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.
[arxiv]
[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.
to appear 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]