Gasper Tkacik

Tkacik Group

82 Publications

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[82]
2020 | Preprint | IST-REx-ID: 7673 | OA
Kavcic B, Tkačik G, Bollenbach T. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020.
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[81]
2020 | Preprint | IST-REx-ID: 7675 | OA
Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020.
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[80]
2020 | Journal Article | IST-REx-ID: 7652
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
View | Files available | DOI
 
[79]
2020 | 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
View | Files available | DOI | PubMed | Europe PMC
 
[78]
2020 | Preprint | IST-REx-ID: 7553 | OA
Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of biological systems. bioRxiv.
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[77]
2019 | Preprint | IST-REx-ID: 7083 | OA
Kavcic B, Tkačik G, Bollenbach T. Mechanistic origin of drug interactions between translation-inhibiting antibiotics. bioRxiv.
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[76]
2019 | Preprint | IST-REx-ID: 7552 | OA
Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:191208579.
View | Download Preprint (ext.) | arXiv
 
[75]
2019 | Journal Article | IST-REx-ID: 5945
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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[74]
2019 | 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
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[73]
2019 | 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
View | Files available | DOI | PubMed | Europe PMC
 
[72]
2019 | 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; 2019:8989292. doi:10.1109/ITW44776.2019.8989292
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[71]
2018 | 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
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[70]
2018 | Research Data | IST-REx-ID: 5587 | OA
De Martino D, Tkačik G. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria; 2018. doi:10.15479/AT:ISTA:62
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[69]
2018 | Journal Article | IST-REx-ID: 281 | OA
Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkacik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115
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[68]
2018 | 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
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[67]
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. IST Austria; 2018. doi:10.15479/AT:ISTA:98
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[66]
2018 | Journal Article | IST-REx-ID: 31 | OA
Ferrari U, Deny S, Chalk MJ, Tkacik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4):042410. doi:10.1103/PhysRevE.98.042410
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[65]
2018 | 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
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[64]
2018 | Journal Article | IST-REx-ID: 543 | OA
Chalk MJ, Marre O, Tkacik 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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[63]
2018 | 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
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[62]
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. IST Austria; 2018. doi:10.15479/AT:ISTA:108
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[61]
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. IST Austria; 2017. doi:10.15479/AT:ISTA:61
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[60]
2017 | 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
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[59]
2017 | 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
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[58]
2017 | 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
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[57]
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. IST Austria; 2017. doi:doi:10.15479/AT:ISTA:53
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[56]
2017 | 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
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[55]
2017 | Journal Article | IST-REx-ID: 725 | OA
Harpaz R, Tkacik 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
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[54]
2017 | Journal Article | IST-REx-ID: 730
Savin C, Tkacik 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
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[53]
2017 | 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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[52]
2017 | 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
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[51]
2016 | 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
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[50]
2016 | 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
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[49]
2016 | Conference Paper | IST-REx-ID: 1082 | OA
Chalk MJ, Marre O, Tkacik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems; 2016:1965-1973.
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[48]
2016 | Conference Paper | IST-REx-ID: 1105
Savin C, Tkacik 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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[47]
2016 | Journal Article | IST-REx-ID: 1171
Tkacik 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
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[46]
2016 | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski TR, Walczak A, Bialek W, Tkacik 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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[45]
2016 | Journal Article | IST-REx-ID: 1248 | OA
Tkacik 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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[44]
2016 | 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
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[43]
2016 | Journal Article | IST-REx-ID: 1420 | OA
Bod’ová K, Tkacik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127
View | DOI | Download Preprint (ext.) | arXiv
 
[42]
2015 | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez SA, Rieckh G, Tkacik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24). doi:10.1103/PhysRevLett.115.248101
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[41]
2015 | 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
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[40]
2015 | Journal Article | IST-REx-ID: 1701 | OA
Tkacik 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
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[39]
2015 | 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
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[38]
2015 | Journal Article | IST-REx-ID: 1885 | OA
Tkacik 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
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[37]
2015 | Journal Article | IST-REx-ID: 1940 | OA
Sokolowski TR, Tkacik 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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[36]
2014 | 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
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[35]
2014 | 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
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[34]
2014 | Journal Article | IST-REx-ID: 2231 | OA
Rieckh G, Tkacik 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
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[33]
2014 | 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
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[32]
2013 | 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
View | Files available | DOI | Download Published Version (ext.) | arXiv
 
[31]
2013 | 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
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[30]
2013 | Journal Article | IST-REx-ID: 2850 | OA
Tkacik 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):P03011. doi:10.1088/1742-5468/2013/03/P03011
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[29]
2013 | Journal Article | IST-REx-ID: 2851
Berry M, Tkacik 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
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[28]
2013 | 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
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[27]
2013 | Journal Article | IST-REx-ID: 2913 | OA
Tkacik 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
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[26]
2013 | Journal Article | IST-REx-ID: 2818 | OA
Rajan K, Marre O, Tkacik G. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692. doi:10.1162/NECO_a_00463
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[25]
2013 | 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
View | Files available | DOI | PubMed | Europe PMC
 
[24]
2012 | Journal Article | IST-REx-ID: 3262 | OA
Tkacik 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
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[23]
2011 | 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 | Journal Article | IST-REx-ID: 3401
Little S, Tkacik 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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[21]
2011 | 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
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[20]
2011 | Journal Article | IST-REx-ID: 3374 | OA
Tkacik 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
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[19]
2010 | Conference Paper | IST-REx-ID: 3430 | OA
Tkacik G. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. In: Elsevier; 2010.
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[18]
2010 | Journal Article | IST-REx-ID: 3735
Tkacik 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 | Journal Article | IST-REx-ID: 3736
Tkacik 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 | Journal Article | IST-REx-ID: 3738
Walczak A, Tkacik 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 | Preprint | IST-REx-ID: 3743 | OA
Tkacik G. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv. 2010;q-MN:1-52.
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[14]
2009 | Preprint | IST-REx-ID: 3732 | OA
Tkacik 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 | Journal Article | IST-REx-ID: 3733
Kryazhimskiy S, Tkacik 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 | Journal Article | IST-REx-ID: 3737
Tkacik 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 | Journal Article | IST-REx-ID: 3745
Tkacik 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
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[10]
2009 | Book Chapter | IST-REx-ID: 3747
Tkacik 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
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[9]
2008 | Journal Article | IST-REx-ID: 3734 | OA
Tkacik 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 | Journal Article | IST-REx-ID: 3739
Tkacik 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
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[7]
2008 | Journal Article | IST-REx-ID: 3740 | OA
Tkacik 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 | Journal Article | IST-REx-ID: 3744 | OA
Tkacik 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 | Journal Article | IST-REx-ID: 3731
Kinney J, Tkacik 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 | Preprint | IST-REx-ID: 3742 | OA
Broderick T, Dudik M, Tkacik G, Schapire R, Bialek W. Faster solutions of the inverse pairwise Ising problem. ArXiv. 2007;q-QM.
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[3]
2006 | Preprint | IST-REx-ID: 3431 | OA
Tkacik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4.
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[2]
2005 | Journal Article | IST-REx-ID: 3741 | OA
Slonim N, Atwal G, Tkacik G, Bialek W. Information-based clustering. PNAS. 2005;102(51):18297-18302. doi:10.1073/pnas.0507432102
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[1]
2005 | Preprint | IST-REx-ID: 3746 | OA
Slonim N, Atwal G, Tkacik G, Bialek W. Estimating mutual information and multi-information in large networks. ArXiv. 2005:1-11.
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82 Publications

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[82]
2020 | Preprint | IST-REx-ID: 7673 | OA
Kavcic B, Tkačik G, Bollenbach T. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020.
View | Download Preprint (ext.)
 
[81]
2020 | Preprint | IST-REx-ID: 7675 | OA
Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020.
View | Files available | Download Preprint (ext.)
 
[80]
2020 | Journal Article | IST-REx-ID: 7652
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
View | Files available | DOI
 
[79]
2020 | 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
View | Files available | DOI | PubMed | Europe PMC
 
[78]
2020 | Preprint | IST-REx-ID: 7553 | OA
Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of biological systems. bioRxiv.
View | Download Preprint (ext.)
 
[77]
2019 | Preprint | IST-REx-ID: 7083 | OA
Kavcic B, Tkačik G, Bollenbach T. Mechanistic origin of drug interactions between translation-inhibiting antibiotics. bioRxiv.
View | Download Preprint (ext.)
 
[76]
2019 | Preprint | IST-REx-ID: 7552 | OA
Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:191208579.
View | Download Preprint (ext.) | arXiv
 
[75]
2019 | Journal Article | IST-REx-ID: 5945
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
View | Files available | DOI
 
[74]
2019 | 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
View | Files available | DOI
 
[73]
2019 | 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
View | Files available | DOI | PubMed | Europe PMC
 
[72]
2019 | 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; 2019:8989292. doi:10.1109/ITW44776.2019.8989292
View | DOI | Download Preprint (ext.) | arXiv
 
[71]
2018 | 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
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[70]
2018 | Research Data | IST-REx-ID: 5587 | OA
De Martino D, Tkačik G. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria; 2018. doi:10.15479/AT:ISTA:62
View | Files available | DOI
 
[69]
2018 | Journal Article | IST-REx-ID: 281 | OA
Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkacik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115
View | Files available | DOI | Download Preprint (ext.) | PubMed | Europe PMC
 
[68]
2018 | 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
View | Files available | DOI
 
[67]
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. IST Austria; 2018. doi:10.15479/AT:ISTA:98
View | Files available | DOI
 
[66]
2018 | Journal Article | IST-REx-ID: 31 | OA
Ferrari U, Deny S, Chalk MJ, Tkacik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4):042410. doi:10.1103/PhysRevE.98.042410
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[65]
2018 | 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
View | Files available | DOI
 
[64]
2018 | Journal Article | IST-REx-ID: 543 | OA
Chalk MJ, Marre O, Tkacik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115
View | DOI | Download Submitted Version (ext.)
 
[63]
2018 | 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
View | Files available | DOI
 
[62]
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. IST Austria; 2018. doi:10.15479/AT:ISTA:108
View | Files available | DOI
 
[61]
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. IST Austria; 2017. doi:10.15479/AT:ISTA:61
View | Files available | DOI
 
[60]
2017 | 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
View | Files available | DOI
 
[59]
2017 | 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
View | Files available | DOI
 
[58]
2017 | 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
 
[57]
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. IST Austria; 2017. doi:doi:10.15479/AT:ISTA:53
View | Files available | DOI
 
[56]
2017 | 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
View | Files available | DOI
 
[55]
2017 | Journal Article | IST-REx-ID: 725 | OA
Harpaz R, Tkacik 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
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[54]
2017 | Journal Article | IST-REx-ID: 730
Savin C, Tkacik 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
 
[53]
2017 | 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
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[52]
2017 | 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
View | Files available | DOI
 
[51]
2016 | 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
View | Files available | DOI
 
[50]
2016 | 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
View | Files available | DOI
 
[49]
2016 | Conference Paper | IST-REx-ID: 1082 | OA
Chalk MJ, Marre O, Tkacik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems; 2016:1965-1973.
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[48]
2016 | Conference Paper | IST-REx-ID: 1105
Savin C, Tkacik 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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[47]
2016 | Journal Article | IST-REx-ID: 1171
Tkacik 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
 
[46]
2016 | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski TR, Walczak A, Bialek W, Tkacik 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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[45]
2016 | Journal Article | IST-REx-ID: 1248 | OA
Tkacik 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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[44]
2016 | 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
View | Files available | DOI
 
[43]
2016 | Journal Article | IST-REx-ID: 1420 | OA
Bod’ová K, Tkacik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127
View | DOI | Download Preprint (ext.) | arXiv
 
[42]
2015 | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez SA, Rieckh G, Tkacik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24). doi:10.1103/PhysRevLett.115.248101
View | Files available | DOI | Download Preprint (ext.)
 
[41]
2015 | 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
View | Files available | DOI
 
[40]
2015 | Journal Article | IST-REx-ID: 1701 | OA
Tkacik 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
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[39]
2015 | 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
View | Files available | DOI
 
[38]
2015 | Journal Article | IST-REx-ID: 1885 | OA
Tkacik 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
View | DOI | Download Preprint (ext.)
 
[37]
2015 | Journal Article | IST-REx-ID: 1940 | OA
Sokolowski TR, Tkacik 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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[36]
2014 | 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
View | Files available | DOI | Download Published Version (ext.)
 
[35]
2014 | 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
View | Files available | DOI
 
[34]
2014 | Journal Article | IST-REx-ID: 2231 | OA
Rieckh G, Tkacik 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
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[33]
2014 | 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
View | Files available | DOI
 
[32]
2013 | 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
View | Files available | DOI | Download Published Version (ext.) | arXiv
 
[31]
2013 | 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
View | Files available | DOI
 
[30]
2013 | Journal Article | IST-REx-ID: 2850 | OA
Tkacik 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):P03011. doi:10.1088/1742-5468/2013/03/P03011
View | DOI | Download Preprint (ext.) | arXiv
 
[29]
2013 | Journal Article | IST-REx-ID: 2851
Berry M, Tkacik 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
 
[28]
2013 | 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
View | Files available | DOI
 
[27]
2013 | Journal Article | IST-REx-ID: 2913 | OA
Tkacik 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
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[26]
2013 | Journal Article | IST-REx-ID: 2818 | OA
Rajan K, Marre O, Tkacik G. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692. doi:10.1162/NECO_a_00463
View | DOI | Download Preprint (ext.) | arXiv
 
[25]
2013 | 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
View | Files available | DOI | PubMed | Europe PMC
 
[24]
2012 | Journal Article | IST-REx-ID: 3262 | OA
Tkacik 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
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[23]
2011 | 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 | Journal Article | IST-REx-ID: 3401
Little S, Tkacik 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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[21]
2011 | 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
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[20]
2011 | Journal Article | IST-REx-ID: 3374 | OA
Tkacik 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
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[19]
2010 | Conference Paper | IST-REx-ID: 3430 | OA
Tkacik G. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. In: Elsevier; 2010.
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[18]
2010 | Journal Article | IST-REx-ID: 3735
Tkacik 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 | Journal Article | IST-REx-ID: 3736
Tkacik 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 | Journal Article | IST-REx-ID: 3738
Walczak A, Tkacik 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 | Preprint | IST-REx-ID: 3743 | OA
Tkacik G. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv. 2010;q-MN:1-52.
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[14]
2009 | Preprint | IST-REx-ID: 3732 | OA
Tkacik 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 | Journal Article | IST-REx-ID: 3733
Kryazhimskiy S, Tkacik 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 | Journal Article | IST-REx-ID: 3737
Tkacik 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 | Journal Article | IST-REx-ID: 3745
Tkacik 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
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[10]
2009 | Book Chapter | IST-REx-ID: 3747
Tkacik 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 | Journal Article | IST-REx-ID: 3734 | OA
Tkacik 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 | Journal Article | IST-REx-ID: 3739
Tkacik 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
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[7]
2008 | Journal Article | IST-REx-ID: 3740 | OA
Tkacik 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 | Journal Article | IST-REx-ID: 3744 | OA
Tkacik 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 | Journal Article | IST-REx-ID: 3731
Kinney J, Tkacik 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 | Preprint | IST-REx-ID: 3742 | OA
Broderick T, Dudik M, Tkacik G, Schapire R, Bialek W. Faster solutions of the inverse pairwise Ising problem. ArXiv. 2007;q-QM.
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[3]
2006 | Preprint | IST-REx-ID: 3431 | OA
Tkacik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4.
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[2]
2005 | Journal Article | IST-REx-ID: 3741 | OA
Slonim N, Atwal G, Tkacik G, Bialek W. Information-based clustering. PNAS. 2005;102(51):18297-18302. doi:10.1073/pnas.0507432102
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[1]
2005 | Preprint | IST-REx-ID: 3746 | OA
Slonim N, Atwal G, Tkacik G, Bialek W. Estimating mutual information and multi-information in large networks. ArXiv. 2005:1-11.
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