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135 Publications

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: 1270 | OA
Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “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: 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 | 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: 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 | 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: 1358 | OA
Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications 7 (2016). https://doi.org/10.1038/ncomms12307.
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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 | 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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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 | 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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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 | 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 | Thesis | IST-REx-ID: 1128 | OA
Rieckh, Georg. Studying the Complexities of Transcriptional Regulation. IST Austria, 2016.
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2015 | Journal Article | IST-REx-ID: 1564 | OA
Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience 9, no. 11 (2015). https://doi.org/10.3389/fncom.2015.00145.
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2015 | Journal Article | IST-REx-ID: 1570 | OA
Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS 112, no. 45 (2015): E6224–32. https://doi.org/10.1073/pnas.1508400112.
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2015 | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez, Sarah A, Georg Rieckh, and Gasper Tkacik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters 115, no. 24 (2015). https://doi.org/10.1103/PhysRevLett.115.248101.
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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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2015 | Conference Paper | IST-REx-ID: 1658
Bogomolov, Sergiy, Thomas A Henzinger, Andreas Podelski, Jakob Ruess, and Christian Schilling. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-23401-4_8.
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2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “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, Gašper Tkačik, 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: 1701 | OA
Tkacik, Gasper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer, Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS 112, no. 37 (2015): 11508–13. https://doi.org/10.1073/pnas.1514188112.
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2015 | Journal Article | IST-REx-ID: 1827 | OA
Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology 11, no. 3 (2015). https://doi.org/10.1371/journal.pcbi.1004055.
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2015 | Journal Article | IST-REx-ID: 1861
Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation 25, no. 2 (2015). https://doi.org/10.1145/2688906.
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2015 | Journal Article | IST-REx-ID: 1885 | OA
Tkacik, Gasper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics 199, no. 1 (2015): 39–59. https://doi.org/10.1534/genetics.114.171850.
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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: 1538 | OA
Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS 112, no. 26 (2015): 8148–53. https://doi.org/10.1073/pnas.1423947112.
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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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2014 | Journal Article | IST-REx-ID: 2231 | OA
Rieckh, Georg, and Gasper Tkacik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal 106, no. 5 (2014): 1194–1204. https://doi.org/10.1016/j.bpj.2014.01.014.
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2014 | Journal Article | IST-REx-ID: 2257 | OA
Tkačik, Gašper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology 10, no. 1 (2014). https://doi.org/10.1371/journal.pcbi.1003408.
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2014 | Journal Article | IST-REx-ID: 537 | OA
Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution 4, no. 15 (2014): 3139–45. https://doi.org/10.1002/ece3.1150.
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2014 | Conference Paper | IST-REx-ID: 1708
Savin, Cristina, and Sophie Denève. “Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks,” 3:2024–32. Neural Information Processing Systems, 2014.
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2014 | Journal Article | IST-REx-ID: 1886 | OA
Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November (2014). https://doi.org/10.7554/eLife.03722.
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2014 | Journal Article | IST-REx-ID: 1896 | OA
Kollár, Richard, Katarína Bod’ová, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics 89, no. 3 (2014). https://doi.org/10.1103/PhysRevE.89.032701.
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2014 | Journal Article | IST-REx-ID: 1909 | OA
Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology 28, no. 3 (2014): 693–701. https://doi.org/10.1111/1365-2435.12207.
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2014 | Journal Article | IST-REx-ID: 1928
Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology 360 (2014): 149–62. https://doi.org/10.1016/j.jtbi.2014.06.039.
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2014 | Journal Article | IST-REx-ID: 1931 | OA
Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience 8, no. MAY (2014). https://doi.org/10.3389/fncom.2014.00057.
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2014 | Journal Article | IST-REx-ID: 3263 | OA
Tkačik, Gašper, Anandamohan Ghosh, Elad Schneidman, and Ronen Segev. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” PLoS One 9, no. 1 (2014). https://doi.org/10.1371/journal.pone.0085841.
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2013 | Journal Article | IST-REx-ID: 2277 | OA
Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology 9, no. 12 (2013). https://doi.org/10.1371/journal.pcbi.1003344.
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2013 | Book Chapter | IST-REx-ID: 2413
Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” In Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson. Wiley-VCH, 2013. https://doi.org/10.1002/9783527671632.ch08.
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2013 | Journal Article | IST-REx-ID: 499
Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” Science 339, no. 6115 (2013): 91–95. https://doi.org/10.1126/science.1229858.
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2013 | Journal Article | IST-REx-ID: 2818 | OA
Rajan, Kanaka, Olivier Marre, and Gasper Tkacik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation 25, no. 7 (2013): 1661–92. https://doi.org/10.1162/NECO_a_00463.
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2013 | Journal Article | IST-REx-ID: 2850 | OA
Tkacik, Gasper, Olivier Marre, Thierry Mora, Dario Amodei, Michael Berry, and William Bialek. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment 2013, no. 3 (2013): P03011. https://doi.org/10.1088/1742-5468/2013/03/P03011.
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2013 | Journal Article | IST-REx-ID: 2851
Berry, Michael, Gasper Tkacik, Julien Dubuis, Olivier Marre, and Ravá Da Silveira. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal of Statistical Mechanics Theory and Experiment 2013, no. 3 (2013). https://doi.org/10.1088/1742-5468/2013/03/P03015.
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2013 | Journal Article | IST-REx-ID: 2861
Botella Soler, Vicente, José Oteo, Javier Ros, and Paul Glendinning. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” Journal of Physics A: Mathematical and Theoretical 46, no. 12 (2013). https://doi.org/10.1088/1751-8113/46/12/125101.
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2013 | Journal Article | IST-REx-ID: 2863 | OA
Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology 9, no. 3 (2013). https://doi.org/10.1371/journal.pcbi.1002922.
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2013 | Journal Article | IST-REx-ID: 2913 | OA
Tkacik, Gasper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters 110, no. 5 (2013). https://doi.org/10.1103/PhysRevLett.110.058104.
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2013 | Journal Article | IST-REx-ID: 2914 | OA
Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical Thermodynamics of Natural Images.” Physical Review Letters 110, no. 1 (2013). https://doi.org/10.1103/PhysRevLett.110.018701.
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