Publications

1. M. Ruiz Ortega, M.V. Pogorelyy, A.A. Minervina, P.G. Thomas, A.M. Walczak, T. Mora, Learning predictive signatures of HLA type from T-cell repertoires bioarxiv (2024)

2. M.-F. Abbate, T. Dupic, E. Vigne, M.A. Shahsavarian, A.M. Walczak, T. Mora, Computational detection of antigen specific B cell receptors following immunization bioarxiv (2023)

3. X. Chen, M. Winiarski, A. Puscian, E.Knapska, T. Mora, A. M. Walczak, Modelling collective behavior in groups of mice housed under semi-naturalistic conditions,  bioarxiv (2023) elife (2024) 

4. V. Karnaukhov, A. Le Gac., L. Bilonda, T. Mora, A. M. Walczak, O. Lantz, TCR repertoire analysis indicates TCR-independent lineage choice of MAIT cells, PNAS (2024)

5. G. Isacchini, V. Quiniou, H. Vantomme, P. Stys, E. Mariotti-Ferandiz, D. Klatzmann, A. M. Walczak, T. Mora and A. Nourmohammad, Variability in the local and global composition of human T-cell receptor repertoires during thymic development across cell types and individuals, PRX Life (2024)

6. B. Meynard-Piganeau, M. Weigt, C. Feinauer, A. M. Walczak, T. Mora, TULIP Transformer based Unsupervised Language modeling for the Interacting Peptide TCR, bioarxiv (2023) PNAS (2024)

7. T. Mora and A. M. Walczak, Quantitative theory of viral-immune coevolution may be within reach,  PRX Life (2023)

8. F. Camaglia, I. Nemenman, T. Mora, A. M. Walczak, Bayesian estimation of the Kullback-Leibler divergence for categorical systems using mixtures of Dirichlet priors,PRE (2024)

9. V. Chardes, A. Mazzolini, T. Mora, A. M. Walczak, Evolutionary stability of antigenically escaping viruses, PNAS 120 (44) e2307712120 (2023)

10. B. Bravi, A. Di Gioacchino, J. Fernandez-de-Cossio-Diaz, A. M. Walczak, T. Mora, S. Cocco, R. Monasson, A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity, bioarxiv (2023)  elife (2023) 

11. T. Mora and A. M. Walczak, Towards a quantitative theory of tolerance,  arxiv (2023), Trends in Immunology (2023)

12. J. Crocker, J. L. Payne, A. M. Walczak and P. J. Wittkopp, Interdisciplinary approaches to predicting evolutionary biology,  Phil. Trans. B (2023)

13. L. Hahn, A. M. Walczak and T. Mora, Dynamical information synergy in biochemical signaling networks, arxiv (2023), PRL (2023)

14. 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]

15. N. Spisak, G. Athènes, T. Dupic, T. Mora and A. M. Walczak, Combining mutation and recombination statistics to infer clonal families in antibody repertoires,  arxiv (2022)

16. P. Meysman, J. Barton, B. Bravi, L. Cohen-Lavi, V. Karnaukhov, E. Lilleskov, A. Montemurro, M. Nielsen, T. Mora,P.Pereira,A.Postovskaya,M.RodriguezMartinez,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, bioRxiv (2022), ImmunoInformatics (2023)

17. A. Mazzolini, T. Mora*, A. M. Walczak* Inspecting the interaction between HIV and the immune system through genetic turnover, bioRxiv (2022), Phil. Trans. B (2023)

18. X. Chen, M. Winiarski, A. Puscian, E. Knapska, A. M. Walczak*, T. Mora* Generalized Glauber dynamics for inference in biology,  bioRxiv (2022) PRX (2023)

19. X. Chen, F. Ginoux, T. Mora*, A. M. Walczak*, C. Wyart* Granger causality analysis for calcium transients in neuronal networks : challenges and improvements, bioRxiv (2022), eLife (2023)

20. 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), Nature Comm. (2023)

21. J. Urbanus, J. Cosgrove, J. Beltman, Y. Elhanati, R. de Andrade Mora, C. Conrad, J. van Heijst, E. Tubeuf, A. Velds, L. Kok, C. Merle, J. Magnusson, J. Frisen, S. Fre, A. M Walczak, T. Mora, H. Jacobs, T. N. Schumacher and L. Perie DRAG in situ barcoding reveals an increase in the number of HSPCs contributing to myelopoiesis with age, bioRxiv (2022), Nature Comm. (2023)

22. 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, arxiv (2022), PRE (2022)

23. M. Bensouda Koraichi, S. Ferri, A.M. Walczak*, T. Mora*, Inferring the T-cells repertoire dynamics of healthy individuals,  bioRxiv (2022), PNAS (2023)

24. E. A. Galpern, J. Marchi, T. Mora, A.M. Walczak, D.U. Ferreiro, From evolution to folding of repeat proteins,  bioRxiv (2022), PNAS (2022)

25. T. Mora, C. Poletto, M. Sales-Pardo, A.M. Walczak, Physics research against pandemics, European Physical Society Grand Challenges Physics for Society at the Horizon 2050 (2022)

26. V. Chardes, M. Vergassola, A. M. Walczak*, T. Mora*, Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints, bioRxiv (2021), PNAS (2022)

27. M. Łuksza, Z. M. Sethna, L. A. Rojas, J. Lihm, B. Bravi, Y. Elhanati, K Soares, M. Amisaki, D. Hoyos, A. Dobrin, P. Guasp, A. Zebboud, R. Yu, A. K. 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, C. Iacobuzio-Donahue, R. Monasson, T. Mora, A. M. Walczak, S. Cocco, B. D. Greenbaum, and V. P. Balachandran, Neoantigen quality predicts immunoediting and clonal evolution in pancreatic cancer survivors, Nature (2023)

28. F. Camaglia, A. Ryvkin, E. Greenstein, S. Reich-Zeliger, B. Chain, T. Mora*, A. M. Walczak*, N. Friedman, Population based selection shapes the T cell receptor repertoire during thymic development, bioRxiv (2021), eLife (2023)

29. 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, bioRxiv (2021), PloS Genetics (2023)

30. C. Lupo, N. Spisak, A. M. Walczak*, T. Mora*, Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies,   arXiv (2021), PloS CB (2022)

31. G. Fernandes, H. Tran, M. Andrieu, Y. Diaw, C.A.Perez-Romero, C. Fradin, A.M. Walczak*, N. Dostatni* Synthetic deconstruction of hunchback regulation by Bicoid, bioRxiv (2021), eLife (2022)

32. G. Isacchini, N. Spisak, A. Nourmohammad*, T. Mora*, A.M. Walczak*,  MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories arXiv (2021), PRE (2022)

33. 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 bioRxiv (2021),  eLife (2021)

34. 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, arXiv (2021), elife (2021)

35. M. Bensouda Koraichi, M. Puelma Touzel, T. Mora*, A.M. Walczak*, NoisET: Noise learning and Expansion detection of T-cell receptors with Python arXiv (2021), J. Chem. Phys. A (2022)

36. J. Marchi, M. Lässig, A.M. Walczak*, T. Mora*, Antigenic waves of virus-immune co-evolution arXiv (2021), PNAS (2022)

37. 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]

38. F. Ferretti, V. Chardès, T. Mora, A.M. Walczak, T. Giardina
    The Connection between Discrete- and Continuous-Time Descriptions of Gaussian Continuous Processes arXiv (2021), PRE (2022)

39. D. Conti, T. Mora, Non-equilibrium dynamics of adaptation in sensory systems, arXiv (2020), PRE (2020)

40. 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] 

41. 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]

42. 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] 

43. 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] 

44. 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, bioRxiv (2020), eLife (2021) 

45. 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] 

46. V. Sachdeva, T. Mora, A.M. Walczak, S. Palmer, Optimal prediction with resource constraints using the information bottleneck, bioRxiv (2020),  PloS CB (2021)

47. 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]

48. 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] 

49. 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] 

50. 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]

51. 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] 

52. M. Puelma Touzel, A.M. Walczak, T. Mora, Inferring the immune response from repertoire sequencing, PLoS Computational Biology 16(4) e1007873 (2020) [pdf] [arXiv] 

53. G. Isacchini, Z. Sethna, Y. Elhanati, A. Nourmohammad, A.M. Walczak, T. Mora, On generative models of T-cell receptor sequences, Phys Rev E 101 062414 (2020) [pdf] [arXiv] 

54. 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] 

55. P. Szymańska-Rożek, D. Villamaina, J. Miekisz, A.M. Walczak, Dissipation in non-steady state regulatory circuits [arxiv] 

56. 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.

57. H. Tran, A. M. Walczak, N. Dostatni, Constraints and limitations on decoding positional information : the Bicoid case-study [biorxiv] 

58. T. Mora, A.M. Walczak, How many different clonotypes do immune repertoires contain? Current Opinion in Systems Biology pre-proof (2019) [arXiv]

59. G. Altan-Bonnet*, T. Mora*, A.M. Walczak*, Quantitative Immunology for Physicists, Physics Reports, 849 1-83 (2020) [pdf] [arXiv] 

60. J. Desponds, M. Vergassola, A.M. Walczak, hunchback Promoters Can Readout Morphogenetic Positional Information in Less Than a Minute eLife 9:e49758. 

61. 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]

62. 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]

63. S. Bradde, T. Mora*, A. M. Walczak*, Cost and benefits of CRISPR spacer acquisition, Phil. Trans. R. Soc. B 374 20180095 (2019) [pdf] [arXiv]

64. 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]

65. H. Tran, J. Desponds, C.A. Perez-Romero, M. Coppey, C. Fradin, N. Dostatni, A.M Walczak, Precision in a rush: trade-offs between positioning and steepness of the hunchback expression pattern PloS Computational Biology (2018) [bioRxiv]

66. T. Lucas, H. Tran, C.A. Perez-Romero, A. Guillou, M. Coppey, C. Fradin, A.M Walczak, N. Dostatni, 3 minutes to precisely measure morphogen concentration PloS Genetics (2018) [bioRxiv]

67. R.A. Neher and A. M. Walczak, Progress and open problems in evolutionary dynamics, Proceedings of the 24th Solvay Conference in Physics -- The Physics of Living Matter : Space, Time and Information in Biology, Worldpress (2018) [arxiv]

68. 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]

69. 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]

70. 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 btz035 (2019) [pdf] [arXiv]

71. T. Dupic, T. Mora*, A. M. Walczak*, Genesis of the αβ T-cell receptor, PLoS Comp. Biol. 15(3): e1006874 (2019) [pdf] [arXiv],

72. C. Gardella, O. Marre*, T. Mora*, Modeling the correlated activity of neural populations: A review, Neural Computation 31(2) 233-269 (2019) [arXiv]

73. 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]

74. H. Tran, C.A. Perez-Romero, T. Ferraro, C. Fradin, N. Dostatni, M. Coppey, A.M Walczak, LiveFly - a toolbox for the analysis of transcription dynamics in live Drosophila embryos, Methods in Molecular Biology (2018)

75. C.A. Perez-Romero, H. Tran, M. Coppey, A.M. Walczak, C. Fradin, N. Dostatni, Live imaging of mRNA transcription in Drosophila Embryos, Methods in Molecular Biology (2018) 

76. 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]

77. 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]

78. 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]

79. 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]

80. 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]

81. 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] 

82. 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 msz143 (2019) [pdf] [arXiv]

83. 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]

84. 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]

85. 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]

86. 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]

87. C. Gardella, O. Marre*, T. Mora*, Blindfold learning of an accurate neural metric, Proc Natl Acad Sci 115 (13) 3267 (2018) [pdf] [arXiv]

88. 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]

89. K. Krishnamurthy, A. M. Hermundstad, T. Mora, A. M. Walczak, V. Balasubramanian, Disorder and the neural representation of complex odors: smelling in the real world, arXiv (2017)

90. Q. Marcou, T. Mora*, A. M. Walczak*, High-throughput immune repertoire analysis with IGoR, Nature Communications 9 561 (2018) [pdf] [arXiv]

91. J. W. Larkin, X. Zhai, K. Kikuchi, S. Redford, A. Prindle, J. Liu, A. M. Walczak, J. Garcia-Ojalvo, A. Mugler and G. M. Suel, Signal Percolation within a Bacterial Community Cell Systems (2018) [arxiv]

92. 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]

93. 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]

94. J. Desponds, A. Mayer, T. Mora, A. M. Walczak, Population dynamics of immune repertoires, To be published as book chapter (2017) [arXiv]

95. 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]

96. 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]

97. U. Ferrari, T. Obuchi, T. Mora, Random versus maximum entropy models of neural population activity, Phys. Rev. E 95 042321 (2017) [pdf] [arXiv]

98. 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]

99. 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]

100. 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]

101. 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]

102. 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]

103. 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]

104. M. Laessig, V. Mustonen and A. M. Walczak, Predicting evolution, Nature Ecology & Evolution (2017) [pdf] 

105. 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]

106. 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]

107. T. Mora, A. M. Walczak, Rényi entropy, abundance distribution and the equivalence of ensembles, Phys. Rev. E 93 052418 (2016) [pdf] [arXiv]

108. 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]

109. J. Desponds, H. Tran, T. Ferraro, T. Lucas, C. Perez Romero, A. Guillou, C. Fradin, M. Coppey, N. Dostatni, A. M. Walczak, Precision of readout at the hunchback gene, PLoS Comp. Biol. (2016) [arxiv] [biorxiv] [pdf] 

110. 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]

111. 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]

112. 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]

113. A. Mugler, M. Kittisopikul, L. Hayden, J. Liu, C. H. Wiggins, G. M. Suel and A. M. Walczak, Noise expands the response range of the Bacillus subtilis competence circuit, PLoS Comp. Biol. (2016) [ abs] [arxiv] [pdf]

114. T. R. Sokolowski, A. M. Walczak, W. Bialek, and G. Tkacik, Extending the dynamic range of transcription factor action by translational regulation, Phys. Rev. E 93 022404(2016) [arxiv] [pdf]

115. T. Ferraro, T. Lucas, M. Clemot, J. De Las Heras Chanes, J. Despond, M. Coppey, A. M. Walczak and N. Dostatni, New methods to image transcription in living fly embryos : the insights so far, and the prospects. WIREs Developmental Biology 10 221(2016) [pdf]

116. T. Ferraro, E. Esposito, L. Mancini, N. Sam, T. Lucas, M. Coppey, N. Dostatni, A. M. Walczak, M. Levine and M. Lagha, Transcriptional memory in the Drosophila embryo, Current Biology 26 1(2015) [abs] [pdf]

117. M. M. Desai and A. M. Walczak, Flexible gene pools, Science 348 977 (2015) [abs] [pdf] 

118. 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]

119. F. Mancini, M. Marsili and A. M. Walczak, Trade-offs in delayed information transmission in biochemical networks, J. Stat. Phys (2015) [arxiv] [pdf]

120. A. M. Walczak, Tiling solutions for optimal biological sensing Comptes Rendus Physique (2015) [arxiv] [pdf] 

121. 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. 1500753 (2015) [pdf]

122. 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]

123. T. Mora, Physical limit to concentration sensing amid spurious ligands, Phys. Rev. Lett. 115 038102 (2015) [pdf] [arXiv]

124. 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]

125. 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]

126. 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]

127. 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]

128. R. Espada, R.G. Parra, T. Mora, A.M. Walczak, D. Ferreiro, Capturing coevolutionary signals in repeat proteins, BMC Bioinformatics 16207 (2015) [pdf] [arXiv]

129. A. Cappuccio, R. Zollinger, M. Schenk, A.M. Walczak, N. Servant, E. Barillot, P. Hupe, R. Modlin, V. Soumelis, The combinatorial code governing innate immune cell response to complex stimuli, Nature Comm. 6 6847 (2015) [abs] [pdf] 

130. 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]

131. A. H. Lang, C. K. Fisher, T. Mora, P. Mehta, Thermodynamics of statistical inference by cells, Phys. Rev. Lett. 113 148103 (2014) [pdf] [arxiv]

132. 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]

133. 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].

134. 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]

135. T. Lucas, T. Ferraro, B. Roelens, J. De Las Heras Chanes, A. M. Walczak, M. Coppey, N. Dostatni, Live Imaging of Bicoid-Dependent Transcription in Drosophila Embryos, Current Biology 23 1(2013) [abs] [pdf], featured in Development [abs][pdf] 

136. 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]

137. 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]

138. B. Good, A. M. Walczak, R. Neher and M. M. Desai, Genetic Diversity in the Interference Selection Limit, PLoS Genetics 10 e1004222(2014) [arxiv] [abs] [pdf] 

139. T. Mora, A.M. Walczak, Effect of Phenotypic Selection on Stochastic Gene Expression, J. Phys. Chem. B 117(42) 13194-13205 (2013) [pdf] [arxiv]

140. 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]

141. 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]

142. 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]

143. F. Mancini, C. H. Wiggins, M. Marsili and A. M. Walczak, Time-dependent information transmission in a model regulatory circuit, Phys. Rev. E 88 022708 (2013) [arxiv] [pdf] 

144. 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]

145. M. M. Desai, A. M. Walczak and D. F. Fisher, Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations, Genetics 193 565 (2013) [arxiv] [abs] [pdf]

146. A. Burger, A. M. Walczak and P. G. Wolynes, Abduction and asylum in the lives of transcription factors, Phys. Rev. E 86 041920(2012) [arxiv] [pdf] 

147. T. Mora, A.M. Walczak, F. Zamponi, Transition path sampling algorithm for discrete many-body systems, Phys. Rev. E, 85 036710 (2012) [pdf] [arxiv]

148. G. Tkacik, A. M. Walczak and W. Bialek, Optimizing information flow in small genetic networks. III: A self-interacting gene, Phys. Rev. E 85 041903(2012) [arxiv] [abs] [pdf] 

149. 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]

150. T. Mora, W. Bialek, Are Biological Systems Poised at Criticality? J. Stat. Phys. 144(2) 268-302 (2011) [pdf] [arxiv]

151. 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]

152. 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]

153. G. Tkacik and A. M. Walczak, Information transmission in genetic regulatory networks: a review, J. Phys. : Condens. Matter 23 153102 (2011) [arxiv] [abs] [pdf]

154. A. M. Walczak, L. E. Nicolaisen, J. B. Plotkin and M. M. Desai The Structure of Genealogies in the Presence of Purifying Selection: An Effective Coalescent Theory, Genetics 190 753 (2011) [arxiv] [abs] [pdf] [Supplement]

155. M. M. Desai, L. E. Nicolaisen, A. M. Walczak and J. B. Plotkin, The Structure of Allelic Diversity in the Presence of Purifying Selection, Theoretical Population Biology 81 144 (2011) [arxiv] [abs] [pdf]

156. A. M. Walczak, A. Mugler and C. H. Wiggins, Analytic methods for modeling stochastic regulatory networks, appeared as a chapter in "Methods in Molecular Biology" Eds. M. Betterton and X. Liu, Springer Verlag [arxiv] [abs] [pdf]

157. A. Mugler, A. M. Walczak and C. H. Wiggins, Telling time with an intrinsically noisy clock, Phys. Rev. Lett. 105 058101 (2010) [arxiv] [abs] [pdf]

158. A. M. Walczak, G. Tkacik and W. Bialek, Optimizing information flow in small genetic networks. II: Feed forward interactions, Phys. Rev. E 81 041905 (2010) [arxiv] [abs] [pdf] 

159. 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]

160. A. Burger, A. M. Walczak and P. G. Wolynes, Abduction and asylum in the lives of transcription factors, Proc Natl Acad Sci USA 107 4016 (2010) [abs] [pdf]

161. 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]

162. T. Mora, H. Yu, Y. Sowa, N.S. Wingreen, Steps in the bacterial flagellar motor, PLoS Comput. Biol. 5(10): e1000540 (2009) [pdf] [arxiv] 

163. M. Mézard, T. Mora, Constraint satisfaction problems and neural networks: a statistical physics perspective, J. Physiol. Paris 103 (2009) 107-113 [pdf] [arxiv]

164. A. Mugler, A. M. Walczak and C. H. Wiggins, Spectral solutions to stochastic models of gene expression with bursts and regulation, Phys. Rev. E 80 041921 (2009) [arxiv] [abs] [pdf]

165. G. Tkacik, A. M. Walczak and W. Bialek, Optimizing information flow in small genetic networks, Phys. Rev. E 80 031920 (2009) [arxiv] [abs] [pdf]

166. A. M. Walczak, A. Mugler and C. H. Wiggins, A stochastic spectral analysis of transcriptional regulatory cascades, Proc Natl Acad Sci USA 106 6529 (2009) [arxiv] [abs] [pdf]

167. A. M. Walczak and P. G. Wolynes, Gene-gene cooperativity in small networks, Biophys. J. 96 4525 (2009) [arxiv] [abs] [pdf]

168. T. Mora, L. Zdeborová, Random subcubes as a toy model for constraint satisfaction problems, J. Stat. Mech. 131, 1121-113 (2008). [pdf] [arxiv]

169. 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]

170. D. Schultz, A. M. Walczak, J. N. Onuchic and P. G. Wolynes, Absolute rate theories of epigenetic stability, Proc Natl Acad Sci USA 105 19165 (2008) [abs] [pdf]

171. J. D. Stevenson, A. M. Walczak, R. W. Hall and P. G. Wolynes, Journal of Chemical Physics 129 194505 (2008) [arxiv] [abs] [pdf]

172. A. M. Walczak, D. U. Ferreiro, E. A. Komives and P. G. Wolynes, The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity and the Folding Funnels of One-Dimensional Architectures, PLoS Computational Biology 4 e1000070(2008) [abs] [pdf]

173. T. Mora, M. Mézard, Geometrical organization of solutions to random linear Boolean equations, J. Stat. Mech. (2006) P10007. [pdf] [arXiv]

174. T. Mora, O. Rivoire, Statistical mechanics of error exponents for error-correcting codes, Phys. Rev. E. 74, 056110 (2006). [pdf] [arxiv]

175. 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] 

176. A. M. Walczak, F. Alet and M. P. A. Fisher, Exotic quantum phase transitions in correlated matter, Physica A 369 122 (2006) [arxiv] [abs] [pdf]

177. T. Mora, A. Boudaoud, Buckling of swelling gels, Eur. Phys. J. E 20, 119-124 (2006) [pdf] [arXiv]

178. J. E. M. Hornos, D. Schultz, G. C. P. Innocentini, J. Wang, A. M. Walczak, J. N. Onuchic and P. G. Wolynes, Self-regulating gene: an exact solution. Phys. Rev. E 72 51907 (2005) [abs] [pdf]A. M. Walczak, J. N. Onuchic and P. G. Wolynes, Absolute rate theories of epigenetic stability, Proc Natl Acad Sci USA 102 18926 (2005) [arxiv] [abs] [pdf]

179. A. M. Walczak, M. Sasai and P.G. Wolynes, Self-Consistent Proteomic Field Theory of Stochastic Gene Switches, Biophys. J. 88 828 (2005) [arxiv] [abs] [pdf]

180. M. Mézard, T. Mora, R. Zecchina, Clustering of solutions in the random satisfiability problem, Phys. Rev. Lett. 94, 197205 (2005). [pdf] [arXiv]

181. 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]

182. 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]

183. T. Mora, A. Boudaoud, Thin elastic plates: On the core of developable cones, Europhysics Letters, 59, 41 (2002). [pdf]

184. A. M. Walczak and J. M. Antosiewicz, Langevin Dynamics of Proteins at Constant pH, Phys. Rev. E 66 051911 (2002) [abs] [pdf] 

In French

1. 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] 

2. 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] 

3. 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] 

4. T. Mora, La physique statistique : entre l'unité et le tout,TDC, no 110, L'individuel et le collectif p. 62 (2017).