Casillas Perez BE, Bodova K, Grasse AV, Tkadik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232.

Lombardi F, Pepic S, Shriki O, Tkadik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263.

Reinhardt M, Tkadik G, Ten Wolde PR. 2023. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 13(4), 041017.

Nardin M, Csicsvari JL, Tkadik G, Savin C. 2023. The structure of hippocampal C interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.

Zoller B, Gregor T, Tkadik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.

Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkadik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543.

Mlynarski WF, Tkadik G. 2022. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 20(12), e3001889.

Hledik M, Barton NH, Tkadik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.

Lombardi F, Pepic S, Shriki O, Tkadik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches.10.48550/ARXIV.2108.06686 .

Kavcic B, Tkadik G. Token-driven totally asymmetric simple exclusion process. arXiv, 2112.13558.

Tkadik G, Gregor T. 2021. The many bits of positional information. Development. 148(2), de6065.

Chalk MJ, Tkadik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.

Kavcic B, Tkadik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.

Mlynarski WF, Hledik M, Sokolowski TR, Tkadik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.

Nardin M, Csicsvari JL, Tkadik G, Savin C. The structure of hippocampal C interactions optimizes spatial coding across experience. bioRxiv,10.1101/2021.09.28.460602 .

Berry MJ, Tkadik G. 2020. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 14, 20.

Maoz O, Tkadik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073.

Grah R, Zoller B, Tkadik G. 2020. Nonequilibrium models of optimal enhancer function. PNAS. 117(50), 31614–31622.

Grah R, Zoller B, Tkadik G. 2020. Normative models of enhancer function. bioRxiv,10.1101/2020.04.08.029405 .

Kavcic B, Tkadik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013.

Kavcic B, Tkadik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv,10.1101/2020.04.18.047886 .

Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkadik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology &; Evolution. 4(4), 612–625.

Bialek W, Gregor T, Tkadik G. Action at a distance in transcriptional regulation. arXiv:1912.08579, .

Petkova MD, Tkadik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15.

Ruess J, Pleska M, Guet CC, Tkadik G. 2019. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.

Ruess J, Pleska M, Guet CC, Tkadik G. 2019. Supporting text and results, Public Library of Science,10.1371/journal.pcbi.1007168.s001 .

Cepeda Humerez SA, Ruess J, Tkadik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290.

Hledik M, Sokolowski TR, Tkadik G. 2019. A tight upper bound on mutual information. IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.

Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkadik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.

Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkadik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).

Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkadik G. 2018. Implementation of the inference method in Matlab, Public Library of Science,10.1371/journal.pone.0193049.s001 .

Ferrari U, Deny S, Chalk MJ, Tkadik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410.

Chalk MJ, Marre O, Tkadik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.

Botella Soler V, Deny S, Martius GS, Marre O, Tkadik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5), e1006057.

Deny S, Marre O, Botella-Soler V, Martius GS, Tkadik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria,10.15479/AT:ISTA:98 .

De Martino D, Mc AA, Bergmiller T, Guet CC, Tkadik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.

De Martino D, Tkadik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria,10.15479/AT:ISTA:62 .

Igler C, Lagator M, Tkadik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643.

Igler C, Lagator M, Tkadik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria,10.15479/AT:ISTA:108 .

Chait RP, Ruess J, Bergmiller T, Tkadik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535.

Humplik J, Tkadik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.

Harpaz R, Tkadik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.

Prentice J, Marre O, Ioffe M, Loback A, Tkadik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad,10.5061/dryad.1f1rc .

Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkadik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964.

Friedlander T, Prizak R, Barton NH, Tkadik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.

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.

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

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 .

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 .

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.

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.

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.

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.

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.

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

Bodova K, Tkadik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.

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.

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.

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 .

Hillenbrand P, Gerland U, Tkadik G. 2016. Error bound on an estimator of position, Public Library of Science,10.1371/journal.pone.0163628.s001 .

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 .

Friedlander T, Prizak R, Guet CC, Barton NH, Tkadik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.

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.

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.

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.

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.

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 .

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

Cepeda Humerez SA, Rieckh G, Tkadik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101.

Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkadik G. 2014. Variance predicts salience in central sensory processing. eLife. (November), e03722.

Rieckh G, Tkadik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204.

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.

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 .

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.

Rajan K, Marre O, Tkadik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692.

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.

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.

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.

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.

Dubuis J, Tkadik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information, in bits. PNAS. 110(41), 16301–16308.

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.

Stephens G, Mora T, Tkadik G, Bialek W. 2013. Statistical thermodynamics of natural images. Physical Review Letters. 110(1), 018701.

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.

Tkadik G, Walczak A. 2011. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 23(15), 153102.

Prentice J, Homann J, Simmons K, Tkadik G, Balasubramanian V, Nelson P. 2011. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 6(7).

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.

Little S, Tkadik G, Kneeland T, Wieschaus E, Gregor T. 2011. The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source. PLoS Biology. 9(3), e1000596.

Tkadik G, Prentice J, Victor J, Balasubramanian V. 2010. Local statistics in natural scenes predict the saliency of synthetic textures. PNAS. 107(42), 18149–18154.

Tkadik G, Prentice J, Balasubramanian V, Schneidman E. 2010. Optimal population coding by noisy spiking neurons. PNAS. 107(32), 14419–14424.

Walczak A, Tkadik G, Bialek W. 2010. Optimizing information flow in small genetic networks. II. Feed-forward interactions. Physical Review E Statistical Nonlinear and Soft Matter Physics. 81(4).

Tkadik G. 2010. Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics. Summer School on Quantitative Evolutionary and Comparative Genomics.

Tkadik G. 2010. From statistical mechanics to information theory: understanding biophysical information-processing systems. ArXiv, q-MN, 1–52, .

Tkadik G, Walczak A, Bialek W. 2009. Optimizing information flow in small genetic networks. Physical Review E Statistical Nonlinear and Soft Matter Physics. 80(3).

Kryazhimskiy S, Tkadik G, Plotkin J. 2009. The dynamics of adaptation on correlated fitness landscapes. PNAS. 106(44), 18638–18643.

Tkadik G, Schneidman E, Berry M, Bialek W. 2009. Spin glass models for a network of real neurons. ArXiv, q-NC, .

Tkadik G, Bialek W. 2009.Cell Biology: Networks, regulation, pathways. In: Encyclopedia of Complexity and Systems Science. , 719–741.

Tkadik G, Bialek W. 2009. Diffusion, dimensionality, and noise in transcriptional regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 79(5).

Tkadik G, Gregor T, Bialek W. 2008. The role of input noise in transcriptional regulation. PLoS One. 3(7).

Tkadik G, Callan C, Bialek W. 2008. Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 78(1).

Tkadik G, Callan C, Bialek W. 2008. Information flow and optimization in transcriptional regulation. PNAS. 105(34), 12265–12270.

Tkadik G, Magnasco M. 2008. Decoding spike timing: The differential reverse-correlation method. Biosystems. 93(1–2), 90–100.

Kinney J, Tkadik G, Callan C. 2007. Precise physical models of protein-DNA interaction from high-throughput data. PNAS. 104(2), 501–506.

Broderick T, Dudik M, Tkadik G, Schapire R, Bialek W. 2007. Faster solutions of the inverse pairwise Ising problem. ArXiv, q-QM, .

Tkadik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks of real neurons. ArXiv, 1–4, .

Slonim N, Atwal G, Tkadik G, Bialek W. 2005. Information-based clustering. PNAS. 102(51), 18297–18302.

Slonim N, Atwal G, Tkadik G, Bialek W. 2005. Estimating mutual information and multi-information in large networks. ArXiv, 1–11, .