Gasper Tkacik

Tkacik Group

114 Publications

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[114]
2025 | Research Data | IST-REx-ID: 19294 | OA
Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. Data for “Pulsatile basal gene expression as a fitness determinant in bacteria.” 2025. doi:10.15479/AT:ISTA:19294
[Published Version] View | Files available | DOI
 
[113]
2025 | Published | Journal Article | IST-REx-ID: 19453 | OA
Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. Learning reshapes the hippocampal representation hierarchy. Proceedings of the National Academy of Sciences. 2025;122(11). doi:10.1073/pnas.2417025122
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[112]
2025 | Published | Journal Article | IST-REx-ID: 18850 | OA
Perkins, Mindy Liu, 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 122 (1). 2025
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[111]
2025 | Published | Journal Article | IST-REx-ID: 18849 | OA
Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences of the United States of America. 2025;122(1). doi:10.1073/pnas.2402925121
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[110]
2025 | Published | Journal Article | IST-REx-ID: 18936 | OA
Grah R, Guet CC, Tkačik G, Lagator M. Linking molecular mechanisms to their evolutionary consequences: a primer. Genetics. 2025;229(2). doi:10.1093/genetics/iyae191
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[109]
2024 | Published | Journal Article | IST-REx-ID: 17123 | OA
Brückner, David, Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America 121 (23). 2024
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[108]
2024 | Published | Journal Article | IST-REx-ID: 18902 | OA
Zagorski, Marcin, Assessing the precision of morphogen gradients in neural tube development. Nature Communications 15. 2024
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[107]
2024 | Published | Journal Article | IST-REx-ID: 18525 | OA
Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(44). doi:10.1073/pnas.2402340121
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[106]
2023 | Published | Journal Article | IST-REx-ID: 14515 | OA
Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 2023;13(4). doi:10.1103/PhysRevX.13.041017
[Published Version] View | Files available | DOI | arXiv
 
[105]
2023 | Published | Journal Article | IST-REx-ID: 13127 | OA
Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 2023;14. doi:10.1038/s41467-023-38947-y
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[104]
2023 | Published | Journal Article | IST-REx-ID: 12762 | OA
Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9
[Published Version] View | Files available | DOI | PubMed | Europe PMC | arXiv
 
[103]
2023 | Published | Journal Article | IST-REx-ID: 14656 | OA
Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[102]
2022 | Published | Journal Article | IST-REx-ID: 12156 | OA
Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 2022;31(9). doi:10.1016/j.coisb.2022.100435
[Published Version] View | Files available | DOI
 
[101]
2022 | Published | Journal Article | IST-REx-ID: 12332 | OA
Mlynarski WF, Tkačik G. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 2022;20(12):e3001889. doi:10.1371/journal.pbio.3001889
[Published Version] View | Files available | DOI | WoS
 
[100]
2022 | Published | Journal Article | IST-REx-ID: 10736 | OA
Lagator M, Sarikas S, Steinrück M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[99]
2022 | Published | Journal Article | IST-REx-ID: 12081 | OA
Hledik, Michal, Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences of the United States of America 119 (36). 2022
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[98]
2021 | Submitted | Preprint | IST-REx-ID: 10579 | OA
Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. arXiv. doi:10.48550/arXiv.2112.13558
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[97]
2021 | Published | Journal Article | IST-REx-ID: 9362 | OA
Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[96]
2021 | Published | Journal Article | IST-REx-ID: 9226 | OA
Tkačik G, Gregor T. The many bits of positional information. Development. 2021;148(2). doi:10.1242/dev.176065
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[95]
2021 | Submitted | Preprint | IST-REx-ID: 10912 | OA
Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. doi:10.48550/ARXIV.2108.06686
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[94]
2021 | Published | Journal Article | IST-REx-ID: 8997 | OA
Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529
[Published Version] View | Files available | DOI | WoS
 
[93]
2021 | Published | Journal Article | IST-REx-ID: 7553 | OA
Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS
 
[92]
2021 | Draft | Preprint | IST-REx-ID: 10077 | OA
Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[91]
2020 | Published | Journal Article | IST-REx-ID: 7656 | OA
Berry MJ, Tkačik G. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 2020;14. doi:10.3389/fncom.2020.00020
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[90]
2020 | Published | Journal Article | IST-REx-ID: 8698 | OA
Maoz, Ori, Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America 117 (40). 2020
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[89]
2020 | Published | Journal Article | IST-REx-ID: 9000 | OA
Grah, Rok, Nonequilibrium models of optimal enhancer function. Proceedings of the National Academy of Sciences of the United States of America 117 (50). 2020
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[88]
2020 | Published | Preprint | IST-REx-ID: 7675 | OA
Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405
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[87]
2020 | Published | Journal Article | IST-REx-ID: 7652 | OA
Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7
[Submitted Version] View | Files available | DOI | WoS
 
[86]
2020 | Published | Journal Article | IST-REx-ID: 8250 | OA
Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z
[Published Version] View | Files available | DOI | WoS
 
[85]
2020 | Published | Preprint | IST-REx-ID: 7673 | OA
Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[84]
2019 | Published | Journal Article | IST-REx-ID: 6900 | OA
Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. PLoS computational biology. 2019;15(9):e1007290. doi:10.1371/journal.pcbi.1007290
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[83]
2019 | Published | Journal Article | IST-REx-ID: 5945 | OA
Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15. doi:10.1016/j.cell.2019.01.007
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[82]
2019 | Submitted | Preprint | IST-REx-ID: 7552 | OA
Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:191208579.
[Preprint] View | Download Preprint (ext.) | arXiv
 
[81]
2019 | Published | Journal Article | IST-REx-ID: 6784 | OA
Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168
[Published Version] View | Files available | DOI | WoS
 
[80]
2019 | Research Data Reference | IST-REx-ID: 9786
Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001
[Published Version] View | Files available | DOI
 
[79]
2019 | Published | Conference Paper | IST-REx-ID: 7606 | OA
Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information. In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | arXiv
 
[78]
2018 | Published | Journal Article | IST-REx-ID: 281 | OA
Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | PubMed | Europe PMC
 
[77]
2018 | Published | Journal Article | IST-REx-ID: 406 | OA
Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049
[Submitted Version] View | Files available | DOI | WoS
 
[76]
2018 | Research Data Reference | IST-REx-ID: 9831
Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001
[Published Version] View | Files available | DOI
 
[75]
2018 | Published | Journal Article | IST-REx-ID: 161 | OA
De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9
[Published Version] View | Files available | DOI | WoS
 
[74]
2018 | Research Data | IST-REx-ID: 5587 | OA
De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62
[Published Version] View | Files available | DOI
 
[73]
2018 | Published | Journal Article | IST-REx-ID: 292 | OA
Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5). doi:10.1371/journal.pcbi.1006057
[Published Version] View | Files available | DOI | WoS
 
[72]
2018 | Research Data | IST-REx-ID: 5584 | OA
Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98
[Published Version] View | Files available | DOI
 
[71]
2018 | Published | Journal Article | IST-REx-ID: 543 | OA
Chalk, Matthew J, Toward a unified theory of efficient, predictive, and sparse coding. Proceedings of the National Academy of Sciences of the United States of America 115 (1). 2018
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[70]
2018 | Published | Journal Article | IST-REx-ID: 31 | OA
Ferrari, Ulisse, Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E 98 (4). 2018
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[69]
2018 | Published | Journal Article | IST-REx-ID: 67 | OA
Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y
[Submitted Version] View | Files available | DOI | WoS
 
[68]
2018 | Research Data | IST-REx-ID: 5585 | OA
Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108
[Published Version] View | Files available | DOI
 
[67]
2017 | Published | Journal Article | IST-REx-ID: 725 | OA
Harpaz, Roy, Discrete modes of social information processing predict individual behavior of fish in a group. PNAS 114 (38). 2017
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[66]
2017 | Research Data | IST-REx-ID: 5560 | OA
Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:10.15479/AT:ISTA:53
[Published Version] View | Files available | DOI
 
[65]
2017 | Published | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science 356 (6335). 2017
View | Files available | DOI
 
[64]
2017 | Published | Journal Article | IST-REx-ID: 943 | OA
Zagórski, Marcin P, Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science 356 (6345). 2017
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[63]
2017 | Published | Journal Article | IST-REx-ID: 730
Savin C, Tkačik G. Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology. 2017;46:120-126. doi:10.1016/j.conb.2017.08.001
View | DOI | WoS
 
[62]
2017 | Research Data Reference | IST-REx-ID: 9709 | OA
Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[61]
2017 | Published | Journal Article | IST-REx-ID: 955 | OA
Friedlander, Tamar, Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications 8 (1). 2017
[Published Version] View | Files available | DOI | WoS
 
[60]
2017 | Published | Journal Article | IST-REx-ID: 1104 | OA
Deny, Stephane, Multiplexed computations in retinal ganglion cells of a single type. Nature Communications 8 (1). 2017
[Published Version] View | Files available | DOI | WoS
 
[59]
2017 | Published | Journal Article | IST-REx-ID: 613 | OA
Chait, Remy P, Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications 8 (1). 2017
[Published Version] View | Files available | DOI
 
[58]
2017 | Published | Journal Article | IST-REx-ID: 720 | OA
Humplik, Jan, Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology 13 (9). 2017
[Published Version] View | Files available | DOI
 
[57]
2017 | Research Data | IST-REx-ID: 5562 | OA
Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61
[Published Version] View | Files available | DOI
 
[56]
2016 | Published | Journal Article | IST-REx-ID: 1171
Tkačik G. 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. 2016;17:166-167. doi:10.1016/j.plrev.2016.06.005
View | DOI
 
[55]
2016 | Published | Journal Article | IST-REx-ID: 1270 | OA
Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 2016;11(9). doi:10.1371/journal.pone.0163628
[Published Version] View | Files available | DOI
 
[54]
2016 | Published | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404
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[53]
2016 | Research Data Reference | IST-REx-ID: 9870
Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:10.1371/journal.pone.0163628.s002
[Published Version] View | Files available | DOI
 
[52]
2016 | Research Data Reference | IST-REx-ID: 9869
Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:10.1371/journal.pone.0163628.s001
[Published Version] View | Files available | DOI
 
[51]
2016 | Research Data Reference | IST-REx-ID: 9871
Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003
[Published Version] View | Files available | DOI
 
[50]
2016 | Published | Conference Paper | IST-REx-ID: 1105
Savin, Cristina, Estimating nonlinear neural response functions using GP priors and Kronecker methods. 29. 2016
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[49]
2016 | Published | Journal Article | IST-REx-ID: 1420 | OA
Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[48]
2016 | Published | Journal Article | IST-REx-ID: 1358 | OA
Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307
[Published Version] View | Files available | DOI
 
[47]
2016 | Published | Journal Article | IST-REx-ID: 1197 | OA
Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes of the retinal population code. PLoS Computational Biology. 2016;12(11). doi:10.1371/journal.pcbi.1005148
[Published Version] View | Files available | DOI
 
[46]
2016 | Published | Journal Article | IST-REx-ID: 1248 | OA
Tkačik G, Bialek W. Information processing in living systems. Annual Review of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803
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[45]
2016 | Published | Conference Paper | IST-REx-ID: 1082 | OA
Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973.
[Preprint] View | Files available | Download Preprint (ext.) | arXiv
 
[44]
2015 | Published | Journal Article | IST-REx-ID: 1885 | OA
Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 2015;199(1):39-59. doi:10.1534/genetics.114.171850
[Preprint] View | DOI | Download Preprint (ext.)
 
[43]
2015 | Published | Journal Article | IST-REx-ID: 1940 | OA
Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710
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[42]
2015 | Published | Journal Article | IST-REx-ID: 1666 | OA
Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
[Published Version] View | Files available | DOI
 
[41]
2015 | Published | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24). doi:10.1103/PhysRevLett.115.248101
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[40]
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
[Published Version] View | Files available | DOI
 
[39]
2015 | Published | Journal Article | IST-REx-ID: 1697 | OA
Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 2015;11(7). doi:10.1371/journal.pcbi.1004304
[Published Version] View | Files available | DOI
 
[38]
2015 | Published | Journal Article | IST-REx-ID: 1701 | OA
Tkačik G, Mora T, Marre O, et al. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 2015;112(37):11508-11513. doi:10.1073/pnas.1514188112
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[37]
2014 | Published | Journal Article | IST-REx-ID: 3263 | OA
Tkačik G, Ghosh A, Schneidman E, Segev R. Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One. 2014;9(1). doi:10.1371/journal.pone.0085841
[Published Version] View | Files available | DOI
 
[36]
2014 | Research Data Reference | IST-REx-ID: 9752 | OA
Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:10.5061/dryad.246qg
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[35]
2014 | Published | Journal Article | IST-REx-ID: 2231 | OA
Rieckh, Georg, Noise and information transmission in promoters with multiple internal states. Biophysical Journal 106 (5). 2014
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[34]
2014 | Published | Journal Article | IST-REx-ID: 1886 | OA
Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722
[Published Version] View | Files available | DOI
 
[33]
2014 | Published | Journal Article | IST-REx-ID: 2257 | OA
Tkacik, Gasper, Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology 10 (1). 2014
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[32]
2013 | Published | Journal Article | IST-REx-ID: 2277 | OA
Simmons K, Prentice J, Tkačik G, et al. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003344
[Published Version] View | Files available | DOI
 
[31]
2013 | Published | Journal Article | IST-REx-ID: 2818 | OA
Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692. doi:10.1162/NECO_a_00463
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[30]
2013 | Published | Journal Article | IST-REx-ID: 2863 | OA
Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 2013;9(3). doi:10.1371/journal.pcbi.1002922
[Published Version] View | Files available | DOI
 
[29]
2013 | Published | Journal Article | IST-REx-ID: 2913 | OA
Tkačik G, Granot Atedgi E, Segev R, Schneidman E. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 2013;110(5). doi:10.1103/PhysRevLett.110.058104
[Preprint] View | DOI | Download Preprint (ext.)
 
[28]
2013 | Published | Journal Article | IST-REx-ID: 2914 | OA
Stephens G, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural images. Physical Review Letters. 2013;110(1). doi:10.1103/PhysRevLett.110.018701
[Published Version] View | Files available | DOI | arXiv
 
[27]
2013 | Published | Journal Article | IST-REx-ID: 3261 | OA
Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information, in bits. PNAS. 2013;110(41):16301-16308. doi:10.1073/pnas.1315642110
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[26]
2013 | Published | Journal Article | IST-REx-ID: 2850 | OA
Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03011
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[25]
2013 | Published | Journal Article | IST-REx-ID: 2851
Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03015
View | DOI
 
[24]
2012 | Published | Journal Article | IST-REx-ID: 3262 | OA
Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E statistical nonlinear and soft matter physics . 2012;85(4). doi:10.1103/PhysRevE.85.041903
[Preprint] View | DOI | Download Preprint (ext.)
 
[23]
2011 | Published | Journal Article | IST-REx-ID: 3276 | OA
Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0019884
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[22]
2011 | Published | Journal Article | IST-REx-ID: 3384 | OA
Tkačik G, Garrigan P, Ratliff C, et al. Natural images from the birthplace of the human eye. PLoS One. 2011;6(6). doi:10.1371/journal.pone.0020409
[Published Version] View | Files available | DOI
 
[21]
2011 | Published | Journal Article | IST-REx-ID: 3401
Little S, Tkačik G, Kneeland T, Wieschaus E, Gregor T. The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source. PLoS Biology. 2011;9(3). doi:10.1371/journal.pbio.1000596
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[20]
2011 | Published | Journal Article | IST-REx-ID: 3374 | OA
Tkacik, Gasper, Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter 23 (15). 2011
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[19]
2010 | Published | Conference Paper | IST-REx-ID: 3430 | OA
Tkačik G. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. In: Elsevier; 2010.
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[18]
2010 | Published | Journal Article | IST-REx-ID: 3735
Tkačik G, Prentice J, Victor J, Balasubramanian V. Local statistics in natural scenes predict the saliency of synthetic textures. PNAS. 2010;107(42):18149-18154. doi:10.1073/pnas.0914916107
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[17]
2010 | Published | Journal Article | IST-REx-ID: 3736
Tkačik G, Prentice J, Balasubramanian V, Schneidman E. Optimal population coding by noisy spiking neurons. PNAS. 2010;107(32):14419-14424. doi:10.1073/pnas.1004906107
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[16]
2010 | Published | Journal Article | IST-REx-ID: 3738
Walczak A, Tkačik G, Bialek W. Optimizing information flow in small genetic networks. II. Feed-forward interactions. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2010;81(4). doi:10.1103/PhysRevE.81.041905
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[15]
2010 | Published | Preprint | IST-REx-ID: 3743 | OA
Tkačik G. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv. 2010;q-MN:1-52.
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[14]
2009 | Published | Preprint | IST-REx-ID: 3732 | OA
Tkačik G, Schneidman E, Berry M, Bialek W. Spin glass models for a network of real neurons. ArXiv. 2009;q-NC.
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[13]
2009 | Published | Journal Article | IST-REx-ID: 3733
Kryazhimskiy S, Tkačik G, Plotkin J. The dynamics of adaptation on correlated fitness landscapes. PNAS. 2009;106(44):18638-18643. doi:10.1073/pnas.0905497106
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[12]
2009 | Published | Journal Article | IST-REx-ID: 3737
Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2009;80(3). doi:10.1103/PhysRevE.80.031920
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[11]
2009 | Published | Journal Article | IST-REx-ID: 3745
Tkačik G, Bialek W. Diffusion, dimensionality, and noise in transcriptional regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2009;79(5). doi:10.1103/PhysRevE.79.051901
View | DOI
 
[10]
2009 | Published | Book Chapter | IST-REx-ID: 3747
Tkačik G, Bialek W. Cell Biology: Networks, regulation, pathways. In: Meyers R, ed. Encyclopedia of Complexity and Systems Science. Springer; 2009:719-741. doi:10.1007/978-0-387-30440-3_48
View | DOI
 
[9]
2008 | Published | Journal Article | IST-REx-ID: 3734 | OA
Tkačik G, Gregor T, Bialek W. The role of input noise in transcriptional regulation. PLoS One. 2008;3(7). doi:10.1371/journal.pone.0002774
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[8]
2008 | Published | Journal Article | IST-REx-ID: 3739
Tkačik G, Callan C, Bialek W. Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2008;78(1). doi:10.1103/PhysRevE.78.011910
View | DOI
 
[7]
2008 | Published | Journal Article | IST-REx-ID: 3740 | OA
Tkačik G, Callan C, Bialek W. Information flow and optimization in transcriptional regulation. PNAS. 2008;105(34):12265-12270. doi:10.1073/pnas.0806077105
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[6]
2008 | Published | Journal Article | IST-REx-ID: 3744 | OA
Tkačik G, Magnasco M. Decoding spike timing: The differential reverse-correlation method. Biosystems. 2008;93(1-2):90-100. doi:10.1016/j.biosystems.2008.04.011
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[5]
2007 | Published | Journal Article | IST-REx-ID: 3731
Kinney J, Tkačik G, Callan C. Precise physical models of protein-DNA interaction from high-throughput data. PNAS. 2007;104(2):501-506. doi:10.1073/pnas.0609908104
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[4]
2007 | Published | Preprint | IST-REx-ID: 3742 | OA
Broderick T, Dudik M, Tkačik G, Schapire R, Bialek W. Faster solutions of the inverse pairwise Ising problem. ArXiv. 2007;q-QM.
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[3]
2006 | Published | Preprint | IST-REx-ID: 3431 | OA
Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4.
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[2]
2005 | Published | Journal Article | IST-REx-ID: 3741 | OA
Slonim N, Atwal G, Tkačik G, Bialek W. Information-based clustering. PNAS. 2005;102(51):18297-18302. doi:10.1073/pnas.0507432102
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[1]
2005 | Published | Preprint | IST-REx-ID: 3746 | OA
Slonim N, Atwal G, Tkačik G, Bialek W. Estimating mutual information and multi-information in large networks. ArXiv. 2005:1-11.
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114 Publications

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[114]
2025 | Research Data | IST-REx-ID: 19294 | OA
Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. Data for “Pulsatile basal gene expression as a fitness determinant in bacteria.” 2025. doi:10.15479/AT:ISTA:19294
[Published Version] View | Files available | DOI
 
[113]
2025 | Published | Journal Article | IST-REx-ID: 19453 | OA
Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. Learning reshapes the hippocampal representation hierarchy. Proceedings of the National Academy of Sciences. 2025;122(11). doi:10.1073/pnas.2417025122
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[112]
2025 | Published | Journal Article | IST-REx-ID: 18850 | OA
Perkins, Mindy Liu, 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 122 (1). 2025
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[111]
2025 | Published | Journal Article | IST-REx-ID: 18849 | OA
Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences of the United States of America. 2025;122(1). doi:10.1073/pnas.2402925121
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[110]
2025 | Published | Journal Article | IST-REx-ID: 18936 | OA
Grah R, Guet CC, Tkačik G, Lagator M. Linking molecular mechanisms to their evolutionary consequences: a primer. Genetics. 2025;229(2). doi:10.1093/genetics/iyae191
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[109]
2024 | Published | Journal Article | IST-REx-ID: 17123 | OA
Brückner, David, Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America 121 (23). 2024
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[108]
2024 | Published | Journal Article | IST-REx-ID: 18902 | OA
Zagorski, Marcin, Assessing the precision of morphogen gradients in neural tube development. Nature Communications 15. 2024
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[107]
2024 | Published | Journal Article | IST-REx-ID: 18525 | OA
Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(44). doi:10.1073/pnas.2402340121
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[106]
2023 | Published | Journal Article | IST-REx-ID: 14515 | OA
Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 2023;13(4). doi:10.1103/PhysRevX.13.041017
[Published Version] View | Files available | DOI | arXiv
 
[105]
2023 | Published | Journal Article | IST-REx-ID: 13127 | OA
Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 2023;14. doi:10.1038/s41467-023-38947-y
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[104]
2023 | Published | Journal Article | IST-REx-ID: 12762 | OA
Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9
[Published Version] View | Files available | DOI | PubMed | Europe PMC | arXiv
 
[103]
2023 | Published | Journal Article | IST-REx-ID: 14656 | OA
Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[102]
2022 | Published | Journal Article | IST-REx-ID: 12156 | OA
Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 2022;31(9). doi:10.1016/j.coisb.2022.100435
[Published Version] View | Files available | DOI
 
[101]
2022 | Published | Journal Article | IST-REx-ID: 12332 | OA
Mlynarski WF, Tkačik G. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 2022;20(12):e3001889. doi:10.1371/journal.pbio.3001889
[Published Version] View | Files available | DOI | WoS
 
[100]
2022 | Published | Journal Article | IST-REx-ID: 10736 | OA
Lagator M, Sarikas S, Steinrück M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[99]
2022 | Published | Journal Article | IST-REx-ID: 12081 | OA
Hledik, Michal, Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences of the United States of America 119 (36). 2022
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[98]
2021 | Submitted | Preprint | IST-REx-ID: 10579 | OA
Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. arXiv. doi:10.48550/arXiv.2112.13558
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[97]
2021 | Published | Journal Article | IST-REx-ID: 9362 | OA
Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[96]
2021 | Published | Journal Article | IST-REx-ID: 9226 | OA
Tkačik G, Gregor T. The many bits of positional information. Development. 2021;148(2). doi:10.1242/dev.176065
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[95]
2021 | Submitted | Preprint | IST-REx-ID: 10912 | OA
Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. doi:10.48550/ARXIV.2108.06686
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[94]
2021 | Published | Journal Article | IST-REx-ID: 8997 | OA
Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529
[Published Version] View | Files available | DOI | WoS
 
[93]
2021 | Published | Journal Article | IST-REx-ID: 7553 | OA
Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS
 
[92]
2021 | Draft | Preprint | IST-REx-ID: 10077 | OA
Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[91]
2020 | Published | Journal Article | IST-REx-ID: 7656 | OA
Berry MJ, Tkačik G. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 2020;14. doi:10.3389/fncom.2020.00020
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[90]
2020 | Published | Journal Article | IST-REx-ID: 8698 | OA
Maoz, Ori, Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America 117 (40). 2020
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[89]
2020 | Published | Journal Article | IST-REx-ID: 9000 | OA
Grah, Rok, Nonequilibrium models of optimal enhancer function. Proceedings of the National Academy of Sciences of the United States of America 117 (50). 2020
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2020 | Published | Preprint | IST-REx-ID: 7675 | OA
Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[87]
2020 | Published | Journal Article | IST-REx-ID: 7652 | OA
Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7
[Submitted Version] View | Files available | DOI | WoS
 
[86]
2020 | Published | Journal Article | IST-REx-ID: 8250 | OA
Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z
[Published Version] View | Files available | DOI | WoS
 
[85]
2020 | Published | Preprint | IST-REx-ID: 7673 | OA
Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[84]
2019 | Published | Journal Article | IST-REx-ID: 6900 | OA
Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. PLoS computational biology. 2019;15(9):e1007290. doi:10.1371/journal.pcbi.1007290
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[83]
2019 | Published | Journal Article | IST-REx-ID: 5945 | OA
Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15. doi:10.1016/j.cell.2019.01.007
[Published Version] View | Files available | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[82]
2019 | Submitted | Preprint | IST-REx-ID: 7552 | OA
Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:191208579.
[Preprint] View | Download Preprint (ext.) | arXiv
 
[81]
2019 | Published | Journal Article | IST-REx-ID: 6784 | OA
Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168
[Published Version] View | Files available | DOI | WoS
 
[80]
2019 | Research Data Reference | IST-REx-ID: 9786
Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001
[Published Version] View | Files available | DOI
 
[79]
2019 | Published | Conference Paper | IST-REx-ID: 7606 | OA
Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information. In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | arXiv
 
[78]
2018 | Published | Journal Article | IST-REx-ID: 281 | OA
Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | PubMed | Europe PMC
 
[77]
2018 | Published | Journal Article | IST-REx-ID: 406 | OA
Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049
[Submitted Version] View | Files available | DOI | WoS
 
[76]
2018 | Research Data Reference | IST-REx-ID: 9831
Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001
[Published Version] View | Files available | DOI
 
[75]
2018 | Published | Journal Article | IST-REx-ID: 161 | OA
De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9
[Published Version] View | Files available | DOI | WoS
 
[74]
2018 | Research Data | IST-REx-ID: 5587 | OA
De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62
[Published Version] View | Files available | DOI
 
[73]
2018 | Published | Journal Article | IST-REx-ID: 292 | OA
Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5). doi:10.1371/journal.pcbi.1006057
[Published Version] View | Files available | DOI | WoS
 
[72]
2018 | Research Data | IST-REx-ID: 5584 | OA
Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98
[Published Version] View | Files available | DOI
 
[71]
2018 | Published | Journal Article | IST-REx-ID: 543 | OA
Chalk, Matthew J, Toward a unified theory of efficient, predictive, and sparse coding. Proceedings of the National Academy of Sciences of the United States of America 115 (1). 2018
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS
 
[70]
2018 | Published | Journal Article | IST-REx-ID: 31 | OA
Ferrari, Ulisse, Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E 98 (4). 2018
[Preprint] View | DOI | Download Preprint (ext.) | WoS
 
[69]
2018 | Published | Journal Article | IST-REx-ID: 67 | OA
Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y
[Submitted Version] View | Files available | DOI | WoS
 
[68]
2018 | Research Data | IST-REx-ID: 5585 | OA
Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108
[Published Version] View | Files available | DOI
 
[67]
2017 | Published | Journal Article | IST-REx-ID: 725 | OA
Harpaz, Roy, Discrete modes of social information processing predict individual behavior of fish in a group. PNAS 114 (38). 2017
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[66]
2017 | Research Data | IST-REx-ID: 5560 | OA
Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:10.15479/AT:ISTA:53
[Published Version] View | Files available | DOI
 
[65]
2017 | Published | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science 356 (6335). 2017
View | Files available | DOI
 
[64]
2017 | Published | Journal Article | IST-REx-ID: 943 | OA
Zagórski, Marcin P, Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science 356 (6345). 2017
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[63]
2017 | Published | Journal Article | IST-REx-ID: 730
Savin C, Tkačik G. Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology. 2017;46:120-126. doi:10.1016/j.conb.2017.08.001
View | DOI | WoS
 
[62]
2017 | Research Data Reference | IST-REx-ID: 9709 | OA
Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[61]
2017 | Published | Journal Article | IST-REx-ID: 955 | OA
Friedlander, Tamar, Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications 8 (1). 2017
[Published Version] View | Files available | DOI | WoS
 
[60]
2017 | Published | Journal Article | IST-REx-ID: 1104 | OA
Deny, Stephane, Multiplexed computations in retinal ganglion cells of a single type. Nature Communications 8 (1). 2017
[Published Version] View | Files available | DOI | WoS
 
[59]
2017 | Published | Journal Article | IST-REx-ID: 613 | OA
Chait, Remy P, Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications 8 (1). 2017
[Published Version] View | Files available | DOI
 
[58]
2017 | Published | Journal Article | IST-REx-ID: 720 | OA
Humplik, Jan, Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology 13 (9). 2017
[Published Version] View | Files available | DOI
 
[57]
2017 | Research Data | IST-REx-ID: 5562 | OA
Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61
[Published Version] View | Files available | DOI
 
[56]
2016 | Published | Journal Article | IST-REx-ID: 1171
Tkačik G. 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. 2016;17:166-167. doi:10.1016/j.plrev.2016.06.005
View | DOI
 
[55]
2016 | Published | Journal Article | IST-REx-ID: 1270 | OA
Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 2016;11(9). doi:10.1371/journal.pone.0163628
[Published Version] View | Files available | DOI
 
[54]
2016 | Published | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404
[Preprint] View | DOI | Download Preprint (ext.)
 
[53]
2016 | Research Data Reference | IST-REx-ID: 9870
Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:10.1371/journal.pone.0163628.s002
[Published Version] View | Files available | DOI
 
[52]
2016 | Research Data Reference | IST-REx-ID: 9869
Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:10.1371/journal.pone.0163628.s001
[Published Version] View | Files available | DOI
 
[51]
2016 | Research Data Reference | IST-REx-ID: 9871
Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003
[Published Version] View | Files available | DOI
 
[50]
2016 | Published | Conference Paper | IST-REx-ID: 1105
Savin, Cristina, Estimating nonlinear neural response functions using GP priors and Kronecker methods. 29. 2016
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[49]
2016 | Published | Journal Article | IST-REx-ID: 1420 | OA
Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[48]
2016 | Published | Journal Article | IST-REx-ID: 1358 | OA
Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307
[Published Version] View | Files available | DOI
 
[47]
2016 | Published | Journal Article | IST-REx-ID: 1197 | OA
Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes of the retinal population code. PLoS Computational Biology. 2016;12(11). doi:10.1371/journal.pcbi.1005148
[Published Version] View | Files available | DOI
 
[46]
2016 | Published | Journal Article | IST-REx-ID: 1248 | OA
Tkačik G, Bialek W. Information processing in living systems. Annual Review of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803
[Preprint] View | DOI | Download Preprint (ext.)
 
[45]
2016 | Published | Conference Paper | IST-REx-ID: 1082 | OA
Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973.
[Preprint] View | Files available | Download Preprint (ext.) | arXiv
 
[44]
2015 | Published | Journal Article | IST-REx-ID: 1885 | OA
Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 2015;199(1):39-59. doi:10.1534/genetics.114.171850
[Preprint] View | DOI | Download Preprint (ext.)
 
[43]
2015 | Published | Journal Article | IST-REx-ID: 1940 | OA
Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710
[Preprint] View | DOI | Download Preprint (ext.)
 
[42]
2015 | Published | Journal Article | IST-REx-ID: 1666 | OA
Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
[Published Version] View | Files available | DOI
 
[41]
2015 | Published | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24). doi:10.1103/PhysRevLett.115.248101
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[40]
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
[Published Version] View | Files available | DOI
 
[39]
2015 | Published | Journal Article | IST-REx-ID: 1697 | OA
Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 2015;11(7). doi:10.1371/journal.pcbi.1004304
[Published Version] View | Files available | DOI
 
[38]
2015 | Published | Journal Article | IST-REx-ID: 1701 | OA
Tkačik G, Mora T, Marre O, et al. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 2015;112(37):11508-11513. doi:10.1073/pnas.1514188112
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[37]
2014 | Published | Journal Article | IST-REx-ID: 3263 | OA
Tkačik G, Ghosh A, Schneidman E, Segev R. Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One. 2014;9(1). doi:10.1371/journal.pone.0085841
[Published Version] View | Files available | DOI
 
[36]
2014 | Research Data Reference | IST-REx-ID: 9752 | OA
Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:10.5061/dryad.246qg
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[35]
2014 | Published | Journal Article | IST-REx-ID: 2231 | OA
Rieckh, Georg, Noise and information transmission in promoters with multiple internal states. Biophysical Journal 106 (5). 2014
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[34]
2014 | Published | Journal Article | IST-REx-ID: 1886 | OA
Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722
[Published Version] View | Files available | DOI
 
[33]
2014 | Published | Journal Article | IST-REx-ID: 2257 | OA
Tkacik, Gasper, Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology 10 (1). 2014
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[32]
2013 | Published | Journal Article | IST-REx-ID: 2277 | OA
Simmons K, Prentice J, Tkačik G, et al. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003344
[Published Version] View | Files available | DOI
 
[31]
2013 | Published | Journal Article | IST-REx-ID: 2818 | OA
Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692. doi:10.1162/NECO_a_00463
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[30]
2013 | Published | Journal Article | IST-REx-ID: 2863 | OA
Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 2013;9(3). doi:10.1371/journal.pcbi.1002922
[Published Version] View | Files available | DOI
 
[29]
2013 | Published | Journal Article | IST-REx-ID: 2913 | OA
Tkačik G, Granot Atedgi E, Segev R, Schneidman E. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 2013;110(5). doi:10.1103/PhysRevLett.110.058104
[Preprint] View | DOI | Download Preprint (ext.)
 
[28]
2013 | Published | Journal Article | IST-REx-ID: 2914 | OA
Stephens G, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural images. Physical Review Letters. 2013;110(1). doi:10.1103/PhysRevLett.110.018701
[Published Version] View | Files available | DOI | arXiv
 
[27]
2013 | Published | Journal Article | IST-REx-ID: 3261 | OA
Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information, in bits. PNAS. 2013;110(41):16301-16308. doi:10.1073/pnas.1315642110
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[26]
2013 | Published | Journal Article | IST-REx-ID: 2850 | OA
Tkačik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03011
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[25]
2013 | Published | Journal Article | IST-REx-ID: 2851
Berry M, Tkačik G, Dubuis J, Marre O, Da Silveira R. A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(3). doi:10.1088/1742-5468/2013/03/P03015
View | DOI
 
[24]
2012 | Published | Journal Article | IST-REx-ID: 3262 | OA
Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E statistical nonlinear and soft matter physics . 2012;85(4). doi:10.1103/PhysRevE.85.041903
[Preprint] View | DOI | Download Preprint (ext.)
 
[23]
2011 | Published | Journal Article | IST-REx-ID: 3276 | OA
Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0019884
View | Files available | DOI
 
[22]
2011 | Published | Journal Article | IST-REx-ID: 3384 | OA
Tkačik G, Garrigan P, Ratliff C, et al. Natural images from the birthplace of the human eye. PLoS One. 2011;6(6). doi:10.1371/journal.pone.0020409
[Published Version] View | Files available | DOI
 
[21]
2011 | Published | Journal Article | IST-REx-ID: 3401
Little S, Tkačik G, Kneeland T, Wieschaus E, Gregor T. The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source. PLoS Biology. 2011;9(3). doi:10.1371/journal.pbio.1000596
View | DOI
 
[20]
2011 | Published | Journal Article | IST-REx-ID: 3374 | OA
Tkacik, Gasper, Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter 23 (15). 2011
[Submitted Version] View | DOI | Download Submitted Version (ext.)
 
[19]
2010 | Published | Conference Paper | IST-REx-ID: 3430 | OA
Tkačik G. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. In: Elsevier; 2010.
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[18]
2010 | Published | Journal Article | IST-REx-ID: 3735
Tkačik G, Prentice J, Victor J, Balasubramanian V. Local statistics in natural scenes predict the saliency of synthetic textures. PNAS. 2010;107(42):18149-18154. doi:10.1073/pnas.0914916107
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[17]
2010 | Published | Journal Article | IST-REx-ID: 3736
Tkačik G, Prentice J, Balasubramanian V, Schneidman E. Optimal population coding by noisy spiking neurons. PNAS. 2010;107(32):14419-14424. doi:10.1073/pnas.1004906107
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[16]
2010 | Published | Journal Article | IST-REx-ID: 3738
Walczak A, Tkačik G, Bialek W. Optimizing information flow in small genetic networks. II. Feed-forward interactions. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2010;81(4). doi:10.1103/PhysRevE.81.041905
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[15]
2010 | Published | Preprint | IST-REx-ID: 3743 | OA
Tkačik G. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv. 2010;q-MN:1-52.
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[14]
2009 | Published | Preprint | IST-REx-ID: 3732 | OA
Tkačik G, Schneidman E, Berry M, Bialek W. Spin glass models for a network of real neurons. ArXiv. 2009;q-NC.
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[13]
2009 | Published | Journal Article | IST-REx-ID: 3733
Kryazhimskiy S, Tkačik G, Plotkin J. The dynamics of adaptation on correlated fitness landscapes. PNAS. 2009;106(44):18638-18643. doi:10.1073/pnas.0905497106
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[12]
2009 | Published | Journal Article | IST-REx-ID: 3737
Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2009;80(3). doi:10.1103/PhysRevE.80.031920
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[11]
2009 | Published | Journal Article | IST-REx-ID: 3745
Tkačik G, Bialek W. Diffusion, dimensionality, and noise in transcriptional regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2009;79(5). doi:10.1103/PhysRevE.79.051901
View | DOI
 
[10]
2009 | Published | Book Chapter | IST-REx-ID: 3747
Tkačik G, Bialek W. Cell Biology: Networks, regulation, pathways. In: Meyers R, ed. Encyclopedia of Complexity and Systems Science. Springer; 2009:719-741. doi:10.1007/978-0-387-30440-3_48
View | DOI
 
[9]
2008 | Published | Journal Article | IST-REx-ID: 3734 | OA
Tkačik G, Gregor T, Bialek W. The role of input noise in transcriptional regulation. PLoS One. 2008;3(7). doi:10.1371/journal.pone.0002774
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[8]
2008 | Published | Journal Article | IST-REx-ID: 3739
Tkačik G, Callan C, Bialek W. Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2008;78(1). doi:10.1103/PhysRevE.78.011910
View | DOI
 
[7]
2008 | Published | Journal Article | IST-REx-ID: 3740 | OA
Tkačik G, Callan C, Bialek W. Information flow and optimization in transcriptional regulation. PNAS. 2008;105(34):12265-12270. doi:10.1073/pnas.0806077105
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[6]
2008 | Published | Journal Article | IST-REx-ID: 3744 | OA
Tkačik G, Magnasco M. Decoding spike timing: The differential reverse-correlation method. Biosystems. 2008;93(1-2):90-100. doi:10.1016/j.biosystems.2008.04.011
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[5]
2007 | Published | Journal Article | IST-REx-ID: 3731
Kinney J, Tkačik G, Callan C. Precise physical models of protein-DNA interaction from high-throughput data. PNAS. 2007;104(2):501-506. doi:10.1073/pnas.0609908104
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[4]
2007 | Published | Preprint | IST-REx-ID: 3742 | OA
Broderick T, Dudik M, Tkačik G, Schapire R, Bialek W. Faster solutions of the inverse pairwise Ising problem. ArXiv. 2007;q-QM.
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[3]
2006 | Published | Preprint | IST-REx-ID: 3431 | OA
Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4.
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[2]
2005 | Published | Journal Article | IST-REx-ID: 3741 | OA
Slonim N, Atwal G, Tkačik G, Bialek W. Information-based clustering. PNAS. 2005;102(51):18297-18302. doi:10.1073/pnas.0507432102
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[1]
2005 | Published | Preprint | IST-REx-ID: 3746 | OA
Slonim N, Atwal G, Tkačik G, Bialek W. Estimating mutual information and multi-information in large networks. ArXiv. 2005:1-11.
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