Gasper Tkacik

Tkacik Group

106 Publications

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[106]
2023 | Journal Article | IST-REx-ID: 13127 | OA
Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/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, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.
[Published Version] View | Files available | DOI | arXiv
 
[104]
2023 | Journal Article | IST-REx-ID: 14515 | OA
Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.041017.
[Published Version] View | Files available | DOI | arXiv
 
[103]
2023 | Journal Article | IST-REx-ID: 14656 | OA
Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023. https://doi.org/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, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology. Elsevier, 2022. https://doi.org/10.1016/j.coisb.2022.100435.
[Published Version] View | Files available | DOI
 
[101]
2022 | Journal Article | IST-REx-ID: 10736 | OA
Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications, 2022. https://doi.org/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. Public Library of Science, 2022. https://doi.org/10.1371/journal.pbio.3001889.
[Published Version] View | Files available | DOI | WoS
 
[99]
2022 | Journal Article | IST-REx-ID: 12081 | OA
Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.
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[98]
2021 | Preprint | IST-REx-ID: 10912 | OA
Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Quantifying the Coexistence of Neuronal Oscillations and Avalanches.” arXiv, n.d. https://doi.org/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, n.d. https://doi.org/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. The Company of Biologists, 2021. https://doi.org/10.1242/dev.176065.
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[95]
2021 | Journal Article | IST-REx-ID: 9362 | OA
Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science, 2021. https://doi.org/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, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.
[Published Version] View | Files available | DOI | WoS
 
[93]
2021 | Journal Article | IST-REx-ID: 7553 | OA
Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press, 2021. https://doi.org/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, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/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. Frontiers, 2020. https://doi.org/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, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/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, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006731117.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2020 | Preprint | IST-REx-ID: 7675 | OA
Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/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, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z.
[Published Version] View | Files available | DOI | WoS
 
[86]
2020 | Preprint | IST-REx-ID: 7673 | OA
Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/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, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7.
[Submitted Version] View | Files available | DOI | WoS
 
[84]
2019 | Preprint | IST-REx-ID: 7552 | OA
Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d.
[Preprint] View | Download Preprint (ext.) | arXiv
 
[83]
2019 | Journal Article | IST-REx-ID: 5945 | OA
Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007.
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[82]
2019 | Journal Article | IST-REx-ID: 6784 | OA
Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.
[Published Version] View | Files available | DOI | WoS
 
[81]
2019 | Research Data Reference | IST-REx-ID: 9786
Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting Text and Results.” Public Library of Science, 2019. https://doi.org/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, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/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, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper Bound on Mutual Information.” In IEEE Information Theory Workshop, ITW 2019. IEEE, 2019. https://doi.org/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, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1716659115.
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[77]
2018 | Journal Article | IST-REx-ID: 406 | OA
Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.
[Submitted Version] View | Files available | DOI | WoS
 
[76]
2018 | Research Data Reference | IST-REx-ID: 9831
Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.
[Published Version] View | Files available | DOI
 
[75]
2018 | Journal Article | IST-REx-ID: 31 | OA
Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410.
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[74]
2018 | Journal Article | IST-REx-ID: 543 | OA
Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/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, Stephane Deny, Georg S Martius, Olivier Marre, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pcbi.1006057.
[Published Version] View | Files available | DOI | WoS
 
[72]
2018 | Research Data | IST-REx-ID: 5584 | OA
Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.
[Published Version] View | Files available | DOI
 
[71]
2018 | Journal Article | IST-REx-ID: 161 | OA
De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/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. https://doi.org/10.15479/AT:ISTA:62.
[Published Version] View | Files available | DOI
 
[69]
2018 | Journal Article | IST-REx-ID: 67 | OA
Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution. Nature Publishing Group, 2018. https://doi.org/10.1038/s41559-018-0651-y.
[Submitted Version] View | Files available | DOI | WoS
 
[68]
2018 | Research Data | IST-REx-ID: 5585 | OA
Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108.
[Published Version] View | Files available | DOI
 
[67]
2017 | Journal Article | IST-REx-ID: 613 | OA
Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/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. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.
[Published Version] View | Files available | DOI
 
[65]
2017 | Journal Article | IST-REx-ID: 725 | OA
Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114.
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[64]
2017 | Research Data Reference | IST-REx-ID: 9709 | OA
Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/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, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-02159-y.
[Published Version] View | Files available | DOI | WoS
 
[62]
2017 | Journal Article | IST-REx-ID: 955 | OA
Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/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, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science. American Association for the Advancement of Science, 2017. https://doi.org/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. Elsevier, 2017. https://doi.org/10.1016/j.conb.2017.08.001.
View | DOI | WoS
 
[59]
2017 | Research Data | IST-REx-ID: 5562 | OA
Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:61.
[Published Version] View | Files available | DOI
 
[58]
2017 | Research Data | IST-REx-ID: 5560 | OA
Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:53.
[Published Version] View | Files available | DOI
 
[57]
2017 | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aaf4762.
View | Files available | DOI
 
[56]
2016 | Conference Paper | IST-REx-ID: 1082 | OA
Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems, 2016.
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[55]
2016 | Conference Paper | IST-REx-ID: 1105
Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems, 2016.
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[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. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.005.
View | DOI
 
[53]
2016 | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022404.
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[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. Annual Reviews, 2016. https://doi.org/10.1146/annurev-conmatphys-031214-014803.
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[51]
2016 | Journal Article | IST-REx-ID: 1420 | OA
Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[50]
2016 | Journal Article | IST-REx-ID: 1197 | OA
Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148.
[Published Version] View | Files available | DOI
 
[49]
2016 | Journal Article | IST-REx-ID: 1270 | OA
Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.
[Published Version] View | Files available | DOI
 
[48]
2016 | Research Data Reference | IST-REx-ID: 9870
Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s002.
[Published Version] View | Files available | DOI
 
[47]
2016 | Research Data Reference | IST-REx-ID: 9869
Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s001.
[Published Version] View | Files available | DOI
 
[46]
2016 | Research Data Reference | IST-REx-ID: 9871
Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s003.
[Published Version] View | Files available | DOI
 
[45]
2016 | Journal Article | IST-REx-ID: 1358 | OA
Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.
[Published Version] View | Files available | DOI
 
[44]
2015 | Journal Article | IST-REx-ID: 1697 | OA
Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora, Gašper Tkačik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004304.
[Published Version] View | Files available | DOI
 
[43]
2015 | Journal Article | IST-REx-ID: 1701 | OA
Tkačik, Gašper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer, Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS. National Academy of Sciences, 2015. https://doi.org/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, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics. Genetics Society of America, 2015. https://doi.org/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. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710.
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[40]
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.
[Published Version] View | Files available | DOI
 
[39]
2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.
[Published Version] View | Files available | DOI
 
[38]
2015 | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.115.248101.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[37]
2014 | Journal Article | IST-REx-ID: 1886 | OA
Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” ELife. eLife Sciences Publications, 2014. https://doi.org/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. Biophysical Society, 2014. https://doi.org/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, Anandamohan Ghosh, Elad Schneidman, and Ronen Segev. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0085841.
[Published Version] View | Files available | DOI
 
[34]
2014 | Research Data Reference | IST-REx-ID: 9752 | OA
Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. https://doi.org/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, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology. Public Library of Science, 2014. https://doi.org/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, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation. MIT Press , 2013. https://doi.org/10.1162/NECO_a_00463.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[31]
2013 | Journal Article | IST-REx-ID: 2850 | OA
Tkačik, Gašper, Olivier Marre, Thierry Mora, Dario Amodei, Michael Berry, and William Bialek. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/03/P03011.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[30]
2013 | Journal Article | IST-REx-ID: 2851
Berry, Michael, Gašper Tkačik, Julien Dubuis, Olivier Marre, and Ravá Da Silveira. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/03/P03015.
View | DOI
 
[29]
2013 | Journal Article | IST-REx-ID: 2863 | OA
Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1002922.
[Published Version] View | Files available | DOI
 
[28]
2013 | Journal Article | IST-REx-ID: 2913 | OA
Tkačik, Gašper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.058104.
[Preprint] View | DOI | Download Preprint (ext.)
 
[27]
2013 | Journal Article | IST-REx-ID: 3261 | OA
Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William Bialek. “Positional Information, in Bits.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1315642110.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[26]
2013 | Journal Article | IST-REx-ID: 2277 | OA
Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003344.
[Published Version] View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2914 | OA
Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical Thermodynamics of Natural Images.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.018701.
[Published Version] View | Files available | DOI | arXiv
 
[24]
2012 | Journal Article | IST-REx-ID: 3262 | OA
Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2012. https://doi.org/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. IOP Publishing Ltd., 2011. https://doi.org/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, Jan Homann, Kristina Simmons, Gašper Tkačik, Vijay Balasubramanian, and Philip Nelson. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0019884.
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[21]
2011 | Journal Article | IST-REx-ID: 3384 | OA
Tkačik, Gašper, Patrick Garrigan, Charles Ratliff, Grega Milcinski, Jennifer Klein, Lucia Seyfarth, Peter Sterling, David Brainard, and Vijay Balasubramanian. “Natural Images from the Birthplace of the Human Eye.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0020409.
[Published Version] View | Files available | DOI
 
[20]
2011 | Journal Article | IST-REx-ID: 3401
Little, Shawn, Gašper Tkačik, Thomas Kneeland, Eric Wieschaus, and Thomas Gregor. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized Source.” PLoS Biology. Public Library of Science, 2011. https://doi.org/10.1371/journal.pbio.1000596.
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[19]
2010 | Journal Article | IST-REx-ID: 3735
Tkačik, Gašper, Jason Prentice, Jonathan Victor, and Vijay Balasubramanian. “Local Statistics in Natural Scenes Predict the Saliency of Synthetic Textures.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.0914916107.
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[18]
2010 | Journal Article | IST-REx-ID: 3736
Tkačik, Gašper, Jason Prentice, Vijay Balasubramanian, and Elad Schneidman. “Optimal Population Coding by Noisy Spiking Neurons.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1004906107.
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[17]
2010 | Journal Article | IST-REx-ID: 3738
Walczak, Aleksandra, Gašper Tkačik, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2010. https://doi.org/10.1103/PhysRevE.81.041905.
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[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.
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[15]
2010 | Preprint | IST-REx-ID: 3743 | OA
Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” ArXiv. ArXiv, 2010.
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[14]
2009 | Journal Article | IST-REx-ID: 3737
Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2009. https://doi.org/10.1103/PhysRevE.80.031920.
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[13]
2009 | Journal Article | IST-REx-ID: 3733
Kryazhimskiy, Sergey, Gašper Tkačik, and Joshua Plotkin. “The Dynamics of Adaptation on Correlated Fitness Landscapes.” PNAS. National Academy of Sciences, 2009. https://doi.org/10.1073/pnas.0905497106.
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[12]
2009 | Preprint | IST-REx-ID: 3732 | OA
Tkačik, Gašper, Elad Schneidman, Michael Berry, and William Bialek. “Spin Glass Models for a Network of Real Neurons.” ArXiv. ArXiv, 2009.
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[11]
2009 | Book Chapter | IST-REx-ID: 3747
Tkačik, Gašper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.” In Encyclopedia of Complexity and Systems Science, edited by R. Meyers, 719–41. Springer, 2009. https://doi.org/10.1007/978-0-387-30440-3_48.
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[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. American Institute of Physics, 2009. https://doi.org/10.1103/PhysRevE.79.051901.
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[9]
2008 | Journal Article | IST-REx-ID: 3734 | OA
Tkačik, Gašper, Thomas Gregor, and William Bialek. “The Role of Input Noise in Transcriptional Regulation.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002774.
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[8]
2008 | Journal Article | IST-REx-ID: 3739
Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Capacity of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2008. https://doi.org/10.1103/PhysRevE.78.011910.
View | DOI
 
[7]
2008 | Journal Article | IST-REx-ID: 3740 | OA
Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Flow and Optimization in Transcriptional Regulation.” PNAS. National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0806077105.
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[6]
2008 | Journal Article | IST-REx-ID: 3744 | OA
Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” Biosystems. Elsevier, 2008. https://doi.org/10.1016/j.biosystems.2008.04.011.
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[5]
2007 | Journal Article | IST-REx-ID: 3731
Kinney, Justin, Gašper Tkačik, and Curtis Callan. “Precise Physical Models of Protein-DNA Interaction from High-Throughput Data.” PNAS. National Academy of Sciences, 2007. https://doi.org/10.1073/pnas.0609908104.
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[4]
2007 | Preprint | IST-REx-ID: 3742 | OA
Broderick, Tamara, Miroslav Dudik, Gašper Tkačik, Robert Schapire, and William Bialek. “Faster Solutions of the Inverse Pairwise Ising Problem.” ArXiv. ArXiv, 2007.
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[3]
2006 | Preprint | IST-REx-ID: 3431 | OA
Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models for Networks of Real Neurons.” ArXiv. ArXiv, 2006.
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[2]
2005 | Journal Article | IST-REx-ID: 3741 | OA
Slonim, N., G. Atwal, Gašper Tkačik, and William Bialek. “Information-Based Clustering.” PNAS. National Academy of Sciences, 2005. https://doi.org/10.1073/pnas.0507432102.
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[1]
2005 | Preprint | IST-REx-ID: 3746 | OA
Slonim, Noam, Gurinder Atwal, Gašper Tkačik, and William Bialek. “Estimating Mutual Information and Multi-Information in Large Networks.” ArXiv. ArXiv, 2005.
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[106]
2023 | Journal Article | IST-REx-ID: 13127 | OA
Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/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, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.
[Published Version] View | Files available | DOI | arXiv
 
[104]
2023 | Journal Article | IST-REx-ID: 14515 | OA
Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.041017.
[Published Version] View | Files available | DOI | arXiv
 
[103]
2023 | Journal Article | IST-REx-ID: 14656 | OA
Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023. https://doi.org/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, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology. Elsevier, 2022. https://doi.org/10.1016/j.coisb.2022.100435.
[Published Version] View | Files available | DOI
 
[101]
2022 | Journal Article | IST-REx-ID: 10736 | OA
Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications, 2022. https://doi.org/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. Public Library of Science, 2022. https://doi.org/10.1371/journal.pbio.3001889.
[Published Version] View | Files available | DOI | WoS
 
[99]
2022 | Journal Article | IST-REx-ID: 12081 | OA
Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[98]
2021 | Preprint | IST-REx-ID: 10912 | OA
Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Quantifying the Coexistence of Neuronal Oscillations and Avalanches.” arXiv, n.d. https://doi.org/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, n.d. https://doi.org/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. The Company of Biologists, 2021. https://doi.org/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, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science, 2021. https://doi.org/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, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.
[Published Version] View | Files available | DOI | WoS
 
[93]
2021 | Journal Article | IST-REx-ID: 7553 | OA
Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press, 2021. https://doi.org/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, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/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. Frontiers, 2020. https://doi.org/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, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/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, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006731117.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2020 | Preprint | IST-REx-ID: 7675 | OA
Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/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, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z.
[Published Version] View | Files available | DOI | WoS
 
[86]
2020 | Preprint | IST-REx-ID: 7673 | OA
Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/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, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7.
[Submitted Version] View | Files available | DOI | WoS
 
[84]
2019 | Preprint | IST-REx-ID: 7552 | OA
Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d.
[Preprint] View | Download Preprint (ext.) | arXiv
 
[83]
2019 | Journal Article | IST-REx-ID: 5945 | OA
Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell. Cell Press, 2019. https://doi.org/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, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.
[Published Version] View | Files available | DOI | WoS
 
[81]
2019 | Research Data Reference | IST-REx-ID: 9786
Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting Text and Results.” Public Library of Science, 2019. https://doi.org/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, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/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, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper Bound on Mutual Information.” In IEEE Information Theory Workshop, ITW 2019. IEEE, 2019. https://doi.org/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, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/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, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.
[Submitted Version] View | Files available | DOI | WoS
 
[76]
2018 | Research Data Reference | IST-REx-ID: 9831
Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.
[Published Version] View | Files available | DOI
 
[75]
2018 | Journal Article | IST-REx-ID: 31 | OA
Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410.
[Preprint] View | DOI | Download Preprint (ext.) | WoS
 
[74]
2018 | Journal Article | IST-REx-ID: 543 | OA
Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/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, Stephane Deny, Georg S Martius, Olivier Marre, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pcbi.1006057.
[Published Version] View | Files available | DOI | WoS
 
[72]
2018 | Research Data | IST-REx-ID: 5584 | OA
Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.
[Published Version] View | Files available | DOI
 
[71]
2018 | Journal Article | IST-REx-ID: 161 | OA
De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/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. https://doi.org/10.15479/AT:ISTA:62.
[Published Version] View | Files available | DOI
 
[69]
2018 | Journal Article | IST-REx-ID: 67 | OA
Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution. Nature Publishing Group, 2018. https://doi.org/10.1038/s41559-018-0651-y.
[Submitted Version] View | Files available | DOI | WoS
 
[68]
2018 | Research Data | IST-REx-ID: 5585 | OA
Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108.
[Published Version] View | Files available | DOI
 
[67]
2017 | Journal Article | IST-REx-ID: 613 | OA
Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/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. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.
[Published Version] View | Files available | DOI
 
[65]
2017 | Journal Article | IST-REx-ID: 725 | OA
Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS. National Academy of Sciences, 2017. https://doi.org/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, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/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, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-02159-y.
[Published Version] View | Files available | DOI | WoS
 
[62]
2017 | Journal Article | IST-REx-ID: 955 | OA
Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/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, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science. American Association for the Advancement of Science, 2017. https://doi.org/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. Elsevier, 2017. https://doi.org/10.1016/j.conb.2017.08.001.
View | DOI | WoS
 
[59]
2017 | Research Data | IST-REx-ID: 5562 | OA
Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:61.
[Published Version] View | Files available | DOI
 
[58]
2017 | Research Data | IST-REx-ID: 5560 | OA
Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:53.
[Published Version] View | Files available | DOI
 
[57]
2017 | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aaf4762.
View | Files available | DOI
 
[56]
2016 | Conference Paper | IST-REx-ID: 1082 | OA
Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems, 2016.
[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,” 29:3610–18. Neural Information Processing Systems, 2016.
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[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. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.005.
View | DOI
 
[53]
2016 | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2016. https://doi.org/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. Annual Reviews, 2016. https://doi.org/10.1146/annurev-conmatphys-031214-014803.
[Preprint] View | DOI | Download Preprint (ext.)
 
[51]
2016 | Journal Article | IST-REx-ID: 1420 | OA
Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[50]
2016 | Journal Article | IST-REx-ID: 1197 | OA
Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148.
[Published Version] View | Files available | DOI
 
[49]
2016 | Journal Article | IST-REx-ID: 1270 | OA
Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.
[Published Version] View | Files available | DOI
 
[48]
2016 | Research Data Reference | IST-REx-ID: 9870
Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s002.
[Published Version] View | Files available | DOI
 
[47]
2016 | Research Data Reference | IST-REx-ID: 9869
Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s001.
[Published Version] View | Files available | DOI
 
[46]
2016 | Research Data Reference | IST-REx-ID: 9871
Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s003.
[Published Version] View | Files available | DOI
 
[45]
2016 | Journal Article | IST-REx-ID: 1358 | OA
Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.
[Published Version] View | Files available | DOI
 
[44]
2015 | Journal Article | IST-REx-ID: 1697 | OA
Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora, Gašper Tkačik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004304.
[Published Version] View | Files available | DOI
 
[43]
2015 | Journal Article | IST-REx-ID: 1701 | OA
Tkačik, Gašper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer, Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS. National Academy of Sciences, 2015. https://doi.org/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, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics. Genetics Society of America, 2015. https://doi.org/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. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710.
[Preprint] View | DOI | Download Preprint (ext.)
 
[40]
2015 | Research Data Reference | IST-REx-ID: 9712
Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.
[Published Version] View | Files available | DOI
 
[39]
2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.
[Published Version] View | Files available | DOI
 
[38]
2015 | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.115.248101.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[37]
2014 | Journal Article | IST-REx-ID: 1886 | OA
Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” ELife. eLife Sciences Publications, 2014. https://doi.org/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. Biophysical Society, 2014. https://doi.org/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, Anandamohan Ghosh, Elad Schneidman, and Ronen Segev. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0085841.
[Published Version] View | Files available | DOI
 
[34]
2014 | Research Data Reference | IST-REx-ID: 9752 | OA
Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. https://doi.org/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, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology. Public Library of Science, 2014. https://doi.org/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, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation. MIT Press , 2013. https://doi.org/10.1162/NECO_a_00463.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[31]
2013 | Journal Article | IST-REx-ID: 2850 | OA
Tkačik, Gašper, Olivier Marre, Thierry Mora, Dario Amodei, Michael Berry, and William Bialek. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/03/P03011.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[30]
2013 | Journal Article | IST-REx-ID: 2851
Berry, Michael, Gašper Tkačik, Julien Dubuis, Olivier Marre, and Ravá Da Silveira. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/03/P03015.
View | DOI
 
[29]
2013 | Journal Article | IST-REx-ID: 2863 | OA
Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1002922.
[Published Version] View | Files available | DOI
 
[28]
2013 | Journal Article | IST-REx-ID: 2913 | OA
Tkačik, Gašper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.058104.
[Preprint] View | DOI | Download Preprint (ext.)
 
[27]
2013 | Journal Article | IST-REx-ID: 3261 | OA
Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William Bialek. “Positional Information, in Bits.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1315642110.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[26]
2013 | Journal Article | IST-REx-ID: 2277 | OA
Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003344.
[Published Version] View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2914 | OA
Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical Thermodynamics of Natural Images.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.018701.
[Published Version] View | Files available | DOI | arXiv
 
[24]
2012 | Journal Article | IST-REx-ID: 3262 | OA
Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2012. https://doi.org/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. IOP Publishing Ltd., 2011. https://doi.org/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, Jan Homann, Kristina Simmons, Gašper Tkačik, Vijay Balasubramanian, and Philip Nelson. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0019884.
View | Files available | DOI
 
[21]
2011 | Journal Article | IST-REx-ID: 3384 | OA
Tkačik, Gašper, Patrick Garrigan, Charles Ratliff, Grega Milcinski, Jennifer Klein, Lucia Seyfarth, Peter Sterling, David Brainard, and Vijay Balasubramanian. “Natural Images from the Birthplace of the Human Eye.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0020409.
[Published Version] View | Files available | DOI
 
[20]
2011 | Journal Article | IST-REx-ID: 3401
Little, Shawn, Gašper Tkačik, Thomas Kneeland, Eric Wieschaus, and Thomas Gregor. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized Source.” PLoS Biology. Public Library of Science, 2011. https://doi.org/10.1371/journal.pbio.1000596.
View | DOI
 
[19]
2010 | Journal Article | IST-REx-ID: 3735
Tkačik, Gašper, Jason Prentice, Jonathan Victor, and Vijay Balasubramanian. “Local Statistics in Natural Scenes Predict the Saliency of Synthetic Textures.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.0914916107.
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[18]
2010 | Journal Article | IST-REx-ID: 3736
Tkačik, Gašper, Jason Prentice, Vijay Balasubramanian, and Elad Schneidman. “Optimal Population Coding by Noisy Spiking Neurons.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1004906107.
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[17]
2010 | Journal Article | IST-REx-ID: 3738
Walczak, Aleksandra, Gašper Tkačik, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2010. https://doi.org/10.1103/PhysRevE.81.041905.
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[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.
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[15]
2010 | Preprint | IST-REx-ID: 3743 | OA
Tkačik, Gašper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” ArXiv. ArXiv, 2010.
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[14]
2009 | Journal Article | IST-REx-ID: 3737
Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2009. https://doi.org/10.1103/PhysRevE.80.031920.
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[13]
2009 | Journal Article | IST-REx-ID: 3733
Kryazhimskiy, Sergey, Gašper Tkačik, and Joshua Plotkin. “The Dynamics of Adaptation on Correlated Fitness Landscapes.” PNAS. National Academy of Sciences, 2009. https://doi.org/10.1073/pnas.0905497106.
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[12]
2009 | Preprint | IST-REx-ID: 3732 | OA
Tkačik, Gašper, Elad Schneidman, Michael Berry, and William Bialek. “Spin Glass Models for a Network of Real Neurons.” ArXiv. ArXiv, 2009.
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[11]
2009 | Book Chapter | IST-REx-ID: 3747
Tkačik, Gašper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.” In Encyclopedia of Complexity and Systems Science, edited by R. Meyers, 719–41. Springer, 2009. https://doi.org/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. American Institute of Physics, 2009. https://doi.org/10.1103/PhysRevE.79.051901.
View | DOI
 
[9]
2008 | Journal Article | IST-REx-ID: 3734 | OA
Tkačik, Gašper, Thomas Gregor, and William Bialek. “The Role of Input Noise in Transcriptional Regulation.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002774.
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[8]
2008 | Journal Article | IST-REx-ID: 3739
Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Capacity of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2008. https://doi.org/10.1103/PhysRevE.78.011910.
View | DOI
 
[7]
2008 | Journal Article | IST-REx-ID: 3740 | OA
Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Flow and Optimization in Transcriptional Regulation.” PNAS. National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0806077105.
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[6]
2008 | Journal Article | IST-REx-ID: 3744 | OA
Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” Biosystems. Elsevier, 2008. https://doi.org/10.1016/j.biosystems.2008.04.011.
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[5]
2007 | Journal Article | IST-REx-ID: 3731
Kinney, Justin, Gašper Tkačik, and Curtis Callan. “Precise Physical Models of Protein-DNA Interaction from High-Throughput Data.” PNAS. National Academy of Sciences, 2007. https://doi.org/10.1073/pnas.0609908104.
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[4]
2007 | Preprint | IST-REx-ID: 3742 | OA
Broderick, Tamara, Miroslav Dudik, Gašper Tkačik, Robert Schapire, and William Bialek. “Faster Solutions of the Inverse Pairwise Ising Problem.” ArXiv. ArXiv, 2007.
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[3]
2006 | Preprint | IST-REx-ID: 3431 | OA
Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models for Networks of Real Neurons.” ArXiv. ArXiv, 2006.
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[2]
2005 | Journal Article | IST-REx-ID: 3741 | OA
Slonim, N., G. Atwal, Gašper Tkačik, and William Bialek. “Information-Based Clustering.” PNAS. National Academy of Sciences, 2005. https://doi.org/10.1073/pnas.0507432102.
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[1]
2005 | Preprint | IST-REx-ID: 3746 | OA
Slonim, Noam, Gurinder Atwal, Gašper Tkačik, and William Bialek. “Estimating Mutual Information and Multi-Information in Large Networks.” ArXiv. ArXiv, 2005.
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