Publications

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

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

  2. 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]

  3. 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]

  4. 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

    arXiv (2018)

  5. 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]

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

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

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

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

  8. 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]

  9. 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]

  10. 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]

  11. 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]

  12. 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]

  13. 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]

  14. 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]

  15. A. Nourmohammad, J. Otwinowski, M. Łuksza, T. Mora*, A.M Walczak*
    Clonal competition in B-cell repertoires during chronic HIV-1 infection

    arXiv (2018)

  16. 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]

  17. 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]

  18. 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]

  19. 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]

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

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

  21. 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]

  22. 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)

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

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

  24. 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]

  25. 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]

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

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

  27. 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]

  28. 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]

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

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

  30. 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]

  31. 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]

  32. 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]

  33. 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]

  34. 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]

  35. 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]

  36. 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]

  37. 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]

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

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

  39. 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]

  40. 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]

  41. 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]

  42. 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]

  43. 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]

  44. 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]

  45. 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]

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

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

  47. 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]

  48. 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]

  49. 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]

  50. 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]

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

    BMC Bioinformatics 16207 (2015) [pdf] [arXiv]

  52. 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]

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

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

  54. 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]

  55. 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]

  56. 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]

  57. 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]

  58. 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]

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

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

  60. 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]

  61. 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]

  62. 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]

  63. 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]

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

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

  65. 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]

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

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

  67. 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]

  68. 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]

  69. 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]

  70. 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]

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

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

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

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

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

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

  74. 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]

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

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

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

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

  77. 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]

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

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

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

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

  80. 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]

  81. 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]

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

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

  83. In French

  84. 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]

  85. 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]

  86. 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]

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

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

Theses