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172 Publications

2016 | Journal Article | IST-REx-ID: 1332 | OA
R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
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2016 | Journal Article | IST-REx-ID: 1342 | OA
M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016.
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2016 | Journal Article | IST-REx-ID: 1358 | OA
T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
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2016 | Journal Article | IST-REx-ID: 1394 | OA
D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016.
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2016 | Journal Article | IST-REx-ID: 1485 | OA
D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” Physical Biology, vol. 13, no. 1. IOP Publishing Ltd., 2016.
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2016 | Conference Paper | IST-REx-ID: 948
T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.
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2016 | Research Data Reference | IST-REx-ID: 9869
P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.
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2016 | Research Data Reference | IST-REx-ID: 9870
P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.
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2016 | Research Data Reference | IST-REx-ID: 9871
P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.
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2016 | Journal Article | IST-REx-ID: 1420 | OA
K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.
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2016 | Journal Article | IST-REx-ID: 1197 | OA
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11. Public Library of Science, 2016.
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2015 | Journal Article | IST-REx-ID: 10794 | OA
F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” Frontiers in Environmental Science, vol. 3. Frontiers, 2015.
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2015 | Journal Article | IST-REx-ID: 1538 | OA
J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015.
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2015 | Journal Article | IST-REx-ID: 1539 | OA
J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” Journal of Chemical Physics, vol. 143, no. 24. American Institute of Physics, 2015.
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2015 | Journal Article | IST-REx-ID: 1564 | OA
M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.
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2015 | Journal Article | IST-REx-ID: 1570 | OA
R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015.
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2015 | Journal Article | IST-REx-ID: 1576 | OA
S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24. American Physical Society, 2015.
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2015 | Journal Article | IST-REx-ID: 1655 | OA
G. S. Martius and E. Olbrich, “Quantifying emergent behavior of autonomous robots,” Entropy, vol. 17, no. 10. Multidisciplinary Digital Publishing Institute, pp. 7266–7297, 2015.
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2015 | Conference Paper | IST-REx-ID: 1658
S. Bogomolov, T. A. Henzinger, A. Podelski, J. Ruess, and C. Schilling, “Adaptive moment closure for parameter inference of biochemical reaction networks,” vol. 9308. Springer, pp. 77–89, 2015.
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2015 | Journal Article | IST-REx-ID: 1666 | OA
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.
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2015 | Journal Article | IST-REx-ID: 1697 | OA
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7. Public Library of Science, 2015.
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2015 | Journal Article | IST-REx-ID: 1701 | OA
G. Tkačik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015.
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2015 | Journal Article | IST-REx-ID: 1827 | OA
T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015.
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2015 | Journal Article | IST-REx-ID: 1861
J. Ruess and J. Lygeros, “Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015.
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2015 | Journal Article | IST-REx-ID: 1885 | OA
G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.
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2015 | Journal Article | IST-REx-ID: 1940 | OA
T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.
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2015 | Research Data Reference | IST-REx-ID: 9712
M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.
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2015 | Research Data Reference | IST-REx-ID: 9718
T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.
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2015 | Research Data Reference | IST-REx-ID: 9773
T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.
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2014 | Journal Article | IST-REx-ID: 3263 | OA
G. Tkačik, A. Ghosh, E. Schneidman, and R. Segev, “Adaptation to changes in higher-order stimulus statistics in the salamander retina,” PLoS One, vol. 9, no. 1. Public Library of Science, 2014.
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2014 | Journal Article | IST-REx-ID: 537 | OA
R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal effects,” Ecology and Evolution, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145, 2014.
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2014 | Conference Paper | IST-REx-ID: 1708
C. Savin and S. Denève, “Spatio-temporal representations of uncertainty in spiking neural networks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2014, vol. 3, no. January, pp. 2024–2032.
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2014 | Journal Article | IST-REx-ID: 1886 | OA
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” eLife, no. November. eLife Sciences Publications, 2014.
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2014 | Journal Article | IST-REx-ID: 1909 | OA
T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.
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2014 | Journal Article | IST-REx-ID: 1928
J. Humplik, A. Hill, and M. Nowak, “Evolutionary dynamics of infectious diseases in finite populations,” Journal of Theoretical Biology, vol. 360. Elsevier, pp. 149–162, 2014.
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2014 | Journal Article | IST-REx-ID: 1931 | OA
C. Savin and J. Triesch, “Emergence of task-dependent representations in working memory circuits,” Frontiers in Computational Neuroscience, vol. 8, no. MAY. Frontiers Research Foundation, 2014.
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2014 | Journal Article | IST-REx-ID: 2231 | OA
G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” Biophysical Journal, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014.
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2014 | Journal Article | IST-REx-ID: 2257 | OA
G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching for collective behavior in a large network of sensory neurons,” PLoS Computational Biology, vol. 10, no. 1. Public Library of Science, 2014.
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2014 | Journal Article | IST-REx-ID: 1896 | OA
R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014.
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2014 | Research Data Reference | IST-REx-ID: 9752 | OA
K. Simmons et al., “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.
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2014 | Journal Article | IST-REx-ID: 2028 | OA
K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type II neurons,” Journal of Theoretical Biology, vol. 365. Academic Press, pp. 40–54, 2014.
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2014 | Journal Article | IST-REx-ID: 2183 | OA
V. Botella Soler and P. Glendinning, “Hierarchy and polysynchrony in an adaptive network ,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 6. American Institute of Physics, 2014.
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2013 | Journal Article | IST-REx-ID: 2818 | OA
K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” Neural Computation, vol. 25, no. 7. MIT Press , pp. 1661–1692, 2013.
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2013 | Journal Article | IST-REx-ID: 2850 | OA
G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, and W. Bialek, “The simplest maximum entropy model for collective behavior in a neural network,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3. IOP Publishing Ltd., 2013.
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2013 | Journal Article | IST-REx-ID: 2851
M. Berry, G. Tkačik, J. Dubuis, O. Marre, and R. Da Silveira, “A simple method for estimating the entropy of neural activity,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3. IOP Publishing Ltd., 2013.
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2013 | Journal Article | IST-REx-ID: 2861
V. Botella Soler, J. Oteo, J. Ros, and P. Glendinning, “Lyapunov exponent and topological entropy plateaus in piecewise linear maps,” Journal of Physics A: Mathematical and Theoretical, vol. 46, no. 12. IOP Publishing Ltd., 2013.
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2013 | Journal Article | IST-REx-ID: 2863 | OA
E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent maximum entropy models of neural population codes,” PLoS Computational Biology, vol. 9, no. 3. Public Library of Science, 2013.
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2013 | Journal Article | IST-REx-ID: 2913 | OA
G. Tkačik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric: a stimulus distance measure derived from population neural responses,” Physical Review Letters, vol. 110, no. 5. American Physical Society, 2013.
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2013 | Journal Article | IST-REx-ID: 2914 | OA
G. Stephens, T. Mora, G. Tkačik, and W. Bialek, “Statistical thermodynamics of natural images,” Physical Review Letters, vol. 110, no. 1. American Physical Society, 2013.
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2013 | Journal Article | IST-REx-ID: 3261 | OA
J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” PNAS, vol. 110, no. 41. National Academy of Sciences, pp. 16301–16308, 2013.
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