75 Publications
2019 | Preprint | IST-REx-ID: 7083   

Kavcic B, Tkačik G, Bollenbach T. Mechanistic origin of drug interactions between translation-inhibiting antibiotics. bioRxiv. 2019.
View
| Download (ext.)
2019 | Journal Article | IST-REx-ID: 5945
Petkova MD, Tkacik 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
2019 | Journal Article | IST-REx-ID: 6784   

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
2019 | Journal Article | IST-REx-ID: 6900   

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
2018 | Journal Article | IST-REx-ID: 31   

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). doi:10.1103/PhysRevE.98.042410
View
| DOI
| Download (ext.)
2018 | Journal Article | IST-REx-ID: 543   

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 (ext.)
2018 | Research Data | IST-REx-ID: 5587   

De Martino D, Tkacik 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
2018 | Journal Article | IST-REx-ID: 67
Igler C, Lagator M, Tkacik 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
2018 | Journal Article | IST-REx-ID: 406   

Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkacik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049
View
| Files available
| DOI
2018 | Journal Article | IST-REx-ID: 292
Botella Soler V, Deny S, Martius GS, Marre O, Tkacik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5):e1006057. doi:10.1371/journal.pcbi.1006057
View
| Files available
| DOI
2018 | Research Data | IST-REx-ID: 5584   

Deny S, Marre O, Botella-Soler V, Martius GS, Tkacik G. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. IST Austria; 2018. doi:10.15479/AT:ISTA:98
View
| Files available
| DOI
2018 | Journal Article | IST-REx-ID: 161
De Martino D, Mc AA, Bergmiller T, Guet CC, Tkacik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1):2988. doi:10.1038/s41467-018-05417-9
View
| Files available
| DOI
2018 | Journal Article | IST-REx-ID: 281
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 (ext.)
| PubMed | Europe PMC
2018 | Research Data | IST-REx-ID: 5585
Igler C, Lagator M, Tkacik 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
2017 | Research Data | IST-REx-ID: 5562   

Marre O, Tkacik 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
2017 | Journal Article | IST-REx-ID: 720   

Humplik J, Tkacik 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
2017 | Journal Article | IST-REx-ID: 725   

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 (ext.)
| PubMed | Europe PMC
2017 | Journal Article | IST-REx-ID: 1104   

Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 2017;8(1):1964. doi:10.1038/s41467-017-02159-y
View
| Files available
| DOI
2017 | Journal Article | IST-REx-ID: 613   

Chait RP, Ruess J, Bergmiller T, Tkacik 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
2017 | Journal Article | IST-REx-ID: 943   

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 (ext.)
| PubMed | Europe PMC
2017 | Journal Article | IST-REx-ID: 955   

Friedlander T, Prizak R, Barton NH, Tkacik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1):216. doi:10.1038/s41467-017-00238-8
View
| Files available
| DOI
2017 | Research Data | IST-REx-ID: 5560
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
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
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
2016 | Journal Article | IST-REx-ID: 1197   

Prentice J, Marre O, Ioffe M, Loback A, Tkacik 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
2016 | Journal Article | IST-REx-ID: 1248   

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
View
| DOI
| Download (ext.)
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.
View
| Download (ext.)
2016 | Journal Article | IST-REx-ID: 1270   

Hillenbrand P, Gerland U, Tkacik 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
2016 | Journal Article | IST-REx-ID: 1358
Friedlander T, Prizak R, Guet CC, Barton NH, Tkacik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7:12307. doi:10.1038/ncomms12307
View
| Files available
| DOI
2016 | Conference Paper | IST-REx-ID: 1082   

Chalk MJ, Marre O, Tkacik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems; 2016:1965-1973.
View
| Files available
| Download (ext.)
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
2016 | Journal Article | IST-REx-ID: 1242   

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
View
| DOI
| Download (ext.)
2016 | Journal Article | IST-REx-ID: 1420   

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 (ext.)
| arXiv
2015 | Journal Article | IST-REx-ID: 1666   

Tugrul M, Paixao T, Barton NH, Tkacik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
View
| Files available
| DOI
2015 | Journal Article | IST-REx-ID: 1697   

Marre O, Botella Soler V, Simmons K, Mora T, Tkacik 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
2015 | Journal Article | IST-REx-ID: 1940   

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
View
| DOI
| Download (ext.)
2015 | Journal Article | IST-REx-ID: 1701   

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 (ext.)
| PubMed | Europe PMC
2015 | Journal Article | IST-REx-ID: 1885   

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 (ext.)
2015 | Journal Article | IST-REx-ID: 1576
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 (ext.)
2014 | Journal Article | IST-REx-ID: 3263   

Tkacik 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
2014 | Journal Article | IST-REx-ID: 2231   

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 (ext.)
| PubMed | Europe PMC
2014 | Journal Article | IST-REx-ID: 1886   

Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkacik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722
View
| Files available
| DOI
2014 | Journal Article | IST-REx-ID: 2257
Tkacik 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 (ext.)
2013 | Journal Article | IST-REx-ID: 2277   

Simmons K, Prentice J, Tkacik G, et al. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 2013;9(12):e1003344. doi:10.1371/journal.pcbi.1003344
View
| Files available
| DOI
2013 | Journal Article | IST-REx-ID: 2913   

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
View
| DOI
| Download (ext.)
2013 | Journal Article | IST-REx-ID: 2850   

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). doi:10.1088/1742-5468/2013/03/P03011
View
| DOI
| Download (ext.)
| arXiv
2013 | Journal Article | IST-REx-ID: 2863   

Granot Atedgi E, Tkacik 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
2013 | Journal Article | IST-REx-ID: 2914   

Stephens G, Mora T, Tkacik G, Bialek W. Statistical thermodynamics of natural images. Physical Review Letters. 2013;110(1):018701. doi:10.1103/PhysRevLett.110.018701
View
| Files available
| DOI
| Download (ext.)
| arXiv
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
2013 | Journal Article | IST-REx-ID: 2818   

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 (ext.)
| arXiv
2013 | Journal Article | IST-REx-ID: 3261   

Dubuis J, Tkacik 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
2012 | Journal Article | IST-REx-ID: 3262   

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
View
| DOI
| Download (ext.)
2011 | Journal Article | IST-REx-ID: 3276   

Prentice J, Homann J, Simmons K, Tkacik 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
2011 | Journal Article | IST-REx-ID: 3384   

Tkacik 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
View
| Files available
| DOI
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):e1000596. doi:10.1371/journal.pbio.1000596
View
| DOI
2011 | Journal Article | IST-REx-ID: 3374   

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
View
| DOI
| Download (ext.)
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
View
| DOI
| Download (ext.)
2010 | Conference Paper | IST-REx-ID: 3430   

Tkacik G. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. In: Elsevier; 2010.
View
| Download (ext.)
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
View
| DOI
| Download (ext.)
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
View
| DOI
| Download (ext.)
2010 | Preprint | IST-REx-ID: 3743   

Tkacik G. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv. 2010;q-MN:1-52.
View
| Download (ext.)
2009 | Preprint | IST-REx-ID: 3732   

Tkacik G, Schneidman E, Berry M, Bialek W. Spin glass models for a network of real neurons. ArXiv. 2009;q-NC.
View
| Download (ext.)
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
View
| DOI
| Download (ext.)
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
View
| DOI
| Download (ext.)
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
View
| DOI
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
2008 | Journal Article | IST-REx-ID: 3744   

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
View
| DOI
| Download (ext.)
2008 | Journal Article | IST-REx-ID: 3740   

Tkacik G, Callan C, Bialek W. Information flow and optimization in transcriptional regulation. PNAS. 2008;105(34):12265-12270. doi:10.1073/pnas.0806077105
View
| DOI
| Download (ext.)
2008 | Journal Article | IST-REx-ID: 3734   

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
View
| DOI
| Download (ext.)
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
View
| DOI
2007 | Preprint | IST-REx-ID: 3742   

Broderick T, Dudik M, Tkacik G, Schapire R, Bialek W. Faster solutions of the inverse pairwise Ising problem. ArXiv. 2007;q-QM.
View
| Download (ext.)
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
View
| DOI
| Download (ext.)
2006 | Preprint | IST-REx-ID: 3431   

Tkacik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4.
View
| Download (ext.)
2005 | Journal Article | IST-REx-ID: 3741   

Slonim N, Atwal G, Tkacik G, Bialek W. Information-based clustering. PNAS. 2005;102(51):18297-18302. doi:10.1073/pnas.0507432102
View
| DOI
| Download (ext.)
2005 | Preprint | IST-REx-ID: 3746   

Slonim N, Atwal G, Tkacik G, Bialek W. Estimating mutual information and multi-information in large networks. ArXiv. 2005:1-11.
View
| Download (ext.)
75 Publications
2019 | Preprint | IST-REx-ID: 7083   

Kavcic B, Tkačik G, Bollenbach T. Mechanistic origin of drug interactions between translation-inhibiting antibiotics. bioRxiv. 2019.
View
| Download (ext.)
2019 | Journal Article | IST-REx-ID: 5945
Petkova MD, Tkacik 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
2019 | Journal Article | IST-REx-ID: 6784   

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
2019 | Journal Article | IST-REx-ID: 6900   

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
2018 | Journal Article | IST-REx-ID: 31   

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). doi:10.1103/PhysRevE.98.042410
View
| DOI
| Download (ext.)
2018 | Journal Article | IST-REx-ID: 543   

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 (ext.)
2018 | Research Data | IST-REx-ID: 5587   

De Martino D, Tkacik 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
2018 | Journal Article | IST-REx-ID: 67
Igler C, Lagator M, Tkacik 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
2018 | Journal Article | IST-REx-ID: 406   

Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkacik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049
View
| Files available
| DOI
2018 | Journal Article | IST-REx-ID: 292
Botella Soler V, Deny S, Martius GS, Marre O, Tkacik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5):e1006057. doi:10.1371/journal.pcbi.1006057
View
| Files available
| DOI
2018 | Research Data | IST-REx-ID: 5584   

Deny S, Marre O, Botella-Soler V, Martius GS, Tkacik G. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. IST Austria; 2018. doi:10.15479/AT:ISTA:98
View
| Files available
| DOI
2018 | Journal Article | IST-REx-ID: 161
De Martino D, Mc AA, Bergmiller T, Guet CC, Tkacik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1):2988. doi:10.1038/s41467-018-05417-9
View
| Files available
| DOI
2018 | Journal Article | IST-REx-ID: 281
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 (ext.)
| PubMed | Europe PMC
2018 | Research Data | IST-REx-ID: 5585
Igler C, Lagator M, Tkacik 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
2017 | Research Data | IST-REx-ID: 5562   

Marre O, Tkacik 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
2017 | Journal Article | IST-REx-ID: 720   

Humplik J, Tkacik 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
2017 | Journal Article | IST-REx-ID: 725   

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 (ext.)
| PubMed | Europe PMC
2017 | Journal Article | IST-REx-ID: 1104   

Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 2017;8(1):1964. doi:10.1038/s41467-017-02159-y
View
| Files available
| DOI
2017 | Journal Article | IST-REx-ID: 613   

Chait RP, Ruess J, Bergmiller T, Tkacik 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
2017 | Journal Article | IST-REx-ID: 943   

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 (ext.)
| PubMed | Europe PMC
2017 | Journal Article | IST-REx-ID: 955   

Friedlander T, Prizak R, Barton NH, Tkacik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1):216. doi:10.1038/s41467-017-00238-8
View
| Files available
| DOI
2017 | Research Data | IST-REx-ID: 5560
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
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
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
2016 | Journal Article | IST-REx-ID: 1197   

Prentice J, Marre O, Ioffe M, Loback A, Tkacik 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
2016 | Journal Article | IST-REx-ID: 1248   

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
View
| DOI
| Download (ext.)
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.
View
| Download (ext.)
2016 | Journal Article | IST-REx-ID: 1270   

Hillenbrand P, Gerland U, Tkacik 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
2016 | Journal Article | IST-REx-ID: 1358
Friedlander T, Prizak R, Guet CC, Barton NH, Tkacik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7:12307. doi:10.1038/ncomms12307
View
| Files available
| DOI
2016 | Conference Paper | IST-REx-ID: 1082   

Chalk MJ, Marre O, Tkacik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems; 2016:1965-1973.
View
| Files available
| Download (ext.)
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
2016 | Journal Article | IST-REx-ID: 1242   

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
View
| DOI
| Download (ext.)
2016 | Journal Article | IST-REx-ID: 1420   

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 (ext.)
| arXiv
2015 | Journal Article | IST-REx-ID: 1666   

Tugrul M, Paixao T, Barton NH, Tkacik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
View
| Files available
| DOI
2015 | Journal Article | IST-REx-ID: 1697   

Marre O, Botella Soler V, Simmons K, Mora T, Tkacik 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
2015 | Journal Article | IST-REx-ID: 1940   

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
View
| DOI
| Download (ext.)
2015 | Journal Article | IST-REx-ID: 1701   

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 (ext.)
| PubMed | Europe PMC
2015 | Journal Article | IST-REx-ID: 1885   

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 (ext.)
2015 | Journal Article | IST-REx-ID: 1576
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 (ext.)
2014 | Journal Article | IST-REx-ID: 3263   

Tkacik 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
2014 | Journal Article | IST-REx-ID: 2231   

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 (ext.)
| PubMed | Europe PMC
2014 | Journal Article | IST-REx-ID: 1886   

Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkacik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722
View
| Files available
| DOI
2014 | Journal Article | IST-REx-ID: 2257
Tkacik 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 (ext.)
2013 | Journal Article | IST-REx-ID: 2277   

Simmons K, Prentice J, Tkacik G, et al. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 2013;9(12):e1003344. doi:10.1371/journal.pcbi.1003344
View
| Files available
| DOI
2013 | Journal Article | IST-REx-ID: 2913   

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
View
| DOI
| Download (ext.)
2013 | Journal Article | IST-REx-ID: 2850   

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). doi:10.1088/1742-5468/2013/03/P03011
View
| DOI
| Download (ext.)
| arXiv
2013 | Journal Article | IST-REx-ID: 2863   

Granot Atedgi E, Tkacik 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
2013 | Journal Article | IST-REx-ID: 2914   

Stephens G, Mora T, Tkacik G, Bialek W. Statistical thermodynamics of natural images. Physical Review Letters. 2013;110(1):018701. doi:10.1103/PhysRevLett.110.018701
View
| Files available
| DOI
| Download (ext.)
| arXiv
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
2013 | Journal Article | IST-REx-ID: 2818   

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 (ext.)
| arXiv
2013 | Journal Article | IST-REx-ID: 3261   

Dubuis J, Tkacik 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
2012 | Journal Article | IST-REx-ID: 3262   

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
View
| DOI
| Download (ext.)
2011 | Journal Article | IST-REx-ID: 3276   

Prentice J, Homann J, Simmons K, Tkacik 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
2011 | Journal Article | IST-REx-ID: 3384   

Tkacik 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
View
| Files available
| DOI
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):e1000596. doi:10.1371/journal.pbio.1000596
View
| DOI
2011 | Journal Article | IST-REx-ID: 3374   

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
View
| DOI
| Download (ext.)
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
View
| DOI
| Download (ext.)
2010 | Conference Paper | IST-REx-ID: 3430   

Tkacik G. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. In: Elsevier; 2010.
View
| Download (ext.)
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
View
| DOI
| Download (ext.)
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
View
| DOI
| Download (ext.)
2010 | Preprint | IST-REx-ID: 3743   

Tkacik G. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv. 2010;q-MN:1-52.
View
| Download (ext.)
2009 | Preprint | IST-REx-ID: 3732   

Tkacik G, Schneidman E, Berry M, Bialek W. Spin glass models for a network of real neurons. ArXiv. 2009;q-NC.
View
| Download (ext.)
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
View
| DOI
| Download (ext.)
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
View
| DOI
| Download (ext.)
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
View
| DOI
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
2008 | Journal Article | IST-REx-ID: 3744   

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
View
| DOI
| Download (ext.)
2008 | Journal Article | IST-REx-ID: 3740   

Tkacik G, Callan C, Bialek W. Information flow and optimization in transcriptional regulation. PNAS. 2008;105(34):12265-12270. doi:10.1073/pnas.0806077105
View
| DOI
| Download (ext.)
2008 | Journal Article | IST-REx-ID: 3734   

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
View
| DOI
| Download (ext.)
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
View
| DOI
2007 | Preprint | IST-REx-ID: 3742   

Broderick T, Dudik M, Tkacik G, Schapire R, Bialek W. Faster solutions of the inverse pairwise Ising problem. ArXiv. 2007;q-QM.
View
| Download (ext.)
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
View
| DOI
| Download (ext.)
2006 | Preprint | IST-REx-ID: 3431   

Tkacik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4.
View
| Download (ext.)
2005 | Journal Article | IST-REx-ID: 3741   

Slonim N, Atwal G, Tkacik G, Bialek W. Information-based clustering. PNAS. 2005;102(51):18297-18302. doi:10.1073/pnas.0507432102
View
| DOI
| Download (ext.)
2005 | Preprint | IST-REx-ID: 3746   

Slonim N, Atwal G, Tkacik G, Bialek W. Estimating mutual information and multi-information in large networks. ArXiv. 2005:1-11.
View
| Download (ext.)