Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.”10.1038/s41467-023-38947-y__Nature Communications, vol. 14, 3232, Springer Nature, 2023, doi:10.1038/s41467-023-38947-y.
LibreCat: https://research-explorer.ista.ac.at/record/13127
DOI: 10.1038/s41467-023-38947-y
WoS: 001002562700005
PMID: 37270641

Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.”10.1038/s43588-023-00410-9__Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9.
LibreCat: https://research-explorer.ista.ac.at/record/12762
DOI: 10.1038/s43588-023-00410-9
arXiv: 2108.06686

Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.”10.1103/PhysRevX.13.041017__Physical Review X, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:10.1103/PhysRevX.13.041017.
LibreCat: https://research-explorer.ista.ac.at/record/14515
DOI: 10.1103/PhysRevX.13.041017
arXiv: 2203.03461

Nardin, Michele, et al. “The Structure of Hippocampal C Interactions Optimizes Spatial Coding across Experience.”10.1523/JNEUROSCI.0194-23.2023__The Journal of Neuroscience, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.
LibreCat: https://research-explorer.ista.ac.at/record/14656
DOI: 10.1523/JNEUROSCI.0194-23.2023
PMID: 37758476

Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?”10.1016/j.coisb.2022.100435__Current Opinion in Systems Biology, vol. 31, no. 9, 100435, Elsevier, 2022, doi:10.1016/j.coisb.2022.100435.
LibreCat: https://research-explorer.ista.ac.at/record/12156
DOI: 10.1016/j.coisb.2022.100435

Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.”10.7554/eLife.64543__ELife, vol. 11, e64543, eLife Sciences Publications, 2022, doi:10.7554/eLife.64543.
LibreCat: https://research-explorer.ista.ac.at/record/10736
DOI: 10.7554/eLife.64543
WoS: 000751104400001
PMID: 35080492

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.
LibreCat: https://research-explorer.ista.ac.at/record/12332
DOI: 10.1371/journal.pbio.3001889
WoS: 000925192000001

Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.”10.1073/pnas.2123152119__Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.
LibreCat: https://research-explorer.ista.ac.at/record/12081
DOI: 10.1073/pnas.2123152119
WoS: 000889278400014
PMID: 36037343

Lombardi, Fabrizio, et al. Quantifying the Coexistence of Neuronal Oscillations and Avalanches. arXiv, doi:10.48550/ARXIV.2108.06686.
LibreCat: https://research-explorer.ista.ac.at/record/10912
DOI: 10.48550/ARXIV.2108.06686
arXiv: 2108.06686

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.
LibreCat: https://research-explorer.ista.ac.at/record/10579
DOI: 10.48550/arXiv.2112.13558
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.
LibreCat: https://research-explorer.ista.ac.at/record/9226
DOI: 10.1242/dev.176065
WoS: 000613906000007
PMID: 33526425

Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.”10.1371/journal.pone.0248940__PLoS ONE, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:10.1371/journal.pone.0248940.
LibreCat: https://research-explorer.ista.ac.at/record/9362
DOI: 10.1371/journal.pone.0248940
WoS: 000641474900072
PMID: 33857170

Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.”10.1371/journal.pcbi.1008529__PLOS Computational Biology, vol. 17, e1008529, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008529.
LibreCat: https://research-explorer.ista.ac.at/record/8997
DOI: 10.1371/journal.pcbi.1008529
WoS: 000608045000010

Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.”10.1016/j.neuron.2021.01.020__Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.
LibreCat: https://research-explorer.ista.ac.at/record/7553
DOI: 10.1016/j.neuron.2021.01.020
WoS: 000637809600006

Nardin, Michele, et al. “The Structure of Hippocampal C Interactions Optimizes Spatial Coding across Experience.”10.1101/2021.09.28.460602__BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602.
LibreCat: https://research-explorer.ista.ac.at/record/10077
DOI: 10.1101/2021.09.28.460602

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.
LibreCat: https://research-explorer.ista.ac.at/record/7656
DOI: 10.3389/fncom.2020.00020
WoS: 000525543200001
PMID: 32231528

Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.”10.1073/pnas.1912804117__Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117.
LibreCat: https://research-explorer.ista.ac.at/record/8698
DOI: 10.1073/pnas.1912804117
WoS: 000579045200012
PMID: 32948691

Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.”10.1073/pnas.2006731117__PNAS, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:10.1073/pnas.2006731117.
LibreCat: https://research-explorer.ista.ac.at/record/9000
DOI: 10.1073/pnas.2006731117
WoS: 000600608300015
PMID: 33268497

Grah, Rok, et al. “Normative Models of Enhancer Function.”10.1101/2020.04.08.029405__BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.
LibreCat: https://research-explorer.ista.ac.at/record/7675
DOI: 10.1101/2020.04.08.029405

Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.”10.1038/s41467-020-17734-z__Nature Communications, vol. 11, 4013, Springer Nature, 2020, doi:10.1038/s41467-020-17734-z.
LibreCat: https://research-explorer.ista.ac.at/record/8250
DOI: 10.1038/s41467-020-17734-z
WoS: 000562769300008

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.
LibreCat: https://research-explorer.ista.ac.at/record/7673
DOI: 10.1101/2020.04.18.047886

Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.”10.1038/s41559-020-1132-7__Nature Ecology &; Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.
LibreCat: https://research-explorer.ista.ac.at/record/7652
DOI: 10.1038/s41559-020-1132-7
WoS: 000519008300005

Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579, ArXiv.
LibreCat: https://research-explorer.ista.ac.at/record/7552
arXiv: 1912.08579

Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.”10.1016/j.cell.2019.01.007__Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.
LibreCat: https://research-explorer.ista.ac.at/record/5945
DOI: 10.1016/j.cell.2019.01.007
WoS: 000457969200015
PMID: 30712870

Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.”10.1371/journal.pcbi.1007168__PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.
LibreCat: https://research-explorer.ista.ac.at/record/6784
DOI: 10.1371/journal.pcbi.1007168
WoS: 000481577700032

Ruess, Jakob, et al. Supporting Text and Results. Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.
LibreCat: https://research-explorer.ista.ac.at/record/9786
DOI: 10.1371/journal.pcbi.1007168.s001

Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.”10.1371/journal.pcbi.1007290__PLoS Computational Biology, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:10.1371/journal.pcbi.1007290.
LibreCat: https://research-explorer.ista.ac.at/record/6900
DOI: 10.1371/journal.pcbi.1007290
WoS: 000489741800021
PMID: 31479447

Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.”10.1109/ITW44776.2019.8989292__IEEE Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.
LibreCat: https://research-explorer.ista.ac.at/record/7606
DOI: 10.1109/ITW44776.2019.8989292
WoS: 000540384500015
arXiv: 1812.01475

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.
LibreCat: https://research-explorer.ista.ac.at/record/281
DOI: 10.1073/pnas.1716659115
WoS: 000434114900071
PMID: 29784812

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.
LibreCat: https://research-explorer.ista.ac.at/record/406
DOI: 10.1371/journal.pone.0193049
WoS: 000426896800032

Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab. Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.
LibreCat: https://research-explorer.ista.ac.at/record/9831
DOI: 10.1371/journal.pone.0193049.s001

Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.”10.1103/PhysRevE.98.042410__Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.
LibreCat: https://research-explorer.ista.ac.at/record/31
DOI: 10.1103/PhysRevE.98.042410
WoS: 000447486100004

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.
LibreCat: https://research-explorer.ista.ac.at/record/543
DOI: 10.1073/pnas.1711114115
WoS: 000419128700049

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.
LibreCat: https://research-explorer.ista.ac.at/record/292
DOI: 10.1371/journal.pcbi.1006057
WoS: 000434012100002

Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.
LibreCat: https://research-explorer.ista.ac.at/record/5584
DOI: 10.15479/AT:ISTA:98

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.
LibreCat: https://research-explorer.ista.ac.at/record/161
DOI: 10.1038/s41467-018-05417-9
WoS: 000440149300021

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.
LibreCat: https://research-explorer.ista.ac.at/record/5587
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.
LibreCat: https://research-explorer.ista.ac.at/record/67
DOI: 10.1038/s41559-018-0651-y
WoS: 000447947600021

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.
LibreCat: https://research-explorer.ista.ac.at/record/5585
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.
LibreCat: https://research-explorer.ista.ac.at/record/613
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.
LibreCat: https://research-explorer.ista.ac.at/record/720
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.
LibreCat: https://research-explorer.ista.ac.at/record/725
DOI: 10.1073/pnas.1703817114
PMID: 28874581

Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.
LibreCat: https://research-explorer.ista.ac.at/record/9709
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.
LibreCat: https://research-explorer.ista.ac.at/record/1104
DOI: 10.1038/s41467-017-02159-y
WoS: 000417241200004

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.
LibreCat: https://research-explorer.ista.ac.at/record/955
DOI: 10.1038/s41467-017-00238-8
WoS: 000407198800005

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.
LibreCat: https://research-explorer.ista.ac.at/record/943
DOI: 10.1126/science.aam5887
WoS: 000404351500036
PMID: 28663499

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.
LibreCat: https://research-explorer.ista.ac.at/record/730
DOI: 10.1016/j.conb.2017.08.001
WoS: 000416196400016

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.
LibreCat: https://research-explorer.ista.ac.at/record/5562
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.
LibreCat: https://research-explorer.ista.ac.at/record/5560
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.
LibreCat: https://research-explorer.ista.ac.at/record/665
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.
LibreCat: https://research-explorer.ista.ac.at/record/1082

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.
LibreCat: https://research-explorer.ista.ac.at/record/1105

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.
LibreCat: https://research-explorer.ista.ac.at/record/1171
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.
LibreCat: https://research-explorer.ista.ac.at/record/1242
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.
LibreCat: https://research-explorer.ista.ac.at/record/1248
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.
LibreCat: https://research-explorer.ista.ac.at/record/1420
DOI: 10.1534/genetics.115.184127
arXiv: 1510.08344

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.
LibreCat: https://research-explorer.ista.ac.at/record/1197
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.
LibreCat: https://research-explorer.ista.ac.at/record/1270
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.
LibreCat: https://research-explorer.ista.ac.at/record/9870
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.
LibreCat: https://research-explorer.ista.ac.at/record/9869
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.
LibreCat: https://research-explorer.ista.ac.at/record/9871
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.
LibreCat: https://research-explorer.ista.ac.at/record/1358
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.
LibreCat: https://research-explorer.ista.ac.at/record/1697
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.
LibreCat: https://research-explorer.ista.ac.at/record/1701
DOI: 10.1073/pnas.1514188112
PMID: 26330611

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.
LibreCat: https://research-explorer.ista.ac.at/record/1885
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.
LibreCat: https://research-explorer.ista.ac.at/record/1940
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.
LibreCat: https://research-explorer.ista.ac.at/record/9712
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.
LibreCat: https://research-explorer.ista.ac.at/record/1666
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.
LibreCat: https://research-explorer.ista.ac.at/record/1576
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.
LibreCat: https://research-explorer.ista.ac.at/record/1886
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.
LibreCat: https://research-explorer.ista.ac.at/record/2231
DOI: 10.1016/j.bpj.2014.01.014
PMID: 24606943

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.
LibreCat: https://research-explorer.ista.ac.at/record/3263
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.
LibreCat: https://research-explorer.ista.ac.at/record/9752
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.
LibreCat: https://research-explorer.ista.ac.at/record/2257
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.
LibreCat: https://research-explorer.ista.ac.at/record/2818
DOI: 10.1162/NECO_a_00463
arXiv: 1209.0121

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.
LibreCat: https://research-explorer.ista.ac.at/record/2850
DOI: 10.1088/1742-5468/2013/03/P03011
arXiv: 1207.6319

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.
LibreCat: https://research-explorer.ista.ac.at/record/2851
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.
LibreCat: https://research-explorer.ista.ac.at/record/2863
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.
LibreCat: https://research-explorer.ista.ac.at/record/2913
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.
LibreCat: https://research-explorer.ista.ac.at/record/3261
DOI: 10.1073/pnas.1315642110
PMID: 24089448

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.
LibreCat: https://research-explorer.ista.ac.at/record/2277
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.
LibreCat: https://research-explorer.ista.ac.at/record/2914
DOI: 10.1103/PhysRevLett.110.018701
arXiv: 0806.2694

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.
LibreCat: https://research-explorer.ista.ac.at/record/3262
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.
LibreCat: https://research-explorer.ista.ac.at/record/3374
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.
LibreCat: https://research-explorer.ista.ac.at/record/3276
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.
LibreCat: https://research-explorer.ista.ac.at/record/3384
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.
LibreCat: https://research-explorer.ista.ac.at/record/3401
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.
LibreCat: https://research-explorer.ista.ac.at/record/3735
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.
LibreCat: https://research-explorer.ista.ac.at/record/3736
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.
LibreCat: https://research-explorer.ista.ac.at/record/3738
DOI: 10.1103/PhysRevE.81.041905

Tkadik, Gasper. Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics. Elsevier, 2010.
LibreCat: https://research-explorer.ista.ac.at/record/3430

Tkadik, Gasper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” ArXiv, vol. q-MN, ArXiv, 2010, pp. 1–52.
LibreCat: https://research-explorer.ista.ac.at/record/3743

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.
LibreCat: https://research-explorer.ista.ac.at/record/3737
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.
LibreCat: https://research-explorer.ista.ac.at/record/3733
DOI: 10.1073/pnas.0905497106

Tkadik, Gasper, et al. “Spin Glass Models for a Network of Real Neurons.” ArXiv, vol. q-NC, ArXiv, 2009.
LibreCat: https://research-explorer.ista.ac.at/record/3732

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.
LibreCat: https://research-explorer.ista.ac.at/record/3747
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.
LibreCat: https://research-explorer.ista.ac.at/record/3745
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.
LibreCat: https://research-explorer.ista.ac.at/record/3734
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.
LibreCat: https://research-explorer.ista.ac.at/record/3739
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.
LibreCat: https://research-explorer.ista.ac.at/record/3740
DOI: 10.1073/pnas.0806077105