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130 Publications

2019 | Journal Article | IST-REx-ID: 5817
Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter 15, no. 4 (2019): 602–14. https://doi.org/10.1039/c8sm01956h.
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2019 | Thesis | IST-REx-ID: 6473
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: 6049   OA
De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical 52, no. 4 (2019). https://doi.org/10.1088/1751-8121/aaf2dd.
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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 15, no. 7 (2019). https://doi.org/10.1371/journal.pcbi.1007168.
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2019 | Journal Article | IST-REx-ID: 5945
Petkova, Mariela D., Gasper Tkacik, 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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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 | 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 | 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 99, no. 2 (2019). https://doi.org/10.1103/PhysRevE.99.022423.
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2019 | Thesis | IST-REx-ID: 6071
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 | 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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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: 5587   OA
De Martino, Daniele, and Gasper Tkacik. 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: 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: 67   OA
Igler, Claudia, Mato Lagator, Gasper Tkacik, 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: 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: 316   OA
Bodova, Katarina, 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: 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 | Preprint | IST-REx-ID: 196   OA
Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” ArXiv. ArXiv, 2018.
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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: 406   OA
Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gasper Tkacik. “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: 292   OA
Botella Soler, Vicent, Stephane Deny, Georg S Martius, Olivier Marre, and Gasper Tkacik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology 14, no. 5 (2018): e1006057. https://doi.org/10.1371/journal.pcbi.1006057.
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2018 | Research Data | IST-REx-ID: 5584
Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gasper Tkacik. 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 | 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: 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: 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: 161
De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gasper Tkacik. “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 | Research Data | IST-REx-ID: 5585
Igler, Claudia, Mato Lagator, Gasper Tkacik, 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 | Research Data | IST-REx-ID: 5562   OA
Marre, Olivier, Gasper Tkacik, 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: 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: 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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2017 | Journal Article | IST-REx-ID: 720   OA
Humplik, Jan, and Gasper Tkacik. “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: 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 | 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: 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: 613   OA
Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gasper Tkacik, 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: 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: 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: 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: 955   OA
Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gasper Tkacik. “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: 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: 2016
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: 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: 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 | Research Data | IST-REx-ID: 5560
Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gasper Tkacik, 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 | 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: 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: 666   OA
Mitosch, Karin, Georg Rieckh, and 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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2016 | Thesis | IST-REx-ID: 1128
Rieckh, Georg. Studying the Complexities of Transcriptional Regulation. IST Austria, 2016.
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