Publications: William Bialek

 

Last updated 14 October 2012

 

Links are to pdf versions of the papers, as available.  Users are responsible for compliance with copyright restrictions.

 

To download a pdf version click here.

 

References to the physics e-print archive http://arxiv.org are given where available. For preprints this is a primary reference; for other work there may be slight differences between the e-print and conventional print versions of the paper. Since almost all of my papers are now deposited on the archive before journal publication, more recent papers are ordered by the date of the archive submission.

 

145.  Biophysics: Searching for Principles.  W Bialek (Princeton University Press, 2012).

 

144. The simplest maximum entropy model for collective behavior in a neural network.  G Tkacik, O Marre, D Amodei, MJ Berry II & W Bialek, arXiv.org:1207.6319 [q–bio.NC] (2012).

 

143. Maximally informative Ňstimulus energiesÓ in the analysis of neural responses to natural signals.  K Rajan & W Bialek, arXiv.org:1201.0321 [q–bio.NC] (2012).

 

142. Positional information, in  bits.  JO Dubuis, G Tkacik, EF Wieschaus, T Gregor & W Bialek, arXiv.org:1201.0198 [q–bio.MN] (2012).

 

141. Optimizing information flow in small genetic networks. III. A self--interacting gene.  G Tkacik, AM Walczak & W Bialek,  Phys Rev E  85,  041903 (2012); arXiv.org:1112.5026 [q–bio.MN] (2011).

 

140. Statistical mechanics for natural flocks of birds.  W Bialek, A Cavagna, I Giardina, T Mora, E Silvestri, M Viale & A Walczak, Proc Natl Acad Sci (USA) 109, 4786-4791 (2012); arXiv.org:1107.0604 [physics.bio–ph] (2011).

 

139. When are correlations strong?    F Azhar & W Bialek, arXiv.org:1012.5987 [q–bio.NC] (2010).

 

138. Searching for simplicity:  Approaches to the analysis of neurons and behavior.  GJ Stephens, LC Osborne & W Bialek, Proc NaatŐl Acad Sci (USA) 108, (Suppl 3) 15565-15571 (2011); arXiv.org:1012.3896 [q–bio.NC] (2010).

 

137. Are biological systems poised at criticality? T Mora & W Bialek, J Stat Phys 144, 268-302 (2011); arXiv:1012.2242 [q–bio.QM] (2010).

 

136. Optimizing information flow in small genetic networks. II:  Feed-forward interactions. AM Walczak, G Tkacik & W Bialek, Phys Rev E 81, 041905 (2010); arXiv:0912.5500 [q–bio.MN] (2009).

 

135. Spin glass models for networks of real neurons.  G Tkacik, E Schneidman, MJ Berry II & W Bialek, arXiv:0912.5409 [q–bio.NC] (2009).

 

134. Emergence of long timescales and stereotyped behaviors in Caenorhabditis elegans. GJ Stephens, MB de Mesquita, WS Ryu  & W Bialek, Proc Nat'l Acad Sci (USA) 108, 7286-7289 (2011).

                           For a preliminary account, see The emergence of stereotyped behaviors in C. elegans. GJ Stephens, WS Ryu & W Bialek, arXiv:0912.5232 [q–bio.NC] (2009).

 

133. Maximum entropy models for antibody diversity.  T Mora, AM Walczak, W Bialek & CG Callan, Jr, Proc Nat'l Acad Sci (USA) 107, 5405-5410 (2010); arXv:0912.5175 [q–bio.GN] (2009).

 

132. From modes to movement in C. elegans. GJ Stephens, B Johnson-Kerner, W Bialek & WS Ryu, PLoS One 5, e13914 (2010); arXiv:0912.4760 [q–bio.NC] (2009).

 

131. Optimizing information flow in small genetic networks.   G Tkacik, AM Walczak & W Bialek, Phys Rev E 80, 031920 (2009); arXiv:0903.4491 [q–bio.MN] (2009).

 

130. Thermodynamics of natural images.  GJ Stephens, T Mora, G Tkacik & W Bialek, Phys Rev Lett in press (2012); arXiv:0806.2694 [q–bio.NC] (2008).

 

129. The neural basis for combinatorial coding in a cortical population response. LC Osborne, SE Palmer, SG Lisberger & W Bialek, J Neurosci 28, 13522–13531 (2008). 

                           A preliminary version is Combinatorial coding in neural populations. arXiv:0803.3837 [q–bio.NC] (2008).

 

128. Can we fit all of the data?  W Bialek, T Gregor, DW Tank & EF Wieschaus, Cell 132, 17-18 (2008).

 

127. Statistical mechanics of letters in words. GJ Stephens & W Bialek, Phys Rev E 81, 066119 (2010); arXiv:0801.0253 [q–bio.NC] (2008).

                           The original title, preserved in the arXiv version, was Toward a statistical mechanics of four letter words.  This was ejected without review; the editors claimed that it was Ňnot physics.Ó  Some small changes to the text, some explanation, and a change in title resulted in more serious consideration.

 

126. Rediscovering the power of pairwise interactions.  W Bialek & R Ranganathan, arXiv:0712.4397 [q–bio.QM] (2007).

 

125. Cell biology: Networks, regulation, pathways.  G Tkacik & W Bialek, in Encyclopedia of Complexity and Systems Science, RA Meyers, ed, pp 719-741 (Springer-Verlag, Berlin, 2009); arXiv:0712.4385 [q–bio.MN] (2007).

 

124.  Information and fitness.  SF Taylor, N Tishby & W Bialek, arXiv:0712.4382 [q–bio.PE] (2007).

 

123. Efficient representation as a design principles for neural coding and computation. W Bialek, RR de Ruyter van Steveninck & N Tishby, arXiv:0712.4381 [q–bio.NC] (2007).

                           A preliminary account appears in the Proceedings of the International Symposium on Information Theory 2006, but this seems to be available only on CDs distributed to meeting attendees (!).

 

122. Faster solutions of the inverse pairwise Ising problem.  T Broderick, M Dudik, G Tkacik, RE Schapire & W Bialek, arXiv:0712.2437 [q–bio.QM] (2007).

 

121. Diffusion, dimensionality and noise in transcriptional regulation. G Tkacik & W Bialek, Phys Rev E  79, 051901 (2009); arXiv:0712.1852 [q–bio.MN] (2007).

                           See also the accompanying commentary by R Metzler, Physics 2, 36 (2009).

 

120. Information capacity of genetic regulatory elements. G Tkacik, CG Callan Jr & W Bialek, Phys Rev E 78, 011910 (2008); arXiv:0709.4209 [q–bio.MN] (2007).

 

119. Dimensionality and dynamics in the behavior of C. elegans.  GJ Stephens, B Johnson-Kerner, W Bialek & WS Ryu, PLoS Comp Bio 4, e1000028 (2008); arXiv:0705:1548 [q–bio.OT] (2007).

 

118. Information flow and optimization in transcriptional regulation.  G Tkacik, CG Callan Jr & W Bialek, Proc NatŐl Acad Sci (USA) 105, 12265-12270 (2008); arXiv:0705.0313 [q–bio.MN] (2007).

 

117. Neural decision boundaries for maximal information transmission.  T Sharpee & W Bialek, PLoS One 2, e646 (2007); q–bio.NC/0703046 (2007).

 

116. The role of input noise in transcriptional regulation. G Tkacik, T Gregor & W Bialek, PLoS One 3, e2774 (2008); q–bio.MN/0701002 (2007).

 

115. Neural coding of a natural stimulus ensemble: Information at sub-millisecond resolution. I Nemenman, GD Lewen, W Bialek & RR de Ruyter van Steveninck, PLoS Comp Bio  4, e1000025 (2008); q–bio.NC/0612050 (2006).

 

114. Time course of precision in smooth pursuit eye movements of monkeys. LC Osborne, SS Hohl, W Bialek & SG Lisberger, J Neurosci  27, 2987-2998 (2007).

 

113. Ising models for networks of real neurons. G Tkacik, E Schneidman, MJ Berry II & W Bialek, q–bio.NC/0611072 (2006).

 

112. Probing the limits to positional information.  T Gregor, DW Tank, EF Wieschaus & W Bialek, Cell  130, 153-164 (2007). 

                           See also the accompanying commentary on this and the next article by MC Gibson, Cell 130, 14-15 (2007).

 

111. Stability and nuclear dynamics of the Bicoid morphogen gradient.  T Gregor, EF Wieschaus, AP McGregor, W Bialek & DW Tank, Cell  130, 141-152 (2007).

 

110. Cooperativity, sensitivity and noise in biochemical signaling.  W Bialek & S Setayeshgar, Phys Rev Lett 100, 258101 (2008); q–bio.MN/0601001 (2006).

 

109. Weak pairwise correlations imply strongly correlated network states in a neural population.  E Schneidman, MJ Berry II, R Segev & W Bialek, Nature 440, 1007-1012 (2006); q–bio.NC/0512013 (2005).

 

108. Should you believe that this coin is fair? W Bialek, q–bio.NC/0508044 (2005).

 

107. Synergy from silence in a combinatorial neural code.  E Schneidman, JL Puchalla, RA Harris, W Bialek & MJ Berry II, q–bio.NC/0607017 (2006).

 

106. Diffusion and scaling during early embryonic pattern formation.  T Gregor, W Bialek, RR de Ruyter van Steveninck, DW Tank & EF Wieschaus, Proc NatŐl Acad Sci (USA) 102, 18403-18407 (2005).

 

105. Information based clustering. N Slonim, GS Atwal, G Tkacik & W Bialek, Proc NatŐl Acad Sci (USA) 102, 18297-18302 (2005); q–bio.QM/0511043.  See also Supplementary material, q–bio.QM/0511042 (2005).

 

104. A sensory source for motor variation.  LC Osborne, SG Lisberger & W Bialek, Nature 437, 412-416 (2005).

 

103. Features and dimensions:  Motion estimation in fly vision. W Bialek & RR de Ruyter van Steveninck, q–bio/0505003 (2005).

 

102.  Estimating mutual information and multi–information in large networks.  N Slonim, GS Atwal, G Tkacik & W Bialek, cs.IT/0502017 (2005).

 

101.  Physical limits to biochemical signaling. W Bialek & S Setayeshgar, Proc NatŐl Acad Sci (USA)  102, 10040-10045 (2005); physics/0301001 (2003).

 

100.  How many clusters? An information theoretic perspective. S Still & W Bialek, Neural Comp 16,  2483-2506 (2004); physics/0301011 (2003).

 

99.  Entropy and information in neural spike trains:  Progress on the sampling problem.  I Nemenman, W Bialek & R de Ruyter van Steveninck, Phys Rev E  69, 056111 (2004); physics/0306063 (2003).

 

98.  Time course of information about  motion direction  in visual area  MT of macaque monkeys.  LC Osborne, W Bialek & SG Lisberger, J Neurosci  24, 3210-3222 (2004).

 

97.    Geometric clustering using the information bottleneck method.  S Still, W Bialek & L Bottou, in Advances in Neural Information Processing 16, S Thrun, L Saul & B Schšlkopf, eds, pp 1165-1172  (MIT Press, Cambridge, 2004).

 

96.  Optimal manifold representation of  data:  An information  theoretic perspective. D Chigirev & W Bialek, in Advances in Neural Information Processing 16, S Thrun, L Saul & B Schšlkopf, eds, pp 161-168 (MIT Press, Cambridge, 2004).

 

95. Ambiguous model learning made unambiguous with 1/f  priors. GS Atwal & W Bialek,  in Advances in Neural Information Processing 16,  S Thrun, L Saul & B Schšlkopf, eds, pp 1205-1212 (MIT Press, Cambridge, 2004).

 

94. Introductory science and mathematics education for 21st century biologists.  W Bialek & D Botstein, Science  308, 788-790 (2004).

 

93.  Analyzing neural responses to natural signals: Maximally informative dimensions.  T Sharpee, NC Rust & W Bialek, Neural  Comp  16, 223-250 (2004); physics/0212110 (2002).
For a preliminary account see Maximally informative dimensions: Analyzing neural responses to natural signals, in Advances in Neural Information Processing 15, S Becker, S Thrun & K Obermayer, eds, pp 261-268 (MIT Press, Cambridge, 2003); physics/0208057 (2002).

 

92.  Spike sorting in the frequency domain with overlap detection. D Rinberg, W Bialek, H Davidowitz  & N Tishby, physics/0306056 (2003).

 

91.  Synergy, redundancy, and independence in population codes. E Schneidman, W Bialek & MJ Berry II, J Neurosci  23, 11539-11553 (2003).

 

90.  Network information and connected correlations. E Schneidman, S Still, MJ Berry II & W Bialek, Phys Rev Lett  91, 238701 (2003); physics/0307072 (2003).

 

89.  The information content of receptive fields. TL Adelman, W Bialek & RM Olberg, Neuron  40, 822-833 (2003).

 

88.  Computation in single neurons:  Hodgkin and Huxley revisited. B AgŸera y Arcas, AL Fairhall, & W Bialek, Neural Comp 15, 1715-1749 (2003); physics/0212113 (2002).

For a preliminary account see What can a single neuron compute?, in Advances in Neural Information Processing 13, TK Leen, TG Dietterich & V Tresp, eds, pp 75-81 (MIT Press, Cambridge, 2001).

 

87.  An information theoretic approach to the functional classification of neurons. E Schneidman, W Bialek, & MJ Berry II, in Advances in Neural Information Processing 15, S Becker, S Thrun & K Obermayer, eds, pp 197-204 (MIT Press, Cambridge, 2003); physics/0212114 (2002).

 

86.  Adaptive spike coding. A Fairhall & W Bialek, in The Handbook of Brain Theory and Neural Networks, Second Edition, MA Arbib, ed, pp 90-94 (MIT Press, Cambridge, 2002).

 

85.  Statistical properties of spike trains: Universal and stimulus-dependent aspects. N Brenner, O Agam, W Bialek, & RR de Ruyter van Steveninck, Phys Rev E  66, 031907 (2002);  physics/9902061 (1999).

For  a preliminary account see Universal statistical behavior of neural spike trains, Phys Rev Lett.  81, 4000-4003 (1998);  physics/9801026 (1998).

 

84.  Thinking about the brain. W Bialek, in  Physics of Biomolecules and Cells: Les Houches Session LXXV, H Flyvbjerg, F JŸlicher, P Ormos, & F David, eds, pp 485-577 (EDP Sciences, Les Ulis; Springer-Verlag, Berlin, 2002); physics/0205030 (2002).

 

83.  Entropy and inference, revisited. I Nemenman, F Shafee, & W Bialek, in Advances in Neural Information Processing 14, TG Dietterich, S Becker & Z Ghahramani, eds, pp 471-478 (MIT Press, Cambridge, 2002); physics/0108025 (2001).

 

82.  Spike timing and the coding of naturalistic sounds in a central auditory area of songbirds. BD Wright, K Sen, W Bialek, & AJ Doupe,  in Advances in Neural Information Processing 14,  TG Dietterich, S Becker & Z Ghahramani, eds, pp 309-316 (MIT Press, Cambridge, 2002); physics/0201027 (2002).

 

81.  Timing and counting precision in the blowfly visual system. R de Ruyter van Steveninck & W Bialek,  in Models of Neural Networks IV:   Early Vision and Attention,   JL van Hemmen, J Cowan & E Domany, eds, pp 313-365 (Springer-Verlag, Berlin, 2002); physics/0202014 (2002).

 

80.  Occam factors and model-independent Bayesian learning of continuous distributions. I Nemenman & W Bialek, Phys Rev E  65, 026137 (2002); cond mat/0009165 (2000).

For a preliminary account see Learning continuous distributions: Simulations with a field theoretic prior, in Advances in Neural Information Processing 13, TK Leen, TG Dietterich & V Tresp, eds, pp 287-293 (MIT Press, Cambridge, 2001).

 

79.  Complexity through nonextensivity. W Bialek, I Nemenman & N Tishby, Physica A 302, 89-99 (2001); physics/0103076 (2001).

 

78.  Efficiency and ambiguity in an adaptive neural code. AL Fairhall, GD Lewen, W Bialek  & RR de Ruyter van  Steveninck, Nature 412, 787-792 (2001).

See also the accompanying commentary by P. Reinagel, Nature  412, 776-777 (2001). For a preliminary account see Multiple timescales of adaptation in a neural code, in Advances in Neural Information Processing 13, TK Leen, TG Dietterich & V Tresp, eds, pp 124-130 (MIT Press, Cambridge, 2001).

 

77.  Neural coding of naturalistic motion stimuli.  GD Lewen, W Bialek & RR de Ruyter van Steveninck, Network  12, 317-329 (2001); physics/0103088 (2001).

 

76.  Predictability, complexity and learning. W Bialek, I Nemenman & N Tishby, Neural Comp  13, 2409-2463 (2001); physics/0007070 (2000).

For a preliminary account see Predictive information, W Bialek & N Tishby; cond-mat/9902341.

 

75.  Universality and individuality in a neural code.  E Schneidman,  N Brenner,  N Tishby, RR de Ruyter van Steveninck  & W Bialek, in Advances in Neural Information Processing 13, TK Leen, TG Dietterich & V Tresp,eds, pp 159-165 (MIT Press, Cambridge, 2001); physics/0005043 (2000).

 

74.  Stability and noise in biochemical switches. W Bialek, in Advances in Neural Information Processing 13, TK Leen, TG Dietterich & V Tresp, eds, pp 103-109 (MIT Press, Cambridge, 2001); cond-mat/0005235 (2000).

 

73.  Real time encoding of motion: Answerable questions and questionable answers from the fly's visual system.  R de Ruyter van Steveninck, A Borst & W Bialek, in Processing Visual Motion in the Real World: A Survey of Computational, Neural and Ecological Constraints, JM Zanker & J Zeil, eds, pp 279-306 (Springer-Verlag, Berlin, 2001); physics/0004060 (2000).

 

72.  Adaptive rescaling optimizes information transmission.  N Brenner, W Bialek & R de Ruyter van Steveninck, Neuron  26, 695-702 (2000).

See also the accompanying commentary by M DeWeese, Neuron  26, 546-548 (2000).

 

71.  Synergy in a neural code.  N Brenner, SP Strong, R Koberle, W Bialek & RR de Ruyter van Steveninck,  Neural Comp 12, 1531-1552 (2000); physics/9902067 (1999).

 

70.  Potenialit‡ e limitazioni nella misura della transmission dell'informazione neuronale.  W Bialek, in Frontiere Della Vita, Vol. III: Sistemi Intelligenti, pp 617-629 (Instituto della Enciclopedia Italiana, 1999).

From an English manuscript, Prospects and pitfalls in the measurement of neural information transmission.  English edition:  Frontiers of Life, Vol III:  Intelligent Systems (Academic Press, San Diego, 2002).

 

69.  The information bottleneck method.  N Tishby, FC Pereira, & W Bialek, in Proceedings of the 37th Annual Allerton Conference on Communication, Control and Computing, B Hajek & RS Sreenivas, eds, pp 368-377 (University of Illinois, 1999);  physics/0004057 (2000).

 

68.  Adaptation and optimal chemotactic strategy for E. Coli.  SP Strong, B Freedman, W Bialek & R Koberle, Phys Rev E  57, 4604-4617 (1998); adap-org/9706001 (1997).

 

67.  On the application of information theory to neural spike trains.   SP Strong, RR de Ruyter van Steveninck, W Bialek & R Koberle, in  Pacific Symposium on Biocomputing `98, RB Altman, AK Dunker, L Hunter & TE Klein, eds, pp 621-632 (World Scientific, Singapore, 1998).

 

66.  Entropy and information in neural spike trains.  SP Strong, R Koberle, RR de Ruyter van Steveninck & W Bialek, Phys Rev Lett  80, 197-200 (1998); cond-mat/9603127 (1996).

 

65.  Spikes: Exploring the Neural Code.  F Rieke, D Warland, R de Ruyter van Steveninck & W Bialek (MIT Press, Cambridge, 1997). Introductory chapter

Reviews include:  A King,  The London Times Higher Education Supplement 17 October 1997, p. 35; A Zador,  Science  277, 772 (1997); LF Abbott,  Neuron  19, 5 (1997); M Abeles,  Trends Neurosci.  20, 496 (1997).

 

64.  Statistical mechanics and sensory signal processing.  W Bialek, in Physics of Biological Systems:  From Molecules to Species, H Flyvbjerg, J Hertz, MH Jensen, OG Mouristen & K Sneppen, eds, pp 252-280 (Springer-Verlag, Berlin, 1997).

 

63.  Reproducibility and variability in neural spike trains.  RR de Ruyter van Steveninck, GD Lewen, SP Strong, R Koberle & W Bialek, Science 275, 1805-1808 (1997).

 

62.  Adaptation of retinal processing to image contrast and spatial scale.  S Smirnakis, MJ Berry II, DK Warland, W Bialek & M Meister, Nature 386, 69-73 (1997).

 

61.  Adaptive movement computation by the blowfy visual system.  RR de Ruyter van Steveninck, W Bialek, M Potters, RH Carlson & GD Lewen,  in  Natural and Artificial Parallel Computation: Proceedings of the Fifth NEC Research Symnposium, DL Waltz, ed, 21-41 (SIAM, Philadelphia, 1996).

 

60.  Field theories for learning probability distributions.  W Bialek, CG  Callan & SP Strong,  Phys Rev Lett  77, 4693-4697 (1996); cond-mat/9607180 (1996).

 

59.  Optimality and adaptation in motion estimation by the blowfly visual system.  RR de Ruyter van Steveninck & W Bialek, Proceedings of the IEEE 22nd Annual Northeast  Bioengineering Conference,  40-41 (1996).

 

58.  Naturalistic stimuli increase the rate and efficiency of information transmission by primary auditory neurons.  F Rieke, DA Bodnar & W Bialek, Proc R Soc Lond Ser B  262, 259-265 (1995).

 

57.  Reliability and statistical efficiency of a blowfly movement-sensitive neuron.  R de Ruyter van Steveninck & W Bialek, Phil Trans R Soc Lond Ser B  348, 321-340 (1995).

For a preliminary account see Statistical reliability of a blowfly movement-sensitive neuron, in  Advances in Neural Information Processing 4, J Moody, SJ Hanson & RP Lippman, eds pp 27-34, (Morgan Kaufmann, San Mateo CA, 1992).

 

56.  Random switching and optimal processing in the perception of ambiguous signals.  W Bialek & M DeWeese, Phys Rev Lett  74, 3077-3080 (1995).

 

 

55.  Information flow in sensory neurons.  M DeWeese & W Bialek, Il  Nuovo Cimento  17D, 733-741 (1995).

 

54.  Statistical adaptation and optimal estimation in movement computation by the blowfly visual system.  RR de Ruyter van Steveninck, W Bialek, M Potters & RH Carlson, in Proc IEEE Conf Sys Man Cybern, 302-307 (1994).

 

53.  Statistical mechanics and visual signal processing.  M Potters & W Bialek, J Phys I France  4, 1755-1775 (1994); cond-mat/9401072 (1994).

 

 

52.  Statistics of natural images: Scaling in the woods.  DL Ruderman & W Bialek, Phys Rev Lett  73, 814-817 (1994).

For a preliminary account see Advances in Neural Information Processing 6, JD Cowan, G Tesauro & J Alspector, eds, pp 551-558 (Morgan Kaufmann, San Mateo CA, 1994).

 

51.  Properties and origins of protein secondary structure. N Socci, W Bialek & JN Onuchic,  Phys Rev E  49, 3400-3443 (1994);  cond-mat/9402010 (1994).

 

50.  Visual computation: A fly's eye view.  W Bialek, M Potters, DL Ruderman & R de Ruyter van Steveninck, in  Cognitive Processing for Vision and Voice, Proceedings of the Fourth NEC Research Symposium, T Ishiguro, ed, pp 7-26, (SIAM, Philadelphia, 1993).

 

 

49.  Non-phase-locked auditory cells and envelope detection.  F Rieke, W Yamada, E Lewis & W Bialek, in Analysis and Modeling of Neural Systems 2, F Eeckman, ed, pp 255-263 (Kluwer Academic, 1993).

 

 

48.  Bits and brains: Information flow in the nervous system.  W Bialek, M DeWeese, F Rieke & D Warland, Physica A  200, 581-593 (1993).

 

 

47.  Nonperturbative approach to non-Condon effects:  Must a nonadiabatic transition always occur at the potential surface crossing?  RF Goldstein, S Franzen & W Bialek, J Phys Chem 97, 11168-11174 (1993).

 

46.  Virtual transitions in nonadiabatic condensed phase reactions.  JS Joseph & W Bialek, J Phys Chem  97, 3245-3256 (1993).

 

45.  Coding efficiency and information rates in sensory neurons.  F Rieke, D Warland &  W Bialek,  Europhys Lett  22, 151-156, (1993).

For a preliminary account see Measuring the coding efficiency of sensory neurons, in  Analysis and Modeling of Neural Systems 2, F Eeckman, ed, pp 29-38 (Kluwer Academic, 1993).

 

44.  Statistical mechanics for a network of spiking neurons.  L Kruglyak & W Bialek, Neural Comp  5, 21-31 (1993).

 

43.  Princeton Lectures on Biophysics.  W Bialek, ed (World Scientific, Singapore, 1992).

 

42.  Optimal signal processing in the nervous system.  W Bialek, in [43], pp 321-401 (1992).

See also Optimal real-time signal processing in the nervous system, in  Analysis and Modeling of Neural Systems  2, F Eeckman, ed, pp 5-28 (Kluwer Academic, 1993).

 

41.  Reliability and information transmission in spiking neurons.   W Bialek & F Rieke, Trends Neurosci  15, 428-434 (1992).

 

40.  Real-time coding of complex sounds in the auditory nerve.  F Rieke, W Yamada, K Moortgat, ER Lewis & W Bialek, in Auditory Physiology and Perception: Proceedings of the 8th International Conference on Hearing, Y Cazals, L Demany, & K Horner, eds, pp 315-322 (Pergamon, 1992).

 

39.  Seeing beyond the Nyquist limit.  DL Ruderman & W Bialek, Neural Comp  4, 682-690 (1992).

Reprinted in Neural Codes and Distributed Representations: Foundations of Neural Computation, LF Abbott & TJ Sejnowski, eds (MIT Press, Cambridge, 1999).

 

38.  A new look at the primary charge separation in bacterial photosynthesis.  SS Skourtis, AJR DaSilva, W Bialek & JN Onuchic,  J Phys Chem  96, 8034-8041 (1992).

 

37.  Vibrationally enhanced tunneling as a mechanism for enzymatic hydrogen transfer.  WJ Bruno & W Bialek, Biophys J  63, 689-699 (1992).

 

36.  Virtual intermediates in photosynthetic electron transfer.  JS Joseph & W Bialek, Biophys J  63, 397-411 (1992).

 

35.  Bleaching of the bacteriochlorophyll monomer: Can absorption kinetics distinguish virtual from two-step transfer? JS Joseph, WJ Bruno & W  Bialek, J Phys Chem  95, 6242-6247 (1991).

 

34.  Reading a neural code.  W Bialek, F Rieke, RR de Ruyter van Steveninck & D Warland, Science  252, 1854-1857 (1991).

Reprinted in  Biology and Computation:  A Physicist's Choice, H Gutfreund & G Toulouse, eds (World Scientific, Signapore, 1994). For a preliminary account see  Advances in Neural Information Processing 2, D Touretzky, ed, pp 36-43 (Morgan Kaufmann, San Mateo CA, 1990).

 

33.  Reading between the spikes in the cricket cercal afferent system.  D Warland, M Landolfa, JP Miller & W Bialek, in  Analysis and Modeling of Neural Systems, F Eeckman, ed, pp 327-333 (Kluwer Academic, 1991).

 

32.  Optimal sampling of natural images: A design principle for the visual system?  W Bialek, DL Ruderman & A Zee, in  Advances in Neural Information Processing 3, R Lippman, J Moody & D Touretzky, eds, pp 363-369 (Morgan Kaufmann, San Mateo CA, 1991).

 

 

31.  Analog computation at a critical point: A novel function for neuronal oscillations?  L Kruglyak & W Bialek, in  Advances in Neural Information Processing 3, R Lippman, J Moody & D Touretzky, eds, pp 137-143 (Morgan Kaufmann, San Mateo CA, 1991).

 

30.  Optimal filtering in the salamander retina.  F Rieke, WG Owen, & W Bialek, in Advances in Neural Information Processing 3, R Lippman, J Moody & D Touretzky, eds, pp 377-383 (Morgan Kaufmann, San Mateo CA, 1991).

See also Analysis and Modeling of Neural Systems, F Eeckman, ed, pp 231-237 (Kluwer Academic, 1991).

 

29.  Theoretical physics meets experimental neurobiology.  W Bialek, in 1989 Lectures in Complex Systems, SFI Studies in the Sciences of Complexity, Lect. Vol. II, E Jen, ed,  pp 513-595 (Addison-Wesley, Menlo Park CA, 1990).

 

28.  Biomolecular dynamics—Quantum or classical?: Results for photosynthetic electron transfer.  JN Onuchic, RF Goldstein & W Bialek, in  Perspectives in Photosynthesis: Proceedings of the 22nd Jerusalem Symposium on Quantum Chemistry and Biochemistry, J Jortner & B Pullman, eds, pp 185-210 (Kluwer Academic, Dordrecht, 1990).

 

27.  Temporal filtering in retinal bipolar cells: Elements of an optimal computation?  W Bialek & WG Owen, Biophys J 58, 1227-1233 (1990).

 

26.  Non–Boltzmann dynamics in networks of spiking neurons.  MC Crair & W Bialek, in  Advances in Neural Information Processing 2, D. Touretzky, ed, pp 109-116 (Morgan Kaufmann, San Mateo CA, 1990).

 

25.  Coding and computation with neural spike trains.  W Bialek & A Zee, J Stat Phys  59, 103-115 (1990).

 

24.  Quantum and classical dynamics in biochemical reactions.  W Bialek, WJ Bruno, JS Joseph & JN Onuchic, Photosyn Res  22, 17-25 (1989).

 

23.  Optimal performance of a feed–forward network at statistical discrimination tasks.   W Bialek, R Scalettar & A Zee, J Stat Phys 57, 141-156 (1989).

 

22.  Understanding the efficiency of human perception.  W Bialek & A Zee, Phys Rev Lett  61, 1512-1515 (1988).

 

21.  Real–time performance of a movement sensitive neuron in the blowfly visual system: Coding and information transfer in short spike sequences.  R de Ruyter van Steveninck & W Bialek, Proc R Soc London Ser B 234, 379-414 (1988).

20.  Protein dynamics and reaction rates: Mode–specific chemistry in large molecules?.  W Bialek & JN Onuchic,  Proc  NatŐl  Acad  Sci (USA)  85, 5908-5912 (1988).

 

19.  Physical limits to sensation and perception.  W Bialek, Ann. Rev Biophys Biophys Chem 16, 455-478 (1987).

 

18.  Statistical mechanics and invariant perception.  W Bialek & A Zee, Phys Rev Lett  58, 741-744 (1987).

 

17.  Tunneling spectroscopy of a macroscopic variable.  W Bialek, S Chakravarty & S Kivelson, Phys Rev B  35, 120-123 (1987).

 

16.  Simple models for the dynamics of biomolecules: How far can we go?  W Bialek, RF Goldstein & S Kivelson, in Structure, Dynamics and Function of Biomolecules: The First EBSA Workshop, A Ehrenberg, R Rigler, A GrŠslund & LJ Nilsson, eds, pp 65-69 (Springer-Verlag, Berlin, 1987).

 

15.  Protein dynamics, tunneling, and all that.  W Bialek & RF Goldstein, Phys Scr  34, 273-282 (1986).

 

14.  Protein dynamics and reaction rates: Are simple models useful?  RF Goldstein & W Bialek, Comments Mol Cell Biophys  3, 407-438 (1986).

 

13.  Macroscopic T non-conservation: Prospects for a new experiment.  W Bialek, J Moody & F Wilczek, Phys Rev Lett  56, 1623-1626 (1986).

 

12.  The Vertebrate Inner Ear.  ER Lewis, EL Leverenz & W Bialek (CRC Press, Boca Raton, 1985).

 

11.  Quantum noise and the threshold of hearing.  W Bialek & A Schweitzer, Phys Rev Lett  54, 725-728 (1985). Erratum  56, 996 (1986).

 

10.  Do vibrational spectroscopies uniquely describe protein dynamics?: The case for myoglobin.  W Bialek & RF Goldstein, Biophys J  48, 1027-1044 (1985).

For a preliminary account see Protein vibrations can markedly affect reaction kinetics: Interpretation of Myoglobin–CO recombination, in  Protein Structure: Molecular and Electronic Reactivity, RH Austin, E Buhks, B Chance, D DeVault, PL Dutton, H Frauenfelder & VI Gol'danskii, eds, pp 187-199 (Springer-Verlag, Berlin, 1987).

 

9.  Quantum limits to oscillator stability: Theory and experiments on an acoustic emission from the human ear.  W Bialek & HP Wit, Phys Lett A 104, 173-178 (1984).

 

8.  Phonon super-radiance.  W Bialek, Phys Lett  A 103, 349-352 (1984).

 

7.  Quantum noise and active feedback.  W Bialek, Phys Rev D  28,  2096-2098 (1983).

 

6.  Vibronically coupled two-level systems: Radiationless transitions in the slow regime.  RF Goldstein & W Bialek, Phys Rev B 27, 7431-7439 (1983).

 

5.  Quantum effects in the dynamics of biological systems.  W Bialek, Doctoral Dissertation (University of California, Berkeley, 1983).

 

4.  Thermal and quantum noise in the inner ear.  W Bialek, in  Mechanics of Hearing, E de Boer & MA Viergever, eds, pp 185-192 (Nijhof, the Hague, 1983).

 

3.  Thermal  noise and active processes in the inner ear: Relating theory to experiment.  W Bialek, in  Hearing: Physiological Bases and Psychophysics, R Klinke & R Hartmann, eds, pp 51-57 (Springer-Verlag, Berlin, 1983).

 

2.  Kinetics and mechanism of force production in muscle.  W Bialek, Undergraduate Honors Thesis (University of California, Berkeley, 1979).

 

1.  Contraction of glycerinated muscle fibers as a function of the ATP concentration.  R Cooke & W Bialek, Biophys J  28, 241-258 (1979).