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114 Publications

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): 1964. https://doi.org/10.1038/s41467-017-02159-y.
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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: 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 | 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 | 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: 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): 216. https://doi.org/10.1038/s41467-017-00238-8.
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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: 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 | 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: 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: 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: 658   OA
Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics 11, no. MAR (2017): 00008. https://doi.org/10.3389/fnbot.2017.00008.
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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
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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2016 | Journal Article | IST-REx-ID: 1197   OA
Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gasper Tkacik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology 12, no. 11 (2016). https://doi.org/10.1371/journal.pcbi.1005148.
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2016 | Journal Article | IST-REx-ID: 1248   OA
Tkacik, Gasper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics 7 (2016): 89–117. https://doi.org/10.1146/annurev-conmatphys-031214-014803.
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2016 | Journal Article | IST-REx-ID: 1332   OA
Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications 7 (2016). https://doi.org/10.1038/ncomms10333.
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2016 | Conference Paper | IST-REx-ID: 1320
Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,” Vol. 2016–July. IEEE, 2016. https://doi.org/10.1109/ACC.2016.7526722.
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2016 | Journal Article | IST-REx-ID: 1394   OA
De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology 13, no. 3 (2016). https://doi.org/10.1088/1478-3975/13/3/036005.
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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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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: 1270   OA
Hillenbrand, Patrick, Ulrich Gerland, and Gasper Tkacik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One 11, no. 9 (2016). https://doi.org/10.1371/journal.pone.0163628.
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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 113, no. 7 (2016): 1811–16. https://doi.org/10.1073/pnas.1419248113.
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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 149 (2016): 15–25. 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 38, no. 6 (2016): B988–1008. https://doi.org/10.1137/15M103306X.
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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 | Journal Article | IST-REx-ID: 1290   OA
Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology 12, no. 11 (2016): 902–4. https://doi.org/10.1038/nchembio.2176.
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2016 | Journal Article | IST-REx-ID: 1485   OA
De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” Physical Biology 13, no. 1 (2016). https://doi.org/10.1088/1478-3975/13/1/016003.
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2016 | Journal Article | IST-REx-ID: 1358
Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gasper Tkacik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications 7 (2016): 12307. https://doi.org/10.1038/ncomms12307.
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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 | Journal Article | IST-REx-ID: 1171
Tkacik, Gasper. “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 17 (2016): 166–67. 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 2016, no. 12 (2016): 123502. https://doi.org/10.1088/1742-5468/aa4e8f.
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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 54, no. 12 (2016): 3010–17. https://doi.org/10.1128/JCM.01511-16.
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2016 | Journal Article | IST-REx-ID: 1260   OA
De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C 27, no. 6 (2016). https://doi.org/10.1142/S0129183116500674.
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2016 | Journal Article | IST-REx-ID: 1342   OA
Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science 353, no. 6304 (2016): 1147–51. https://doi.org/10.1126/science.aag0822.
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2016 | Journal Article | IST-REx-ID: 1266   OA
Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife 5, no. 2016JULY (2016). https://doi.org/10.7554/eLife.13824.
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2016 | Journal Article | IST-REx-ID: 1242   OA
Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gasper Tkacik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics 93, no. 2 (2016). https://doi.org/10.1103/PhysRevE.93.022404.
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2016 | Journal Article | IST-REx-ID: 1420   OA
Bod’ová, Katarína, Gasper Tkacik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics 202, no. 4 (2016): 1523–48. https://doi.org/10.1534/genetics.115.184127.
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2015 | Journal Article | IST-REx-ID: 1539   OA
Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics 143, no. 24 (2015). https://doi.org/10.1063/1.4937937.
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2015 | Journal Article | IST-REx-ID: 1666   OA
Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gasper Tkacik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics 11, no. 11 (2015). https://doi.org/10.1371/journal.pgen.1005639.
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2015 | Journal Article | IST-REx-ID: 1697   OA
Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora, Gasper Tkacik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology 11, no. 7 (2015). https://doi.org/10.1371/journal.pcbi.1004304.
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2015 | Journal Article | IST-REx-ID: 1940   OA
Sokolowski, Thomas R, and Gasper Tkacik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics 91, no. 6 (2015). https://doi.org/10.1103/PhysRevE.91.062710.
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2015 | Journal Article | IST-REx-ID: 1655   OA
Martius, Georg S, and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy 17, no. 10 (2015): 7266–97. https://doi.org/10.3390/e17107266.
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