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183 Publications
2016 |Published| Journal Article | IST-REx-ID: 1420 |
A general approximation for the dynamics of quantitative traits
K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.
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K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.
2016 |Published| Journal Article | IST-REx-ID: 1485 |
Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis
D. De Martino, Physical Biology 13 (2016).
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D. De Martino, Physical Biology 13 (2016).
2016 |Published| Journal Article | IST-REx-ID: 1148
Adaptive moment closure for parameter inference of biochemical reaction networks
C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.
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C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.
2016 |Published| Conference Paper | IST-REx-ID: 8094 |
Self-organized control of an tendon driven arm by differential extrinsic plasticity
G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.
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G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.
2016 |Published| Journal Article | IST-REx-ID: 1197 |
Error-robust modes of the retinal population code
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).
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J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).
2016 |Published| Conference Paper | IST-REx-ID: 948
Neurons equipped with intrinsic plasticity learn stimulus intensity statistics
T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.
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T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.
2016 |Published| Journal Article | IST-REx-ID: 1270 |
Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information
P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).
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P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).
2016 | Research Data Reference | IST-REx-ID: 9870
Computation of positional information in an Ising model
P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
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P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
2016 | Research Data Reference | IST-REx-ID: 9869
Error bound on an estimator of position
P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
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P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
2016 | Research Data Reference | IST-REx-ID: 9871
Computation of positional information in a discrete morphogen field
P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
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P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
2016 |Published| Thesis | IST-REx-ID: 1128 |
Studying the complexities of transcriptional regulation
G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.
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G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.
2016 |Published| Journal Article | IST-REx-ID: 1358 |
Intrinsic limits to gene regulation by global crosstalk
T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).
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T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).
2015 |Published| Journal Article | IST-REx-ID: 10794 |
Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study
F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).
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F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).
2015 |Published| Journal Article | IST-REx-ID: 1539 |
Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space
J. Ruess, Journal of Chemical Physics 143 (2015).
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J. Ruess, Journal of Chemical Physics 143 (2015).
2015 |Published| Journal Article | IST-REx-ID: 1538 |
Iterative experiment design guides the characterization of a light-inducible gene expression circuit
J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.
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J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.
2015 |Published| Journal Article | IST-REx-ID: 1564 |
Editorial: Emergent neural computation from the interaction of different forms of plasticity
M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015).
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M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015).
2015 |Published| Journal Article | IST-REx-ID: 1570 |
Novel plasticity rule can explain the development of sensorimotor intelligence
R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.
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R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.
2015 |Published| Conference Paper | IST-REx-ID: 1658
Adaptive moment closure for parameter inference of biochemical reaction networks
S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, C. Schilling, 9308 (2015) 77–89.
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S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, C. Schilling, 9308 (2015) 77–89.
2015 |Published| Journal Article | IST-REx-ID: 1697 |
High accuracy decoding of dynamical motion from a large retinal population
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015).
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O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015).
2015 |Published| Journal Article | IST-REx-ID: 1701 |
Thermodynamics and signatures of criticality in a network of neurons
G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.
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G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.
2015 |Published| Journal Article | IST-REx-ID: 1861
Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks
J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015).
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J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015).
2015 |Published| Journal Article | IST-REx-ID: 1885 |
Positional information, positional error, and readout precision in morphogenesis: A mathematical framework
G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.
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G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.
2015 |Published| Journal Article | IST-REx-ID: 1940 |
Optimizing information flow in small genetic networks. IV. Spatial coupling
T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
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T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
2015 | Research Data Reference | IST-REx-ID: 9718
Supporting information text
T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
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T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
2015 |Published| Journal Article | IST-REx-ID: 1827 |
Evolution of bow-tie architectures in biology
T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).
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T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).
2015 | Research Data Reference | IST-REx-ID: 9773
Evolutionary simulation code
T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
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T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
2015 | Research Data Reference | IST-REx-ID: 9712
Other fitness models for comparison & for interacting TFBSs
M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).
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M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).
2015 |Published| Journal Article | IST-REx-ID: 1666 |
Dynamics of transcription factor binding site evolution
M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).
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M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).
2015 |Published| Journal Article | IST-REx-ID: 1576 |
Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).
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S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).
2015 |Published| Journal Article | IST-REx-ID: 1655 |
Quantifying emergent behavior of autonomous robots
G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.
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G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.
2014 |Published| Conference Paper | IST-REx-ID: 1708
Spatio-temporal representations of uncertainty in spiking neural networks
C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp. 2024–2032.
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C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp. 2024–2032.
2014 |Published| Journal Article | IST-REx-ID: 1886 |
Variance predicts salience in central sensory processing
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).
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A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).
2014 |Published| Journal Article | IST-REx-ID: 1896 |
Mathematical model of alternative mechanism of telomere length maintenance
R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).
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R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).
2014 |Published| Journal Article | IST-REx-ID: 1909 |
The fitness costs of adaptation via phenotypic plasticity and maternal effects
T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.
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T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.
2014 |Published| Journal Article | IST-REx-ID: 1928
Evolutionary dynamics of infectious diseases in finite populations
J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162.
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J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162.
2014 |Published| Journal Article | IST-REx-ID: 1931 |
Emergence of task-dependent representations in working memory circuits
C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).
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C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).
2014 |Published| Journal Article | IST-REx-ID: 2028 |
Characterizing spiking in noisy type II neurons
K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014) 40–54.
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K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014) 40–54.
2014 |Published| Journal Article | IST-REx-ID: 2183 |
Hierarchy and polysynchrony in an adaptive network
V. Botella Soler, P. Glendinning, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).
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V. Botella Soler, P. Glendinning, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).
2014 |Published| Journal Article | IST-REx-ID: 2231 |
Noise and information transmission in promoters with multiple internal states
G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.
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G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.
2014 |Published| Journal Article | IST-REx-ID: 3263 |
Adaptation to changes in higher-order stimulus statistics in the salamander retina
G. Tkačik, A. Ghosh, E. Schneidman, R. Segev, PLoS One 9 (2014).
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G. Tkačik, A. Ghosh, E. Schneidman, R. Segev, PLoS One 9 (2014).
2014 |Published| Journal Article | IST-REx-ID: 537 |
Fitness consequences of maternal and grandmaternal effects
R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.
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R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.
2014 | Research Data Reference | IST-REx-ID: 9752 |
Data from: Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).
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K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).
2014 |Published| Journal Article | IST-REx-ID: 2257 |
Searching for collective behavior in a large network of sensory neurons
G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).
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G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).
2013 |Published| Book Chapter | IST-REx-ID: 2413
Neuronal oscillations scale up and scale down the brain dynamics
M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH, 2013.
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M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH, 2013.
2013 |Published| Journal Article | IST-REx-ID: 2818 |
Learning quadratic receptive fields from neural responses to natural stimuli
K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.
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K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.
2013 |Published| Journal Article | IST-REx-ID: 2850 |
The simplest maximum entropy model for collective behavior in a neural network
G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
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G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
2013 |Published| Journal Article | IST-REx-ID: 2851
A simple method for estimating the entropy of neural activity
M. Berry, G. Tkačik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
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M. Berry, G. Tkačik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
2013 |Published| Journal Article | IST-REx-ID: 2863 |
Stimulus-dependent maximum entropy models of neural population codes
E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).
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E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).
2013 |Published| Journal Article | IST-REx-ID: 2861
Lyapunov exponent and topological entropy plateaus in piecewise linear maps
V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A: Mathematical and Theoretical 46 (2013).
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V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A: Mathematical and Theoretical 46 (2013).
2013 |Published| Journal Article | IST-REx-ID: 2913 |
Retinal metric: a stimulus distance measure derived from population neural responses
G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).
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G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).