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132 Publications

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 15, no. 9 (2019): e1007290. https://doi.org/10.1371/journal.pcbi.1007290.
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2019 | Preprint | IST-REx-ID: 7083 | OA
Kavcic, Bor, Gašper Tkačik, and Tobias Bollenbach. “Mechanistic Origin of Drug Interactions between Translation-Inhibiting Antibiotics.” BioRxiv. Cold Spring Harbor Laboratory, n.d.
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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 15, no. 11 (2019). https://doi.org/10.1371/journal.pcbi.1007268.
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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 150, no. 5 (2019): 054108. 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, 8989292. IEEE, 2019. https://doi.org/10.1109/ITW44776.2019.8989292.
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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 116, no. 8 (2019): 2821–30. https://doi.org/10.1073/pnas.1812015116.
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2019 | Journal Article | IST-REx-ID: 5945
Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell 176, no. 4 (2019): 844–855.e15. https://doi.org/10.1016/j.cell.2019.01.007.
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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 35, no. 11 (2018): 2669–84. https://doi.org/10.1093/molbev/msy163.
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2018 | Journal Article | IST-REx-ID: 281 | OA
Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gasper Tkacik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS 115, no. 23 (2018): 6088–93. https://doi.org/10.1073/pnas.1716659115.
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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 2, no. 2 (2018): 359–66. https://doi.org/10.1038/s41559-017-0424-z.
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2018 | Journal Article | IST-REx-ID: 543 | OA
Chalk, Matthew J, Olivier Marre, and Gasper Tkacik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS 115, no. 1 (2018): 186–91. https://doi.org/10.1073/pnas.1711114115.
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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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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
Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena 376–377 (2018): 108–20. https://doi.org/10.1016/j.physd.2017.10.015.
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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 2, no. 10 (2018): 1633–43. https://doi.org/10.1038/s41559-018-0651-y.
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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 1771 (2018): 183–202. 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 4, no. 4 (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, Gasper Tkacik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E 98, no. 4 (2018): 042410. https://doi.org/10.1103/PhysRevE.98.042410.
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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 13, no. 3 (2018). https://doi.org/10.1371/journal.pone.0193049.
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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 9, no. 1 (2018). https://doi.org/10.1038/s41467-018-05417-9.
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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 209, no. 3 (2018): 861–83. https://doi.org/10.1534/genetics.118.300748.
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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 14, no. 5 (2018). https://doi.org/10.1371/journal.pcbi.1006057.
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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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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 44, no. 2 (2017): 285–306. https://doi.org/10.1111/sjos.12251.
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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 96, no. 6 (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 8, no. 1 (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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2017 | Journal Article | IST-REx-ID: 658 | OA
Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics 11, no. MAR (2017). https://doi.org/10.3389/fnbot.2017.00008.
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2017 | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gasper Tkacik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science 356, no. 6335 (2017): 311–15. https://doi.org/10.1126/science.aaf4762.
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2017 | Journal Article | IST-REx-ID: 666 | OA
Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems 4, no. 4 (2017): 393–403. https://doi.org/10.1016/j.cels.2017.03.001.
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2017 | Journal Article | IST-REx-ID: 680 | OA
Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational Biology 13, no. 6 (2017). https://doi.org/10.1371/journal.pcbi.1005582.
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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 13, no. 9 (2017). https://doi.org/10.1371/journal.pcbi.1005763.
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2017 | Journal Article | IST-REx-ID: 725 | OA
Harpaz, Roy, Gasper Tkacik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS 114, no. 38 (2017): 10149–54. https://doi.org/10.1073/pnas.1703817114.
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2017 | Journal Article | IST-REx-ID: 730
Savin, Cristina, and Gasper Tkacik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” Current Opinion in Neurobiology 46 (2017): 120–26. 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 43, no. 2 (2017): 198–211. https://doi.org/10.1016/j.devcel.2017.09.014.
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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 2017, no. 9 (2017). https://doi.org/10.1088/1742-5468/aa85c3.
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2017 | Journal Article | IST-REx-ID: 943 | OA
Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gasper Tkacik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science 356, no. 6345 (2017): 1379–83. https://doi.org/10.1126/science.aam5887.
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2017 | Journal Article | IST-REx-ID: 947 | OA
De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics 96, no. 1 (2017). https://doi.org/10.1103/PhysRevE.96.010401.
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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 8, no. 1 (2017). https://doi.org/10.1038/s41467-017-00238-8.
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2017 | Journal Article | IST-REx-ID: 959 | OA
De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics 95, no. 6 (2017): 062419. https://doi.org/10.1103/PhysRevE.95.062419.
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2017 | Journal Article | IST-REx-ID: 993 | OA
Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications 8 (2017). https://doi.org/10.1038/ncomms15140.
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2017 | Journal Article | IST-REx-ID: 1007 | OA
Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” Automatica 81C (2017): 46–55. https://doi.org/10.1016/j.automatica.2017.03.030.
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2017 | Journal Article | IST-REx-ID: 1104 | OA
Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gasper Tkacik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications 8, no. 1 (2017). https://doi.org/10.1038/s41467-017-02159-y.
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2016 | Conference Paper | IST-REx-ID: 8094 | OA
Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In Proceedings of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029.
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2016 | Conference Paper | IST-REx-ID: 948
Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems, 2016.
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2016 | Conference Paper | IST-REx-ID: 1082 | OA
Chalk, Matthew J, Olivier Marre, and Gasper Tkacik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems, 2016.
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2016 | Conference Paper | IST-REx-ID: 1105
Savin, Cristina, and Gasper Tkacik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems, 2016.
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