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160 Publications

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: 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: 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: 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 | 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: 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 | 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.
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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: 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. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.
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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. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.
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2018 | Research Data Reference | IST-REx-ID: 9813
Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.
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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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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: 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 | 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: 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.
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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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2017 | Journal Article | IST-REx-ID: 658 | OA
Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics. Frontiers Research Foundation, 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, 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.
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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. Cell Press, 2017. 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. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.
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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. IFAC, the International Federation of Automatic Control, 2017. https://doi.org/10.1016/j.automatica.2017.03.030.
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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: 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.
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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 . American Institute of Physics, 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. Nature Publishing Group, 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 . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.95.062419.
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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.
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2017 | Research Data Reference | IST-REx-ID: 9855
Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary Appendix.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.s001.
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2017 | Journal Article | IST-REx-ID: 993 | OA
Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15140.
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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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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: 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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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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2016 | Thesis | IST-REx-ID: 1128 | OA
Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” IST Austria, 2016.
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2016 | Journal Article | IST-REx-ID: 1148
Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Biosystems. Elsevier, 2016. https://doi.org/10.1016/j.biosystems.2016.07.005.
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2016 | Journal Article | IST-REx-ID: 1170
Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M103306X.
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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.
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2016 | Journal Article | IST-REx-ID: 1188 | OA
De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.
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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.
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2016 | Journal Article | IST-REx-ID: 1203 | OA
Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology. American Society for Microbiology, 2016. https://doi.org/10.1128/JCM.01511-16.
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2016 | Conference Paper | IST-REx-ID: 1214
Martius, Georg S, Raphael Hostettler, Alois Knoll, and Ralf Der. “Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm,” Vol. 2016–November. IEEE, 2016. https://doi.org/10.1109/IROS.2016.7759138.
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2016 | Conference Paper | IST-REx-ID: 1220 | OA
Mikić, Gregor, Alex Stoll, Joe Bevirt, Rok Grah, and Mark Moore. “Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency,” 1–19. AIAA, 2016. https://doi.org/10.2514/6.2016-3764.
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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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2016 | Journal Article | IST-REx-ID: 1244 | OA
Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1419248113.
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