De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 95(6), 062419.
LibreCat: https://research-explorer.ista.ac.at/record/959
DOI: 10.1103/PhysRevE.95.062419
WoS: 000404546400004

De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 010401.
LibreCat: https://research-explorer.ista.ac.at/record/947
DOI: 10.1103/PhysRevE.96.010401
WoS: 000405194200002

Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkadik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383.
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PMID: 28663499

Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems.  Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.
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Savin C, Tkadik G. 2017. Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology. 46, 120–126.
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De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6), 060401.
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Lang M, Sontag E. 2017. Zeros of nonlinear systems with input invariances. Automatica. 81C, 46–55.
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Marre O, Tkadik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode array recording from salamander retinal ganglion cells, Institute of Science and Technology Austria,10.15479/AT:ISTA:61 .
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Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkadik G, Guet CC. 2017. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity, Institute of Science and Technology Austria,10.15479/AT:ISTA:53 .
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Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkadik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.
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Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211.
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Chalk MJ, Marre O, Tkadik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.
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Savin C, Tkadik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618.
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Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), 8–08.
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Tkadik G. 2016. 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. Physics of Life Reviews. 17, 166–167.
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De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism &;amp; growth.  Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.
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Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017.
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Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International Conference on Intelligent Robots and Systems IROS  vol. 2016–November, 7759138.
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Miki G, Stoll A, Bevirt J, Grah R, Moore M. 2016. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. AIAA: Aviation Technology, Integration, and Operations Conference, 1–19.
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Sokolowski TR, Walczak A, Bialek W, Tkadik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.
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Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.
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Tkadik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117.
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De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067.
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Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.
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Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904.
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Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July, 7526722.
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Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333.
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Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304), 1147–1151.
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De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 13(3), 036005.
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Bodova K, Tkadik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.
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De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003.
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Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25.
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Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.
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Prentice J, Marre O, Ioffe M, Loback A, Tkadik G, Berry M. 2016. Error-robust modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.
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Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.
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Hillenbrand P, Gerland U, Tkadik G. 2016. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 11(9), e0163628.
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Hillenbrand P, Gerland U, Tkadik G. 2016. Computation of positional information in an Ising model, Public Library of Science,10.1371/journal.pone.0163628.s002 .
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Hillenbrand P, Gerland U, Tkadik G. 2016. Error bound on an estimator of position, Public Library of Science,10.1371/journal.pone.0163628.s001 .
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Hillenbrand P, Gerland U, Tkadik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science,10.1371/journal.pone.0163628.s003 .
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Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.
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Friedlander T, Prizak R, Guet CC, Barton NH, Tkadik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.
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Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.
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Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103.
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Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153.
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Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.
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Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), 24–32.
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Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. 2015. Adaptive moment closure for parameter inference of biochemical reaction networks. 9308, 77–89.
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Marre O, Botella Soler V, Simmons K, Mora T, Tkadik G, Berry M. 2015. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 11(7), e1004304.
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Tkadik G, Mora T, Marre O, Amodei D, Palmer S, Berry Ii M, Bialek W. 2015. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 112(37), 11508–11513.
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Ruess J, Lygeros J. 2015. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 25(2), 8.
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Tkadik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 199(1), 39–59.
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Sokolowski TR, Tkadik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6), 062710.
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Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science,10.1371/journal.pcbi.1004055.s001 .
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Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).
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Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science,10.1371/journal.pcbi.1004055.s002 .
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Tugrul M, Paixao T, Barton NH, Tkadik G. 2015. Other fitness models for comparison &; for interacting TFBSs, Public Library of Science,10.1371/journal.pgen.1005639.s001 .
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Tugrul M, Paixao T, Barton NH, Tkadik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).
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Cepeda Humerez SA, Rieckh G, Tkadik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101.
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Martius GS, Olbrich E. 2015. Quantifying emergent behavior of autonomous robots. Entropy. 17(10), 7266–7297.
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Savin C, Denève S. 2014. Spatio-temporal representations of uncertainty in spiking neural networks. NIPS: Neural Information Processing Systems vol. 3, 2024–2032.
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Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkadik G. 2014. Variance predicts salience in central sensory processing. eLife. (November), e03722.
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Kollár R, Bodova K, Nosek J, Tomáska d. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.
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Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701.
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Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 360, 149–162.
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Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57.
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Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons.  Journal of Theoretical Biology. 365, 40–54.
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Botella Soler V, Glendinning P. 2014. Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(6), 062809.
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Rieckh G, Tkadik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204.
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Tkadik G, Ghosh A, Schneidman E, Segev R. 2014. Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One. 9(1), e85841.
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Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145.
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Simmons K, Prentice J, Tkadik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad,10.5061/dryad.246qg .
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Tkadik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. 2014. Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. 10(1), e1003408.
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Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity, .
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Rajan K, Marre O, Tkadik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692.
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DOI: 10.1162/NECO_a_00463
arXiv: 1209.0121

Tkadik G, Marre O, Mora T, Amodei D, Berry M, Bialek W. 2013. The simplest maximum entropy model for collective behavior in a neural network. Journal of Statistical Mechanics Theory and Experiment. 2013(3), 011.
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arXiv: 1207.6319

Berry M, Tkadik G, Dubuis J, Marre O, Da Silveira R. 2013. A simple method for estimating the entropy of neural activity. Journal of Statistical Mechanics Theory and Experiment. 2013(3), 015.
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Granot Atedgi E, Tkadik G, Segev R, Schneidman E. 2013. Stimulus-dependent maximum entropy models of neural population codes. PLoS Computational Biology. 9(3), e1002922.
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Botella Soler V, Oteo J, Ros J, Glendinning P. 2013. Lyapunov exponent and topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical and Theoretical. 46(12), 125101.
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Tkadik G, Granot Atedgi E, Segev R, Schneidman E. 2013. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 110(5), 058104.
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Dubuis J, Tkadik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information, in bits. PNAS. 110(41), 16301–16308.
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Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95.
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Simmons K, Prentice J, Tkadik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2013. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 9(12), e1003344.
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Stephens G, Mora T, Tkadik G, Bialek W. 2013. Statistical thermodynamics of natural images. Physical Review Letters. 110(1), 018701.
LibreCat: https://research-explorer.ista.ac.at/record/2914
DOI: 10.1103/PhysRevLett.110.018701
arXiv: 0806.2694

Tkadik G, Walczak A, Bialek W. 2012. Optimizing information flow in small genetic networks. III. A self-interacting gene.  Physical Review E statistical nonlinear and soft matter physics . 85(4), 041903.
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Rieckh G, Kreuzer W, Waubke H, Balazs P. 2012. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil.  Engineering Analysis with Boundary Elements. 36(6), 960–967.
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Tkadik G, Walczak A. 2011. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 23(15), 153102.
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Tkadik G, Garrigan P, Ratliff C, Milcinski G, Klein J, Seyfarth L, Sterling P, Brainard D, Balasubramanian V. 2011. Natural images from the birthplace of the human eye. PLoS One. 6(6), e20409.
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