75 Publications

Mark all

[75]
2019 | Preprint | IST-REx-ID: 7083   OA
B. Kavcic, G. Tkačik, and T. Bollenbach, “Mechanistic origin of drug interactions between translation-inhibiting antibiotics,” bioRxiv. Cold Spring Harbor Laboratory, 2019.
View | Download (ext.)
 
[74]
2019 | Journal Article | IST-REx-ID: 6784   OA
J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7, 2019.
View | Files available | DOI
 
[73]
2019 | Journal Article | IST-REx-ID: 5945
M. D. Petkova, G. Tkacik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4, p. 844–855.e15, 2019.
View | Files available | DOI
 
[72]
2019 | Journal Article | IST-REx-ID: 6900   OA
S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” PLoS computational biology, vol. 15, no. 9, p. e1007290, 2019.
View | Files available | DOI | PubMed | Europe PMC
 
[71]
2018 | Journal Article | IST-REx-ID: 31   OA
U. Ferrari, S. Deny, M. J. Chalk, G. Tkacik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4, 2018.
View | DOI | Download (ext.)
 
[70]
2018 | Journal Article | IST-REx-ID: 67
C. Igler, M. Lagator, G. Tkacik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10, pp. 1633–1643, 2018.
View | Files available | DOI
 
[69]
2018 | Journal Article | IST-REx-ID: 543   OA
M. J. Chalk, O. Marre, and G. Tkacik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1, pp. 186–191, 2018.
View | DOI | Download (ext.)
 
[68]
2018 | Research Data | IST-REx-ID: 5587   OA
D. De Martino and G. Tkacik, Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria, 2018.
View | Files available | DOI
 
[67]
2018 | Journal Article | IST-REx-ID: 406   OA
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkacik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3, 2018.
View | Files available | DOI
 
[66]
2018 | Journal Article | IST-REx-ID: 292
V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkacik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5, 2018.
View | Files available | DOI
 
[65]
2018 | Research Data | IST-REx-ID: 5584   OA
S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkacik, Nonlinear decoding of a complex movie from the mammalian retina. IST Austria, 2018.
View | Files available | DOI
 
[64]
2018 | Research Data | IST-REx-ID: 5585
C. Igler, M. Lagator, G. Tkacik, J. P. Bollback, and C. C. Guet, Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. IST Austria, 2018.
View | Files available | DOI
 
[63]
2018 | Journal Article | IST-REx-ID: 281   OA
A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkacik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23, pp. 6088–6093, 2018.
View | Files available | DOI | Download (ext.) | PubMed | Europe PMC
 
[62]
2018 | Journal Article | IST-REx-ID: 161
D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkacik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1, 2018.
View | Files available | DOI
 
[61]
2017 | Research Data | IST-REx-ID: 5562   OA
O. Marre, G. Tkacik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, Multi-electrode array recording from salamander retinal ganglion cells. IST Austria, 2017.
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[60]
2017 | Journal Article | IST-REx-ID: 725   OA
R. Harpaz, G. Tkacik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38, pp. 10149–10154, 2017.
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[59]
2017 | Journal Article | IST-REx-ID: 1104   OA
S. Deny et al., “Multiplexed computations in retinal ganglion cells of a single type,” Nature Communications, vol. 8, no. 1, 2017.
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[58]
2017 | Journal Article | IST-REx-ID: 720   OA
J. Humplik and G. Tkacik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9, 2017.
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[57]
2017 | Journal Article | IST-REx-ID: 613   OA
R. P. Chait, J. Ruess, T. Bergmiller, G. Tkacik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1, 2017.
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[56]
2017 | Journal Article | IST-REx-ID: 943   OA
M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345, pp. 1379–1383, 2017.
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[55]
2017 | Journal Article | IST-REx-ID: 955   OA
T. Friedlander, R. Prizak, N. H. Barton, and G. Tkacik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1, 2017.
View | Files available | DOI
 
[54]
2017 | Journal Article | IST-REx-ID: 730
C. Savin and G. Tkacik, “Maximum entropy models as a tool for building precise neural controls,” Current Opinion in Neurobiology, vol. 46, pp. 120–126, 2017.
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[53]
2017 | Research Data | IST-REx-ID: 5560
T. Bergmiller et al., Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. IST Austria, 2017.
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[52]
2017 | Journal Article | IST-REx-ID: 665
T. Bergmiller et al., “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science, vol. 356, no. 6335, pp. 311–315, 2017.
View | Files available | DOI
 
[51]
2016 | Journal Article | IST-REx-ID: 1248   OA
G. Tkacik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7, pp. 89–117, 2016.
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[50]
2016 | Journal Article | IST-REx-ID: 1197   OA
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkacik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11, 2016.
View | Files available | DOI
 
[49]
2016 | Conference Paper | IST-REx-ID: 1105
C. Savin and G. Tkacik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.
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[48]
2016 | Journal Article | IST-REx-ID: 1270   OA
P. Hillenbrand, U. Gerland, and G. Tkacik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9, 2016.
View | Files available | DOI
 
[47]
2016 | Journal Article | IST-REx-ID: 1358
T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkacik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7, 2016.
View | Files available | DOI
 
[46]
2016 | Conference Paper | IST-REx-ID: 1082   OA
M. J. Chalk, O. Marre, and G. Tkacik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.
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[45]
2016 | Journal Article | IST-REx-ID: 1171
G. Tkacik, “Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.,” Physics of Life Reviews, vol. 17, pp. 166–167, 2016.
View | DOI
 
[44]
2016 | Journal Article | IST-REx-ID: 1420   OA
K. Bod’ová, G. Tkacik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4, pp. 1523–1548, 2016.
View | DOI | Download (ext.) | arXiv
 
[43]
2016 | Journal Article | IST-REx-ID: 1242   OA
T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkacik, “Extending the dynamic range of transcription factor action by translational regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2, 2016.
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[42]
2015 | Journal Article | IST-REx-ID: 1666   OA
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkacik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11, 2015.
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[41]
2015 | Journal Article | IST-REx-ID: 1940   OA
T. R. Sokolowski and G. Tkacik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 2015.
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[40]
2015 | Journal Article | IST-REx-ID: 1697   OA
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkacik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7, 2015.
View | Files available | DOI
 
[39]
2015 | Journal Article | IST-REx-ID: 1701   OA
G. Tkacik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37, pp. 11508–11513, 2015.
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[38]
2015 | Journal Article | IST-REx-ID: 1885   OA
G. Tkacik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1, pp. 39–59, 2015.
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[37]
2015 | Journal Article | IST-REx-ID: 1576
S. A. Cepeda Humerez, G. Rieckh, and G. Tkacik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24, 2015.
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[36]
2014 | Journal Article | IST-REx-ID: 3263   OA
G. Tkacik, A. Ghosh, E. Schneidman, and R. Segev, “Adaptation to changes in higher-order stimulus statistics in the salamander retina,” PLoS One, vol. 9, no. 1, 2014.
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[35]
2014 | Journal Article | IST-REx-ID: 2231   OA
G. Rieckh and G. Tkacik, “Noise and information transmission in promoters with multiple internal states,” Biophysical Journal, vol. 106, no. 5, pp. 1194–1204, 2014.
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[34]
2014 | Journal Article | IST-REx-ID: 2257
G. Tkacik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching for collective behavior in a large network of sensory neurons,” PLoS Computational Biology, vol. 10, no. 1, 2014.
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[33]
2014 | Journal Article | IST-REx-ID: 1886   OA
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkacik, “Variance predicts salience in central sensory processing,” eLife, no. November, 2014.
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[32]
2013 | Journal Article | IST-REx-ID: 2277   OA
K. Simmons et al., “Transformation of stimulus correlations by the retina,” PLoS Computational Biology, vol. 9, no. 12, 2013.
View | Files available | DOI
 
[31]
2013 | Journal Article | IST-REx-ID: 2913   OA
G. Tkacik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric: a stimulus distance measure derived from population neural responses,” Physical Review Letters, vol. 110, no. 5, 2013.
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[30]
2013 | Journal Article | IST-REx-ID: 2850   OA
G. Tkacik, O. Marre, T. Mora, D. Amodei, M. Berry, and W. Bialek, “The simplest maximum entropy model for collective behavior in a neural network,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, 2013.
View | DOI | Download (ext.) | arXiv
 
[29]
2013 | Journal Article | IST-REx-ID: 2863   OA
E. Granot Atedgi, G. Tkacik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” PLoS Computational Biology, vol. 9, no. 3, 2013.
View | Files available | DOI
 
[28]
2013 | Journal Article | IST-REx-ID: 2914   OA
G. Stephens, T. Mora, G. Tkacik, and W. Bialek, “Statistical thermodynamics of natural images,” Physical Review Letters, vol. 110, no. 1, 2013.
View | Files available | DOI | Download (ext.) | arXiv
 
[27]
2013 | Journal Article | IST-REx-ID: 2851
M. Berry, G. Tkacik, J. Dubuis, O. Marre, and R. Da Silveira, “A simple method for estimating the entropy of neural activity,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, 2013.
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[26]
2013 | Journal Article | IST-REx-ID: 2818   OA
K. Rajan, O. Marre, and G. Tkacik, “Learning quadratic receptive fields from neural responses to natural stimuli,” Neural Computation, vol. 25, no. 7, pp. 1661–1692, 2013.
View | DOI | Download (ext.) | arXiv
 
[25]
2013 | Journal Article | IST-REx-ID: 3261   OA
J. Dubuis, G. Tkacik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” PNAS, vol. 110, no. 41, pp. 16301–16308, 2013.
View | Files available | DOI | PubMed | Europe PMC
 
[24]
2012 | Journal Article | IST-REx-ID: 3262   OA
G. Tkacik, A. Walczak, and W. Bialek, “Optimizing information flow in small genetic networks. III. A self-interacting gene,” Physical Review E statistical nonlinear and soft matter physics , vol. 85, no. 4, 2012.
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[23]
2011 | Journal Article | IST-REx-ID: 3276   OA
J. Prentice, J. Homann, K. Simmons, G. Tkacik, V. Balasubramanian, and P. Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,” PLoS One, vol. 6, no. 7, 2011.
View | Files available | DOI
 
[22]
2011 | Journal Article | IST-REx-ID: 3384   OA
G. Tkacik et al., “Natural images from the birthplace of the human eye,” PLoS One, vol. 6, no. 6, 2011.
View | Files available | DOI
 
[21]
2011 | Journal Article | IST-REx-ID: 3401
S. Little, G. Tkacik, T. Kneeland, E. Wieschaus, and T. Gregor, “The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source,” PLoS Biology, vol. 9, no. 3, 2011.
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[20]
2011 | Journal Article | IST-REx-ID: 3374   OA
G. Tkacik and A. Walczak, “Information transmission in genetic regulatory networks a review,” Journal of Physics: Condensed Matter, vol. 23, no. 15, 2011.
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[19]
2010 | Journal Article | IST-REx-ID: 3738
A. Walczak, G. Tkacik, and W. Bialek, “Optimizing information flow in small genetic networks. II. Feed-forward interactions,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 81, no. 4, 2010.
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[18]
2010 | Conference Paper | IST-REx-ID: 3430   OA
G. Tkacik, “Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics,” presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, 2010.
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[17]
2010 | Journal Article | IST-REx-ID: 3735
G. Tkacik, J. Prentice, J. Victor, and V. Balasubramanian, “Local statistics in natural scenes predict the saliency of synthetic textures,” PNAS, vol. 107, no. 42, pp. 18149–18154, 2010.
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[16]
2010 | Journal Article | IST-REx-ID: 3736
G. Tkacik, J. Prentice, V. Balasubramanian, and E. Schneidman, “Optimal population coding by noisy spiking neurons,” PNAS, vol. 107, no. 32, pp. 14419–14424, 2010.
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[15]
2010 | Preprint | IST-REx-ID: 3743   OA
G. Tkacik, “From statistical mechanics to information theory: understanding biophysical information-processing systems,” ArXiv, vol. q-MN. ArXiv, pp. 1–52, 2010.
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[14]
2009 | Preprint | IST-REx-ID: 3732   OA
G. Tkacik, E. Schneidman, M. Berry, and W. Bialek, “Spin glass models for a network of real neurons,” ArXiv, vol. q-NC. ArXiv, 2009.
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[13]
2009 | Journal Article | IST-REx-ID: 3737
G. Tkacik, A. Walczak, and W. Bialek, “Optimizing information flow in small genetic networks,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 80, no. 3, 2009.
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[12]
2009 | Journal Article | IST-REx-ID: 3733
S. Kryazhimskiy, G. Tkacik, and J. Plotkin, “The dynamics of adaptation on correlated fitness landscapes,” PNAS, vol. 106, no. 44, pp. 18638–18643, 2009.
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[11]
2009 | Journal Article | IST-REx-ID: 3745
G. Tkacik and W. Bialek, “Diffusion, dimensionality, and noise in transcriptional regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5, 2009.
View | DOI
 
[10]
2009 | Book Chapter | IST-REx-ID: 3747
G. Tkacik and W. Bialek, “Cell Biology: Networks, regulation, pathways,” in Encyclopedia of Complexity and Systems Science, R. Meyers, Ed. Springer, 2009, pp. 719–741.
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[9]
2008 | Journal Article | IST-REx-ID: 3744   OA
G. Tkacik and M. Magnasco, “Decoding spike timing: The differential reverse-correlation method,” Biosystems, vol. 93, no. 1–2, pp. 90–100, 2008.
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[8]
2008 | Journal Article | IST-REx-ID: 3740   OA
G. Tkacik, C. Callan, and W. Bialek, “Information flow and optimization in transcriptional regulation,” PNAS, vol. 105, no. 34, pp. 12265–12270, 2008.
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[7]
2008 | Journal Article | IST-REx-ID: 3734   OA
G. Tkacik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional regulation,” PLoS One, vol. 3, no. 7, 2008.
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[6]
2008 | Journal Article | IST-REx-ID: 3739
G. Tkacik, C. Callan, and W. Bialek, “Information capacity of genetic regulatory elements,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1, 2008.
View | DOI
 
[5]
2007 | Preprint | IST-REx-ID: 3742   OA
T. Broderick, M. Dudik, G. Tkacik, R. Schapire, and W. Bialek, “Faster solutions of the inverse pairwise Ising problem,” ArXiv, vol. q-QM. ArXiv, 2007.
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[4]
2007 | Journal Article | IST-REx-ID: 3731
J. Kinney, G. Tkacik, and C. Callan, “Precise physical models of protein-DNA interaction from high-throughput data,” PNAS, vol. 104, no. 2, pp. 501–506, 2007.
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[3]
2006 | Preprint | IST-REx-ID: 3431   OA
G. Tkacik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006.
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[2]
2005 | Journal Article | IST-REx-ID: 3741   OA
N. Slonim, G. Atwal, G. Tkacik, and W. Bialek, “Information-based clustering,” PNAS, vol. 102, no. 51, pp. 18297–18302, 2005.
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[1]
2005 | Preprint | IST-REx-ID: 3746   OA
N. Slonim, G. Atwal, G. Tkacik, and W. Bialek, “Estimating mutual information and multi-information in large networks,” ArXiv. ArXiv, pp. 1–11, 2005.
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75 Publications

Mark all

[75]
2019 | Preprint | IST-REx-ID: 7083   OA
B. Kavcic, G. Tkačik, and T. Bollenbach, “Mechanistic origin of drug interactions between translation-inhibiting antibiotics,” bioRxiv. Cold Spring Harbor Laboratory, 2019.
View | Download (ext.)
 
[74]
2019 | Journal Article | IST-REx-ID: 6784   OA
J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7, 2019.
View | Files available | DOI
 
[73]
2019 | Journal Article | IST-REx-ID: 5945
M. D. Petkova, G. Tkacik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4, p. 844–855.e15, 2019.
View | Files available | DOI
 
[72]
2019 | Journal Article | IST-REx-ID: 6900   OA
S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” PLoS computational biology, vol. 15, no. 9, p. e1007290, 2019.
View | Files available | DOI | PubMed | Europe PMC
 
[71]
2018 | Journal Article | IST-REx-ID: 31   OA
U. Ferrari, S. Deny, M. J. Chalk, G. Tkacik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4, 2018.
View | DOI | Download (ext.)
 
[70]
2018 | Journal Article | IST-REx-ID: 67
C. Igler, M. Lagator, G. Tkacik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10, pp. 1633–1643, 2018.
View | Files available | DOI
 
[69]
2018 | Journal Article | IST-REx-ID: 543   OA
M. J. Chalk, O. Marre, and G. Tkacik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1, pp. 186–191, 2018.
View | DOI | Download (ext.)
 
[68]
2018 | Research Data | IST-REx-ID: 5587   OA
D. De Martino and G. Tkacik, Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria, 2018.
View | Files available | DOI
 
[67]
2018 | Journal Article | IST-REx-ID: 406   OA
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkacik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3, 2018.
View | Files available | DOI
 
[66]
2018 | Journal Article | IST-REx-ID: 292
V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkacik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5, 2018.
View | Files available | DOI
 
[65]
2018 | Research Data | IST-REx-ID: 5584   OA
S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkacik, Nonlinear decoding of a complex movie from the mammalian retina. IST Austria, 2018.
View | Files available | DOI
 
[64]
2018 | Research Data | IST-REx-ID: 5585
C. Igler, M. Lagator, G. Tkacik, J. P. Bollback, and C. C. Guet, Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. IST Austria, 2018.
View | Files available | DOI
 
[63]
2018 | Journal Article | IST-REx-ID: 281   OA
A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkacik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23, pp. 6088–6093, 2018.
View | Files available | DOI | Download (ext.) | PubMed | Europe PMC
 
[62]
2018 | Journal Article | IST-REx-ID: 161
D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkacik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1, 2018.
View | Files available | DOI
 
[61]
2017 | Research Data | IST-REx-ID: 5562   OA
O. Marre, G. Tkacik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, Multi-electrode array recording from salamander retinal ganglion cells. IST Austria, 2017.
View | Files available | DOI
 
[60]
2017 | Journal Article | IST-REx-ID: 725   OA
R. Harpaz, G. Tkacik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38, pp. 10149–10154, 2017.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[59]
2017 | Journal Article | IST-REx-ID: 1104   OA
S. Deny et al., “Multiplexed computations in retinal ganglion cells of a single type,” Nature Communications, vol. 8, no. 1, 2017.
View | Files available | DOI
 
[58]
2017 | Journal Article | IST-REx-ID: 720   OA
J. Humplik and G. Tkacik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9, 2017.
View | Files available | DOI
 
[57]
2017 | Journal Article | IST-REx-ID: 613   OA
R. P. Chait, J. Ruess, T. Bergmiller, G. Tkacik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1, 2017.
View | Files available | DOI
 
[56]
2017 | Journal Article | IST-REx-ID: 943   OA
M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345, pp. 1379–1383, 2017.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[55]
2017 | Journal Article | IST-REx-ID: 955   OA
T. Friedlander, R. Prizak, N. H. Barton, and G. Tkacik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1, 2017.
View | Files available | DOI
 
[54]
2017 | Journal Article | IST-REx-ID: 730
C. Savin and G. Tkacik, “Maximum entropy models as a tool for building precise neural controls,” Current Opinion in Neurobiology, vol. 46, pp. 120–126, 2017.
View | DOI
 
[53]
2017 | Research Data | IST-REx-ID: 5560
T. Bergmiller et al., Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. IST Austria, 2017.
View | Files available | DOI
 
[52]
2017 | Journal Article | IST-REx-ID: 665
T. Bergmiller et al., “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science, vol. 356, no. 6335, pp. 311–315, 2017.
View | Files available | DOI
 
[51]
2016 | Journal Article | IST-REx-ID: 1248   OA
G. Tkacik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7, pp. 89–117, 2016.
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[50]
2016 | Journal Article | IST-REx-ID: 1197   OA
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkacik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11, 2016.
View | Files available | DOI
 
[49]
2016 | Conference Paper | IST-REx-ID: 1105
C. Savin and G. Tkacik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.
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[48]
2016 | Journal Article | IST-REx-ID: 1270   OA
P. Hillenbrand, U. Gerland, and G. Tkacik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9, 2016.
View | Files available | DOI
 
[47]
2016 | Journal Article | IST-REx-ID: 1358
T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkacik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7, 2016.
View | Files available | DOI
 
[46]
2016 | Conference Paper | IST-REx-ID: 1082   OA
M. J. Chalk, O. Marre, and G. Tkacik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.
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[45]
2016 | Journal Article | IST-REx-ID: 1171
G. Tkacik, “Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.,” Physics of Life Reviews, vol. 17, pp. 166–167, 2016.
View | DOI
 
[44]
2016 | Journal Article | IST-REx-ID: 1420   OA
K. Bod’ová, G. Tkacik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4, pp. 1523–1548, 2016.
View | DOI | Download (ext.) | arXiv
 
[43]
2016 | Journal Article | IST-REx-ID: 1242   OA
T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkacik, “Extending the dynamic range of transcription factor action by translational regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2, 2016.
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[42]
2015 | Journal Article | IST-REx-ID: 1666   OA
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkacik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11, 2015.
View | Files available | DOI
 
[41]
2015 | Journal Article | IST-REx-ID: 1940   OA
T. R. Sokolowski and G. Tkacik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 2015.
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[40]
2015 | Journal Article | IST-REx-ID: 1697   OA
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkacik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7, 2015.
View | Files available | DOI
 
[39]
2015 | Journal Article | IST-REx-ID: 1701   OA
G. Tkacik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37, pp. 11508–11513, 2015.
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[38]
2015 | Journal Article | IST-REx-ID: 1885   OA
G. Tkacik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1, pp. 39–59, 2015.
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[37]
2015 | Journal Article | IST-REx-ID: 1576
S. A. Cepeda Humerez, G. Rieckh, and G. Tkacik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24, 2015.
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[36]
2014 | Journal Article | IST-REx-ID: 3263   OA
G. Tkacik, A. Ghosh, E. Schneidman, and R. Segev, “Adaptation to changes in higher-order stimulus statistics in the salamander retina,” PLoS One, vol. 9, no. 1, 2014.
View | Files available | DOI
 
[35]
2014 | Journal Article | IST-REx-ID: 2231   OA
G. Rieckh and G. Tkacik, “Noise and information transmission in promoters with multiple internal states,” Biophysical Journal, vol. 106, no. 5, pp. 1194–1204, 2014.
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[34]
2014 | Journal Article | IST-REx-ID: 2257
G. Tkacik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching for collective behavior in a large network of sensory neurons,” PLoS Computational Biology, vol. 10, no. 1, 2014.
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[33]
2014 | Journal Article | IST-REx-ID: 1886   OA
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkacik, “Variance predicts salience in central sensory processing,” eLife, no. November, 2014.
View | Files available | DOI
 
[32]
2013 | Journal Article | IST-REx-ID: 2277   OA
K. Simmons et al., “Transformation of stimulus correlations by the retina,” PLoS Computational Biology, vol. 9, no. 12, 2013.
View | Files available | DOI
 
[31]
2013 | Journal Article | IST-REx-ID: 2913   OA
G. Tkacik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric: a stimulus distance measure derived from population neural responses,” Physical Review Letters, vol. 110, no. 5, 2013.
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[30]
2013 | Journal Article | IST-REx-ID: 2850   OA
G. Tkacik, O. Marre, T. Mora, D. Amodei, M. Berry, and W. Bialek, “The simplest maximum entropy model for collective behavior in a neural network,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, 2013.
View | DOI | Download (ext.) | arXiv
 
[29]
2013 | Journal Article | IST-REx-ID: 2863   OA
E. Granot Atedgi, G. Tkacik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” PLoS Computational Biology, vol. 9, no. 3, 2013.
View | Files available | DOI
 
[28]
2013 | Journal Article | IST-REx-ID: 2914   OA
G. Stephens, T. Mora, G. Tkacik, and W. Bialek, “Statistical thermodynamics of natural images,” Physical Review Letters, vol. 110, no. 1, 2013.
View | Files available | DOI | Download (ext.) | arXiv
 
[27]
2013 | Journal Article | IST-REx-ID: 2851
M. Berry, G. Tkacik, J. Dubuis, O. Marre, and R. Da Silveira, “A simple method for estimating the entropy of neural activity,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, 2013.
View | DOI
 
[26]
2013 | Journal Article | IST-REx-ID: 2818   OA
K. Rajan, O. Marre, and G. Tkacik, “Learning quadratic receptive fields from neural responses to natural stimuli,” Neural Computation, vol. 25, no. 7, pp. 1661–1692, 2013.
View | DOI | Download (ext.) | arXiv
 
[25]
2013 | Journal Article | IST-REx-ID: 3261   OA
J. Dubuis, G. Tkacik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” PNAS, vol. 110, no. 41, pp. 16301–16308, 2013.
View | Files available | DOI | PubMed | Europe PMC
 
[24]
2012 | Journal Article | IST-REx-ID: 3262   OA
G. Tkacik, A. Walczak, and W. Bialek, “Optimizing information flow in small genetic networks. III. A self-interacting gene,” Physical Review E statistical nonlinear and soft matter physics , vol. 85, no. 4, 2012.
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[23]
2011 | Journal Article | IST-REx-ID: 3276   OA
J. Prentice, J. Homann, K. Simmons, G. Tkacik, V. Balasubramanian, and P. Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,” PLoS One, vol. 6, no. 7, 2011.
View | Files available | DOI
 
[22]
2011 | Journal Article | IST-REx-ID: 3384   OA
G. Tkacik et al., “Natural images from the birthplace of the human eye,” PLoS One, vol. 6, no. 6, 2011.
View | Files available | DOI
 
[21]
2011 | Journal Article | IST-REx-ID: 3401
S. Little, G. Tkacik, T. Kneeland, E. Wieschaus, and T. Gregor, “The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source,” PLoS Biology, vol. 9, no. 3, 2011.
View | DOI
 
[20]
2011 | Journal Article | IST-REx-ID: 3374   OA
G. Tkacik and A. Walczak, “Information transmission in genetic regulatory networks a review,” Journal of Physics: Condensed Matter, vol. 23, no. 15, 2011.
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[19]
2010 | Journal Article | IST-REx-ID: 3738
A. Walczak, G. Tkacik, and W. Bialek, “Optimizing information flow in small genetic networks. II. Feed-forward interactions,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 81, no. 4, 2010.
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[18]
2010 | Conference Paper | IST-REx-ID: 3430   OA
G. Tkacik, “Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics,” presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, 2010.
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[17]
2010 | Journal Article | IST-REx-ID: 3735
G. Tkacik, J. Prentice, J. Victor, and V. Balasubramanian, “Local statistics in natural scenes predict the saliency of synthetic textures,” PNAS, vol. 107, no. 42, pp. 18149–18154, 2010.
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[16]
2010 | Journal Article | IST-REx-ID: 3736
G. Tkacik, J. Prentice, V. Balasubramanian, and E. Schneidman, “Optimal population coding by noisy spiking neurons,” PNAS, vol. 107, no. 32, pp. 14419–14424, 2010.
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[15]
2010 | Preprint | IST-REx-ID: 3743   OA
G. Tkacik, “From statistical mechanics to information theory: understanding biophysical information-processing systems,” ArXiv, vol. q-MN. ArXiv, pp. 1–52, 2010.
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[14]
2009 | Preprint | IST-REx-ID: 3732   OA
G. Tkacik, E. Schneidman, M. Berry, and W. Bialek, “Spin glass models for a network of real neurons,” ArXiv, vol. q-NC. ArXiv, 2009.
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[13]
2009 | Journal Article | IST-REx-ID: 3737
G. Tkacik, A. Walczak, and W. Bialek, “Optimizing information flow in small genetic networks,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 80, no. 3, 2009.
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[12]
2009 | Journal Article | IST-REx-ID: 3733
S. Kryazhimskiy, G. Tkacik, and J. Plotkin, “The dynamics of adaptation on correlated fitness landscapes,” PNAS, vol. 106, no. 44, pp. 18638–18643, 2009.
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[11]
2009 | Journal Article | IST-REx-ID: 3745
G. Tkacik and W. Bialek, “Diffusion, dimensionality, and noise in transcriptional regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5, 2009.
View | DOI
 
[10]
2009 | Book Chapter | IST-REx-ID: 3747
G. Tkacik and W. Bialek, “Cell Biology: Networks, regulation, pathways,” in Encyclopedia of Complexity and Systems Science, R. Meyers, Ed. Springer, 2009, pp. 719–741.
View | DOI
 
[9]
2008 | Journal Article | IST-REx-ID: 3744   OA
G. Tkacik and M. Magnasco, “Decoding spike timing: The differential reverse-correlation method,” Biosystems, vol. 93, no. 1–2, pp. 90–100, 2008.
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[8]
2008 | Journal Article | IST-REx-ID: 3740   OA
G. Tkacik, C. Callan, and W. Bialek, “Information flow and optimization in transcriptional regulation,” PNAS, vol. 105, no. 34, pp. 12265–12270, 2008.
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[7]
2008 | Journal Article | IST-REx-ID: 3734   OA
G. Tkacik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional regulation,” PLoS One, vol. 3, no. 7, 2008.
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[6]
2008 | Journal Article | IST-REx-ID: 3739
G. Tkacik, C. Callan, and W. Bialek, “Information capacity of genetic regulatory elements,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1, 2008.
View | DOI
 
[5]
2007 | Preprint | IST-REx-ID: 3742   OA
T. Broderick, M. Dudik, G. Tkacik, R. Schapire, and W. Bialek, “Faster solutions of the inverse pairwise Ising problem,” ArXiv, vol. q-QM. ArXiv, 2007.
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[4]
2007 | Journal Article | IST-REx-ID: 3731
J. Kinney, G. Tkacik, and C. Callan, “Precise physical models of protein-DNA interaction from high-throughput data,” PNAS, vol. 104, no. 2, pp. 501–506, 2007.
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[3]
2006 | Preprint | IST-REx-ID: 3431   OA
G. Tkacik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006.
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[2]
2005 | Journal Article | IST-REx-ID: 3741   OA
N. Slonim, G. Atwal, G. Tkacik, and W. Bialek, “Information-based clustering,” PNAS, vol. 102, no. 51, pp. 18297–18302, 2005.
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[1]
2005 | Preprint | IST-REx-ID: 3746   OA
N. Slonim, G. Atwal, G. Tkacik, and W. Bialek, “Estimating mutual information and multi-information in large networks,” ArXiv. ArXiv, pp. 1–11, 2005.
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