Publications

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

  • B. Good, A. M. Walczak, R. Neher and M. M. Desai, Effect of Phenotypic Selection on Stochastic Gene Expression. [arxiv] [pdf]

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

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

  • F. Mancini, C. H. Wiggins, M. Marsili and A. M. Walczak, Time-dependent information transmission in a model regulatory circuit. [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 (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]