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127 Publications

2016 | Journal Article | IST-REx-ID: 1420 | OA
Bod’ová K, Tkacik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.
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2016 | Journal Article | IST-REx-ID: 1485 | OA
De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003.
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2016 | Conference Paper | IST-REx-ID: 1082 | OA
Chalk MJ, Marre O, Tkacik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29. 1965–1973.
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2016 | Conference Paper | IST-REx-ID: 1105
Savin C, Tkacik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29. 3610–3618.
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2016 | Journal Article | IST-REx-ID: 1148
Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25.
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2016 | Journal Article | IST-REx-ID: 1170
Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.
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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.
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2016 | Thesis | IST-REx-ID: 1128 | OA
Rieckh G. 2016. Studying the complexities of transcriptional regulation, IST Austria, 114p.
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2015 | Journal Article | IST-REx-ID: 1564 | OA
Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11).
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2015 | Journal Article | IST-REx-ID: 1570 | OA
Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.
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2015 | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez SA, Rieckh G, Tkacik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101.
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2015 | Journal Article | IST-REx-ID: 1655 | OA
Martius GS, Olbrich E. 2015. Quantifying emergent behavior of autonomous robots. Entropy. 17(10), 7266–7297.
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2015 | Conference Paper | IST-REx-ID: 1658
Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. 2015. Adaptive moment closure for parameter inference of biochemical reaction networks. 9308, 77–89.
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2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).
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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. 2015. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 11(7).
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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.
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2015 | Journal Article | IST-REx-ID: 1827 | OA
Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).
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2015 | Journal Article | IST-REx-ID: 1861
Ruess J, Lygeros J. 2015. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 25(2), 8.
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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.
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2015 | Journal Article | IST-REx-ID: 1940 | OA
Sokolowski TR, Tkacik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6), 062710.
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2015 | Journal Article | IST-REx-ID: 1538 | OA
Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153.
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2015 | Journal Article | IST-REx-ID: 1539 | OA
Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24).
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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.
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2014 | Journal Article | IST-REx-ID: 2257 | OA
Tkačik 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).
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2014 | Journal Article | IST-REx-ID: 537 | OA
Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145.
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2014 | Conference Paper | IST-REx-ID: 1708
Savin C, Denève S. 2014. Spatio-temporal representations of uncertainty in spiking neural networks. NIPS: Neural Information Processing Systems vol. 3. 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. 2014. Variance predicts salience in central sensory processing. eLife. (November).
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2014 | Journal Article | IST-REx-ID: 1896 | OA
Kollár R, Bod’ová K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.
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2014 | Journal Article | IST-REx-ID: 1909 | OA
Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701.
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2014 | Journal Article | IST-REx-ID: 1928
Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 360, 149–162.
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2014 | Journal Article | IST-REx-ID: 1931 | OA
Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57.
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2014 | Journal Article | IST-REx-ID: 3263 | OA
Tkačik G, Ghosh A, Schneidman E, Segev R. 2014. Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One. 9(1).
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2013 | Journal Article | IST-REx-ID: 2277 | OA
Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2013. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 9(12).
View | Files available | DOI
 
2013 | Book Chapter | IST-REx-ID: 2413
Valderrama M, Botella Soler V, Le Van Quyen M. 2013. Neuronal oscillations scale up and scale down the brain dynamics . Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. , Reviews of Nonlinear Dynamics and Complexity,
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2013 | Journal Article | IST-REx-ID: 499
Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95.
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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.
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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), P03011.
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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), P03015.
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2013 | Journal Article | IST-REx-ID: 2861
Botella Soler V, Oteo J, Ros J, Glendinning P. 2013. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 46(12), 125101.
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2013 | Journal Article | IST-REx-ID: 2863 | OA
Granot Atedgi E, Tkačik G, Segev R, Schneidman E. 2013. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 9(3).
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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), 058104.
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2013 | Journal Article | IST-REx-ID: 2914 | OA
Stephens G, Mora T, Tkačik G, Bialek W. 2013. Statistical thermodynamics of natural images. Physical Review Letters. 110(1).
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. 2013. Positional information, in bits. PNAS. 110(41), 16301–16308.
View | Files available | DOI | PubMed | Europe PMC
 
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), 041903.
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2012 | Journal Article | IST-REx-ID: 3274
Rieckh G, Kreuzer W, Waubke H, Balazs P. 2012. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. 36(6), 960–967.
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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), 153102.
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2011 | Journal Article | IST-REx-ID: 3384 | OA
Tkačik G, Garrigan P, Ratliff C, Milcinski G, Klein J, Seyfarth L, Sterling P, Brainard D, Balasubramanian V. 2011. Natural images from the birthplace of the human eye. PLoS One. 6(6).
View | Files available | DOI
 

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