Publications

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  • 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

    [arxiv] [biorxiv] [pdf]

  • 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

    [arxiv] [biorxiv] [pdf]

  • T. Mora and A. M. Walczak, Quantifying lymphocyte receptor diversity

    [arxiv] [biorxiv] [pdf]

  • T. Mora and A. M. Walczak, Renyi entropy, abundance distribution and the equivalence of ensembles

    [arxiv] [pdf]

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

    [arxiv] [biorxiv] [pdf]

  • R.M. Adams, J.B. Kinney, T. Mora, A. M. Walczak, Diversity of immune strategies explained by adaptation to pathogen statistics

    [arxiv] [biorxiv] [pdf]

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

    PNAS 113 8630(2016) [arxiv] [biorxiv] [pdf]

  • T. Mora, A. M. Walczak, L. Del Castello, F. Ginelli, S. Melillo, L. Parisi, M. Viale, A. Cavagna and I. Giardina, Questioning the activity of active matter in natural flocks of birds

    Nature Physics (2016) [arxiv] [pdf]

  • 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 (2016) [arxiv] [biorxiv] [pdf]

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

    [arxiv] [pdf]

  • 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]

  • 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]

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

    PNAS 113 274(2016) [arxiv] [biorxiv] [pdf]

  • 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]

  • 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]

  • M. M. Desai and A. M. Walczak, Flexible gene pools

    Science 348 977 (2015) [abs] [pdf]

  • R. Espada, R. Gonzalo Parra, M. J. Sippl, T. Mora, A. M. Walczak and D. U. Ferreiro
    Repeat Proteins challenge the concept of structural domains.

    Biochemical Society Transactions 43 844 (2015) [abs]

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

    Philosophical Transactions B 370 20140243 (2015) [arxiv] [biorxiv] [abs] [pdf]

  • F. Mancini, M. Marsili and A. M. Walczak, Trade-offs in delayed information transmission in biochemical networks.

    J. Stat. Phys (2015) [arxiv] [pdf]

  • A. M. Walczak
    Tiling solutions for optimal biological sensing

    Comptes Rendus Physique (2015)

    [arxiv] [pdf]

  • D. Bagnara, M. Squillario, D. Kipling, T. Mora, A. M. Walczak, L. Da Silva, S. Weller, D. Dunn-Walters, J.-C. Weill, C.-A. Reynaud, A redefinition of IgM memory subsets in humans

    Journal of Immunology (2015)

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

    Proc Natl Acad Sci USA 112 5950 (2015)

    [arxiv] [abs] [pdf]

    featured in [phys.org|medicalxpress ]

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

    BMC Bioinformatics 16 207 (2015)

    [arxiv] [abs] [pdf]

  • 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]

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

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

  • 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) [arxiv] [abs] [pdf]

  • A. Cavagna, I. Giardina, F. Ginelli, T. Mora, D. Poviani, R. Tavarone, A. M. Walczak, Dynamical Maximum Entropy Approach to Flocking.

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

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

    Frontiers in Immunology 4 413(2013) [abs] [pdf]

  • 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]

  • 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 (2014) [arxiv] [abs] [pdf]

  • 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]

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

    J. Phys. Chem. 117 13194 (2013) [arxiv] [abs] [pdf]

  • 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]

  • A. Murugan, T. Mora, A. M. Walczak and C. G. Callan, Statistical inference of the mechanisms of T-cell receptor diversity generation from sequence repertoires.

    Proc Natl Acad Sci USA 109 16161 (2012) [arxiv] [abs] [pdf]

  • 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]

  • 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]

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

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

  • 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]

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

    Proc Natl Acad Sci USA 109 4786(2012) [arxiv] [abs] [pdf]

  • G. Tkacik and A. M. Walczak, Information transmission in genetic regulatory networks: a review.

    J. Phys. : Condens. Matter 23 153102 (2011) [arxiv] [abs] [pdf]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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) [arxiv] [abs] [pdf]

  • 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]

  • 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]

  • G. Tkacik, A. M. Walczak and W. Bialek, Optimizing information flow in small genetic networks.

    Phys. Rev. E 80 031920 (2009) [arxiv] [abs] [pdf]

  • 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]

  • A. M. Walczak and P. G. Wolynes, Gene-gene cooperativity in small networks.

    Biophys. J. 96 4525 (2009) [arxiv] [abs] [pdf]

  • 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]

  • J. D. Stevenson, A. M. Walczak, R. W. Hall and P. G. Wolynes,

    Journal of Chemical Physics 129 194505 (2008) [arxiv] [abs] [pdf]

  • 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]

  • 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]

  • 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]

  • 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, M. Sasai and P.G. Wolynes, Self-Consistent Proteomic Field Theory of Stochastic Gene Switches.

    Biophys. J. 88 828 (2005) [arxiv] [abs] [pdf]

  • A. M. Walczak and J. M. Antosiewicz, Langevin Dynamics of Proteins at Constant pH.

    Phys. Rev. E 66 051911 (2002) [abs] [pdf]