Gasper Tkacik

Tkacik Group

108 Publications

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[108]
2024 | Published | Journal Article | IST-REx-ID: 17123 | OA
Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. PNAS. 2024;121(23). doi:10.1073/pnas.2322326121
[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
 
[106]
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
 
[105]
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
 
[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 | 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
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[102]
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
 
[101]
2022 | Published | Journal Article | IST-REx-ID: 12081 | OA
Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 2022;119(36). doi:10.1073/pnas.2123152119
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[100]
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
 
[99]
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
 
[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: 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
 
[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 | 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
 
[94]
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
 
[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 | Submitted | 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: 8698 | OA
Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[90]
2020 | Published | Journal Article | IST-REx-ID: 9000 | OA
Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. PNAS. 2020;117(50):31614-31622. doi:10.1073/pnas.2006731117
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[89]
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
 
[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: 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
 
[86]
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.)
 
[85]
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
 
[84]
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
 
[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 | 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
 
[80]
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
 
[79]
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
 
[78]
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
 
[77]
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
 
[76]
2018 | Published | Journal Article | IST-REx-ID: 31 | OA
Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410
[Preprint] View | DOI | Download Preprint (ext.) | WoS
 
[75]
2018 | Published | Journal Article | IST-REx-ID: 543 | OA
Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115
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[74]
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
 
[73]
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
 
[72]
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
 
[71]
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
 
[70]
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
 
[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 | 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.)
 
[66]
2017 | Published | Journal Article | IST-REx-ID: 943 | OA
Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887
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[65]
2017 | Published | Journal Article | IST-REx-ID: 1104 | OA
Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y
[Published Version] View | Files available | DOI | WoS
 
[64]
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
 
[63]
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
 
[62]
2017 | Published | Journal Article | IST-REx-ID: 613 | OA
Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01683-1
[Published Version] View | Files available | DOI
 
[61]
2017 | Published | Journal Article | IST-REx-ID: 665
Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 2017;356(6335):311-315. doi:10.1126/science.aaf4762
View | Files available | DOI
 
[60]
2017 | Published | Journal Article | IST-REx-ID: 720 | OA
Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 2017;13(9). doi:10.1371/journal.pcbi.1005763
[Published Version] View | Files available | DOI
 
[59]
2017 | Published | Journal Article | IST-REx-ID: 725 | OA
Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[58]
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
 
[57]
2017 | Published | Journal Article | IST-REx-ID: 955 | OA
Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8
[Published Version] View | Files available | DOI | WoS
 
[56]
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
 
[55]
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
 
[54]
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
 
[53]
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
 
[52]
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; 2016:1965-1973.
[Preprint] View | Files available | Download Preprint (ext.)
 
[51]
2016 | Published | Conference Paper | IST-REx-ID: 1105
Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems; 2016:3610-3618.
View | Download None (ext.)
 
[50]
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
 
[49]
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
 
[48]
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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[47]
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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[46]
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
 
[45]
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
 
[44]
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
 
[43]
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
 
[42]
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
 
[41]
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.)
 
[40]
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.)
 
[39]
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.)
 
[38]
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
 
[37]
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.)
 
[36]
2014 | Published | Journal Article | IST-REx-ID: 2257 | OA
Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. 2014;10(1). doi:10.1371/journal.pcbi.1003408
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[35]
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
 
[34]
2014 | Published | Journal Article | IST-REx-ID: 2231 | OA
Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 2014;106(5):1194-1204. doi:10.1016/j.bpj.2014.01.014
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[33]
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
 
[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: 3374 | OA
Tkačik G, Walczak A. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 2011;23(15). doi:10.1088/0953-8984/23/15/153102
[Submitted Version] View | DOI | Download Submitted Version (ext.)
 
[21]
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
 
[20]
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
 
[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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108 Publications

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[108]
2024 | Published | Journal Article | IST-REx-ID: 17123 | OA
Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. PNAS. 2024;121(23). doi:10.1073/pnas.2322326121
[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
 
[106]
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
 
[105]
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
 
[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 | 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 | Download Published Version (ext.) | PubMed | Europe PMC
 
[102]
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
 
[101]
2022 | Published | Journal Article | IST-REx-ID: 12081 | OA
Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 2022;119(36). doi:10.1073/pnas.2123152119
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[100]
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
 
[99]
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
 
[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: 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
 
[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 | 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
 
[94]
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
 
[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 | Submitted | 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: 8698 | OA
Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[90]
2020 | Published | Journal Article | IST-REx-ID: 9000 | OA
Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. PNAS. 2020;117(50):31614-31622. doi:10.1073/pnas.2006731117
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[89]
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
 
[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: 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
 
[86]
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.)
 
[85]
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
 
[84]
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
 
[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 | 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
 
[80]
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
 
[79]
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
 
[78]
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
 
[77]
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
 
[76]
2018 | Published | Journal Article | IST-REx-ID: 31 | OA
Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410
[Preprint] View | DOI | Download Preprint (ext.) | WoS
 
[75]
2018 | Published | Journal Article | IST-REx-ID: 543 | OA
Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS
 
[74]
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
 
[73]
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
 
[72]
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
 
[71]
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
 
[70]
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
 
[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 | 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.)
 
[66]
2017 | Published | Journal Article | IST-REx-ID: 943 | OA
Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[65]
2017 | Published | Journal Article | IST-REx-ID: 1104 | OA
Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y
[Published Version] View | Files available | DOI | WoS
 
[64]
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
 
[63]
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
 
[62]
2017 | Published | Journal Article | IST-REx-ID: 613 | OA
Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01683-1
[Published Version] View | Files available | DOI
 
[61]
2017 | Published | Journal Article | IST-REx-ID: 665
Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 2017;356(6335):311-315. doi:10.1126/science.aaf4762
View | Files available | DOI
 
[60]
2017 | Published | Journal Article | IST-REx-ID: 720 | OA
Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 2017;13(9). doi:10.1371/journal.pcbi.1005763
[Published Version] View | Files available | DOI
 
[59]
2017 | Published | Journal Article | IST-REx-ID: 725 | OA
Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[58]
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
 
[57]
2017 | Published | Journal Article | IST-REx-ID: 955 | OA
Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8
[Published Version] View | Files available | DOI | WoS
 
[56]
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
 
[55]
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
 
[54]
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
 
[53]
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
 
[52]
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; 2016:1965-1973.
[Preprint] View | Files available | Download Preprint (ext.)
 
[51]
2016 | Published | Conference Paper | IST-REx-ID: 1105
Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems; 2016:3610-3618.
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[50]
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
 
[49]
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
 
[48]
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.)
 
[47]
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.)
 
[46]
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
 
[45]
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
 
[44]
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
 
[43]
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
 
[42]
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
 
[41]
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.)
 
[40]
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.)
 
[39]
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.)
 
[38]
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
 
[37]
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.)
 
[36]
2014 | Published | Journal Article | IST-REx-ID: 2257 | OA
Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. 2014;10(1). doi:10.1371/journal.pcbi.1003408
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[35]
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
 
[34]
2014 | Published | Journal Article | IST-REx-ID: 2231 | OA
Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 2014;106(5):1194-1204. doi:10.1016/j.bpj.2014.01.014
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[33]
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
 
[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: 3374 | OA
Tkačik G, Walczak A. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 2011;23(15). doi:10.1088/0953-8984/23/15/153102
[Submitted Version] View | DOI | Download Submitted Version (ext.)
 
[21]
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
 
[20]
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
 
[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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