List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

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E. Schneidman, Berry, M. J., Segev, R., and Bialek, W., “Weak pairwise correlations imply strongly correlated network states in a neural population.”, Nature, vol. 440, no. 7087, pp. 1007-12, 2006.
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L. C. Osborne, Hohl, S. S., Bialek, W., and Lisberger, S. G., “Time course of precision in smooth-pursuit eye movements of monkeys.”, J Neurosci, vol. 27, no. 11, pp. 2987-98, 2007.
L. C. Osborne, Bialek, W., and Lisberger, S. G., “Time course of information about motion direction in visual area MT of macaque monkeys.”, J Neurosci, vol. 24, no. 13, pp. 3210-22, 2004.
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E. Schneidman, Bialek, W., and Berry, M. J., “Synergy, redundancy, and independence in population codes.”, J Neurosci, vol. 23, no. 37, pp. 11539-53, 2003.
E. Schneidman, Puchalla, J. L., Segev, R., Harris, R. A., Bialek, W., and Berry, M. J., “Synergy from silence in a combinatorial neural code.”, J Neurosci, vol. 31, no. 44, pp. 15732-41, 2011.
G. J. Stephens, Mora, T., Tkačik, G., and Bialek, W., “Statistical thermodynamics of natural images.”, Phys Rev Lett, vol. 110, no. 1, p. 018701, 2013.
N. Brenner, Agam, O., Bialek, W., and van Steveninck, Rde Ruyter, “Statistical properties of spike trains: universal and stimulus-dependent aspects.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 66, no. 3 Pt 1, p. 031907, 2002.
G. J. Stephens and Bialek, W., “Statistical mechanics of letters in words.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 81, no. 6 Pt 2, p. 066119, 2010.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Silvestri, E., Viale, M., and Walczak, A. M., “Statistical mechanics for natural flocks of birds.”, Proc Natl Acad Sci U S A, vol. 109, no. 13, pp. 4786-91, 2012.
T. Gregor, Wieschaus, E. F., McGregor, A. P., Bialek, W., and Tank, D. W., “Stability and nuclear dynamics of the bicoid morphogen gradient.”, Cell, vol. 130, no. 1, pp. 141-52, 2007.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Pohl, O., Silvestri, E., Viale, M., and Walczak, A. M., “Social interactions dominate speed control in poising natural flocks near criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 20, pp. 7212-7, 2014.
L. C. Osborne, Lisberger, S. G., and Bialek, W., “A sensory source for motor variation.”, Nature, vol. 437, no. 7057, pp. 412-6, 2005.
G. J. Stephens, Osborne, L. C., and Bialek, W., “Searching for simplicity in the analysis of neurons and behavior.”, Proc Natl Acad Sci U S A, vol. 108 Suppl 3, pp. 15565-71, 2011.
G. Tkačik, Marre, O., Amodei, D., Schneidman, E., Bialek, W., and Berry, M. J., “Searching for collective behavior in a large network of sensory neurons.”, PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
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G. Tkačik, Gregor, T., and Bialek, W., “The role of input noise in transcriptional regulation.”, PLoS One, vol. 3, no. 7, p. e2774, 2008.
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W. Bialek, “QnAs with William Bialek.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, p. 16288, 2013.
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T. Gregor, Tank, D. W., Wieschaus, E. F., and Bialek, W., “Probing the limits to positional information.”, Cell, vol. 130, no. 1, pp. 153-64, 2007.
G. J. Berman, Bialek, W., and Shaevitz, J. W., “Predictability and hierarchy in Drosophila behavior.”, Proc Natl Acad Sci U S A, vol. 113, no. 42, pp. 11943-11948, 2016.
J. O. Dubuis, Tkačik, G., Wieschaus, E. F., Gregor, T., and Bialek, W., “Positional information, in bits.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
W. Bialek and Setayeshgar, S., “Physical limits to biochemical signaling.”, Proc Natl Acad Sci U S A, vol. 102, no. 29, pp. 10040-5, 2005.
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G. Tkačik, Walczak, A. M., and Bialek, W., “Optimizing information flow in small genetic networks. III. A self-interacting gene.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 85, no. 4 Pt 1, p. 041903, 2012.
A. M. Walczak, Tkačik, G., and Bialek, W., “Optimizing information flow in small genetic networks. II. Feed-forward interactions.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 81, no. 4 Pt 1, p. 041905, 2010.
G. Tkačik, Walczak, A. M., and Bialek, W., “Optimizing information flow in small genetic networks.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 3 Pt 1, p. 031920, 2009.
I. Nemenman and Bialek, W., “Occam factors and model independent Bayesian learning of continuous distributions.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 65, no. 2 Pt 2, p. 026137, 2002.
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T. Sharpee and Bialek, W., “Neural decision boundaries for maximal information transmission.”, PLoS One, vol. 2, no. 7, p. e646, 2007.
I. Nemenman, Lewen, G. D., Bialek, W., and van Steveninck, R. R. de Ruyte, “Neural coding of natural stimuli: information at sub-millisecond resolution.”, PLoS Comput Biol, vol. 4, no. 3, p. e1000025, 2008.
L. C. Osborne, Palmer, S. E., Lisberger, S. G., and Bialek, W., “The neural basis for combinatorial coding in a cortical population response.”, J Neurosci, vol. 28, no. 50, pp. 13522-31, 2008.
E. Schneidman, Still, S., Berry, M. J., and Bialek, W., “Network information and connected correlations.”, Phys Rev Lett, vol. 91, no. 23, p. 238701, 2003.
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D. Krotov, Dubuis, J. O., Gregor, T., and Bialek, W., “Morphogenesis at criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
T. Mora, Walczak, A. M., Bialek, W., and Callan, C. G., “Maximum entropy models for antibody diversity.”, Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5405-10, 2010.
K. Rajan and Bialek, W., “Maximally informative "stimulus energies" in the analysis of neural responses to natural signals.”, PLoS One, vol. 8, no. 11, p. e71959, 2013.
G. J. Berman, Choi, D. M., Bialek, W., and Shaevitz, J. W., “Mapping the stereotyped behaviour of freely moving fruit flies.”, J R Soc Interface, vol. 11, no. 99, 2014.
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M. Castellana and Bialek, W., “Inverse spin glass and related maximum entropy problems.”, Phys Rev Lett, vol. 113, no. 11, p. 117204, 2014.
W. Bialek and Botstein, D., “Introductory science and mathematics education for 21st-Century biologists.”, Science, vol. 303, no. 5659, pp. 788-90, 2004.
N. Slonim, Atwal, G. Singh, Tkačik, G., and Bialek, W., “Information-based clustering.”, Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18297-302, 2005.
G. Tkačik, Callan, C. G., and Bialek, W., “Information flow and optimization in transcriptional regulation.”, Proc Natl Acad Sci U S A, vol. 105, no. 34, pp. 12265-70, 2008.
T. L. Adelman, Bialek, W., and Olberg, R. M., “The information content of receptive fields.”, Neuron, vol. 40, no. 4, pp. 823-33, 2003.
G. Tkačik, Callan, C. G., and Bialek, W., “Information capacity of genetic regulatory elements.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, no. 1 Pt 1, p. 011910, 2008.
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S. Still and Bialek, W., “How many clusters? An information-theoretic perspective.”, Neural Comput, vol. 16, no. 12, pp. 2483-506, 2004.
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G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
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I. Nemenman, Bialek, W., and van Steveninck, Rde Ruyter, “Entropy and information in neural spike trains: progress on the sampling problem.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 69, no. 5 Pt 2, p. 056111, 2004.
G. J. Stephens, de Mesquita, M. Bueno, Ryu, W. S., and Bialek, W., “Emergence of long timescales and stereotyped behaviors in Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7286-9, 2011.
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G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “Dimensionality and dynamics in the behavior of C. elegans.”, PLoS Comput Biol, vol. 4, no. 4, p. e1000028, 2008.
G. Tkačik and Bialek, W., “Diffusion, dimensionality, and noise in transcriptional regulation.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 79, no. 5 Pt 1, p. 051901, 2009.
T. Gregor, Bialek, W., van Steveninck, R. R. de Ruyte, Tank, D. W., and Wieschaus, E. F., “Diffusion and scaling during early embryonic pattern formation.”, Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18403-7, 2005.
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W. Bialek and Setayeshgar, S., “Cooperativity, sensitivity, and noise in biochemical signaling.”, Phys Rev Lett, vol. 100, no. 25, p. 258101, 2008.
B. Agüera y Arcas, Fairhall, A. L., and Bialek, W., “Computation in a single neuron: Hodgkin and Huxley revisited.”, Neural Comput, vol. 15, no. 8, pp. 1715-49, 2003.
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T. Sharpee, Rust, N. C., and Bialek, W., “Analyzing neural responses to natural signals: maximally informative dimensions.”, Neural Comput, vol. 16, no. 2, pp. 223-50, 2004.