Publications

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

    arXiv (2018)

  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

    arXiv (2018)

  3. 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)

  4. 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

    arXiv (2018)

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

    arXiv (2018)

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

    Neural Computation In press (2018) [arXiv]

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

    arXiv (2018)

  8. 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]

  9. 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

    arXiv (2018)

  10. 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]

  11. 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]

  12. 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]

  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
    How Can Systems Biology Test Principles and Tools Using Immune Cells as a Model?

    Cell Systems 6 146 (2018) [pdf]

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

    arXiv (2018)

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

    bioRxiv (2018)

  16. 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]

  17. 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) [arXiv]

  18. R.M. Adams, J.B. Kinney, A.M. Walczak*, T. Mora*
    Physical epistatic landscape of antibody binding affinity

    arXiv (2017)

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

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

  20. 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]

  21. 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)

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

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

  23. 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]

  24. 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]

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

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

  26. 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]

  27. 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]

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

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

  29. 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]

  30. 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]

  31. 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]

  32. 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]

  33. 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]

  34. 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]

  35. 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]

  36. 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]

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

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

  38. 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]

  39. 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]

  40. 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]

  41. 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]

  42. 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]

  43. 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]

  44. 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]

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

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

  46. 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]

  47. 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]

  48. 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]

  49. 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]

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

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

  51. 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]

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

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

  53. 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]

  54. 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]

  55. 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]

  56. 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]

  57. 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]

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

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

  59. 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]

  60. 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]

  61. 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]

  62. 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]

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

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

  64. 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]

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

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

  66. 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]

  67. 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]

  68. 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]

  69. 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]

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

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

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

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

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

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

  73. 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]

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

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

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

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

  76. 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]

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

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

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

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

  79. 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]

  80. 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]

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

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

  82. In French

  83. 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]

  84. 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]

  85. 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]

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

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

Theses