Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system
K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.

Probabilistic models of individual and collective animal behavior
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkadik, PLoS One 13 (2018).

Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity
M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.

Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons
U. Ferrari, S. Deny, M.J. Chalk, G. Tkadik, O. Marre, T. Mora, Physical Review E 98 (2018).

Toward a unified theory of efficient, predictive, and sparse coding
M.J. Chalk, O. Marre, G. Tkadik, PNAS 115 (2018) 186–191.

Well posedness and maximum entropy approximation for the dynamics of quantitative traits
K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.

Nonoptimal gene expression creates latent potential for antibiotic resistance
A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.

Nonlinear decoding of a complex movie from the mammalian retina
V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkadik, PLoS Computational Biology 14 (2018).

Statistical mechanics for metabolic networks during steady state growth
D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkadik, Nature Communications 9 (2018).

Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkadik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.

Shaping bacterial population behavior through computer interfaced control of individual cells
R.P. Chait, J. Ruess, T. Bergmiller, G. Tkadik, C.C. Guet, Nature Communications 8 (2017).

Dynamical self consistency leads to behavioral development and emergent social interactions in robots
R. Der, G.S. Martius, in:, IEEE, 2017.

Self organized behavior generation for musculoskeletal robots
R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).

Probabilistic models for neural populations that naturally capture global coupling and criticality
J. Humplik, G. Tkadik, PLoS Computational Biology 13 (2017).

Discrete modes of social information processing predict individual behavior of fish in a group
R. Harpaz, G. Tkadik, E. Schneidman, PNAS 114 (2017) 10149–10154.

Sensory noise predicts divisive reshaping of receptive fields
M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13 (2017).

Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment
K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.

Exact goodness-of-fit testing for the Ising model
A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.

Multiplexed computations in retinal ganglion cells of a single type
S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkadik, O. Marre, Nature Communications 8 (2017).

Subsampling scaling
A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).

Evolution of new regulatory functions on biophysically realistic fitness landscapes
T. Friedlander, R. Prizak, N.H. Barton, G. Tkadik, Nature Communications 8 (2017).

Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics
D. De Martino,  Physical Review E Statistical Nonlinear and Soft Matter Physics  95 (2017) 062419.

Quantifying the entropic cost of cellular growth control
D. De Martino, F. Capuani, A. De Martino,  Physical Review E Statistical Nonlinear and Soft Matter Physics  96 (2017).

Decoding of position in the developing neural tube from antiparallel morphogen gradients
M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkadik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.

Phase transitions in integer linear problems
S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari,  Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).

Maximum entropy models as a tool for building precise neural controls
C. Savin, G. Tkadik, Current Opinion in Neurobiology 46 (2017) 120–126.

Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes
D. De Martino, Physical Review E 96 (2017).

Zeros of nonlinear systems with input invariances
M. Lang, E. Sontag, Automatica 81C (2017) 46–55.

Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity
T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkadik, C.C. Guet, Science 356 (2017) 311–315.

An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate
V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.

Relevant sparse codes with variational information bottleneck
M.J. Chalk, O. Marre, G. Tkadik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.

Estimating nonlinear neural response functions using GP priors and Kronecker methods
C. Savin, G. Tkadik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.

Modular parameter identification of biomolecular networks
M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) 8–08.

Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot; by O. C. Martin et al.
G. Tkadik, Physics of Life Reviews 17 (2016) 166–167.

Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth
D. De Martino, D. Masoero,  Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).

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.

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.

Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency
G. Miki, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.

Extending the dynamic range of transcription factor action by translational regulation
T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkadik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).

Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells
P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.

Information processing in living systems
G. Tkadik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.

The dual of the space of interactions in neural network models
D. De Martino, International Journal of Modern Physics C 27 (2016).

Neural oscillations as a signature of efficient coding in the presence of synaptic delays
M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).

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.

Scale-invariant systems realize nonlinear differential operators
M. Lang, E. Sontag, in:, IEEE, 2016.

Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments
R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).

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.

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).

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).

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

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).