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142 Publications

2020 | Preprint | IST-REx-ID: 7553 | OA
Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Biological Systems.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/848374.
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2020 | Journal Article | IST-REx-ID: 7569 | OA
Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.
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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.
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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.
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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.
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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.
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2020 | Research Data | IST-REx-ID: 8930 | OA
Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.
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2020 | Journal Article | IST-REx-ID: 8955 | OA
Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology. Frontiers, 2020. https://doi.org/10.3389/fphys.2020.558070.
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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.
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2019 | Journal Article | IST-REx-ID: 196 | OA
Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.
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2019 | Journal Article | IST-REx-ID: 7422 | OA
Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.
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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.
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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.
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2019 | Journal Article | IST-REx-ID: 5817 | OA
Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8sm01956h.
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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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2019 | Journal Article | IST-REx-ID: 6046 | OA
Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470.
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2019 | Journal Article | IST-REx-ID: 6049 | OA
De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd.
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2019 | Thesis | IST-REx-ID: 6071 | OA
Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” IST Austria, 2019. https://doi.org/10.15479/at:ista:th6071.
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2019 | Journal Article | IST-REx-ID: 6090 | OA
Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. APS, 2019. https://doi.org/10.1103/PhysRevE.99.022423.
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2019 | Thesis | IST-REx-ID: 6473 | OA
Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6473.
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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.
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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.
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2019 | Journal Article | IST-REx-ID: 7103 | OA
Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLOS Computational Biology. PLoS, 2019. https://doi.org/10.1371/journal.pcbi.1007268.
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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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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.
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2018 | Journal Article | IST-REx-ID: 19 | OA
Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution. NLM , 2018. https://doi.org/10.1093/molbev/msy163.
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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.
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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.” IST Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.
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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.’” IST Austria, 2018. https://doi.org/10.15479/AT:ISTA:62.
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2018 | Journal Article | IST-REx-ID: 607 | OA
Bod’ová, Katarína, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.
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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.
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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.
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2018 | Journal Article | IST-REx-ID: 457
Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0424-z.
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2018 | Journal Article | IST-REx-ID: 305
Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15.
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2018 | Journal Article | IST-REx-ID: 306 | OA
De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.
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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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2018 | Journal Article | IST-REx-ID: 316 | OA
Bod’ová, Katarína, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.
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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.
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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.” IST Austria, 2018. https://doi.org/10.15479/AT:ISTA:108.
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2017 | Journal Article | IST-REx-ID: 823 | OA
Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.
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2017 | Journal Article | IST-REx-ID: 2016 | OA
Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal of Statistics. Wiley-Blackwell, 2017. https://doi.org/10.1111/sjos.12251.
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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.
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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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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.
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2017 | Journal Article | IST-REx-ID: 735
Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.014.
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2017 | Journal Article | IST-REx-ID: 548 | OA
De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E. American Physiological Society, 2017. https://doi.org/10.1103/PhysRevE.96.060401.
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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.” IST Austria, 2017. https://doi.org/doi:10.15479/AT:ISTA:53.
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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.” IST Austria, 2017. https://doi.org/10.15479/AT:ISTA:61.
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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.
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2017 | Conference Paper | IST-REx-ID: 652
Der, Ralf, and Georg S Martius. “Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots.” IEEE, 2017. https://doi.org/10.1109/DEVLRN.2016.7846789.
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