Hillenbrand P, Gerland U, Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/1270
DOI: 10.1371/journal.pone.0163628

Hillenbrand P, Gerland U, Tkadik G. Computation of positional information in an Ising model. 2016. doi:10.1371/journal.pone.0163628.s002
LibreCat: https://research-explorer.ista.ac.at/record/9870
DOI: 10.1371/journal.pone.0163628.s002

Hillenbrand P, Gerland U, Tkadik G. Error bound on an estimator of position. 2016. doi:10.1371/journal.pone.0163628.s001
LibreCat: https://research-explorer.ista.ac.at/record/9869
DOI: 10.1371/journal.pone.0163628.s001

Hillenbrand P, Gerland U, Tkadik G. Computation of positional information in a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003
LibreCat: https://research-explorer.ista.ac.at/record/9871
DOI: 10.1371/journal.pone.0163628.s003

Rieckh G. Studying the complexities of transcriptional regulation. 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1128

Friedlander T, Prizak R, Guet CC, Barton NH, Tkadik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307
LibreCat: https://research-explorer.ista.ac.at/record/1358
DOI: 10.1038/ncomms12307

Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042
LibreCat: https://research-explorer.ista.ac.at/record/10794
DOI: 10.3389/fenvs.2015.00042

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
LibreCat: https://research-explorer.ista.ac.at/record/1539
DOI: 10.1063/1.4937937

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
LibreCat: https://research-explorer.ista.ac.at/record/1538
DOI: 10.1073/pnas.1423947112
PMID: 26085136

Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 2015;9(11). doi:10.3389/fncom.2015.00145
LibreCat: https://research-explorer.ista.ac.at/record/1564
DOI: 10.3389/fncom.2015.00145

Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 2015;112(45):24-32. doi:10.1073/pnas.1508400112
LibreCat: https://research-explorer.ista.ac.at/record/1570
DOI: 10.1073/pnas.1508400112
PMID: 26504200

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
LibreCat: https://research-explorer.ista.ac.at/record/1658
DOI: 10.1007/978-3-319-23401-4_8

Marre O, Botella Soler V, Simmons K, Mora T, Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/1697
DOI: 10.1371/journal.pcbi.1004304

Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/1701
DOI: 10.1073/pnas.1514188112
PMID: 26330611

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
LibreCat: https://research-explorer.ista.ac.at/record/1861
DOI: 10.1145/2688906

Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/1885
DOI: 10.1534/genetics.114.171850

Sokolowski TR, Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/1940
DOI: 10.1103/PhysRevE.91.062710

Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:10.1371/journal.pcbi.1004055.s001
LibreCat: https://research-explorer.ista.ac.at/record/9718
DOI: 10.1371/journal.pcbi.1004055.s001

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
LibreCat: https://research-explorer.ista.ac.at/record/1827
DOI: 10.1371/journal.pcbi.1004055

Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002
LibreCat: https://research-explorer.ista.ac.at/record/9773
DOI: 10.1371/journal.pcbi.1004055.s002

Tugrul M, Paixao T, Barton NH, Tkadik G. Other fitness models for comparison &; for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
LibreCat: https://research-explorer.ista.ac.at/record/9712
DOI: 10.1371/journal.pgen.1005639.s001

Tugrul M, Paixao T, Barton NH, Tkadik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
LibreCat: https://research-explorer.ista.ac.at/record/1666
DOI: 10.1371/journal.pgen.1005639

Cepeda Humerez SA, Rieckh G, Tkadik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24). doi:10.1103/PhysRevLett.115.248101
LibreCat: https://research-explorer.ista.ac.at/record/1576
DOI: 10.1103/PhysRevLett.115.248101

Martius GS, Olbrich E. Quantifying emergent behavior of autonomous robots. Entropy. 2015;17(10):7266-7297. doi:10.3390/e17107266
LibreCat: https://research-explorer.ista.ac.at/record/1655
DOI: 10.3390/e17107266

Savin C, Denève S. Spatio-temporal representations of uncertainty in spiking neural networks. In: Vol 3. Neural Information Processing Systems; 2014:2024-2032.
LibreCat: https://research-explorer.ista.ac.at/record/1708

Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkadik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722
LibreCat: https://research-explorer.ista.ac.at/record/1886
DOI: 10.7554/eLife.03722

Kollár R, Bodova K, Nosek J, Tomáska d. 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
LibreCat: https://research-explorer.ista.ac.at/record/1896
DOI: 10.1103/PhysRevE.89.032701

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
LibreCat: https://research-explorer.ista.ac.at/record/1909
DOI: 10.1111/1365-2435.12207

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
LibreCat: https://research-explorer.ista.ac.at/record/1928
DOI: 10.1016/j.jtbi.2014.06.039

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
LibreCat: https://research-explorer.ista.ac.at/record/1931
DOI: 10.3389/fncom.2014.00057

Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. 10.1016/j.jtbi.2014.09.041__Journal of Theoretical Biology. 2014;365:40-54. doi:10.1016/j.jtbi.2014.09.041
LibreCat: https://research-explorer.ista.ac.at/record/2028
DOI: 10.1016/j.jtbi.2014.09.041

Botella Soler V, Glendinning P. Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(6). doi:10.1103/PhysRevE.89.062809
LibreCat: https://research-explorer.ista.ac.at/record/2183
DOI: 10.1103/PhysRevE.89.062809

Rieckh G, Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/2231
DOI: 10.1016/j.bpj.2014.01.014
PMID: 24606943

Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/3263
DOI: 10.1371/journal.pone.0085841

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
LibreCat: https://research-explorer.ista.ac.at/record/537
DOI: 10.1002/ece3.1150

Simmons K, Prentice J, Tkadik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:10.5061/dryad.246qg
LibreCat: https://research-explorer.ista.ac.at/record/9752
DOI: 10.5061/dryad.246qg

Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/2257
DOI: 10.1371/journal.pcbi.1003408

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
LibreCat: https://research-explorer.ista.ac.at/record/2413
DOI: 10.1002/9783527671632.ch08

Rajan K, Marre O, Tkadik G. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692. doi:10.1162/NECO_a_00463
LibreCat: https://research-explorer.ista.ac.at/record/2818
DOI: 10.1162/NECO_a_00463
arXiv: 1209.0121

Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/2850
DOI: 10.1088/1742-5468/2013/03/P03011
arXiv: 1207.6319

Berry M, Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/2851
DOI: 10.1088/1742-5468/2013/03/P03015

Granot Atedgi E, Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/2863
DOI: 10.1371/journal.pcbi.1002922

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
LibreCat: https://research-explorer.ista.ac.at/record/2861
DOI: 10.1088/1751-8113/46/12/125101

Tkadik 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
LibreCat: https://research-explorer.ista.ac.at/record/2913
DOI: 10.1103/PhysRevLett.110.058104

Dubuis J, Tkadik G, Wieschaus E, Gregor T, Bialek W. Positional information, in bits. PNAS. 2013;110(41):16301-16308. doi:10.1073/pnas.1315642110
LibreCat: https://research-explorer.ista.ac.at/record/3261
DOI: 10.1073/pnas.1315642110
PMID: 24089448

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
LibreCat: https://research-explorer.ista.ac.at/record/499
DOI: 10.1126/science.1229858

Simmons K, Prentice J, Tkadik G, et al. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003344
LibreCat: https://research-explorer.ista.ac.at/record/2277
DOI: 10.1371/journal.pcbi.1003344

Stephens G, Mora T, Tkadik G, Bialek W. Statistical thermodynamics of natural images. Physical Review Letters. 2013;110(1). doi:10.1103/PhysRevLett.110.018701
LibreCat: https://research-explorer.ista.ac.at/record/2914
DOI: 10.1103/PhysRevLett.110.018701
arXiv: 0806.2694

Tkadik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. III. A self-interacting gene. 10.1103/PhysRevE.85.041903__Physical Review E statistical nonlinear and soft matter physics . 2012;85(4). doi:10.1103/PhysRevE.85.041903
LibreCat: https://research-explorer.ista.ac.at/record/3262
DOI: 10.1103/PhysRevE.85.041903

Rieckh G, Kreuzer W, Waubke H, Balazs P. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. 10.1016/j.enganabound.2011.12.014__Engineering Analysis with Boundary Elements. 2012;36(6):960-967. doi:10.1016/j.enganabound.2011.12.014
LibreCat: https://research-explorer.ista.ac.at/record/3274
DOI: 10.1016/j.enganabound.2011.12.014