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114 Publications

2016 | Journal Article | IST-REx-ID: 1170
Modular parameter identification of biomolecular networks
M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.
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2016 | Conference Paper | IST-REx-ID: 1214
Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm
G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016.
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2016 | Journal Article | IST-REx-ID: 1290   OA
Compounds that select against the tetracycline-resistance efflux pump
L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.
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2016 | Journal Article | IST-REx-ID: 1485   OA View | DOI | Download (ext.)
 
2016 | 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. Tkacik, Nature Communications 7 (2016) 12307.
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2016 | 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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2016 | Conference Paper | IST-REx-ID: 1082   OA
Relevant sparse codes with variational information bottleneck
M.J. Chalk, O. Marre, G. Tkacik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.
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2016 | Journal Article | IST-REx-ID: 1188   OA
Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth
D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016) 123502.
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2016 | Journal Article | IST-REx-ID: 1203   OA
Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination
F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.
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2016 | Journal Article | IST-REx-ID: 1260   OA
The dual of the space of interactions in neural network models
D. De Martino, International Journal of Modern Physics C 27 (2016).
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2016 | Journal Article | IST-REx-ID: 1342   OA
Spatiotemporal microbial evolution on antibiotic landscapes
M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151.
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2016 | Journal Article | IST-REx-ID: 1266   OA View | Files available | DOI
 
2016 | Journal Article | IST-REx-ID: 1242   OA
Extending the dynamic range of transcription factor action by translational regulation
T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkacik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).
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2016 | Journal Article | IST-REx-ID: 1420   OA
A general approximation for the dynamics of quantitative traits
K. Bod’ová, G. Tkacik, N.H. Barton, Genetics 202 (2016) 1523–1548.
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2015 | Journal Article | IST-REx-ID: 1539   OA View | Files available | DOI
 
2015 | Journal Article | IST-REx-ID: 1666   OA
Dynamics of transcription factor binding site evolution
M. Tugrul, T. Paixao, N.H. Barton, G. Tkacik, PLoS Genetics 11 (2015).
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2015 | Journal Article | IST-REx-ID: 1697   OA
High accuracy decoding of dynamical motion from a large retinal population
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkacik, M. Berry, PLoS Computational Biology 11 (2015).
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2015 | Journal Article | IST-REx-ID: 1940   OA
Optimizing information flow in small genetic networks. IV. Spatial coupling
T.R. Sokolowski, G. Tkacik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
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2015 | Journal Article | IST-REx-ID: 1655   OA
Quantifying emergent behavior of autonomous robots
G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.
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2015 | Journal Article | IST-REx-ID: 1701   OA
Thermodynamics and signatures of criticality in a network of neurons
G. Tkacik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.
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2015 | Journal Article | IST-REx-ID: 1827   OA
Evolution of bow-tie architectures in biology
T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).
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2015 | Journal Article | IST-REx-ID: 1570   OA
Novel plasticity rule can explain the development of sensorimotor intelligence
R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.
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2015 | 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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2015 | Journal Article | IST-REx-ID: 1885   OA
Positional information, positional error, and readout precision in morphogenesis: A mathematical framework
G. Tkacik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.
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2015 | Journal Article | IST-REx-ID: 1564   OA
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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2015 | Journal Article | IST-REx-ID: 1538   OA
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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2015 | 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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2015 | Journal Article | IST-REx-ID: 1576
Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
S.A. Cepeda Humerez, G. Rieckh, G. Tkacik, Physical Review Letters 115 (2015).
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2014 | Journal Article | IST-REx-ID: 3263   OA
Adaptation to changes in higher-order stimulus statistics in the salamander retina
G. Tkacik, A. Ghosh, E. Schneidman, R. Segev, PLoS One 9 (2014).
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2014 | Journal Article | IST-REx-ID: 1896   OA
Mathematical model of alternative mechanism of telomere length maintenance
R. Kollár, K. Bod’ová, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).
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2014 | 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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2014 | Journal Article | IST-REx-ID: 1909   OA
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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2014 | Journal Article | IST-REx-ID: 2231   OA
Noise and information transmission in promoters with multiple internal states
G. Rieckh, G. Tkacik, Biophysical Journal 106 (2014) 1194–1204.
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2014 | Journal Article | IST-REx-ID: 537   OA
Fitness consequences of maternal and grandmaternal effects
R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.
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2014 | 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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2014 | Journal Article | IST-REx-ID: 1931   OA
Emergence of task-dependent representations in working memory circuits
C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).
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2014 | Journal Article | IST-REx-ID: 1886   OA
Variance predicts salience in central sensory processing
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkacik, ELife (2014).
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2014 | Journal Article | IST-REx-ID: 2257
Searching for collective behavior in a large network of sensory neurons
G. Tkacik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).
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2013 | Journal Article | IST-REx-ID: 2277   OA
Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkacik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, PLoS Computational Biology 9 (2013) e1003344.
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2013 | 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) 125101.
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2013 | 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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2013 | Journal Article | IST-REx-ID: 2913   OA
Retinal metric: a stimulus distance measure derived from population neural responses
G. Tkacik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).
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2013 | Journal Article | IST-REx-ID: 2850   OA
The simplest maximum entropy model for collective behavior in a neural network
G. Tkacik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
View | DOI | Download (ext.) | arXiv
 
2013 | Journal Article | IST-REx-ID: 2863   OA
Stimulus-dependent maximum entropy models of neural population codes
E. Granot Atedgi, G. Tkacik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).
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2013 | Journal Article | IST-REx-ID: 2914   OA
Statistical thermodynamics of natural images
G. Stephens, T. Mora, G. Tkacik, W. Bialek, Physical Review Letters 110 (2013) 018701.
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2013 | Journal Article | IST-REx-ID: 2851
A simple method for estimating the entropy of neural activity
M. Berry, G. Tkacik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
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2013 | Journal Article | IST-REx-ID: 2818   OA
Learning quadratic receptive fields from neural responses to natural stimuli
K. Rajan, O. Marre, G. Tkacik, Neural Computation 25 (2013) 1661–1692.
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2013 | Journal Article | IST-REx-ID: 3261   OA
Positional information, in bits
J. Dubuis, G. Tkacik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308.
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2013 | Journal Article | IST-REx-ID: 499
Dynamic persistence of antibiotic-stressed mycobacteria
Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.
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