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126 Publications

2015 | Journal Article | IST-REx-ID: 1655 | OA
Martius GS, Olbrich E. Quantifying emergent behavior of autonomous robots. Entropy. 2015;17(10):7266-7297. doi:10.3390/e17107266
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2015 | Conference Paper | IST-REx-ID: 1658
Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. Adaptive moment closure for parameter inference of biochemical reaction networks. 2015;9308:77-89. doi:10.1007/978-3-319-23401-4_8
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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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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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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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2015 | Journal Article | IST-REx-ID: 1827 | OA
Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055
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2015 | Journal Article | IST-REx-ID: 1861
Ruess J, Lygeros J. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 2015;25(2). doi:10.1145/2688906
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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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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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2015 | Journal Article | IST-REx-ID: 1538 | OA
Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112
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2015 | Journal Article | IST-REx-ID: 1539 | OA
Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 2015;143(24). doi:10.1063/1.4937937
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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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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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2014 | Journal Article | IST-REx-ID: 537 | OA
Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 2014;4(15):3139-3145. doi:10.1002/ece3.1150
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2014 | Conference Paper | IST-REx-ID: 1708
Savin C, Denève S. Spatio-temporal representations of uncertainty in spiking neural networks. In: Vol 3. Neural Information Processing Systems; 2014:2024-2032.
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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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2014 | Journal Article | IST-REx-ID: 1896 | OA
Kollár R, Bod’ová K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701
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2014 | Journal Article | IST-REx-ID: 1909 | OA
Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207
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2014 | Journal Article | IST-REx-ID: 1928
Humplik J, Hill A, Nowak M. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 2014;360:149-162. doi:10.1016/j.jtbi.2014.06.039
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2014 | Journal Article | IST-REx-ID: 1931 | OA
Savin C, Triesch J. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 2014;8(MAY). doi:10.3389/fncom.2014.00057
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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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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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2013 | Book Chapter | IST-REx-ID: 2413
Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH; 2013. doi:10.1002/9783527671632.ch08
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2013 | Journal Article | IST-REx-ID: 499
Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858
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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
 
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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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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2013 | Journal Article | IST-REx-ID: 2861
Botella Soler V, Oteo J, Ros J, Glendinning P. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 2013;46(12). doi:10.1088/1751-8113/46/12/125101
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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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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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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
 
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
 
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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2012 | Journal Article | IST-REx-ID: 3274
Rieckh G, Kreuzer W, Waubke H, Balazs P. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. 2012;36(6):960-967. doi:10.1016/j.enganabound.2011.12.014
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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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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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