M. Walczak, T. Mora
    SOS: Online probability estimation and generation of T and B cell receptors

    Bioinformatics 36(16) 4510-4512 (2020) [pdf] [arXiv]

  45. Z. Sethna, G. Isacchini, T. Dupic, T. Mora, A.M. Walczak, Y. Elhanati
    Population variability in the generation and thymic selection of T-cell repertoires

    PLoS Computational Biology 16(12) e1008394 (2020) [pdf] [arXiv]

  46. C. Kreer, H. Gruell, T. Mora, A.M. Walczak, F. Klein
    Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies

    Vaccines 8(1) 13 (2020) [pdf]

  47. F. Ferretti, V. Chardès, T. Mora, A.M. Walczak, I. Giardina
    Building general Langevin models from discrete data sets

    Phys Rev X 10 031018 (2020) [pdf] [arXiv]

  48. M. Puelma Touzel, A.M. Walczak, T. Mora
    Inferring the immune response from repertoire sequencing

    PLoS Computational Biology 16(4) e1007873 (2020) [pdf] [arXiv]

  49. G. Isacchini, Z. Sethna, Y. Elhanati, A. Nourmohammad, A.M. Walczak, T. Mora
    Generative models of T-cell receptor sequences

    Phys Rev E 101 062414 (2020) [pdf] [arXiv]

  50. A.A. Minervina, M.V. Pogorelyy, E.A. Komech, V.K. Karnaukhov, P. Bacher, E. Rosati, A. Franke, D.M. Chudakov, I.Z. Mamedov, Y.B. Lebedev, T. Mora, A.M. Walczak
    Comprehensive analysis of antiviral adaptive immunity formation and reactivation down to single-cell level

    eLife 2020;9:e53704 (2020) [pdf] [arXiv]

  51. T. Mora, I. Nemenman
    Physical limit to concentration sensing in a changing environment

    Phys. Rev. Lett. 123 198101 (2019) [pdf] [arXiv]

    See also the synopsis in Physics:
    A Biological Cell As a Chemical Sensor

  52. T. Mora, A.M. Walczak
    How many different clonotypes do immune repertoires contain?

    Current Opinion in Systems Biology 18 104 (2019) [pdf] [arXiv]

  53. G. Altan-Bonnet*, T. Mora*, A.M. Walczak*
    Quantitative Immunology for Physicists

    Physics Reports, 849 1-83 (2020) [pdf] [arXiv]

  54. J. Marchi, M. Lässig, T. Mora*, A.M. Walczak*
    Multi-lineage evolution in viral populations driven by host immune systems

    Pathogens 8 115 (2019) [pdf] [arXiv]

  55. J. Marchi, E.A. Galpern, R. Espada, D.U. Ferreiro, A.M. Walczak*, T. Mora*
    Size and structure of the sequence space of repeat proteins

    PLoS Comp. Biol. 15(8): e1007282 (2019) [pdf] [arXiv]

  56. S. Bradde, T. Mora*, A. M. Walczak*
    Cost and benefits of CRISPR spacer acquisition

    Phil. Trans. R. Soc. B 374 20180095 (2019) [pdf] [arXiv]

  57. M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman*, T. Mora*
    Receptor crosstalk improves concentration sensing of multiple ligands

    Phys Rev E 99 022423 (2019) [pdf] [arXiv]

  58. S. Magadan, L. Jouneau, M. Puelma Touzel, S. Marillet, W. Chara, A. Six, E. Quillet, T. Mora, A.M. Walczak, F. Cazals, O. Sunyer, S. Fillatreau, P. Boudinot
    Origin of Public Memory B Cell Clones in Fish After Antiviral Vaccination

    Front. Immunol. 9 2115 (2018) [pdf]

  59. M. V. Pogorelyy, A. A. Minervina, M. Shugay, D. M. Chudakov, Y. B. Lebedev*, T. Mora*, A. M. Walczak*
    Detecting T-cell receptors involved in immune responses from single repertoire snapshots

    PLoS Biology 17(6):e3000314 (2019) [pdf] [arXiv]

  60. Z. Sethna, Y. Elhanati, G. G. Callan Jr., A.M. Walczak*, T. Mora*
    OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs

    Bioinformatics 35(17) 2974-2981 (2019) [pdf] [arXiv]

  61. T. Dupic, T. Mora*, A. M. Walczak*
    Genesis of the αβ T-cell receptor

    PLoS Comp. Biol. 15(3):e1006874 (2019) [pdf] [arXiv]

  62. C. Gardella, O. Marre*, T. Mora*
    Modeling the correlated activity of neural populations: A review

    Neural Computation 31(2) 233-269 (2019) [arXiv]

  63. A. Mayer, V. Balasubramanian, A. M. Walczak*, T. Mora*
    How a well-adapting immune system remembers

    Proc Natl Acad Sci 116(18) 8815-8823 (2019) [pdf] [arXiv]

  64. A. Toledano, Y. Elhanati, J. I. C. Benichou, A. M. Walczak, T. Mora, Y. Louzoun
    Evidence for Shaping of Light Chain Repertoire by Structural Selection

    Front. Immunol. 9 1307 (2018) [pdf]

  65. M. V. Pogorelyy, A. A. Minervina, M. Puelma Touzel, A. L. Sycheva, E. A. Komech, E. I. Kovalenko, G. G. Karganova, E. S. Egorov, A. Yu. Komkov, D. M. Chudakov, I. Z. Mamedov, T. Mora*, A. M. Walczak*, Y. B. Lebedev*
    Precise tracking of vaccine-responding T-cell clones reveals convergent and personalized response in identical twins

    Proc Natl Acad Sci 115(50) 12704 (2018) [pdf] [arXiv]

  66. A. Cavagna, I. Giardina, T. Mora, A. M. Walczak
    Physical constraints in biological collective behaviour

    Current Opinion in Systems Biology 9 49-54 (2018) [pdf]

  67. Y. Elhanati, Z. Sethna, G. G. Callan Jr., T. Mora*, A.M. Walczak*
    Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination

    Immunological Reviews 284(1) 167-179 (2018) [pdf] [arXiv]

  68. R. N. Germain, B. D. Greenbaum, A. Hoffmann, K. Miller-Jensen, T. Mora, A. M. Walczak, E. Segal, T. Vogl, S. Klompus, S. Peled-Liviatan, A. Weinberger, S. T. Smale, J. S. Tsang
    What Can Immunologists Learn from Systems Approaches?

    Trends in Immunology 39(3) 163 (2018) [pdf]

  69. R. N. Germain, B. D. Greenbaum, A. Hoffmann, K. Miller-Jensen, T. Mora, A. M. Walczak, E. Segal, T. Vogl, S. Klompus, S. Peled-Liviatan, A. Weinberger, S. T. Smale, J. S. Tsang
    How Can Systems Biology Test Principles and Tools Using Immune Cells as a Model?

    Cell Systems 6 146 (2018) [pdf]

  70. A. Nourmohammad, J. Otwinowski, M. Łuksza, T. Mora*, A.M Walczak*
    Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1

    Molecular Biology and Evolution 36(10) 2184-2194 (2019) [pdf] [arXiv]

  71. N.A. Rossi, T. Mora, A.M. Walczak, M.J. Dunlop
    Active degradation of a regulator controls coordination of downstream genes

    PLoS Comp. Biol. 14(12): e1006634 (2018) [pdf] [bioRxiv]

  72. U. Ferrari, S. Deny, M. Chalk, G. Tkacik, O. Marre*, T. Mora*
    Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons

    Phys Rev E 98 042410 (2018) [pdf] [arXiv]

  73. U. Ferrari, S. Deny, O. Marre*, T. Mora*
    A simple model for low variability in neural spike trains

    Neural Computation 30(11) 3009-3016 (2018) [pdf] [arXiv]

  74. R.M. Adams, J.B. Kinney, A.M. Walczak*, T. Mora*
    Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy

    Cell Systems 8 86-93 (2019) [pdf] [arXiv]

  75. C. Gardella, O. Marre*, T. Mora*
    Blindfold learning of an accurate neural metric

    Proc Natl Acad Sci 115 (13) 3267 (2018) [pdf] [arXiv]

  76. M. V. Pogorelyy, A. A. Minervina, D. M. Chudakov, I. Z. Mamedov, Y. B. Lebedev*, T. Mora*, A. M. Walczak*
    Method for identification of condition-associated public antigen receptor sequences

    eLife 2018;7:e33050 (2018) [pdf] [arXiv]

  77. K. Krishnamurthy, A. M. Hermundstad, T. Mora, A. M. Walczak, V. Balasubramanian
    Disorder and the neural representation of complex odors

    Front. Comput. Neurosci. 16 (2022) [pdf] [arXiv (2017)]

  78. Q. Marcou, T. Mora*, A. M. Walczak*
    High-throughput immune repertoire analysis with IGoR

    Nature Communications 9 561 (2018) [pdf] [arXiv]

  79. A. Mayer, T. Mora, O. Rivoire, A. M. Walczak
    Transitions in optimal adaptive strategies for populations in fluctuating environments

    Phys. Rev. E 96 032412 (2017) [pdf] [arXiv]

  80. R. Espada, R. G. Parra, T. Mora, A. M. Walczak, D. U. Ferreiro
    Inferring repeat protein energetics from evolutionary information

    PLoS Comput. Biol. 13(6) e1005584 (2017) [pdf] [arXiv]

  81. J. Desponds, A. Mayer, T. Mora, A. M. Walczak
    Population dynamics of immune repertoires

    To be published as book chapter (2017) [arXiv]

  82. M.-C. Duvernoy, T. Mora, M. Ardre, V. Croquette, D. Bensimon, C. Quilliet, J.-M. Ghigo, M. Balland, C. Beloin, S. Lecuyer, N. Desprat
    Asymmetric adhesion of rod-shaped bacteria controls microcolony morphogenesis

    Nature Communications, 9 1120 (2018) [pdf] [bioRxiv]

  83. U. Ferrari, C. Gardella, O. Marre*, T. Mora*
    Closed-loop estimation of retinal network sensitivity reveals signature of efficient coding

    eNeuro 4(6) e0166-17.2017 (2018) [pdf] [arXiv]

  84. U. Ferrari, T. Obuchi, T. Mora
    Random versus maximum entropy models of neural population activity

    Phys. Rev. E 95 042321 (2017) [pdf] [arXiv]

  85. Q. Marcou, I. Carmi-Levy, C. Trichot, V. Soumelis*, T. Mora*, A. M. Walczak*
    A model for the integration of conflicting exogenous and endogenous signals by dendritic cells

    Phys. Biol. 15 056001 (2018) [pdf] [arXiv]

  86. T. Mora, A. M. Walczak
    Quantifying lymphocyte receptor diversity

    in Systems Immunology: An Introduction to Modeling Methods for Scientists, eds. J. Das, and C. Jayaprakash (2018) [arXiv]

  87. M. V. Pogorelyy, Y. Elhanati, Q. Marcou, A. L. Sycheva, E. A. Komech, V. I. Nazarov, O. V. Britanova, D. M. Chudakov, I. Z. Mamedov, Y. B. Lebedev*, T. Mora*, A. M. Walczak*
    Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

    PLoS Comput. Biol. 13(7) e1005572 (2017) [pdf] [arXiv]

  88. C. K. Fisher, T. Mora and A. M. Walczak
    Habitat Fluctuations Drive Species Covariation in the Human Microbiota

    PLoS Comput. Biol. 13(4) e1005435 (2017) [pdf] [arXiv]

  89. Z. Sethna, Y. Elhanati, C. S. Dudgeon, C. G. Callan Jr., A. Levine, T. Mora, A. M. Walczak
    Insights into immune system development and function from mouse T-cell repertoires

    Proc Natl Acad Sci USA 114(9) 2253-2258 (2017) [pdf] [arXiv]

  90. R. M. Adams, T. Mora*, A. M. Walczak*, J. B. Kinney*
    Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves

    eLife 2016;5:e23156 (2016) [pdf] [arXiv]

  91. C. G. Callan, T. Mora and A. M. Walczak
    Repertoire sequencing and the statistical ensemble approach to adaptive immunity

    Current Opinion in Systems Biology, 1 44 (2017) [pdf]

  92. C. Gardella, O. Marre*, T. Mora*
    A tractable method for describing complex couplings between neurons and population rate

    eNeuro 3(4) e0160-15.2016 (2016) [pdf] [arXiv]

  93. T. Mora, A. M. Walczak
    Rényi entropy, abundance distribution and the equivalence of ensembles

    Phys. Rev. E 93 052418 (2016) [pdf] [arXiv]

  94. A. Mayer, T. Mora, O. Rivoire, A. M. Walczak
    Diversity of immune strategies explained by adaptation to pathogen statistics

    Proc Natl Acad Sci USA 113(31) 8630 (2016) [pdf] [arXiv]

  95. T. Mora, A. M. Walczak, L. Del Castello, F. Ginelli, S. Melillo, L. Parisi, M. Viale, A. Cavagna and I. Giardina
    Local equilibrium in bird flocks

    Nature Physics 12 1153 (2016) [pdf] [arXiv]

  96. Y. Elhanati, Q. Marcou, T. Mora and A. M. Walczak
    repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data

    Bioinformatics 32(13) 1943 (2016) [pdf] [arXiv]

  97. J. Desponds, T. Mora and A. M. Walczak
    Fluctuating fitness shapes the clone size distribution of immune repertoires

    Proc Natl Acad Sci USA 113(2) 274 (2016) [pdf] [arXiv]

  98. R. Espada, R.G. Parra, M.J. Sippl, T. Mora, A.M. Walczak, D.U. Ferreiro
    Repeat proteins challenge the concept of structural domains

    Biochemical Society Transactions 43 844 (2015) [pdf]

  99. D. Bagnara, M. Squillario, D. Kipling, T. Mora, A.M. Walczak, L. Da Silva, S. Weller, D.K. Dunn-Walters, J.-C. Weill, C.-A. Reynaud
    A Reassessment of IgM Memory Subsets in Humans

    J. Immunol. 195(8) 3716-3724 (2015) [pdf]

  100. G. Tkacik, T. Mora, O. Marre, D. Amodei, S.E. Palmer, M.J. Berry, W. Bialek
    Thermodynamics and signatures of criticality in a network of neurons

    Proc Natl Acad Sci USA 112(37) 11508 (2015) [pdf] [arxiv]

  101. T. Mora
    Physical limit to concentration sensing amid spurious ligands

    Phys. Rev. Lett. 115 038102 (2015) [pdf] [arXiv]

  102. Y. Elhanati, Z. Sethna, Q. Marcou, C. G. Callan Jr., T. Mora and A. M. Walczak
    Inferring processes underlying B-cell repertoire diversity

    Phil. Trans. R. Soc. B 370 20140243 (2015) [pdf] [arXiv]

  103. T. Mora, S. Deny and O. Marre
    Dynamical criticality in the collective activity of a population of retinal neurons.

    Phys. Rev. Lett. 115 078105 (2015) [pdf] [arxiv]

  104. O. Marre, Vicente Botella-Soler, K.D. Simmons, T. Mora, G. Tkacik and M.J. Berry II
    High accuracy decoding of dynamical motion from a large retinal population.

    PLoS Comput. Biol. 11(7): e1004304 (2015) [pdf] [arXiv]

  105. A. Mayer, V. Balasubramanian, T. Mora, A.M. Walczak
    How a well-adapted immune system is organized.

    Proc Natl Acad Sci USA 112(19) 5950 (2015) [pdf] [arxiv]

  106. R. Espada, R.G. Parra, T. Mora, A.M. Walczak, D. Ferreiro
    Capturing coevolutionary signals in repeat proteins.

    BMC Bioinformatics 16 207 (2015) [pdf] [arXiv]

  107. M. Santolini, T. Mora, V. Hakim
    A General Pairwise Interaction Model Provides an Accurate Description of In Vivo Transcription Factor Binding Sites.

    PLoS One 9(6): e99015 (2014) [pdf] [arxiv]

  108. A. H. Lang, C. K. Fisher, T. Mora, P. Mehta
    Thermodynamics of statistical inference by cells.

    Phys. Rev. Lett. 113 148103 (2014) [pdf] [arxiv]

  109. Y. Elhanati, A. Murugan, C. G. Callan Jr., T. Mora, A. M. Walczak
    Quantifying selection in immune receptor repertoires.

    Proc Natl Acad Sci USA 111(27) 9875-9880 (2014) [pdf] [arxiv] [biorxiv]

  110. A. Cavagna, L. Del Castello, I. Giardina, T. Grigera, A. Jelic, S. Melillo, T. Mora, L. Parisi, E. Silvestri, M. Viale, A. M. Walczak
    Flocking and turning: a new model for self-organized collective motion.

    J. Stat. Phys 158(3) 601-627 (2014) [pdf] [arxiv]

  111. A. Cavagna, I. Giardina, F. Ginelli, T. Mora, D. Piovani, R. Tavarone, A. M. Walczak,
    Dynamical maximum entropy approach to flocking.

    Phys. Rev. E 89 042707 (2014) [pdf] [arxiv]

  112. W. Bialek, A. Cavagna, I. Giardina, T. Mora, O. Pohl, E. Silvestri, M. Viale, A. Walczak,
    Social interactions dominate speed control in driving natural flocks toward criticality.

    Proc Natl Acad Sci USA 111(20) 7212-7217 (2014) [pdf] [arxiv]

  113. A. Six, E. Mariotti-Ferrandiz, W. Chaara, S. Magadan, H.-P. Pham, M.-P. Lefranc, T. Mora, V. Thomas-Vaslin, A. M. Walczak and P. Boudinot,
    The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis.

    Front. Immunol. 4:413 (2013) [pdf]

  114. T. Mora, A.M. Walczak,
    Effect of Phenotypic Selection on Stochastic Gene Expression.

    J. Phys. Chem. B 117(42) 13194-13205 (2013) [pdf] [arxiv]

  115. T. Julou*, T. Mora* L. Guillon, V. Croquette, I. Schalk, D. Bensimon, N. Desprat,
    Cell-cell contacts confine public goods diffusion inside Pseudomonas aeruginosa clonal microcolonies.

    Proc Natl Acad Sci USA 110(31) 12577-12582 (2013) [pdf]

  116. G. Tkacik, O. Marre, T. Mora, D. Amodei, M.J. Berry II, W. Bialek,
    The simplest maximum entropy model for collective behavior in a neural network.

    J. Stat. Mech. P03011 (2013) [arxiv] [pdf]

  117. G. J. Stephens*, T. Mora*, G. Tkacik and B. Bialek,
    Statistical Thermodynamics of Natural Images.

    Phys. Rev. Lett. 110 018701 (2013) [pdf]
    An earlier version is available on the [arxiv]

  118. A. Murugan, T. Mora, A.M. Walczak, C.G. Callan Jr.,
    Statistical inference of the generation probability of T-cell receptors from sequence repertoires.

    Proc Natl Acad Sci USA 109(40) 16161-16166 (2012) [pdf] [arxiv]

  119. T. Mora, A.M. Walczak, F. Zamponi,
    Transition path sampling algorithm for discrete many-body systems.

    Phys. Rev. E, 85 036710 (2012) [pdf] [arxiv]

  120. W. Bialek, A. Cavagna, I. Giardina, T. Mora, E. Silvestri, M. Viale, A.M. Walczak,
    Statistical mechanics for natural flocks of birds.

    Proc Natl Acad Sci USA 109(13) 4786-4791 (2012) [pdf] [arxiv]

  121. T. Mora, W. Bialek,
    Are Biological Systems Poised at Criticality?

    J. Stat. Phys. 144(2) 268-302 (2011) [pdf] [arxiv]

  122. T. Mora, F. Bai, Y.-S. Che, T. Minamino, K. Namba, N.S. Wingreen,
    Non-genetic individuality in Escherichia coli motor switching.

    Physical biology 8(2) 024001 (2011) [pdf]

  123. T. Mora, N.S. Wingreen,
    Limits of sensing temporal concentration changes by single cells.

    Phys. Rev. Lett. 104 248101 (2010) [pdf] [arxiv]

    See also the viewpoint by Sima Setayeshgar:
    Improving accuracy by leaps and unbounds, Physics 3 49 (2010) [pdf]

  124. T. Mora*, A.M. Walczak*, W. Bialek, C.G. Callan,
    Maximum entropy models for antibody diversity.

    Proc Natl Acad Sci USA 107(12) 5405-5410 (2010) [pdf] [arxiv]

  125. T. Mora, H. Yu, N.S. Wingreen,
    Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor.

    Phys. Rev. Lett. 103 248102 (2009) [pdf] [arxiv]

  126. T. Mora, H. Yu, Y. Sowa, N.S. Wingreen,
    Steps in the bacterial flagellar motor.

    PLoS Comput. Biol. 5(10): e1000540 (2009) [pdf] [arxiv]

  127. M. Mézard, T. Mora,
    Constraint satisfaction problems and neural networks: a statistical physics perspective.

    J. Physiol. Paris 103 (2009) 107-113 [pdf] [arxiv]

  128. T. Mora, L. Zdeborová,
    Random subcubes as a toy model for constraint satisfaction problems.

    J. Stat. Mech. 131, 1121-113 (2008). [pdf] [arxiv]

  129. H. Daudé, M. Mézard, T. Mora and R. Zecchina,
    Pairs of SAT Assignments and Clustering in Random Boolean Formulae.

    Theoretical Computer Science 393 (2008) 260. [pdf] [arXiv]

  130. T. Mora, M. Mézard,
    Geometrical organization of solutions to random linear Boolean equations.

    J. Stat. Mech. (2006) P10007. [pdf] [arXiv]

  131. T. Mora, O. Rivoire,
    Statistical mechanics of error exponents for error-correcting codes.

    Phys. Rev. E. 74, 056110 (2006). [pdf] [arxiv]

  132. T. Mora, O. Rivoire,
    Error Exponents of Low-Density Parity-Check Codes on the Binary Erasure Channel.

    Information Theory Workshop 2006, ITW 06' Chengdu, IEEE, october 2006, pp. 81-85 [pdf] [arxiv]

  133. T. Mora, A. Boudaoud,
    Buckling of swelling gels.

    Eur. Phys. J. E 20, 119-124 (2006) [pdf] [arXiv]

  134. M. Mézard, T. Mora, R. Zecchina,
    Clustering of solutions in the random satisfiability problem.

    Phys. Rev. Lett. 94, 197205 (2005). [pdf] [arXiv]

  135. T. Mora, C. M. Will,
    A Post-Newtonian diagnostic of quasi-equilibrium binary configurations of compact objects.

    Physical Review D, 69, 104021 (2004). [pdf] [arXiv]

  136. T. Mora, C. M. Will,
    Numerically generated quasi-equilibrium orbits of black holes: Circular or eccentric?

    Physical Review D, 66, 101501 (R) (2002). [pdf] [arXiv]

  137. T. Mora, A. Boudaoud,
    Thin elastic plates: On the core of developable cones.

    Europhysics Letters, 59, 41 (2002). [pdf]

  138. In French

  139. T. Mora,
    IGoR : un outil pour apprendre et simuler la génération aléatoire de récepteurs d'antigènes

    Biologie Aujourd'hui, 211(3), 229-231 (2017). [pdf]

  140. T. Mora,
    Diversité et spécificité des récepteurs immunitaires : comment notre corps fabrique des protéines aléatoires spécialisées pour combattre les pathogènes

    L'actualité chimique, 424, 56-60 (2017). [pdf]

  141. A. Mayer, O. Rivoire, T. Mora, A.M. Walczak,
    Explication évolutive de la diversité des stratégies immunitaires

    Med Sci (Paris), 33(6-7), 593 (2017). [pdf]

  142. T. Mora,
    La physique statistique : entre l'unité et le tout

    TDC, no 110, L'individuel et le collectif p. 62 (2017).