Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli
D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016).

A general approximation for the dynamics of quantitative traits
K. Bodova, G. Tkadik, N.H. Barton, Genetics 202 (2016) 1523–1548.

Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis
D. De Martino, Physical Biology 13 (2016).

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.

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.

Error-robust modes of the retinal population code
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkadik, M. Berry, PLoS Computational Biology 12 (2016).

Neurons equipped with intrinsic plasticity learn stimulus intensity statistics
T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.

Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information
P. Hillenbrand, U. Gerland, G. Tkadik, PLoS One 11 (2016).

Computation of positional information in an Ising model
P. Hillenbrand, U. Gerland, G. Tkadik, (2016).

Error bound on an estimator of position
P. Hillenbrand, U. Gerland, G. Tkadik, (2016).

Computation of positional information in a discrete morphogen field
P. Hillenbrand, U. Gerland, G. Tkadik, (2016).

Studying the complexities of transcriptional regulation
G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.

Intrinsic limits to gene regulation by global crosstalk
T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkadik, Nature Communications 7 (2016).

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).

Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space
J. Ruess, Journal of Chemical Physics 143 (2015).

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.

Editorial: Emergent neural computation from the interaction of different forms of plasticity
M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015).

Novel plasticity rule can explain the development of sensorimotor intelligence
R. Der, G.S. Martius, PNAS 112 (2015) 24–32.

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.

High accuracy decoding of dynamical motion from a large retinal population
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkadik, M. Berry, PLoS Computational Biology 11 (2015).

Thermodynamics and signatures of criticality in a network of neurons
G. Tkadik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.

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).

Positional information, positional error, and readout precision in morphogenesis: A mathematical framework
G. Tkadik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.

Optimizing information flow in small genetic networks. IV. Spatial coupling
T.R. Sokolowski, G. Tkadik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).

Supporting information text
T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).

Evolution of bow-tie architectures in biology
T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).

Evolutionary simulation code
T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).

Other fitness models for comparison & for interacting TFBSs
M. Tugrul, T. Paixao, N.H. Barton, G. Tkadik, (2015).

Dynamics of transcription factor binding site evolution
M. Tugrul, T. Paixao, N.H. Barton, G. Tkadik, PLoS Genetics 11 (2015).

Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
S.A. Cepeda Humerez, G. Rieckh, G. Tkadik, Physical Review Letters 115 (2015).

Quantifying emergent behavior of autonomous robots
G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.

Spatio-temporal representations of uncertainty in spiking neural networks
C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp. 2024–2032.

Variance predicts salience in central sensory processing
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkadik, ELife (2014).

Mathematical model of alternative mechanism of telomere length maintenance
R. Kollár, K. Bodova, J. Nosek, d. Tomáska, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).

The fitness costs of adaptation via phenotypic plasticity and maternal effects
T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.

Evolutionary dynamics of infectious diseases in finite populations
J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162.

Emergence of task-dependent representations in working memory circuits
C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).

Characterizing spiking in noisy type II neurons
K. Bodova, D. Paydarfar, D. Forger,  Journal of Theoretical Biology 365 (2014) 40–54.

Hierarchy and polysynchrony in an adaptive network 
V. Botella Soler, P. Glendinning, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).

Noise and information transmission in promoters with multiple internal states
G. Rieckh, G. Tkadik, Biophysical Journal 106 (2014) 1194–1204.

Adaptation to changes in higher-order stimulus statistics in the salamander retina
G. Tkadik, A. Ghosh, E. Schneidman, R. Segev, PLoS One 9 (2014).

Fitness consequences of maternal and grandmaternal effects
R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.

Data from: Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkadik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).

Searching for collective behavior in a large network of sensory neurons
G. Tkadik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).

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.

Learning quadratic receptive fields from neural responses to natural stimuli
K. Rajan, O. Marre, G. Tkadik, Neural Computation 25 (2013) 1661–1692.

The simplest maximum entropy model for collective behavior in a neural network
G. Tkadik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).

A simple method for estimating the entropy of neural activity
M. Berry, G. Tkadik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).

Stimulus-dependent maximum entropy models of neural population codes
E. Granot Atedgi, G. Tkadik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).

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).

Retinal metric: a stimulus distance measure derived from population neural responses
G. Tkadik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).

Positional information, in bits
J. Dubuis, G. Tkadik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308.

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.

Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkadik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, PLoS Computational Biology 9 (2013).

Statistical thermodynamics of natural images
G. Stephens, T. Mora, G. Tkadik, W. Bialek, Physical Review Letters 110 (2013).

Optimizing information flow in small genetic networks. III. A self-interacting gene
G. Tkadik, A. Walczak, W. Bialek,  Physical Review E Statistical Nonlinear and Soft Matter Physics  85 (2012).

A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil
G. Rieckh, W. Kreuzer, H. Waubke, P. Balazs,  Engineering Analysis with Boundary Elements 36 (2012) 960–967.

Information transmission in genetic regulatory networks a review
G. Tkadik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).

Natural images from the birthplace of the human eye
G. Tkadik, P. Garrigan, C. Ratliff, G. Milcinski, J. Klein, L. Seyfarth, P. Sterling, D. Brainard, V. Balasubramanian, PLoS One 6 (2011).