Gasper Tkacik

118 Publications

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[118]
2025 | Published | Journal Article | IST-REx-ID: 19453 | OA
H. S. C. Chiossi, M. Nardin, G. Tkačik, and J. L. Csicsvari, “Learning reshapes the hippocampal representation hierarchy,” Proceedings of the National Academy of Sciences, vol. 122, no. 11. National Academy of Sciences, 2025.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[117]
2025 | Published | Journal Article | IST-REx-ID: 18849 | OA
T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic regulatory network from an optimization principle,” Proceedings of the National Academy of Sciences of the United States of America, vol. 122, no. 1. National Academy of Sciences, 2025.
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[116]
2025 | Published | Journal Article | IST-REx-ID: 19701 | OA
G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” Annual review of biophysics, vol. 54. Annual Reviews, pp. 249–274, 2025.
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[115]
2025 | Published | Journal Article | IST-REx-ID: 18936 | OA
R. Grah, C. C. Guet, G. Tkačik, and M. Lagator, “Linking molecular mechanisms to their evolutionary consequences: a primer,” Genetics, vol. 229, no. 2. Oxford University Press, 2025.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[114]
2025 | Published | Journal Article | IST-REx-ID: 18850 | OA
M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable gene regulation with factors of limited specificity,” Proceedings of the National Academy of Sciences of the United States of America, vol. 122, no. 1. National Academy of Sciences, 2025.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[113]
2025 | Published | Journal Article | IST-REx-ID: 19785 | OA
B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion processes,” Physical Review E, vol. 111, no. 5. American Physical Society, 2025.
[Published Version] View | Files available | DOI
 
[112]
2025 | Research Data | IST-REx-ID: 19658 | OA
G. Tkačik, “Token-driven totally asymmetric simple exclusion processes.” Institute of Science and Technology Austria, 2025.
[Published Version] View | Files available | DOI
 
[111]
2025 | Published | Journal Article | IST-REx-ID: 19626 | OA
K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, and C. C. Guet, “Pulsatile basal gene expression as a fitness determinant in bacteria,” Proceedings of the National Academy of Sciences, vol. 122, no. 15. National Academy of Sciences, 2025.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[110]
2025 | Research Data | IST-REx-ID: 19294 | OA
K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, and C. C. Guet, “Data for ‘Pulsatile basal gene expression as a fitness determinant in bacteria.’” Institute of Science and Technology Austria, 2025.
[Published Version] View | Files available | DOI
 
[109]
2024 | Published | Journal Article | IST-REx-ID: 18525 | OA
N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44. National Academy of Sciences, 2024.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[108]
2024 | Published | Journal Article | IST-REx-ID: 17123 | OA
D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 23. National Academy of Sciences, 2024.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[107]
2024 | Published | Journal Article | IST-REx-ID: 18902 | OA
M. Zagorski et al., “Assessing the precision of morphogen gradients in neural tube development,” Nature Communications, vol. 15. Springer Nature, 2024.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[106]
2023 | Published | Journal Article | IST-REx-ID: 14515 | OA
M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories,” Physical Review X, vol. 13, no. 4. American Physical Society, 2023.
[Published Version] View | Files available | DOI | arXiv
 
[105]
2023 | Published | Journal Article | IST-REx-ID: 13127 | OA
B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” Nature Communications, vol. 14. Springer Nature, 2023.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[104]
2023 | Published | Journal Article | IST-REx-ID: 12762 | OA
F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023.
[Published Version] View | Files available | DOI | PubMed | Europe PMC | arXiv
 
[103]
2023 | Published | Journal Article | IST-REx-ID: 14656 | OA
M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[102]
2022 | Published | Journal Article | IST-REx-ID: 10736 | OA
M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[101]
2022 | Published | Journal Article | IST-REx-ID: 12081 | OA
M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 36. National Academy of Sciences, 2022.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[100]
2022 | Published | Journal Article | IST-REx-ID: 12156 | OA
B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” Current Opinion in Systems Biology, vol. 31, no. 9. Elsevier, 2022.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[99]
2022 | Published | Journal Article | IST-REx-ID: 12332 | OA
W. F. Mlynarski and G. Tkačik, “Efficient coding theory of dynamic attentional modulation,” PLoS Biology, vol. 20, no. 12. Public Library of Science, p. e3001889, 2022.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[98]
2021 | Submitted | Preprint | IST-REx-ID: 10579 | OA
B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion process,” arXiv. .
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[97]
2021 | Published | Journal Article | IST-REx-ID: 9362 | OA
M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of Science, 2021.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[96]
2021 | Published | Journal Article | IST-REx-ID: 9226 | OA
G. Tkačik and T. Gregor, “The many bits of positional information,” Development, vol. 148, no. 2. The Company of Biologists, 2021.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[95]
2021 | Submitted | Preprint | IST-REx-ID: 10912 | OA
F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Quantifying the coexistence of neuronal oscillations and avalanches.” arXiv.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[94]
2021 | Published | Journal Article | IST-REx-ID: 8997 | OA
B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” PLOS Computational Biology, vol. 17. Public Library of Science, 2021.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[93]
2021 | Published | Journal Article | IST-REx-ID: 7553 | OA
W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | PubMed | Europe PMC
 
[92]
2021 | Draft | Preprint | IST-REx-ID: 10077 | OA
M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[91]
2020 | Published | Journal Article | IST-REx-ID: 7656 | OA
M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle for population codes,” Frontiers in Computational Neuroscience, vol. 14. Frontiers, 2020.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[90]
2020 | Published | Preprint | IST-REx-ID: 7675 | OA
R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[89]
2020 | Published | Journal Article | IST-REx-ID: 9000 | OA
R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2020 | Published | Journal Article | IST-REx-ID: 8698 | OA
O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[87]
2020 | Published | Journal Article | IST-REx-ID: 8250 | OA
B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[86]
2020 | Published | Preprint | IST-REx-ID: 7673 | OA
B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[85]
2020 | Published | Journal Article | IST-REx-ID: 7652 | OA
I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.
[Submitted Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[84]
2019 | Published | 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. Public Library of Science, p. e1007290, 2019.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[83]
2019 | Published | Journal Article | IST-REx-ID: 5945 | OA
M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019.
[Published Version] View | Files available | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[82]
2019 | Published | 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. Public Library of Science, 2019.
[Published Version] View | Files available | DOI | WoS
 
[81]
2019 | Research Data Reference | IST-REx-ID: 9786
J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.” Public Library of Science, 2019.
[Published Version] View | Files available | DOI
 
[80]
2019 | Published | Conference Paper | IST-REx-ID: 7606 | OA
M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden, 2019.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | arXiv
 
[79]
2019 | Submitted | Preprint | IST-REx-ID: 7552 | OA
W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” arXiv. ArXiv.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[78]
2018 | Published | Journal Article | IST-REx-ID: 281 | OA
A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | PubMed | Europe PMC
 
[77]
2018 | Published | Journal Article | IST-REx-ID: 406 | OA
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.
[Submitted Version] View | Files available | DOI | WoS
 
[76]
2018 | Research Data Reference | IST-REx-ID: 9831
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018.
[Published Version] View | Files available | DOI
 
[75]
2018 | Published | Journal Article | IST-REx-ID: 161 | OA
D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.
[Published Version] View | Files available | DOI | WoS
 
[74]
2018 | Research Data | IST-REx-ID: 5587 | OA
D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.
[Published Version] View | Files available | DOI
 
[73]
2018 | Published | Journal Article | IST-REx-ID: 292 | OA
V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5. Public Library of Science, 2018.
[Published Version] View | Files available | DOI | WoS
 
[72]
2018 | Research Data | IST-REx-ID: 5584 | OA
S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.
[Published Version] View | Files available | DOI
 
[71]
2018 | Published | Journal Article | IST-REx-ID: 31 | OA
U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018.
[Preprint] View | DOI | Download Preprint (ext.) | WoS
 
[70]
2018 | Published | Journal Article | IST-REx-ID: 543 | OA
M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS
 
[69]
2018 | Published | Journal Article | IST-REx-ID: 67 | OA
C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018.
[Submitted Version] View | Files available | DOI | WoS
 
[68]
2018 | Research Data | IST-REx-ID: 5585 | OA
C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.
[Published Version] View | Files available | DOI
 
[67]
2017 | Published | Journal Article | IST-REx-ID: 730
C. Savin and G. Tkačik, “Maximum entropy models as a tool for building precise neural controls,” Current Opinion in Neurobiology, vol. 46. Elsevier, pp. 120–126, 2017.
View | DOI | WoS
 
[66]
2017 | Research Data Reference | IST-REx-ID: 9709 | OA
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[65]
2017 | Research Data | IST-REx-ID: 5562 | OA
O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017.
[Published Version] View | Files available | DOI
 
[64]
2017 | Published | 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. Nature Publishing Group, 2017.
[Published Version] View | Files available | DOI | WoS
 
[63]
2017 | Published | Journal Article | IST-REx-ID: 613 | OA
R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
[Published Version] View | Files available | DOI
 
[62]
2017 | Published | 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. American Association for the Advancement of Science, pp. 311–315, 2017.
View | Files available | DOI
 
[61]
2017 | Research Data | IST-REx-ID: 5560 | OA
T. Bergmiller et al., “Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science and Technology Austria, 2017.
[Published Version] View | Files available | DOI
 
[60]
2017 | Published | Journal Article | IST-REx-ID: 720 | OA
J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9. Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[59]
2017 | Published | Journal Article | IST-REx-ID: 725 | OA
R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[58]
2017 | Published | 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. American Association for the Advancement of Science, pp. 1379–1383, 2017.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[57]
2017 | Published | Journal Article | IST-REx-ID: 955 | OA
T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
[Published Version] View | Files available | DOI | WoS
 
[56]
2016 | Published | Journal Article | IST-REx-ID: 1171
G. Tkačik, “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. Elsevier, pp. 166–167, 2016.
View | DOI
 
[55]
2016 | Published | Journal Article | IST-REx-ID: 1270 | OA
P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9. Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 
[54]
2016 | Research Data Reference | IST-REx-ID: 9870
P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 
[53]
2016 | Research Data Reference | IST-REx-ID: 9869
P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 
[52]
2016 | Research Data Reference | IST-REx-ID: 9871
P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 
[51]
2016 | Published | Journal Article | IST-REx-ID: 1420 | OA
K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[50]
2016 | Published | Journal Article | IST-REx-ID: 1358 | OA
T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
[Published Version] View | Files available | DOI
 
[49]
2016 | Published | Journal Article | IST-REx-ID: 1197 | OA
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11. Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 
[48]
2016 | Published | Conference Paper | IST-REx-ID: 1082 | OA
M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.
[Preprint] View | Files available | Download Preprint (ext.) | arXiv
 
[47]
2016 | Published | Conference Paper | IST-REx-ID: 1105 | OA
C. Savin and G. Tkačik, “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.
View | Download None (ext.)
 
[46]
2016 | Published | Journal Article | IST-REx-ID: 1242 | OA
T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American Institute of Physics, 2016.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[45]
2016 | Published | Journal Article | IST-REx-ID: 1248 | OA
G. Tkačik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[44]
2015 | Published | Journal Article | IST-REx-ID: 1666 | OA
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 
[43]
2015 | Research Data Reference | IST-REx-ID: 9712
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 
[42]
2015 | Published | Journal Article | IST-REx-ID: 1697 | OA
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7. Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 
[41]
2015 | Published | Journal Article | IST-REx-ID: 1701 | OA
G. Tkačik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[40]
2015 | Published | Journal Article | IST-REx-ID: 1885 | OA
G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[39]
2015 | Published | Journal Article | IST-REx-ID: 1576 | OA
S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24. American Physical Society, 2015.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | arXiv
 
[38]
2015 | Published | Journal Article | IST-REx-ID: 1940 | OA
T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[37]
2014 | Published | Journal Article | IST-REx-ID: 3263 | OA
G. Tkačik, 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. Public Library of Science, 2014.
[Published Version] View | Files available | DOI
 
[36]
2014 | Research Data Reference | IST-REx-ID: 9752 | OA
K. Simmons et al., “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[35]
2014 | Published | Journal Article | IST-REx-ID: 1886 | OA
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” eLife, no. November. eLife Sciences Publications, 2014.
[Published Version] View | Files available | DOI
 
[34]
2014 | Published | Journal Article | IST-REx-ID: 2257 | OA
G. Tkačik, 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. Public Library of Science, 2014.
[Published Version] View | Files available | DOI
 
[33]
2014 | Published | Journal Article | IST-REx-ID: 2231 | OA
G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” Biophysical Journal, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[32]
2013 | Published | 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. Public Library of Science, 2013.
[Published Version] View | Files available | DOI
 
[31]
2013 | Published | Journal Article | IST-REx-ID: 2818 | OA
K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” Neural Computation, vol. 25, no. 7. MIT Press , pp. 1661–1692, 2013.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[30]
2013 | Published | Journal Article | IST-REx-ID: 2863 | OA
E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” PLoS Computational Biology, vol. 9, no. 3. Public Library of Science, 2013.
[Published Version] View | Files available | DOI
 
[29]
2013 | Published | Journal Article | IST-REx-ID: 2914 | OA
G. Stephens, T. Mora, G. Tkačik, and W. Bialek, “Statistical thermodynamics of natural images,” Physical Review Letters, vol. 110, no. 1. American Physical Society, 2013.
[Published Version] View | Files available | DOI | arXiv
 
[28]
2013 | Published | Journal Article | IST-REx-ID: 3261 | OA
J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” PNAS, vol. 110, no. 41. National Academy of Sciences, pp. 16301–16308, 2013.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[27]
2013 | Published | Journal Article | IST-REx-ID: 2850 | OA
G. Tkačik, 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. IOP Publishing, 2013.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[26]
2013 | Published | Journal Article | IST-REx-ID: 2851
M. Berry, G. Tkačik, 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. IOP Publishing, 2013.
View | DOI
 
[25]
2013 | Published | Journal Article | IST-REx-ID: 2913 | OA
G. Tkačik, 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. American Physical Society, 2013.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[24]
2012 | Published | Journal Article | IST-REx-ID: 3262 | OA
G. Tkačik, 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. American Institute of Physics, 2012.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[23]
2011 | Published | Journal Article | IST-REx-ID: 3276 | OA
J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, and P. Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011.
View | Files available | DOI
 
[22]
2011 | Published | Journal Article | IST-REx-ID: 3384 | OA
G. Tkačik et al., “Natural images from the birthplace of the human eye,” PLoS One, vol. 6, no. 6. Public Library of Science, 2011.
[Published Version] View | Files available | DOI
 
[21]
2011 | Published | Journal Article | IST-REx-ID: 3401
S. Little, G. Tkačik, 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. Public Library of Science, 2011.
View | DOI
 
[20]
2011 | Published | Journal Article | IST-REx-ID: 3374 | OA
G. Tkačik and A. Walczak, “Information transmission in genetic regulatory networks a review,” Journal of Physics: Condensed Matter, vol. 23, no. 15. IOP Publishing, 2011.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | arXiv
 
[19]
2010 | Published | Conference Paper | IST-REx-ID: 3430 | OA
G. Tkačik, “Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics,” presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, 2010.
View | Download (ext.)
 
[18]
2010 | Published | Journal Article | IST-REx-ID: 3735
G. Tkačik, J. Prentice, J. Victor, and V. Balasubramanian, “Local statistics in natural scenes predict the saliency of synthetic textures,” PNAS, vol. 107, no. 42. National Academy of Sciences, pp. 18149–18154, 2010.
View | DOI | Download (ext.)
 
[17]
2010 | Published | Journal Article | IST-REx-ID: 3736
G. Tkačik, J. Prentice, V. Balasubramanian, and E. Schneidman, “Optimal population coding by noisy spiking neurons,” PNAS, vol. 107, no. 32. National Academy of Sciences, pp. 14419–14424, 2010.
View | DOI | Download (ext.)
 
[16]
2010 | Published | Journal Article | IST-REx-ID: 3738
A. Walczak, G. Tkačik, 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. American Institute of Physics, 2010.
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[15]
2010 | Published | Preprint | IST-REx-ID: 3743 | OA
G. Tkačik, “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 | Published | Preprint | IST-REx-ID: 3732 | OA
G. Tkačik, 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 | Published | Journal Article | IST-REx-ID: 3733
S. Kryazhimskiy, G. Tkačik, and J. Plotkin, “The dynamics of adaptation on correlated fitness landscapes,” PNAS, vol. 106, no. 44. National Academy of Sciences, pp. 18638–18643, 2009.
View | DOI | Download (ext.)
 
[12]
2009 | Published | Journal Article | IST-REx-ID: 3737
G. Tkačik, 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. American Institute of Physics, 2009.
View | DOI | Download (ext.)
 
[11]
2009 | Published | Journal Article | IST-REx-ID: 3745
G. Tkačik and W. Bialek, “Diffusion, dimensionality, and noise in transcriptional regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5. American Institute of Physics, 2009.
View | DOI
 
[10]
2009 | Published | Book Chapter | IST-REx-ID: 3747
G. Tkačik 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 | Published | Journal Article | IST-REx-ID: 3734 | OA
G. Tkačik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional regulation,” PLoS One, vol. 3, no. 7. Public Library of Science, 2008.
View | DOI | Download (ext.)
 
[8]
2008 | Published | Journal Article | IST-REx-ID: 3739
G. Tkačik, C. Callan, and W. Bialek, “Information capacity of genetic regulatory elements,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1. American Institute of Physics, 2008.
View | DOI
 
[7]
2008 | Published | Journal Article | IST-REx-ID: 3740 | OA
G. Tkačik, C. Callan, and W. Bialek, “Information flow and optimization in transcriptional regulation,” PNAS, vol. 105, no. 34. National Academy of Sciences, pp. 12265–12270, 2008.
View | DOI | Download (ext.)
 
[6]
2008 | Published | Journal Article | IST-REx-ID: 3744 | OA
G. Tkačik and M. Magnasco, “Decoding spike timing: The differential reverse-correlation method,” Biosystems, vol. 93, no. 1–2. Elsevier, pp. 90–100, 2008.
View | DOI | Download (ext.)
 
[5]
2007 | Published | Journal Article | IST-REx-ID: 3731
J. Kinney, G. Tkačik, and C. Callan, “Precise physical models of protein-DNA interaction from high-throughput data,” PNAS, vol. 104, no. 2. National Academy of Sciences, pp. 501–506, 2007.
View | DOI | Download (ext.)
 
[4]
2007 | Published | Preprint | IST-REx-ID: 3742 | OA
T. Broderick, M. Dudik, G. Tkačik, R. Schapire, and W. Bialek, “Faster solutions of the inverse pairwise Ising problem,” ArXiv, vol. q-QM. ArXiv, 2007.
View | Download (ext.)
 
[3]
2006 | Published | Preprint | IST-REx-ID: 3431 | OA
G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006.
View | Download (ext.)
 
[2]
2005 | Published | Journal Article | IST-REx-ID: 3741 | OA
N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Information-based clustering,” PNAS, vol. 102, no. 51. National Academy of Sciences, pp. 18297–18302, 2005.
View | DOI | Download (ext.)
 
[1]
2005 | Published | Preprint | IST-REx-ID: 3746 | OA
N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Estimating mutual information and multi-information in large networks,” ArXiv. ArXiv, pp. 1–11, 2005.
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118 Publications

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[118]
2025 | Published | Journal Article | IST-REx-ID: 19453 | OA
H. S. C. Chiossi, M. Nardin, G. Tkačik, and J. L. Csicsvari, “Learning reshapes the hippocampal representation hierarchy,” Proceedings of the National Academy of Sciences, vol. 122, no. 11. National Academy of Sciences, 2025.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[117]
2025 | Published | Journal Article | IST-REx-ID: 18849 | OA
T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic regulatory network from an optimization principle,” Proceedings of the National Academy of Sciences of the United States of America, vol. 122, no. 1. National Academy of Sciences, 2025.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[116]
2025 | Published | Journal Article | IST-REx-ID: 19701 | OA
G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” Annual review of biophysics, vol. 54. Annual Reviews, pp. 249–274, 2025.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[115]
2025 | Published | Journal Article | IST-REx-ID: 18936 | OA
R. Grah, C. C. Guet, G. Tkačik, and M. Lagator, “Linking molecular mechanisms to their evolutionary consequences: a primer,” Genetics, vol. 229, no. 2. Oxford University Press, 2025.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[114]
2025 | Published | Journal Article | IST-REx-ID: 18850 | OA
M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable gene regulation with factors of limited specificity,” Proceedings of the National Academy of Sciences of the United States of America, vol. 122, no. 1. National Academy of Sciences, 2025.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[113]
2025 | Published | Journal Article | IST-REx-ID: 19785 | OA
B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion processes,” Physical Review E, vol. 111, no. 5. American Physical Society, 2025.
[Published Version] View | Files available | DOI
 
[112]
2025 | Research Data | IST-REx-ID: 19658 | OA
G. Tkačik, “Token-driven totally asymmetric simple exclusion processes.” Institute of Science and Technology Austria, 2025.
[Published Version] View | Files available | DOI
 
[111]
2025 | Published | Journal Article | IST-REx-ID: 19626 | OA
K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, and C. C. Guet, “Pulsatile basal gene expression as a fitness determinant in bacteria,” Proceedings of the National Academy of Sciences, vol. 122, no. 15. National Academy of Sciences, 2025.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[110]
2025 | Research Data | IST-REx-ID: 19294 | OA
K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, and C. C. Guet, “Data for ‘Pulsatile basal gene expression as a fitness determinant in bacteria.’” Institute of Science and Technology Austria, 2025.
[Published Version] View | Files available | DOI
 
[109]
2024 | Published | Journal Article | IST-REx-ID: 18525 | OA
N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44. National Academy of Sciences, 2024.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[108]
2024 | Published | Journal Article | IST-REx-ID: 17123 | OA
D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 23. National Academy of Sciences, 2024.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[107]
2024 | Published | Journal Article | IST-REx-ID: 18902 | OA
M. Zagorski et al., “Assessing the precision of morphogen gradients in neural tube development,” Nature Communications, vol. 15. Springer Nature, 2024.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[106]
2023 | Published | Journal Article | IST-REx-ID: 14515 | OA
M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories,” Physical Review X, vol. 13, no. 4. American Physical Society, 2023.
[Published Version] View | Files available | DOI | arXiv
 
[105]
2023 | Published | Journal Article | IST-REx-ID: 13127 | OA
B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” Nature Communications, vol. 14. Springer Nature, 2023.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[104]
2023 | Published | Journal Article | IST-REx-ID: 12762 | OA
F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023.
[Published Version] View | Files available | DOI | PubMed | Europe PMC | arXiv
 
[103]
2023 | Published | Journal Article | IST-REx-ID: 14656 | OA
M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[102]
2022 | Published | Journal Article | IST-REx-ID: 10736 | OA
M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[101]
2022 | Published | Journal Article | IST-REx-ID: 12081 | OA
M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 36. National Academy of Sciences, 2022.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[100]
2022 | Published | Journal Article | IST-REx-ID: 12156 | OA
B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” Current Opinion in Systems Biology, vol. 31, no. 9. Elsevier, 2022.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[99]
2022 | Published | Journal Article | IST-REx-ID: 12332 | OA
W. F. Mlynarski and G. Tkačik, “Efficient coding theory of dynamic attentional modulation,” PLoS Biology, vol. 20, no. 12. Public Library of Science, p. e3001889, 2022.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[98]
2021 | Submitted | Preprint | IST-REx-ID: 10579 | OA
B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion process,” arXiv. .
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[97]
2021 | Published | Journal Article | IST-REx-ID: 9362 | OA
M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of Science, 2021.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[96]
2021 | Published | Journal Article | IST-REx-ID: 9226 | OA
G. Tkačik and T. Gregor, “The many bits of positional information,” Development, vol. 148, no. 2. The Company of Biologists, 2021.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[95]
2021 | Submitted | Preprint | IST-REx-ID: 10912 | OA
F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Quantifying the coexistence of neuronal oscillations and avalanches.” arXiv.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[94]
2021 | Published | Journal Article | IST-REx-ID: 8997 | OA
B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” PLOS Computational Biology, vol. 17. Public Library of Science, 2021.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[93]
2021 | Published | Journal Article | IST-REx-ID: 7553 | OA
W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | PubMed | Europe PMC
 
[92]
2021 | Draft | Preprint | IST-REx-ID: 10077 | OA
M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[91]
2020 | Published | Journal Article | IST-REx-ID: 7656 | OA
M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle for population codes,” Frontiers in Computational Neuroscience, vol. 14. Frontiers, 2020.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[90]
2020 | Published | Preprint | IST-REx-ID: 7675 | OA
R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[89]
2020 | Published | Journal Article | IST-REx-ID: 9000 | OA
R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2020 | Published | Journal Article | IST-REx-ID: 8698 | OA
O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[87]
2020 | Published | Journal Article | IST-REx-ID: 8250 | OA
B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[86]
2020 | Published | Preprint | IST-REx-ID: 7673 | OA
B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[85]
2020 | Published | Journal Article | IST-REx-ID: 7652 | OA
I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.
[Submitted Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[84]
2019 | Published | 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. Public Library of Science, p. e1007290, 2019.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[83]
2019 | Published | Journal Article | IST-REx-ID: 5945 | OA
M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019.
[Published Version] View | Files available | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[82]
2019 | Published | 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. Public Library of Science, 2019.
[Published Version] View | Files available | DOI | WoS
 
[81]
2019 | Research Data Reference | IST-REx-ID: 9786
J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.” Public Library of Science, 2019.
[Published Version] View | Files available | DOI
 
[80]
2019 | Published | Conference Paper | IST-REx-ID: 7606 | OA
M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden, 2019.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | arXiv
 
[79]
2019 | Submitted | Preprint | IST-REx-ID: 7552 | OA
W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” arXiv. ArXiv.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[78]
2018 | Published | Journal Article | IST-REx-ID: 281 | OA
A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | PubMed | Europe PMC
 
[77]
2018 | Published | Journal Article | IST-REx-ID: 406 | OA
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.
[Submitted Version] View | Files available | DOI | WoS
 
[76]
2018 | Research Data Reference | IST-REx-ID: 9831
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018.
[Published Version] View | Files available | DOI
 
[75]
2018 | Published | Journal Article | IST-REx-ID: 161 | OA
D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.
[Published Version] View | Files available | DOI | WoS
 
[74]
2018 | Research Data | IST-REx-ID: 5587 | OA
D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.
[Published Version] View | Files available | DOI
 
[73]
2018 | Published | Journal Article | IST-REx-ID: 292 | OA
V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5. Public Library of Science, 2018.
[Published Version] View | Files available | DOI | WoS
 
[72]
2018 | Research Data | IST-REx-ID: 5584 | OA
S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.
[Published Version] View | Files available | DOI
 
[71]
2018 | Published | Journal Article | IST-REx-ID: 31 | OA
U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018.
[Preprint] View | DOI | Download Preprint (ext.) | WoS
 
[70]
2018 | Published | Journal Article | IST-REx-ID: 543 | OA
M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS
 
[69]
2018 | Published | Journal Article | IST-REx-ID: 67 | OA
C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018.
[Submitted Version] View | Files available | DOI | WoS
 
[68]
2018 | Research Data | IST-REx-ID: 5585 | OA
C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.
[Published Version] View | Files available | DOI
 
[67]
2017 | Published | Journal Article | IST-REx-ID: 730
C. Savin and G. Tkačik, “Maximum entropy models as a tool for building precise neural controls,” Current Opinion in Neurobiology, vol. 46. Elsevier, pp. 120–126, 2017.
View | DOI | WoS
 
[66]
2017 | Research Data Reference | IST-REx-ID: 9709 | OA
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[65]
2017 | Research Data | IST-REx-ID: 5562 | OA
O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017.
[Published Version] View | Files available | DOI
 
[64]
2017 | Published | 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. Nature Publishing Group, 2017.
[Published Version] View | Files available | DOI | WoS
 
[63]
2017 | Published | Journal Article | IST-REx-ID: 613 | OA
R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
[Published Version] View | Files available | DOI
 
[62]
2017 | Published | 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. American Association for the Advancement of Science, pp. 311–315, 2017.
View | Files available | DOI
 
[61]
2017 | Research Data | IST-REx-ID: 5560 | OA
T. Bergmiller et al., “Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science and Technology Austria, 2017.
[Published Version] View | Files available | DOI
 
[60]
2017 | Published | Journal Article | IST-REx-ID: 720 | OA
J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9. Public Library of Science, 2017.
[Published Version] View | Files available | DOI
 
[59]
2017 | Published | Journal Article | IST-REx-ID: 725 | OA
R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[58]
2017 | Published | 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. American Association for the Advancement of Science, pp. 1379–1383, 2017.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[57]
2017 | Published | Journal Article | IST-REx-ID: 955 | OA
T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
[Published Version] View | Files available | DOI | WoS
 
[56]
2016 | Published | Journal Article | IST-REx-ID: 1171
G. Tkačik, “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. Elsevier, pp. 166–167, 2016.
View | DOI
 
[55]
2016 | Published | Journal Article | IST-REx-ID: 1270 | OA
P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9. Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 
[54]
2016 | Research Data Reference | IST-REx-ID: 9870
P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 
[53]
2016 | Research Data Reference | IST-REx-ID: 9869
P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 
[52]
2016 | Research Data Reference | IST-REx-ID: 9871
P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 
[51]
2016 | Published | Journal Article | IST-REx-ID: 1420 | OA
K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[50]
2016 | Published | Journal Article | IST-REx-ID: 1358 | OA
T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
[Published Version] View | Files available | DOI
 
[49]
2016 | Published | Journal Article | IST-REx-ID: 1197 | OA
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11. Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 
[48]
2016 | Published | Conference Paper | IST-REx-ID: 1082 | OA
M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.
[Preprint] View | Files available | Download Preprint (ext.) | arXiv
 
[47]
2016 | Published | Conference Paper | IST-REx-ID: 1105 | OA
C. Savin and G. Tkačik, “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.
View | Download None (ext.)
 
[46]
2016 | Published | Journal Article | IST-REx-ID: 1242 | OA
T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American Institute of Physics, 2016.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[45]
2016 | Published | Journal Article | IST-REx-ID: 1248 | OA
G. Tkačik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[44]
2015 | Published | Journal Article | IST-REx-ID: 1666 | OA
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 
[43]
2015 | Research Data Reference | IST-REx-ID: 9712
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 
[42]
2015 | Published | Journal Article | IST-REx-ID: 1697 | OA
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7. Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 
[41]
2015 | Published | Journal Article | IST-REx-ID: 1701 | OA
G. Tkačik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[40]
2015 | Published | Journal Article | IST-REx-ID: 1885 | OA
G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[39]
2015 | Published | Journal Article | IST-REx-ID: 1576 | OA
S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24. American Physical Society, 2015.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | arXiv
 
[38]
2015 | Published | Journal Article | IST-REx-ID: 1940 | OA
T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[37]
2014 | Published | Journal Article | IST-REx-ID: 3263 | OA
G. Tkačik, 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. Public Library of Science, 2014.
[Published Version] View | Files available | DOI
 
[36]
2014 | Research Data Reference | IST-REx-ID: 9752 | OA
K. Simmons et al., “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[35]
2014 | Published | Journal Article | IST-REx-ID: 1886 | OA
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” eLife, no. November. eLife Sciences Publications, 2014.
[Published Version] View | Files available | DOI
 
[34]
2014 | Published | Journal Article | IST-REx-ID: 2257 | OA
G. Tkačik, 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. Public Library of Science, 2014.
[Published Version] View | Files available | DOI
 
[33]
2014 | Published | Journal Article | IST-REx-ID: 2231 | OA
G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” Biophysical Journal, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[32]
2013 | Published | 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. Public Library of Science, 2013.
[Published Version] View | Files available | DOI
 
[31]
2013 | Published | Journal Article | IST-REx-ID: 2818 | OA
K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” Neural Computation, vol. 25, no. 7. MIT Press , pp. 1661–1692, 2013.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[30]
2013 | Published | Journal Article | IST-REx-ID: 2863 | OA
E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” PLoS Computational Biology, vol. 9, no. 3. Public Library of Science, 2013.
[Published Version] View | Files available | DOI
 
[29]
2013 | Published | Journal Article | IST-REx-ID: 2914 | OA
G. Stephens, T. Mora, G. Tkačik, and W. Bialek, “Statistical thermodynamics of natural images,” Physical Review Letters, vol. 110, no. 1. American Physical Society, 2013.
[Published Version] View | Files available | DOI | arXiv
 
[28]
2013 | Published | Journal Article | IST-REx-ID: 3261 | OA
J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” PNAS, vol. 110, no. 41. National Academy of Sciences, pp. 16301–16308, 2013.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[27]
2013 | Published | Journal Article | IST-REx-ID: 2850 | OA
G. Tkačik, 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. IOP Publishing, 2013.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[26]
2013 | Published | Journal Article | IST-REx-ID: 2851
M. Berry, G. Tkačik, 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. IOP Publishing, 2013.
View | DOI
 
[25]
2013 | Published | Journal Article | IST-REx-ID: 2913 | OA
G. Tkačik, 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. American Physical Society, 2013.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[24]
2012 | Published | Journal Article | IST-REx-ID: 3262 | OA
G. Tkačik, 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. American Institute of Physics, 2012.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[23]
2011 | Published | Journal Article | IST-REx-ID: 3276 | OA
J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, and P. Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011.
View | Files available | DOI
 
[22]
2011 | Published | Journal Article | IST-REx-ID: 3384 | OA
G. Tkačik et al., “Natural images from the birthplace of the human eye,” PLoS One, vol. 6, no. 6. Public Library of Science, 2011.
[Published Version] View | Files available | DOI
 
[21]
2011 | Published | Journal Article | IST-REx-ID: 3401
S. Little, G. Tkačik, 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. Public Library of Science, 2011.
View | DOI
 
[20]
2011 | Published | Journal Article | IST-REx-ID: 3374 | OA
G. Tkačik and A. Walczak, “Information transmission in genetic regulatory networks a review,” Journal of Physics: Condensed Matter, vol. 23, no. 15. IOP Publishing, 2011.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | arXiv
 
[19]
2010 | Published | Conference Paper | IST-REx-ID: 3430 | OA
G. Tkačik, “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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[18]
2010 | Published | Journal Article | IST-REx-ID: 3735
G. Tkačik, J. Prentice, J. Victor, and V. Balasubramanian, “Local statistics in natural scenes predict the saliency of synthetic textures,” PNAS, vol. 107, no. 42. National Academy of Sciences, pp. 18149–18154, 2010.
View | DOI | Download (ext.)
 
[17]
2010 | Published | Journal Article | IST-REx-ID: 3736
G. Tkačik, J. Prentice, V. Balasubramanian, and E. Schneidman, “Optimal population coding by noisy spiking neurons,” PNAS, vol. 107, no. 32. National Academy of Sciences, pp. 14419–14424, 2010.
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[16]
2010 | Published | Journal Article | IST-REx-ID: 3738
A. Walczak, G. Tkačik, 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. American Institute of Physics, 2010.
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[15]
2010 | Published | Preprint | IST-REx-ID: 3743 | OA
G. Tkačik, “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 | Published | Preprint | IST-REx-ID: 3732 | OA
G. Tkačik, 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 | Published | Journal Article | IST-REx-ID: 3733
S. Kryazhimskiy, G. Tkačik, and J. Plotkin, “The dynamics of adaptation on correlated fitness landscapes,” PNAS, vol. 106, no. 44. National Academy of Sciences, pp. 18638–18643, 2009.
View | DOI | Download (ext.)
 
[12]
2009 | Published | Journal Article | IST-REx-ID: 3737
G. Tkačik, 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. American Institute of Physics, 2009.
View | DOI | Download (ext.)
 
[11]
2009 | Published | Journal Article | IST-REx-ID: 3745
G. Tkačik and W. Bialek, “Diffusion, dimensionality, and noise in transcriptional regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5. American Institute of Physics, 2009.
View | DOI
 
[10]
2009 | Published | Book Chapter | IST-REx-ID: 3747
G. Tkačik 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 | Published | Journal Article | IST-REx-ID: 3734 | OA
G. Tkačik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional regulation,” PLoS One, vol. 3, no. 7. Public Library of Science, 2008.
View | DOI | Download (ext.)
 
[8]
2008 | Published | Journal Article | IST-REx-ID: 3739
G. Tkačik, C. Callan, and W. Bialek, “Information capacity of genetic regulatory elements,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1. American Institute of Physics, 2008.
View | DOI
 
[7]
2008 | Published | Journal Article | IST-REx-ID: 3740 | OA
G. Tkačik, C. Callan, and W. Bialek, “Information flow and optimization in transcriptional regulation,” PNAS, vol. 105, no. 34. National Academy of Sciences, pp. 12265–12270, 2008.
View | DOI | Download (ext.)
 
[6]
2008 | Published | Journal Article | IST-REx-ID: 3744 | OA
G. Tkačik and M. Magnasco, “Decoding spike timing: The differential reverse-correlation method,” Biosystems, vol. 93, no. 1–2. Elsevier, pp. 90–100, 2008.
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[5]
2007 | Published | Journal Article | IST-REx-ID: 3731
J. Kinney, G. Tkačik, and C. Callan, “Precise physical models of protein-DNA interaction from high-throughput data,” PNAS, vol. 104, no. 2. National Academy of Sciences, pp. 501–506, 2007.
View | DOI | Download (ext.)
 
[4]
2007 | Published | Preprint | IST-REx-ID: 3742 | OA
T. Broderick, M. Dudik, G. Tkačik, R. Schapire, and W. Bialek, “Faster solutions of the inverse pairwise Ising problem,” ArXiv, vol. q-QM. ArXiv, 2007.
View | Download (ext.)
 
[3]
2006 | Published | Preprint | IST-REx-ID: 3431 | OA
G. Tkačik, 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 | Published | Journal Article | IST-REx-ID: 3741 | OA
N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Information-based clustering,” PNAS, vol. 102, no. 51. National Academy of Sciences, pp. 18297–18302, 2005.
View | DOI | Download (ext.)
 
[1]
2005 | Published | Preprint | IST-REx-ID: 3746 | OA
N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Estimating mutual information and multi-information in large networks,” ArXiv. ArXiv, pp. 1–11, 2005.
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