Gasper Tkacik

Tkacik Group

106 Publications

Mark all

[106]
2023 | Journal Article | IST-REx-ID: 13127 | OA
Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232, Springer Nature, 2023, doi:10.1038/s41467-023-38947-y.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[105]
2023 | Journal Article | IST-REx-ID: 12762 | OA
Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9.
[Published Version] View | Files available | DOI | arXiv
 
[104]
2023 | Journal Article | IST-REx-ID: 14515 | OA
Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:10.1103/PhysRevX.13.041017.
[Published Version] View | Files available | DOI | arXiv
 
[103]
2023 | Journal Article | IST-REx-ID: 14656 | OA
Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.
[Published Version] View | Files available | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[102]
2022 | Journal Article | IST-REx-ID: 12156 | OA
Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology, vol. 31, no. 9, 100435, Elsevier, 2022, doi:10.1016/j.coisb.2022.100435.
[Published Version] View | Files available | DOI
 
[101]
2022 | Journal Article | IST-REx-ID: 10736 | OA
Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications, 2022, doi:10.7554/eLife.64543.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[100]
2022 | Journal Article | IST-REx-ID: 12332 | OA
Mlynarski, Wiktor F., and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” PLoS Biology, vol. 20, no. 12, Public Library of Science, 2022, p. e3001889, doi:10.1371/journal.pbio.3001889.
[Published Version] View | Files available | DOI | WoS
 
[99]
2022 | Journal Article | IST-REx-ID: 12081 | OA
Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” 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.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[98]
2021 | Preprint | IST-REx-ID: 10912 | OA
Lombardi, Fabrizio, et al. Quantifying the Coexistence of Neuronal Oscillations and Avalanches. arXiv, doi:10.48550/ARXIV.2108.06686.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[97]
2021 | Preprint | IST-REx-ID: 10579 | OA
Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” ArXiv, 2112.13558, doi:10.48550/arXiv.2112.13558.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[96]
2021 | Journal Article | IST-REx-ID: 9226 | OA
Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development, vol. 148, no. 2, dev176065, The Company of Biologists, 2021, doi:10.1242/dev.176065.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[95]
2021 | Journal Article | IST-REx-ID: 9362 | OA
Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:10.1371/journal.pone.0248940.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[94]
2021 | Journal Article | IST-REx-ID: 8997 | OA
Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology, vol. 17, e1008529, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008529.
[Published Version] View | Files available | DOI | WoS
 
[93]
2021 | Journal Article | IST-REx-ID: 7553 | OA
Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS
 
[92]
2021 | Preprint | IST-REx-ID: 10077 | OA
Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[91]
2020 | Journal Article | IST-REx-ID: 7656 | OA
Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” Frontiers in Computational Neuroscience, vol. 14, 20, Frontiers, 2020, doi:10.3389/fncom.2020.00020.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[90]
2020 | Journal Article | IST-REx-ID: 8698 | OA
Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” 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.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[89]
2020 | Journal Article | IST-REx-ID: 9000 | OA
Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:10.1073/pnas.2006731117.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2020 | Preprint | IST-REx-ID: 7675 | OA
Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[87]
2020 | Journal Article | IST-REx-ID: 8250 | OA
Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020, doi:10.1038/s41467-020-17734-z.
[Published Version] View | Files available | DOI | WoS
 
[86]
2020 | Preprint | IST-REx-ID: 7673 | OA
Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[85]
2020 | Journal Article | IST-REx-ID: 7652 | OA
Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.
[Submitted Version] View | Files available | DOI | WoS
 
[84]
2019 | Preprint | IST-REx-ID: 7552 | OA
Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579, ArXiv.
[Preprint] View | Download Preprint (ext.) | arXiv
 
[83]
2019 | Journal Article | IST-REx-ID: 5945 | OA
Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.
[Published Version] View | Files available | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[82]
2019 | Journal Article | IST-REx-ID: 6784 | OA
Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.
[Published Version] View | Files available | DOI | WoS
 
[81]
2019 | Research Data Reference | IST-REx-ID: 9786
Ruess, Jakob, et al. Supporting Text and Results. Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.
[Published Version] View | Files available | DOI
 
[80]
2019 | Journal Article | IST-REx-ID: 6900 | OA
Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:10.1371/journal.pcbi.1007290.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[79]
2019 | Conference Paper | IST-REx-ID: 7606 | OA
Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | arXiv
 
[78]
2018 | Journal Article | IST-REx-ID: 281 | OA
Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | PubMed | Europe PMC
 
[77]
2018 | Journal Article | IST-REx-ID: 406 | OA
Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.
[Submitted Version] View | Files available | DOI | WoS
 
[76]
2018 | Research Data Reference | IST-REx-ID: 9831
Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab. Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.
[Published Version] View | Files available | DOI
 
[75]
2018 | Journal Article | IST-REx-ID: 31 | OA
Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.
[Preprint] View | DOI | Download Preprint (ext.) | WoS
 
[74]
2018 | Journal Article | IST-REx-ID: 543 | OA
Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS
 
[73]
2018 | Journal Article | IST-REx-ID: 292 | OA
Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.
[Published Version] View | Files available | DOI | WoS
 
[72]
2018 | Research Data | IST-REx-ID: 5584 | OA
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.
[Published Version] View | Files available | DOI
 
[71]
2018 | Journal Article | IST-REx-ID: 161 | OA
De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.
[Published Version] View | Files available | DOI | WoS
 
[70]
2018 | Research Data | IST-REx-ID: 5587 | OA
De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.
[Published Version] View | Files available | DOI
 
[69]
2018 | Journal Article | IST-REx-ID: 67 | OA
Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.
[Submitted Version] View | Files available | DOI | WoS
 
[68]
2018 | Research Data | IST-REx-ID: 5585 | OA
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.
[Published Version] View | Files available | DOI
 
[67]
2017 | Journal Article | IST-REx-ID: 613 | OA
Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.
[Published Version] View | Files available | DOI
 
[66]
2017 | Journal Article | IST-REx-ID: 720 | OA
Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.
[Published Version] View | Files available | DOI
 
[65]
2017 | Journal Article | IST-REx-ID: 725 | OA
Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[64]
2017 | Research Data Reference | IST-REx-ID: 9709 | OA
Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[63]
2017 | Journal Article | IST-REx-ID: 1104 | OA
Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:10.1038/s41467-017-02159-y.
[Published Version] View | Files available | DOI | WoS
 
[62]
2017 | Journal Article | IST-REx-ID: 955 | OA
Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
[Published Version] View | Files available | DOI | WoS
 
[61]
2017 | Journal Article | IST-REx-ID: 943 | OA
Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[60]
2017 | Journal Article | IST-REx-ID: 730
Savin, Cristina, and Gašper Tkačik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” Current Opinion in Neurobiology, vol. 46, Elsevier, 2017, pp. 120–26, doi:10.1016/j.conb.2017.08.001.
View | DOI | WoS
 
[59]
2017 | Research Data | IST-REx-ID: 5562 | OA
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.
[Published Version] View | Files available | DOI
 
[58]
2017 | Research Data | IST-REx-ID: 5560 | OA
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.
[Published Version] View | Files available | DOI
 
[57]
2017 | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:10.1126/science.aaf4762.
View | Files available | DOI
 
[56]
2016 | Conference Paper | IST-REx-ID: 1082 | OA
Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems, 2016, pp. 1965–73.
[Preprint] View | Files available | Download Preprint (ext.)
 
[55]
2016 | Conference Paper | IST-REx-ID: 1105
Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18.
View | Download None (ext.)
 
[54]
2016 | Journal Article | IST-REx-ID: 1171
Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function" by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 166–67, doi:10.1016/j.plrev.2016.06.005.
View | DOI
 
[53]
2016 | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” 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.
[Preprint] View | DOI | Download Preprint (ext.)
 
[52]
2016 | Journal Article | IST-REx-ID: 1248 | OA
Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803.
[Preprint] View | DOI | Download Preprint (ext.)
 
[51]
2016 | Journal Article | IST-REx-ID: 1420 | OA
Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[50]
2016 | Journal Article | IST-REx-ID: 1197 | OA
Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005148.
[Published Version] View | Files available | DOI
 
[49]
2016 | Journal Article | IST-REx-ID: 1270 | OA
Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.
[Published Version] View | Files available | DOI
 
[48]
2016 | Research Data Reference | IST-REx-ID: 9870
Hillenbrand, Patrick, et al. Computation of Positional Information in an Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002.
[Published Version] View | Files available | DOI
 
[47]
2016 | Research Data Reference | IST-REx-ID: 9869
Hillenbrand, Patrick, et al. Error Bound on an Estimator of Position. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s001.
[Published Version] View | Files available | DOI
 
[46]
2016 | Research Data Reference | IST-REx-ID: 9871
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.
[Published Version] View | Files available | DOI
 
[45]
2016 | Journal Article | IST-REx-ID: 1358 | OA
Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.
[Published Version] View | Files available | DOI
 
[44]
2015 | Journal Article | IST-REx-ID: 1697 | OA
Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304.
[Published Version] View | Files available | DOI
 
[43]
2015 | Journal Article | IST-REx-ID: 1701 | OA
Tkačik, Gašper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[42]
2015 | Journal Article | IST-REx-ID: 1885 | OA
Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.
[Preprint] View | DOI | Download Preprint (ext.)
 
[41]
2015 | Journal Article | IST-REx-ID: 1940 | OA
Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” 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.
[Preprint] View | DOI | Download Preprint (ext.)
 
[40]
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.
[Published Version] View | Files available | DOI
 
[39]
2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
[Published Version] View | Files available | DOI
 
[38]
2015 | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[37]
2014 | Journal Article | IST-REx-ID: 1886 | OA
Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.
[Published Version] View | Files available | DOI
 
[36]
2014 | Journal Article | IST-REx-ID: 2231 | OA
Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[35]
2014 | Journal Article | IST-REx-ID: 3263 | OA
Tkačik, Gašper, et al. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” PLoS One, vol. 9, no. 1, e85841, Public Library of Science, 2014, doi:10.1371/journal.pone.0085841.
[Published Version] View | Files available | DOI
 
[34]
2014 | Research Data Reference | IST-REx-ID: 9752 | OA
Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[33]
2014 | Journal Article | IST-REx-ID: 2257 | OA
Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[32]
2013 | Journal Article | IST-REx-ID: 2818 | OA
Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:10.1162/NECO_a_00463.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[31]
2013 | Journal Article | IST-REx-ID: 2850 | OA
Tkačik, Gašper, et al. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, P03011, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03011.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[30]
2013 | Journal Article | IST-REx-ID: 2851
Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, P03015, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03015.
View | DOI
 
[29]
2013 | Journal Article | IST-REx-ID: 2863 | OA
Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.
[Published Version] View | Files available | DOI
 
[28]
2013 | Journal Article | IST-REx-ID: 2913 | OA
Tkačik, Gašper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.058104.
[Preprint] View | DOI | Download Preprint (ext.)
 
[27]
2013 | Journal Article | IST-REx-ID: 3261 | OA
Dubuis, Julien, et al. “Positional Information, in Bits.” PNAS, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[26]
2013 | Journal Article | IST-REx-ID: 2277 | OA
Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003344.
[Published Version] View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2914 | OA
Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” Physical Review Letters, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.018701.
[Published Version] View | Files available | DOI | arXiv
 
[24]
2012 | Journal Article | IST-REx-ID: 3262 | OA
Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” 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.
[Preprint] View | DOI | Download Preprint (ext.)
 
[23]
2011 | Journal Article | IST-REx-ID: 3374 | OA
Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” Journal of Physics: Condensed Matter, vol. 23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:10.1088/0953-8984/23/15/153102.
[Submitted Version] View | DOI | Download Submitted Version (ext.)
 
[22]
2011 | Journal Article | IST-REx-ID: 3276 | OA
Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0019884.
View | Files available | DOI
 
[21]
2011 | Journal Article | IST-REx-ID: 3384 | OA
Tkačik, Gašper, et al. “Natural Images from the Birthplace of the Human Eye.” PLoS One, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:10.1371/journal.pone.0020409.
[Published Version] View | Files available | DOI
 
[20]
2011 | Journal Article | IST-REx-ID: 3401
Little, Shawn, et al. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized Source.” PLoS Biology, vol. 9, no. 3, e1000596, Public Library of Science, 2011, doi:10.1371/journal.pbio.1000596.
View | DOI
 
[19]
2010 | Journal Article | IST-REx-ID: 3735
Tkačik, Gašper, et al. “Local Statistics in Natural Scenes Predict the Saliency of Synthetic Textures.” PNAS, vol. 107, no. 42, National Academy of Sciences, 2010, pp. 18149–54, doi:10.1073/pnas.0914916107.
View | DOI | Download (ext.)
 
[18]
2010 | Journal Article | IST-REx-ID: 3736
Tkačik, Gašper, et al. “Optimal Population Coding by Noisy Spiking Neurons.” PNAS, vol. 107, no. 32, National Academy of Sciences, 2010, pp. 14419–24, doi:10.1073/pnas.1004906107.
View | DOI | Download (ext.)
 
[17]
2010 | Journal Article | IST-REx-ID: 3738
Walczak, Aleksandra, et al. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 81, no. 4, American Institute of Physics, 2010, doi:10.1103/PhysRevE.81.041905.
View | DOI | Download (ext.)
 
[16]
2010 | Conference Paper | IST-REx-ID: 3430 | OA
Tkačik, Gašper. Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics. Elsevier, 2010.
View | Download (ext.)
 
[15]
2010 | Preprint | IST-REx-ID: 3743 | OA
Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” ArXiv, vol. q-MN, ArXiv, 2010, pp. 1–52.
View | Download (ext.)
 
[14]
2009 | Journal Article | IST-REx-ID: 3737
Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 80, no. 3, American Institute of Physics, 2009, doi:10.1103/PhysRevE.80.031920.
View | DOI | Download (ext.)
 
[13]
2009 | Journal Article | IST-REx-ID: 3733
Kryazhimskiy, Sergey, et al. “The Dynamics of Adaptation on Correlated Fitness Landscapes.” PNAS, vol. 106, no. 44, National Academy of Sciences, 2009, pp. 18638–43, doi:10.1073/pnas.0905497106.
View | DOI | Download (ext.)
 
[12]
2009 | Preprint | IST-REx-ID: 3732 | OA
Tkačik, Gašper, et al. “Spin Glass Models for a Network of Real Neurons.” ArXiv, vol. q-NC, ArXiv, 2009.
View | Download (ext.)
 
[11]
2009 | Book Chapter | IST-REx-ID: 3747
Tkačik, Gašper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.” Encyclopedia of Complexity and Systems Science, edited by R. Meyers, Springer, 2009, pp. 719–41, doi:10.1007/978-0-387-30440-3_48.
View | DOI
 
[10]
2009 | Journal Article | IST-REx-ID: 3745
Tkačik, Gašper, and William Bialek. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5, American Institute of Physics, 2009, doi:10.1103/PhysRevE.79.051901.
View | DOI
 
[9]
2008 | Journal Article | IST-REx-ID: 3734 | OA
Tkačik, Gašper, et al. “The Role of Input Noise in Transcriptional Regulation.” PLoS One, vol. 3, no. 7, Public Library of Science, 2008, doi:10.1371/journal.pone.0002774.
View | DOI | Download (ext.)
 
[8]
2008 | Journal Article | IST-REx-ID: 3739
Tkačik, Gašper, et al. “Information Capacity of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1, American Institute of Physics, 2008, doi:10.1103/PhysRevE.78.011910.
View | DOI
 
[7]
2008 | Journal Article | IST-REx-ID: 3740 | OA
Tkačik, Gašper, et al. “Information Flow and Optimization in Transcriptional Regulation.” PNAS, vol. 105, no. 34, National Academy of Sciences, 2008, pp. 12265–70, doi:10.1073/pnas.0806077105.
View | DOI | Download (ext.)
 
[6]
2008 | Journal Article | IST-REx-ID: 3744 | OA
Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” Biosystems, vol. 93, no. 1–2, Elsevier, 2008, pp. 90–100, doi:10.1016/j.biosystems.2008.04.011.
View | DOI | Download (ext.)
 
[5]
2007 | Journal Article | IST-REx-ID: 3731
Kinney, Justin, et al. “Precise Physical Models of Protein-DNA Interaction from High-Throughput Data.” PNAS, vol. 104, no. 2, National Academy of Sciences, 2007, pp. 501–06, doi:10.1073/pnas.0609908104.
View | DOI | Download (ext.)
 
[4]
2007 | Preprint | IST-REx-ID: 3742 | OA
Broderick, Tamara, et al. “Faster Solutions of the Inverse Pairwise Ising Problem.” ArXiv, vol. q-QM, ArXiv, 2007.
View | Download (ext.)
 
[3]
2006 | Preprint | IST-REx-ID: 3431 | OA
Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv, ArXiv, 2006, pp. 1–4.
View | Download (ext.)
 
[2]
2005 | Journal Article | IST-REx-ID: 3741 | OA
Slonim, N., et al. “Information-Based Clustering.” PNAS, vol. 102, no. 51, National Academy of Sciences, 2005, pp. 18297–302, doi:10.1073/pnas.0507432102.
View | DOI | Download (ext.)
 
[1]
2005 | Preprint | IST-REx-ID: 3746 | OA
Slonim, Noam, et al. “Estimating Mutual Information and Multi-Information in Large Networks.” ArXiv, ArXiv, 2005, pp. 1–11.
View | Download (ext.)
 
Marked Publication(s)

Search

Filter Publications

    • Display / Sort

    Citation Style: MLA

    Export / Embed

106 Publications

Mark all

[106]
2023 | Journal Article | IST-REx-ID: 13127 | OA
Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232, Springer Nature, 2023, doi:10.1038/s41467-023-38947-y.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[105]
2023 | Journal Article | IST-REx-ID: 12762 | OA
Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9.
[Published Version] View | Files available | DOI | arXiv
 
[104]
2023 | Journal Article | IST-REx-ID: 14515 | OA
Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:10.1103/PhysRevX.13.041017.
[Published Version] View | Files available | DOI | arXiv
 
[103]
2023 | Journal Article | IST-REx-ID: 14656 | OA
Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.
[Published Version] View | Files available | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[102]
2022 | Journal Article | IST-REx-ID: 12156 | OA
Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology, vol. 31, no. 9, 100435, Elsevier, 2022, doi:10.1016/j.coisb.2022.100435.
[Published Version] View | Files available | DOI
 
[101]
2022 | Journal Article | IST-REx-ID: 10736 | OA
Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications, 2022, doi:10.7554/eLife.64543.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[100]
2022 | Journal Article | IST-REx-ID: 12332 | OA
Mlynarski, Wiktor F., and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” PLoS Biology, vol. 20, no. 12, Public Library of Science, 2022, p. e3001889, doi:10.1371/journal.pbio.3001889.
[Published Version] View | Files available | DOI | WoS
 
[99]
2022 | Journal Article | IST-REx-ID: 12081 | OA
Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” 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.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[98]
2021 | Preprint | IST-REx-ID: 10912 | OA
Lombardi, Fabrizio, et al. Quantifying the Coexistence of Neuronal Oscillations and Avalanches. arXiv, doi:10.48550/ARXIV.2108.06686.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[97]
2021 | Preprint | IST-REx-ID: 10579 | OA
Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” ArXiv, 2112.13558, doi:10.48550/arXiv.2112.13558.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[96]
2021 | Journal Article | IST-REx-ID: 9226 | OA
Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development, vol. 148, no. 2, dev176065, The Company of Biologists, 2021, doi:10.1242/dev.176065.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[95]
2021 | Journal Article | IST-REx-ID: 9362 | OA
Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:10.1371/journal.pone.0248940.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[94]
2021 | Journal Article | IST-REx-ID: 8997 | OA
Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology, vol. 17, e1008529, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008529.
[Published Version] View | Files available | DOI | WoS
 
[93]
2021 | Journal Article | IST-REx-ID: 7553 | OA
Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS
 
[92]
2021 | Preprint | IST-REx-ID: 10077 | OA
Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[91]
2020 | Journal Article | IST-REx-ID: 7656 | OA
Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” Frontiers in Computational Neuroscience, vol. 14, 20, Frontiers, 2020, doi:10.3389/fncom.2020.00020.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[90]
2020 | Journal Article | IST-REx-ID: 8698 | OA
Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” 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.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[89]
2020 | Journal Article | IST-REx-ID: 9000 | OA
Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:10.1073/pnas.2006731117.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2020 | Preprint | IST-REx-ID: 7675 | OA
Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[87]
2020 | Journal Article | IST-REx-ID: 8250 | OA
Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020, doi:10.1038/s41467-020-17734-z.
[Published Version] View | Files available | DOI | WoS
 
[86]
2020 | Preprint | IST-REx-ID: 7673 | OA
Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[85]
2020 | Journal Article | IST-REx-ID: 7652 | OA
Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.
[Submitted Version] View | Files available | DOI | WoS
 
[84]
2019 | Preprint | IST-REx-ID: 7552 | OA
Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579, ArXiv.
[Preprint] View | Download Preprint (ext.) | arXiv
 
[83]
2019 | Journal Article | IST-REx-ID: 5945 | OA
Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.
[Published Version] View | Files available | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[82]
2019 | Journal Article | IST-REx-ID: 6784 | OA
Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.
[Published Version] View | Files available | DOI | WoS
 
[81]
2019 | Research Data Reference | IST-REx-ID: 9786
Ruess, Jakob, et al. Supporting Text and Results. Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.
[Published Version] View | Files available | DOI
 
[80]
2019 | Journal Article | IST-REx-ID: 6900 | OA
Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:10.1371/journal.pcbi.1007290.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[79]
2019 | Conference Paper | IST-REx-ID: 7606 | OA
Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | arXiv
 
[78]
2018 | Journal Article | IST-REx-ID: 281 | OA
Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | PubMed | Europe PMC
 
[77]
2018 | Journal Article | IST-REx-ID: 406 | OA
Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.
[Submitted Version] View | Files available | DOI | WoS
 
[76]
2018 | Research Data Reference | IST-REx-ID: 9831
Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab. Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.
[Published Version] View | Files available | DOI
 
[75]
2018 | Journal Article | IST-REx-ID: 31 | OA
Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.
[Preprint] View | DOI | Download Preprint (ext.) | WoS
 
[74]
2018 | Journal Article | IST-REx-ID: 543 | OA
Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS
 
[73]
2018 | Journal Article | IST-REx-ID: 292 | OA
Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.
[Published Version] View | Files available | DOI | WoS
 
[72]
2018 | Research Data | IST-REx-ID: 5584 | OA
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.
[Published Version] View | Files available | DOI
 
[71]
2018 | Journal Article | IST-REx-ID: 161 | OA
De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.
[Published Version] View | Files available | DOI | WoS
 
[70]
2018 | Research Data | IST-REx-ID: 5587 | OA
De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.
[Published Version] View | Files available | DOI
 
[69]
2018 | Journal Article | IST-REx-ID: 67 | OA
Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.
[Submitted Version] View | Files available | DOI | WoS
 
[68]
2018 | Research Data | IST-REx-ID: 5585 | OA
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.
[Published Version] View | Files available | DOI
 
[67]
2017 | Journal Article | IST-REx-ID: 613 | OA
Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.
[Published Version] View | Files available | DOI
 
[66]
2017 | Journal Article | IST-REx-ID: 720 | OA
Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.
[Published Version] View | Files available | DOI
 
[65]
2017 | Journal Article | IST-REx-ID: 725 | OA
Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[64]
2017 | Research Data Reference | IST-REx-ID: 9709 | OA
Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[63]
2017 | Journal Article | IST-REx-ID: 1104 | OA
Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:10.1038/s41467-017-02159-y.
[Published Version] View | Files available | DOI | WoS
 
[62]
2017 | Journal Article | IST-REx-ID: 955 | OA
Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
[Published Version] View | Files available | DOI | WoS
 
[61]
2017 | Journal Article | IST-REx-ID: 943 | OA
Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[60]
2017 | Journal Article | IST-REx-ID: 730
Savin, Cristina, and Gašper Tkačik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” Current Opinion in Neurobiology, vol. 46, Elsevier, 2017, pp. 120–26, doi:10.1016/j.conb.2017.08.001.
View | DOI | WoS
 
[59]
2017 | Research Data | IST-REx-ID: 5562 | OA
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.
[Published Version] View | Files available | DOI
 
[58]
2017 | Research Data | IST-REx-ID: 5560 | OA
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.
[Published Version] View | Files available | DOI
 
[57]
2017 | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:10.1126/science.aaf4762.
View | Files available | DOI
 
[56]
2016 | Conference Paper | IST-REx-ID: 1082 | OA
Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems, 2016, pp. 1965–73.
[Preprint] View | Files available | Download Preprint (ext.)
 
[55]
2016 | Conference Paper | IST-REx-ID: 1105
Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18.
View | Download None (ext.)
 
[54]
2016 | Journal Article | IST-REx-ID: 1171
Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function" by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 166–67, doi:10.1016/j.plrev.2016.06.005.
View | DOI
 
[53]
2016 | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” 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.
[Preprint] View | DOI | Download Preprint (ext.)
 
[52]
2016 | Journal Article | IST-REx-ID: 1248 | OA
Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803.
[Preprint] View | DOI | Download Preprint (ext.)
 
[51]
2016 | Journal Article | IST-REx-ID: 1420 | OA
Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[50]
2016 | Journal Article | IST-REx-ID: 1197 | OA
Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005148.
[Published Version] View | Files available | DOI
 
[49]
2016 | Journal Article | IST-REx-ID: 1270 | OA
Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.
[Published Version] View | Files available | DOI
 
[48]
2016 | Research Data Reference | IST-REx-ID: 9870
Hillenbrand, Patrick, et al. Computation of Positional Information in an Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002.
[Published Version] View | Files available | DOI
 
[47]
2016 | Research Data Reference | IST-REx-ID: 9869
Hillenbrand, Patrick, et al. Error Bound on an Estimator of Position. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s001.
[Published Version] View | Files available | DOI
 
[46]
2016 | Research Data Reference | IST-REx-ID: 9871
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.
[Published Version] View | Files available | DOI
 
[45]
2016 | Journal Article | IST-REx-ID: 1358 | OA
Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.
[Published Version] View | Files available | DOI
 
[44]
2015 | Journal Article | IST-REx-ID: 1697 | OA
Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304.
[Published Version] View | Files available | DOI
 
[43]
2015 | Journal Article | IST-REx-ID: 1701 | OA
Tkačik, Gašper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[42]
2015 | Journal Article | IST-REx-ID: 1885 | OA
Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.
[Preprint] View | DOI | Download Preprint (ext.)
 
[41]
2015 | Journal Article | IST-REx-ID: 1940 | OA
Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” 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.
[Preprint] View | DOI | Download Preprint (ext.)
 
[40]
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.
[Published Version] View | Files available | DOI
 
[39]
2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
[Published Version] View | Files available | DOI
 
[38]
2015 | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[37]
2014 | Journal Article | IST-REx-ID: 1886 | OA
Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.
[Published Version] View | Files available | DOI
 
[36]
2014 | Journal Article | IST-REx-ID: 2231 | OA
Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[35]
2014 | Journal Article | IST-REx-ID: 3263 | OA
Tkačik, Gašper, et al. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” PLoS One, vol. 9, no. 1, e85841, Public Library of Science, 2014, doi:10.1371/journal.pone.0085841.
[Published Version] View | Files available | DOI
 
[34]
2014 | Research Data Reference | IST-REx-ID: 9752 | OA
Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[33]
2014 | Journal Article | IST-REx-ID: 2257 | OA
Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[32]
2013 | Journal Article | IST-REx-ID: 2818 | OA
Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:10.1162/NECO_a_00463.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[31]
2013 | Journal Article | IST-REx-ID: 2850 | OA
Tkačik, Gašper, et al. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, P03011, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03011.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[30]
2013 | Journal Article | IST-REx-ID: 2851
Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, P03015, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03015.
View | DOI
 
[29]
2013 | Journal Article | IST-REx-ID: 2863 | OA
Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.
[Published Version] View | Files available | DOI
 
[28]
2013 | Journal Article | IST-REx-ID: 2913 | OA
Tkačik, Gašper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.058104.
[Preprint] View | DOI | Download Preprint (ext.)
 
[27]
2013 | Journal Article | IST-REx-ID: 3261 | OA
Dubuis, Julien, et al. “Positional Information, in Bits.” PNAS, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[26]
2013 | Journal Article | IST-REx-ID: 2277 | OA
Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003344.
[Published Version] View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2914 | OA
Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” Physical Review Letters, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.018701.
[Published Version] View | Files available | DOI | arXiv
 
[24]
2012 | Journal Article | IST-REx-ID: 3262 | OA
Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” 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.
[Preprint] View | DOI | Download Preprint (ext.)
 
[23]
2011 | Journal Article | IST-REx-ID: 3374 | OA
Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” Journal of Physics: Condensed Matter, vol. 23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:10.1088/0953-8984/23/15/153102.
[Submitted Version] View | DOI | Download Submitted Version (ext.)
 
[22]
2011 | Journal Article | IST-REx-ID: 3276 | OA
Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0019884.
View | Files available | DOI
 
[21]
2011 | Journal Article | IST-REx-ID: 3384 | OA
Tkačik, Gašper, et al. “Natural Images from the Birthplace of the Human Eye.” PLoS One, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:10.1371/journal.pone.0020409.
[Published Version] View | Files available | DOI
 
[20]
2011 | Journal Article | IST-REx-ID: 3401
Little, Shawn, et al. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized Source.” PLoS Biology, vol. 9, no. 3, e1000596, Public Library of Science, 2011, doi:10.1371/journal.pbio.1000596.
View | DOI
 
[19]
2010 | Journal Article | IST-REx-ID: 3735
Tkačik, Gašper, et al. “Local Statistics in Natural Scenes Predict the Saliency of Synthetic Textures.” PNAS, vol. 107, no. 42, National Academy of Sciences, 2010, pp. 18149–54, doi:10.1073/pnas.0914916107.
View | DOI | Download (ext.)
 
[18]
2010 | Journal Article | IST-REx-ID: 3736
Tkačik, Gašper, et al. “Optimal Population Coding by Noisy Spiking Neurons.” PNAS, vol. 107, no. 32, National Academy of Sciences, 2010, pp. 14419–24, doi:10.1073/pnas.1004906107.
View | DOI | Download (ext.)
 
[17]
2010 | Journal Article | IST-REx-ID: 3738
Walczak, Aleksandra, et al. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 81, no. 4, American Institute of Physics, 2010, doi:10.1103/PhysRevE.81.041905.
View | DOI | Download (ext.)
 
[16]
2010 | Conference Paper | IST-REx-ID: 3430 | OA
Tkačik, Gašper. Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics. Elsevier, 2010.
View | Download (ext.)
 
[15]
2010 | Preprint | IST-REx-ID: 3743 | OA
Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” ArXiv, vol. q-MN, ArXiv, 2010, pp. 1–52.
View | Download (ext.)
 
[14]
2009 | Journal Article | IST-REx-ID: 3737
Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 80, no. 3, American Institute of Physics, 2009, doi:10.1103/PhysRevE.80.031920.
View | DOI | Download (ext.)
 
[13]
2009 | Journal Article | IST-REx-ID: 3733
Kryazhimskiy, Sergey, et al. “The Dynamics of Adaptation on Correlated Fitness Landscapes.” PNAS, vol. 106, no. 44, National Academy of Sciences, 2009, pp. 18638–43, doi:10.1073/pnas.0905497106.
View | DOI | Download (ext.)
 
[12]
2009 | Preprint | IST-REx-ID: 3732 | OA
Tkačik, Gašper, et al. “Spin Glass Models for a Network of Real Neurons.” ArXiv, vol. q-NC, ArXiv, 2009.
View | Download (ext.)
 
[11]
2009 | Book Chapter | IST-REx-ID: 3747
Tkačik, Gašper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.” Encyclopedia of Complexity and Systems Science, edited by R. Meyers, Springer, 2009, pp. 719–41, doi:10.1007/978-0-387-30440-3_48.
View | DOI
 
[10]
2009 | Journal Article | IST-REx-ID: 3745
Tkačik, Gašper, and William Bialek. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5, American Institute of Physics, 2009, doi:10.1103/PhysRevE.79.051901.
View | DOI
 
[9]
2008 | Journal Article | IST-REx-ID: 3734 | OA
Tkačik, Gašper, et al. “The Role of Input Noise in Transcriptional Regulation.” PLoS One, vol. 3, no. 7, Public Library of Science, 2008, doi:10.1371/journal.pone.0002774.
View | DOI | Download (ext.)
 
[8]
2008 | Journal Article | IST-REx-ID: 3739
Tkačik, Gašper, et al. “Information Capacity of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1, American Institute of Physics, 2008, doi:10.1103/PhysRevE.78.011910.
View | DOI
 
[7]
2008 | Journal Article | IST-REx-ID: 3740 | OA
Tkačik, Gašper, et al. “Information Flow and Optimization in Transcriptional Regulation.” PNAS, vol. 105, no. 34, National Academy of Sciences, 2008, pp. 12265–70, doi:10.1073/pnas.0806077105.
View | DOI | Download (ext.)
 
[6]
2008 | Journal Article | IST-REx-ID: 3744 | OA
Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” Biosystems, vol. 93, no. 1–2, Elsevier, 2008, pp. 90–100, doi:10.1016/j.biosystems.2008.04.011.
View | DOI | Download (ext.)
 
[5]
2007 | Journal Article | IST-REx-ID: 3731
Kinney, Justin, et al. “Precise Physical Models of Protein-DNA Interaction from High-Throughput Data.” PNAS, vol. 104, no. 2, National Academy of Sciences, 2007, pp. 501–06, doi:10.1073/pnas.0609908104.
View | DOI | Download (ext.)
 
[4]
2007 | Preprint | IST-REx-ID: 3742 | OA
Broderick, Tamara, et al. “Faster Solutions of the Inverse Pairwise Ising Problem.” ArXiv, vol. q-QM, ArXiv, 2007.
View | Download (ext.)
 
[3]
2006 | Preprint | IST-REx-ID: 3431 | OA
Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv, ArXiv, 2006, pp. 1–4.
View | Download (ext.)
 
[2]
2005 | Journal Article | IST-REx-ID: 3741 | OA
Slonim, N., et al. “Information-Based Clustering.” PNAS, vol. 102, no. 51, National Academy of Sciences, 2005, pp. 18297–302, doi:10.1073/pnas.0507432102.
View | DOI | Download (ext.)
 
[1]
2005 | Preprint | IST-REx-ID: 3746 | OA
Slonim, Noam, et al. “Estimating Mutual Information and Multi-Information in Large Networks.” ArXiv, ArXiv, 2005, pp. 1–11.
View | Download (ext.)
 
Marked Publication(s)

Search

Filter Publications

    • Display / Sort

    Citation Style: MLA

    Export / Embed