75 Publications

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[75]
2019 | Preprint | IST-REx-ID: 7083   OA
Kavcic, B., Tkačik, G., & Bollenbach, T. (2019). Mechanistic origin of drug interactions between translation-inhibiting antibiotics. BioRxiv. Cold Spring Harbor Laboratory.
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[74]
2019 | Journal Article | IST-REx-ID: 6784   OA
Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology, 15(7). https://doi.org/10.1371/journal.pcbi.1007168
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[73]
2019 | Journal Article | IST-REx-ID: 5945
Petkova, M. D., Tkacik, G., Bialek, W., Wieschaus, E. F., & Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. Cell, 176(4), 844–855.e15. https://doi.org/10.1016/j.cell.2019.01.007
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[72]
2019 | Journal Article | IST-REx-ID: 6900   OA
Cepeda Humerez, S. A., Ruess, J., & Tkačik, G. (2019). Estimating information in time-varying signals. PLoS Computational Biology, 15(9), e1007290. https://doi.org/10.1371/journal.pcbi.1007290
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[71]
2018 | Journal Article | IST-REx-ID: 31   OA
Ferrari, U., Deny, S., Chalk, M. J., Tkacik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E, 98(4). https://doi.org/10.1103/PhysRevE.98.042410
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[70]
2018 | Journal Article | IST-REx-ID: 67
Igler, C., Lagator, M., Tkacik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution, 2(10), 1633–1643. https://doi.org/10.1038/s41559-018-0651-y
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[69]
2018 | Journal Article | IST-REx-ID: 543   OA
Chalk, M. J., Marre, O., & Tkacik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS, 115(1), 186–191. https://doi.org/10.1073/pnas.1711114115
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[68]
2018 | Research Data | IST-REx-ID: 5587   OA
De Martino, D., & Tkacik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria. https://doi.org/10.15479/AT:ISTA:62
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[67]
2018 | Journal Article | IST-REx-ID: 406   OA
Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkacik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One, 13(3). https://doi.org/10.1371/journal.pone.0193049
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[66]
2018 | Journal Article | IST-REx-ID: 292
Botella Soler, V., Deny, S., Martius, G. S., Marre, O., & Tkacik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology, 14(5). https://doi.org/10.1371/journal.pcbi.1006057
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[65]
2018 | Research Data | IST-REx-ID: 5584   OA
Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkacik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. IST Austria. https://doi.org/10.15479/AT:ISTA:98
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[64]
2018 | Research Data | IST-REx-ID: 5585
Igler, C., Lagator, M., Tkacik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. IST Austria. https://doi.org/10.15479/AT:ISTA:108
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[63]
2018 | Journal Article | IST-REx-ID: 281   OA
Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkacik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS, 115(23), 6088–6093. https://doi.org/10.1073/pnas.1716659115
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[62]
2018 | Journal Article | IST-REx-ID: 161
De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkacik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-05417-9
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[61]
2017 | Research Data | IST-REx-ID: 5562   OA
Marre, O., Tkacik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2017). Multi-electrode array recording from salamander retinal ganglion cells. IST Austria. https://doi.org/10.15479/AT:ISTA:61
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[60]
2017 | Journal Article | IST-REx-ID: 725   OA
Harpaz, R., Tkacik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS, 114(38), 10149–10154. https://doi.org/10.1073/pnas.1703817114
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[59]
2017 | Journal Article | IST-REx-ID: 1104   OA
Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-02159-y
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[58]
2017 | Journal Article | IST-REx-ID: 720   OA
Humplik, J., & Tkacik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology, 13(9). https://doi.org/10.1371/journal.pcbi.1005763
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[57]
2017 | Journal Article | IST-REx-ID: 613   OA
Chait, R. P., Ruess, J., Bergmiller, T., Tkacik, G., & Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-01683-1
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[56]
2017 | Journal Article | IST-REx-ID: 943   OA
Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkacik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science, 356(6345), 1379–1383. https://doi.org/10.1126/science.aam5887
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[55]
2017 | Journal Article | IST-REx-ID: 955   OA
Friedlander, T., Prizak, R., Barton, N. H., & Tkacik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-00238-8
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[54]
2017 | Journal Article | IST-REx-ID: 730
Savin, C., & Tkacik, G. (2017). Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology, 46, 120–126. https://doi.org/10.1016/j.conb.2017.08.001
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[53]
2017 | Research Data | IST-REx-ID: 5560
Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. IST Austria. https://doi.org/doi:10.15479/AT:ISTA:53
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[52]
2017 | Journal Article | IST-REx-ID: 665
Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science, 356(6335), 311–315. https://doi.org/10.1126/science.aaf4762
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[51]
2016 | Journal Article | IST-REx-ID: 1248   OA
Tkacik, G., & Bialek, W. (2016). Information processing in living systems. Annual Review of Condensed Matter Physics, 7, 89–117. https://doi.org/10.1146/annurev-conmatphys-031214-014803
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[50]
2016 | Journal Article | IST-REx-ID: 1197   OA
Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkacik, G., & Berry, M. (2016). Error-robust modes of the retinal population code. PLoS Computational Biology, 12(11). https://doi.org/10.1371/journal.pcbi.1005148
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[49]
2016 | Conference Paper | IST-REx-ID: 1105
Savin, C., & Tkacik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems.
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[48]
2016 | Journal Article | IST-REx-ID: 1270   OA
Hillenbrand, P., Gerland, U., & Tkacik, G. (2016). Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One, 11(9). https://doi.org/10.1371/journal.pone.0163628
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[47]
2016 | Journal Article | IST-REx-ID: 1358
Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkacik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications, 7. https://doi.org/10.1038/ncomms12307
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[46]
2016 | Conference Paper | IST-REx-ID: 1082   OA
Chalk, M. J., Marre, O., & Tkacik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems.
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[45]
2016 | Journal Article | IST-REx-ID: 1171
Tkacik, G. (2016). 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, 17, 166–167. https://doi.org/10.1016/j.plrev.2016.06.005
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[44]
2016 | Journal Article | IST-REx-ID: 1420   OA
Bod’ová, K., Tkacik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics, 202(4), 1523–1548. https://doi.org/10.1534/genetics.115.184127
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[43]
2016 | Journal Article | IST-REx-ID: 1242   OA
Sokolowski, T. R., Walczak, A., Bialek, W., & Tkacik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics, 93(2). https://doi.org/10.1103/PhysRevE.93.022404
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[42]
2015 | Journal Article | IST-REx-ID: 1666   OA
Tugrul, M., Paixao, T., Barton, N. H., & Tkacik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics, 11(11). https://doi.org/10.1371/journal.pgen.1005639
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[41]
2015 | Journal Article | IST-REx-ID: 1940   OA
Sokolowski, T. R., & Tkacik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics, 91(6). https://doi.org/10.1103/PhysRevE.91.062710
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[40]
2015 | Journal Article | IST-REx-ID: 1697   OA
Marre, O., Botella Soler, V., Simmons, K., Mora, T., Tkacik, G., & Berry, M. (2015). High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology, 11(7). https://doi.org/10.1371/journal.pcbi.1004304
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[39]
2015 | Journal Article | IST-REx-ID: 1701   OA
Tkacik, G., Mora, T., Marre, O., Amodei, D., Palmer, S., Berry Ii, M., & Bialek, W. (2015). Thermodynamics and signatures of criticality in a network of neurons. PNAS, 112(37), 11508–11513. https://doi.org/10.1073/pnas.1514188112
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[38]
2015 | Journal Article | IST-REx-ID: 1885   OA
Tkacik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics, 199(1), 39–59. https://doi.org/10.1534/genetics.114.171850
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[37]
2015 | Journal Article | IST-REx-ID: 1576
Cepeda Humerez, S. A., Rieckh, G., & Tkacik, G. (2015). Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters, 115(24). https://doi.org/10.1103/PhysRevLett.115.248101
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[36]
2014 | Journal Article | IST-REx-ID: 3263   OA
Tkacik, G., Ghosh, A., Schneidman, E., & Segev, R. (2014). Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One, 9(1). https://doi.org/10.1371/journal.pone.0085841
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[35]
2014 | Journal Article | IST-REx-ID: 2231   OA
Rieckh, G., & Tkacik, G. (2014). Noise and information transmission in promoters with multiple internal states. Biophysical Journal, 106(5), 1194–1204. https://doi.org/10.1016/j.bpj.2014.01.014
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[34]
2014 | Journal Article | IST-REx-ID: 2257
Tkacik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2014). Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology, 10(1). https://doi.org/10.1371/journal.pcbi.1003408
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[33]
2014 | Journal Article | IST-REx-ID: 1886   OA
Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., & Tkacik, G. (2014). Variance predicts salience in central sensory processing. ELife, (November). https://doi.org/10.7554/eLife.03722
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[32]
2013 | Journal Article | IST-REx-ID: 2277   OA
Simmons, K., Prentice, J., Tkacik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2013). Transformation of stimulus correlations by the retina. PLoS Computational Biology, 9(12). https://doi.org/10.1371/journal.pcbi.1003344
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[31]
2013 | Journal Article | IST-REx-ID: 2913   OA
Tkacik, G., Granot Atedgi, E., Segev, R., & Schneidman, E. (2013). Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters, 110(5). https://doi.org/10.1103/PhysRevLett.110.058104
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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. (2013). The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment, 2013(3). https://doi.org/10.1088/1742-5468/2013/03/P03011
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[29]
2013 | Journal Article | IST-REx-ID: 2863   OA
Granot Atedgi, E., Tkacik, G., Segev, R., & Schneidman, E. (2013). Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology, 9(3). https://doi.org/10.1371/journal.pcbi.1002922
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[28]
2013 | Journal Article | IST-REx-ID: 2914   OA
Stephens, G., Mora, T., Tkacik, G., & Bialek, W. (2013). Statistical thermodynamics of natural images. Physical Review Letters, 110(1). https://doi.org/10.1103/PhysRevLett.110.018701
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[27]
2013 | Journal Article | IST-REx-ID: 2851
Berry, M., Tkacik, G., Dubuis, J., Marre, O., & Da Silveira, R. (2013). A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment, 2013(3). https://doi.org/10.1088/1742-5468/2013/03/P03015
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[26]
2013 | Journal Article | IST-REx-ID: 2818   OA
Rajan, K., Marre, O., & Tkacik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation, 25(7), 1661–1692. https://doi.org/10.1162/NECO_a_00463
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[25]
2013 | Journal Article | IST-REx-ID: 3261   OA
Dubuis, J., Tkacik, G., Wieschaus, E., Gregor, T., & Bialek, W. (2013). Positional information, in bits. PNAS, 110(41), 16301–16308. https://doi.org/10.1073/pnas.1315642110
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[24]
2012 | Journal Article | IST-REx-ID: 3262   OA
Tkacik, G., Walczak, A., & Bialek, W. (2012). Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E Statistical Nonlinear and Soft Matter Physics , 85(4). https://doi.org/10.1103/PhysRevE.85.041903
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[23]
2011 | Journal Article | IST-REx-ID: 3276   OA
Prentice, J., Homann, J., Simmons, K., Tkacik, G., Balasubramanian, V., & Nelson, P. (2011). Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One, 6(7). https://doi.org/10.1371/journal.pone.0019884
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[22]
2011 | Journal Article | IST-REx-ID: 3384   OA
Tkacik, G., Garrigan, P., Ratliff, C., Milcinski, G., Klein, J., Seyfarth, L., … Balasubramanian, V. (2011). Natural images from the birthplace of the human eye. PLoS One, 6(6). https://doi.org/10.1371/journal.pone.0020409
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[21]
2011 | Journal Article | IST-REx-ID: 3401
Little, S., Tkacik, G., Kneeland, T., Wieschaus, E., & Gregor, T. (2011). The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source. PLoS Biology, 9(3). https://doi.org/10.1371/journal.pbio.1000596
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[20]
2011 | Journal Article | IST-REx-ID: 3374   OA
Tkacik, G., & Walczak, A. (2011). Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter, 23(15). https://doi.org/10.1088/0953-8984/23/15/153102
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[19]
2010 | Journal Article | IST-REx-ID: 3738
Walczak, A., Tkacik, G., & Bialek, W. (2010). Optimizing information flow in small genetic networks. II. Feed-forward interactions. Physical Review E Statistical Nonlinear and Soft Matter Physics, 81(4). https://doi.org/10.1103/PhysRevE.81.041905
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[18]
2010 | Conference Paper | IST-REx-ID: 3430   OA
Tkacik, G. (2010). Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. Presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, Elsevier.
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[17]
2010 | Journal Article | IST-REx-ID: 3735
Tkacik, G., Prentice, J., Victor, J., & Balasubramanian, V. (2010). Local statistics in natural scenes predict the saliency of synthetic textures. PNAS, 107(42), 18149–18154. https://doi.org/10.1073/pnas.0914916107
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[16]
2010 | Journal Article | IST-REx-ID: 3736
Tkacik, G., Prentice, J., Balasubramanian, V., & Schneidman, E. (2010). Optimal population coding by noisy spiking neurons. PNAS, 107(32), 14419–14424. https://doi.org/10.1073/pnas.1004906107
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[15]
2010 | Preprint | IST-REx-ID: 3743   OA
Tkacik, G. (2010). From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv. ArXiv.
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[14]
2009 | Preprint | IST-REx-ID: 3732   OA
Tkacik, G., Schneidman, E., Berry, M., & Bialek, W. (2009). Spin glass models for a network of real neurons. ArXiv. ArXiv.
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[13]
2009 | Journal Article | IST-REx-ID: 3737
Tkacik, G., Walczak, A., & Bialek, W. (2009). Optimizing information flow in small genetic networks. Physical Review E Statistical Nonlinear and Soft Matter Physics, 80(3). https://doi.org/10.1103/PhysRevE.80.031920
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[12]
2009 | Journal Article | IST-REx-ID: 3733
Kryazhimskiy, S., Tkacik, G., & Plotkin, J. (2009). The dynamics of adaptation on correlated fitness landscapes. PNAS, 106(44), 18638–18643. https://doi.org/10.1073/pnas.0905497106
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[11]
2009 | Journal Article | IST-REx-ID: 3745
Tkacik, G., & Bialek, W. (2009). Diffusion, dimensionality, and noise in transcriptional regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics, 79(5). https://doi.org/10.1103/PhysRevE.79.051901
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[10]
2009 | Book Chapter | IST-REx-ID: 3747
Tkacik, G., & Bialek, W. (2009). Cell Biology: Networks, regulation, pathways. In R. Meyers (Ed.), Encyclopedia of Complexity and Systems Science (pp. 719–741). Springer. https://doi.org/10.1007/978-0-387-30440-3_48
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[9]
2008 | Journal Article | IST-REx-ID: 3744   OA
Tkacik, G., & Magnasco, M. (2008). Decoding spike timing: The differential reverse-correlation method. Biosystems, 93(1–2), 90–100. https://doi.org/10.1016/j.biosystems.2008.04.011
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[8]
2008 | Journal Article | IST-REx-ID: 3740   OA
Tkacik, G., Callan, C., & Bialek, W. (2008). Information flow and optimization in transcriptional regulation. PNAS, 105(34), 12265–12270. https://doi.org/10.1073/pnas.0806077105
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[7]
2008 | Journal Article | IST-REx-ID: 3734   OA
Tkacik, G., Gregor, T., & Bialek, W. (2008). The role of input noise in transcriptional regulation. PLoS One, 3(7). https://doi.org/10.1371/journal.pone.0002774
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[6]
2008 | Journal Article | IST-REx-ID: 3739
Tkacik, G., Callan, C., & Bialek, W. (2008). Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics, 78(1). https://doi.org/10.1103/PhysRevE.78.011910
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[5]
2007 | Preprint | IST-REx-ID: 3742   OA
Broderick, T., Dudik, M., Tkacik, G., Schapire, R., & Bialek, W. (2007). Faster solutions of the inverse pairwise Ising problem. ArXiv. ArXiv.
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[4]
2007 | Journal Article | IST-REx-ID: 3731
Kinney, J., Tkacik, G., & Callan, C. (2007). Precise physical models of protein-DNA interaction from high-throughput data. PNAS, 104(2), 501–506. https://doi.org/10.1073/pnas.0609908104
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[3]
2006 | Preprint | IST-REx-ID: 3431   OA
Tkacik, G., Schneidman, E., Berry, M., & Bialek, W. (2006). Ising models for networks of real neurons. ArXiv. ArXiv.
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[2]
2005 | Journal Article | IST-REx-ID: 3741   OA
Slonim, N., Atwal, G., Tkacik, G., & Bialek, W. (2005). Information-based clustering. PNAS, 102(51), 18297–18302. https://doi.org/10.1073/pnas.0507432102
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[1]
2005 | Preprint | IST-REx-ID: 3746   OA
Slonim, N., Atwal, G., Tkacik, G., & Bialek, W. (2005). Estimating mutual information and multi-information in large networks. ArXiv. ArXiv.
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75 Publications

Mark all

[75]
2019 | Preprint | IST-REx-ID: 7083   OA
Kavcic, B., Tkačik, G., & Bollenbach, T. (2019). Mechanistic origin of drug interactions between translation-inhibiting antibiotics. BioRxiv. Cold Spring Harbor Laboratory.
View | Download (ext.)
 
[74]
2019 | Journal Article | IST-REx-ID: 6784   OA
Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology, 15(7). https://doi.org/10.1371/journal.pcbi.1007168
View | Files available | DOI
 
[73]
2019 | Journal Article | IST-REx-ID: 5945
Petkova, M. D., Tkacik, G., Bialek, W., Wieschaus, E. F., & Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. Cell, 176(4), 844–855.e15. https://doi.org/10.1016/j.cell.2019.01.007
View | Files available | DOI
 
[72]
2019 | Journal Article | IST-REx-ID: 6900   OA
Cepeda Humerez, S. A., Ruess, J., & Tkačik, G. (2019). Estimating information in time-varying signals. PLoS Computational Biology, 15(9), e1007290. https://doi.org/10.1371/journal.pcbi.1007290
View | Files available | DOI | PubMed | Europe PMC
 
[71]
2018 | Journal Article | IST-REx-ID: 31   OA
Ferrari, U., Deny, S., Chalk, M. J., Tkacik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E, 98(4). https://doi.org/10.1103/PhysRevE.98.042410
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[70]
2018 | Journal Article | IST-REx-ID: 67
Igler, C., Lagator, M., Tkacik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution, 2(10), 1633–1643. https://doi.org/10.1038/s41559-018-0651-y
View | Files available | DOI
 
[69]
2018 | Journal Article | IST-REx-ID: 543   OA
Chalk, M. J., Marre, O., & Tkacik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS, 115(1), 186–191. https://doi.org/10.1073/pnas.1711114115
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[68]
2018 | Research Data | IST-REx-ID: 5587   OA
De Martino, D., & Tkacik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria. https://doi.org/10.15479/AT:ISTA:62
View | Files available | DOI
 
[67]
2018 | Journal Article | IST-REx-ID: 406   OA
Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkacik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One, 13(3). https://doi.org/10.1371/journal.pone.0193049
View | Files available | DOI
 
[66]
2018 | Journal Article | IST-REx-ID: 292
Botella Soler, V., Deny, S., Martius, G. S., Marre, O., & Tkacik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology, 14(5). https://doi.org/10.1371/journal.pcbi.1006057
View | Files available | DOI
 
[65]
2018 | Research Data | IST-REx-ID: 5584   OA
Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkacik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. IST Austria. https://doi.org/10.15479/AT:ISTA:98
View | Files available | DOI
 
[64]
2018 | Research Data | IST-REx-ID: 5585
Igler, C., Lagator, M., Tkacik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. IST Austria. https://doi.org/10.15479/AT:ISTA:108
View | Files available | DOI
 
[63]
2018 | Journal Article | IST-REx-ID: 281   OA
Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkacik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS, 115(23), 6088–6093. https://doi.org/10.1073/pnas.1716659115
View | Files available | DOI | Download (ext.) | PubMed | Europe PMC
 
[62]
2018 | Journal Article | IST-REx-ID: 161
De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkacik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-05417-9
View | Files available | DOI
 
[61]
2017 | Research Data | IST-REx-ID: 5562   OA
Marre, O., Tkacik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2017). Multi-electrode array recording from salamander retinal ganglion cells. IST Austria. https://doi.org/10.15479/AT:ISTA:61
View | Files available | DOI
 
[60]
2017 | Journal Article | IST-REx-ID: 725   OA
Harpaz, R., Tkacik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS, 114(38), 10149–10154. https://doi.org/10.1073/pnas.1703817114
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[59]
2017 | Journal Article | IST-REx-ID: 1104   OA
Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-02159-y
View | Files available | DOI
 
[58]
2017 | Journal Article | IST-REx-ID: 720   OA
Humplik, J., & Tkacik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology, 13(9). https://doi.org/10.1371/journal.pcbi.1005763
View | Files available | DOI
 
[57]
2017 | Journal Article | IST-REx-ID: 613   OA
Chait, R. P., Ruess, J., Bergmiller, T., Tkacik, G., & Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-01683-1
View | Files available | DOI
 
[56]
2017 | Journal Article | IST-REx-ID: 943   OA
Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkacik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science, 356(6345), 1379–1383. https://doi.org/10.1126/science.aam5887
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[55]
2017 | Journal Article | IST-REx-ID: 955   OA
Friedlander, T., Prizak, R., Barton, N. H., & Tkacik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-00238-8
View | Files available | DOI
 
[54]
2017 | Journal Article | IST-REx-ID: 730
Savin, C., & Tkacik, G. (2017). Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology, 46, 120–126. https://doi.org/10.1016/j.conb.2017.08.001
View | DOI
 
[53]
2017 | Research Data | IST-REx-ID: 5560
Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. IST Austria. https://doi.org/doi:10.15479/AT:ISTA:53
View | Files available | DOI
 
[52]
2017 | Journal Article | IST-REx-ID: 665
Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science, 356(6335), 311–315. https://doi.org/10.1126/science.aaf4762
View | Files available | DOI
 
[51]
2016 | Journal Article | IST-REx-ID: 1248   OA
Tkacik, G., & Bialek, W. (2016). Information processing in living systems. Annual Review of Condensed Matter Physics, 7, 89–117. https://doi.org/10.1146/annurev-conmatphys-031214-014803
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[50]
2016 | Journal Article | IST-REx-ID: 1197   OA
Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkacik, G., & Berry, M. (2016). Error-robust modes of the retinal population code. PLoS Computational Biology, 12(11). https://doi.org/10.1371/journal.pcbi.1005148
View | Files available | DOI
 
[49]
2016 | Conference Paper | IST-REx-ID: 1105
Savin, C., & Tkacik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems.
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[48]
2016 | Journal Article | IST-REx-ID: 1270   OA
Hillenbrand, P., Gerland, U., & Tkacik, G. (2016). Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One, 11(9). https://doi.org/10.1371/journal.pone.0163628
View | Files available | DOI
 
[47]
2016 | Journal Article | IST-REx-ID: 1358
Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkacik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications, 7. https://doi.org/10.1038/ncomms12307
View | Files available | DOI
 
[46]
2016 | Conference Paper | IST-REx-ID: 1082   OA
Chalk, M. J., Marre, O., & Tkacik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems.
View | Files available | Download (ext.)
 
[45]
2016 | Journal Article | IST-REx-ID: 1171
Tkacik, G. (2016). 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, 17, 166–167. https://doi.org/10.1016/j.plrev.2016.06.005
View | DOI
 
[44]
2016 | Journal Article | IST-REx-ID: 1420   OA
Bod’ová, K., Tkacik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics, 202(4), 1523–1548. https://doi.org/10.1534/genetics.115.184127
View | DOI | Download (ext.) | arXiv
 
[43]
2016 | Journal Article | IST-REx-ID: 1242   OA
Sokolowski, T. R., Walczak, A., Bialek, W., & Tkacik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics, 93(2). https://doi.org/10.1103/PhysRevE.93.022404
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[42]
2015 | Journal Article | IST-REx-ID: 1666   OA
Tugrul, M., Paixao, T., Barton, N. H., & Tkacik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics, 11(11). https://doi.org/10.1371/journal.pgen.1005639
View | Files available | DOI
 
[41]
2015 | Journal Article | IST-REx-ID: 1940   OA
Sokolowski, T. R., & Tkacik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics, 91(6). https://doi.org/10.1103/PhysRevE.91.062710
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[40]
2015 | Journal Article | IST-REx-ID: 1697   OA
Marre, O., Botella Soler, V., Simmons, K., Mora, T., Tkacik, G., & Berry, M. (2015). High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology, 11(7). https://doi.org/10.1371/journal.pcbi.1004304
View | Files available | DOI
 
[39]
2015 | Journal Article | IST-REx-ID: 1701   OA
Tkacik, G., Mora, T., Marre, O., Amodei, D., Palmer, S., Berry Ii, M., & Bialek, W. (2015). Thermodynamics and signatures of criticality in a network of neurons. PNAS, 112(37), 11508–11513. https://doi.org/10.1073/pnas.1514188112
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[38]
2015 | Journal Article | IST-REx-ID: 1885   OA
Tkacik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics, 199(1), 39–59. https://doi.org/10.1534/genetics.114.171850
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[37]
2015 | Journal Article | IST-REx-ID: 1576
Cepeda Humerez, S. A., Rieckh, G., & Tkacik, G. (2015). Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters, 115(24). https://doi.org/10.1103/PhysRevLett.115.248101
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[36]
2014 | Journal Article | IST-REx-ID: 3263   OA
Tkacik, G., Ghosh, A., Schneidman, E., & Segev, R. (2014). Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One, 9(1). https://doi.org/10.1371/journal.pone.0085841
View | Files available | DOI
 
[35]
2014 | Journal Article | IST-REx-ID: 2231   OA
Rieckh, G., & Tkacik, G. (2014). Noise and information transmission in promoters with multiple internal states. Biophysical Journal, 106(5), 1194–1204. https://doi.org/10.1016/j.bpj.2014.01.014
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[34]
2014 | Journal Article | IST-REx-ID: 2257
Tkacik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2014). Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology, 10(1). https://doi.org/10.1371/journal.pcbi.1003408
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[33]
2014 | Journal Article | IST-REx-ID: 1886   OA
Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., & Tkacik, G. (2014). Variance predicts salience in central sensory processing. ELife, (November). https://doi.org/10.7554/eLife.03722
View | Files available | DOI
 
[32]
2013 | Journal Article | IST-REx-ID: 2277   OA
Simmons, K., Prentice, J., Tkacik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2013). Transformation of stimulus correlations by the retina. PLoS Computational Biology, 9(12). https://doi.org/10.1371/journal.pcbi.1003344
View | Files available | DOI
 
[31]
2013 | Journal Article | IST-REx-ID: 2913   OA
Tkacik, G., Granot Atedgi, E., Segev, R., & Schneidman, E. (2013). Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters, 110(5). https://doi.org/10.1103/PhysRevLett.110.058104
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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. (2013). The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment, 2013(3). https://doi.org/10.1088/1742-5468/2013/03/P03011
View | DOI | Download (ext.) | arXiv
 
[29]
2013 | Journal Article | IST-REx-ID: 2863   OA
Granot Atedgi, E., Tkacik, G., Segev, R., & Schneidman, E. (2013). Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology, 9(3). https://doi.org/10.1371/journal.pcbi.1002922
View | Files available | DOI
 
[28]
2013 | Journal Article | IST-REx-ID: 2914   OA
Stephens, G., Mora, T., Tkacik, G., & Bialek, W. (2013). Statistical thermodynamics of natural images. Physical Review Letters, 110(1). https://doi.org/10.1103/PhysRevLett.110.018701
View | Files available | DOI | Download (ext.) | arXiv
 
[27]
2013 | Journal Article | IST-REx-ID: 2851
Berry, M., Tkacik, G., Dubuis, J., Marre, O., & Da Silveira, R. (2013). A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment, 2013(3). https://doi.org/10.1088/1742-5468/2013/03/P03015
View | DOI
 
[26]
2013 | Journal Article | IST-REx-ID: 2818   OA
Rajan, K., Marre, O., & Tkacik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation, 25(7), 1661–1692. https://doi.org/10.1162/NECO_a_00463
View | DOI | Download (ext.) | arXiv
 
[25]
2013 | Journal Article | IST-REx-ID: 3261   OA
Dubuis, J., Tkacik, G., Wieschaus, E., Gregor, T., & Bialek, W. (2013). Positional information, in bits. PNAS, 110(41), 16301–16308. https://doi.org/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. (2012). Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E Statistical Nonlinear and Soft Matter Physics , 85(4). https://doi.org/10.1103/PhysRevE.85.041903
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[23]
2011 | Journal Article | IST-REx-ID: 3276   OA
Prentice, J., Homann, J., Simmons, K., Tkacik, G., Balasubramanian, V., & Nelson, P. (2011). Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One, 6(7). https://doi.org/10.1371/journal.pone.0019884
View | Files available | DOI
 
[22]
2011 | Journal Article | IST-REx-ID: 3384   OA
Tkacik, G., Garrigan, P., Ratliff, C., Milcinski, G., Klein, J., Seyfarth, L., … Balasubramanian, V. (2011). Natural images from the birthplace of the human eye. PLoS One, 6(6). https://doi.org/10.1371/journal.pone.0020409
View | Files available | DOI
 
[21]
2011 | Journal Article | IST-REx-ID: 3401
Little, S., Tkacik, G., Kneeland, T., Wieschaus, E., & Gregor, T. (2011). The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source. PLoS Biology, 9(3). https://doi.org/10.1371/journal.pbio.1000596
View | DOI
 
[20]
2011 | Journal Article | IST-REx-ID: 3374   OA
Tkacik, G., & Walczak, A. (2011). Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter, 23(15). https://doi.org/10.1088/0953-8984/23/15/153102
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[19]
2010 | Journal Article | IST-REx-ID: 3738
Walczak, A., Tkacik, G., & Bialek, W. (2010). Optimizing information flow in small genetic networks. II. Feed-forward interactions. Physical Review E Statistical Nonlinear and Soft Matter Physics, 81(4). https://doi.org/10.1103/PhysRevE.81.041905
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[18]
2010 | Conference Paper | IST-REx-ID: 3430   OA
Tkacik, G. (2010). Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. Presented at the Summer School on Quantitative Evolutionary and Comparative Genomics, Elsevier.
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[17]
2010 | Journal Article | IST-REx-ID: 3735
Tkacik, G., Prentice, J., Victor, J., & Balasubramanian, V. (2010). Local statistics in natural scenes predict the saliency of synthetic textures. PNAS, 107(42), 18149–18154. https://doi.org/10.1073/pnas.0914916107
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[16]
2010 | Journal Article | IST-REx-ID: 3736
Tkacik, G., Prentice, J., Balasubramanian, V., & Schneidman, E. (2010). Optimal population coding by noisy spiking neurons. PNAS, 107(32), 14419–14424. https://doi.org/10.1073/pnas.1004906107
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[15]
2010 | Preprint | IST-REx-ID: 3743   OA
Tkacik, G. (2010). From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv. ArXiv.
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[14]
2009 | Preprint | IST-REx-ID: 3732   OA
Tkacik, G., Schneidman, E., Berry, M., & Bialek, W. (2009). Spin glass models for a network of real neurons. ArXiv. ArXiv.
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[13]
2009 | Journal Article | IST-REx-ID: 3737
Tkacik, G., Walczak, A., & Bialek, W. (2009). Optimizing information flow in small genetic networks. Physical Review E Statistical Nonlinear and Soft Matter Physics, 80(3). https://doi.org/10.1103/PhysRevE.80.031920
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[12]
2009 | Journal Article | IST-REx-ID: 3733
Kryazhimskiy, S., Tkacik, G., & Plotkin, J. (2009). The dynamics of adaptation on correlated fitness landscapes. PNAS, 106(44), 18638–18643. https://doi.org/10.1073/pnas.0905497106
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[11]
2009 | Journal Article | IST-REx-ID: 3745
Tkacik, G., & Bialek, W. (2009). Diffusion, dimensionality, and noise in transcriptional regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics, 79(5). https://doi.org/10.1103/PhysRevE.79.051901
View | DOI
 
[10]
2009 | Book Chapter | IST-REx-ID: 3747
Tkacik, G., & Bialek, W. (2009). Cell Biology: Networks, regulation, pathways. In R. Meyers (Ed.), Encyclopedia of Complexity and Systems Science (pp. 719–741). Springer. https://doi.org/10.1007/978-0-387-30440-3_48
View | DOI
 
[9]
2008 | Journal Article | IST-REx-ID: 3744   OA
Tkacik, G., & Magnasco, M. (2008). Decoding spike timing: The differential reverse-correlation method. Biosystems, 93(1–2), 90–100. https://doi.org/10.1016/j.biosystems.2008.04.011
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[8]
2008 | Journal Article | IST-REx-ID: 3740   OA
Tkacik, G., Callan, C., & Bialek, W. (2008). Information flow and optimization in transcriptional regulation. PNAS, 105(34), 12265–12270. https://doi.org/10.1073/pnas.0806077105
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[7]
2008 | Journal Article | IST-REx-ID: 3734   OA
Tkacik, G., Gregor, T., & Bialek, W. (2008). The role of input noise in transcriptional regulation. PLoS One, 3(7). https://doi.org/10.1371/journal.pone.0002774
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[6]
2008 | Journal Article | IST-REx-ID: 3739
Tkacik, G., Callan, C., & Bialek, W. (2008). Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics, 78(1). https://doi.org/10.1103/PhysRevE.78.011910
View | DOI
 
[5]
2007 | Preprint | IST-REx-ID: 3742   OA
Broderick, T., Dudik, M., Tkacik, G., Schapire, R., & Bialek, W. (2007). Faster solutions of the inverse pairwise Ising problem. ArXiv. ArXiv.
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[4]
2007 | Journal Article | IST-REx-ID: 3731
Kinney, J., Tkacik, G., & Callan, C. (2007). Precise physical models of protein-DNA interaction from high-throughput data. PNAS, 104(2), 501–506. https://doi.org/10.1073/pnas.0609908104
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[3]
2006 | Preprint | IST-REx-ID: 3431   OA
Tkacik, G., Schneidman, E., Berry, M., & Bialek, W. (2006). Ising models for networks of real neurons. ArXiv. ArXiv.
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[2]
2005 | Journal Article | IST-REx-ID: 3741   OA
Slonim, N., Atwal, G., Tkacik, G., & Bialek, W. (2005). Information-based clustering. PNAS, 102(51), 18297–18302. https://doi.org/10.1073/pnas.0507432102
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[1]
2005 | Preprint | IST-REx-ID: 3746   OA
Slonim, N., Atwal, G., Tkacik, G., & Bialek, W. (2005). Estimating mutual information and multi-information in large networks. ArXiv. ArXiv.
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