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Mlynarski, Wiktor F., and Gasper Tkadik. “Efficient Coding Theory of Dynamic Attentional Modulation.”10.1371/journal.pbio.3001889__PLoS Biology, vol. 20, no. 12, Public Library of Science, 2022, p. e3001889, doi:10.1371/journal.pbio.3001889.

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Kavcic, Bor, and Gasper Tkadik. “Token-Driven Totally Asymmetric Simple Exclusion Process.”10.48550/arXiv.2112.13558__ArXiv, 2112.13558, doi:10.48550/arXiv.2112.13558.

Tkadik, Gasper, and Thomas Gregor. “The Many Bits of Positional Information.”10.1242/dev.176065__Development, vol. 148, no. 2, de6065, The Company of Biologists, 2021, doi:10.1242/dev.176065.

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Berry, Michael J., and Gasper Tkadik. “Clustering of Neural Activity: A Design Principle for Population Codes.”10.3389/fncom.2020.00020__Frontiers in Computational Neuroscience, vol. 14, 20, Frontiers, 2020, doi:10.3389/fncom.2020.00020.

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Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.”10.1101/2020.04.18.047886__BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.

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Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.”10.1073/pnas.1716659115__PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.

Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.”10.1371/journal.pone.0193049__PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.

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Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.”10.1073/pnas.1711114115__PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.

Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.”10.1371/journal.pcbi.1006057__PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.

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De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.”10.1038/s41467-018-05417-9__Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.

De Martino, Daniele, and Gasper Tkadik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.

Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.”10.1038/s41559-018-0651-y__Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.

Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:108.

Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.”10.1038/s41467-017-01683-1__Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.

Humplik, Jan, and Gasper Tkadik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.”10.1371/journal.pcbi.1005763__PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.

Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.”10.1073/pnas.1703817114__PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.

Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.

Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.”10.1038/s41467-017-02159-y__Nature Communications, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:10.1038/s41467-017-02159-y.

Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.”10.1038/s41467-017-00238-8__Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.

Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.”10.1126/science.aam5887__Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.

Savin, Cristina, and Gasper Tkadik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.”10.1016/j.conb.2017.08.001__Current Opinion in Neurobiology, vol. 46, Elsevier, 2017, pp. 120–26, doi:10.1016/j.conb.2017.08.001.

Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:61.

Bergmiller, Tobias, et al. Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:53.

Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.”10.1126/science.aaf4762__Science, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:10.1126/science.aaf4762.

Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems, 2016, pp. 1965–73.

Savin, Cristina, and Gasper Tkadik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18.

Tkadik, Gasper. “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.”10.1016/j.plrev.2016.06.005__Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 166–67, doi:10.1016/j.plrev.2016.06.005.

Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.”10.1103/PhysRevE.93.022404__Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:10.1103/PhysRevE.93.022404.

Tkadik, Gasper, and William Bialek. “Information Processing in Living Systems.”10.1146/annurev-conmatphys-031214-014803__Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803.

Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.”10.1534/genetics.115.184127__Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.

Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.”10.1371/journal.pcbi.1005148__PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005148.

Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.”10.1371/journal.pone.0163628__PLoS One, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.

Hillenbrand, Patrick, et al. Computation of Positional Information in an Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002.

Hillenbrand, Patrick, et al. Error Bound on an Estimator of Position. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s001.

Hillenbrand, Patrick, et al. Computation of Positional Information in a Discrete Morphogen Field. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s003.

Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.”10.1038/ncomms12307__Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.

Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.”10.1371/journal.pcbi.1004304__PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304.

Tkadik, Gasper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.”10.1073/pnas.1514188112__PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112.

Tkadik, Gasper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.”10.1534/genetics.114.171850__Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.

Sokolowski, Thomas R., and Gasper Tkadik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.”10.1103/PhysRevE.91.062710__Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.062710.

Tugrul, Murat, et al. Other Fitness Models for Comparison &; for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.

Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.”10.1371/journal.pgen.1005639__PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.

Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.”10.1103/PhysRevLett.115.248101__Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101.

Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.”10.7554/eLife.03722__ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.

Rieckh, Georg, and Gasper Tkadik. “Noise and Information Transmission in Promoters with Multiple Internal States.”10.1016/j.bpj.2014.01.014__Biophysical Journal, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.

Tkadik, Gasper, et al. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.”10.1371/journal.pone.0085841__PLoS One, vol. 9, no. 1, e85841, Public Library of Science, 2014, doi:10.1371/journal.pone.0085841.

Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.

Tkadik, Gasper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.”10.1371/journal.pcbi.1003408__PLoS Computational Biology, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408.

Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.”10.1162/NECO_a_00463__Neural Computation, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:10.1162/NECO_a_00463.

Tkadik, Gasper, et al. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.”10.1088/1742-5468/2013/03/P03011__Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, 011, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03011.

Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural Activity.”10.1088/1742-5468/2013/03/P03015__Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, 015, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03015.

Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.”10.1371/journal.pcbi.1002922__PLoS Computational Biology, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.

Tkadik, Gasper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.”10.1103/PhysRevLett.110.058104__Physical Review Letters, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.058104.

Dubuis, Julien, et al. “Positional Information, in Bits.”10.1073/pnas.1315642110__PNAS, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110.

Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.”10.1371/journal.pcbi.1003344__PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003344.

Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.”10.1103/PhysRevLett.110.018701__Physical Review Letters, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.018701.

Tkadik, Gasper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.”10.1103/PhysRevE.85.041903__10.1103/PhysRevE.85.041903__Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 85, no. 4, 041903, American Institute of Physics, 2012, doi:10.1103/PhysRevE.85.041903.

Tkadik, Gasper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.”10.1088/0953-8984/23/15/153102__Journal of Physics: Condensed Matter, vol. 23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:10.1088/0953-8984/23/15/153102.

Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.”10.1371/journal.pone.0019884__PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0019884.

Tkadik, Gasper, et al. “Natural Images from the Birthplace of the Human Eye.”10.1371/journal.pone.0020409__PLoS One, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:10.1371/journal.pone.0020409.

Little, Shawn, et al. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized Source.”10.1371/journal.pbio.1000596__PLoS Biology, vol. 9, no. 3, e1000596, Public Library of Science, 2011, doi:10.1371/journal.pbio.1000596.

Tkadik, Gasper, et al. “Local Statistics in Natural Scenes Predict the Saliency of Synthetic Textures.”10.1073/pnas.0914916107__PNAS, vol. 107, no. 42, National Academy of Sciences, 2010, pp. 18149–54, doi:10.1073/pnas.0914916107.

Tkadik, Gasper, et al. “Optimal Population Coding by Noisy Spiking Neurons.”10.1073/pnas.1004906107__PNAS, vol. 107, no. 32, National Academy of Sciences, 2010, pp. 14419–24, doi:10.1073/pnas.1004906107.

Walczak, Aleksandra, et al. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.”10.1103/PhysRevE.81.041905__Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 81, no. 4, American Institute of Physics, 2010, doi:10.1103/PhysRevE.81.041905.

Tkadik, Gasper. Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics. Elsevier, 2010.

Tkadik, Gasper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” ArXiv, vol. q-MN, ArXiv, 2010, pp. 1–52.

Tkadik, Gasper, et al. “Optimizing Information Flow in Small Genetic Networks.”10.1103/PhysRevE.80.031920__Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 80, no. 3, American Institute of Physics, 2009, doi:10.1103/PhysRevE.80.031920.

Kryazhimskiy, Sergey, et al. “The Dynamics of Adaptation on Correlated Fitness Landscapes.”10.1073/pnas.0905497106__PNAS, vol. 106, no. 44, National Academy of Sciences, 2009, pp. 18638–43, doi:10.1073/pnas.0905497106.

Tkadik, Gasper, et al. “Spin Glass Models for a Network of Real Neurons.” ArXiv, vol. q-NC, ArXiv, 2009.

Tkadik, Gasper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.”10.1007/978-0-387-30440-3_48__Encyclopedia of Complexity and Systems Science, edited by R. Meyers, Springer, 2009, pp. 719–41, doi:10.1007/978-0-387-30440-3_48.

Tkadik, Gasper, and William Bialek. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.”10.1103/PhysRevE.79.051901__Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5, American Institute of Physics, 2009, doi:10.1103/PhysRevE.79.051901.

Tkadik, Gasper, et al. “The Role of Input Noise in Transcriptional Regulation.”10.1371/journal.pone.0002774__PLoS One, vol. 3, no. 7, Public Library of Science, 2008, doi:10.1371/journal.pone.0002774.

Tkadik, Gasper, et al. “Information Capacity of Genetic Regulatory Elements.”10.1103/PhysRevE.78.011910__Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1, American Institute of Physics, 2008, doi:10.1103/PhysRevE.78.011910.

Tkadik, Gasper, et al. “Information Flow and Optimization in Transcriptional Regulation.”10.1073/pnas.0806077105__PNAS, vol. 105, no. 34, National Academy of Sciences, 2008, pp. 12265–70, doi:10.1073/pnas.0806077105.