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134 Publications

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, vol. 2016, no. 12, 123502, IOPscience, 2016, doi:10.1088/1742-5468/aa4e8f.
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2016 | Journal Article | IST-REx-ID: 1197 | OA
Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005148.
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2016 | Journal Article | IST-REx-ID: 1203 | OA
Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology, vol. 54, no. 12, American Society for Microbiology, 2016, pp. 3010–17, doi:10.1128/JCM.01511-16.
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2016 | Conference Paper | IST-REx-ID: 1214
Martius, Georg S., et al. Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm. Vol. 2016–November, 7759138, IEEE, 2016, doi:10.1109/IROS.2016.7759138.
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2016 | Conference Paper | IST-REx-ID: 1220 | OA
Mikić, Gregor, et al. Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency. AIAA, 2016, pp. 1–19, doi:10.2514/6.2016-3764.
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2016 | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:10.1103/PhysRevE.93.022404.
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2016 | Journal Article | IST-REx-ID: 1244 | OA
Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS, vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:10.1073/pnas.1419248113.
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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, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803.
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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, vol. 27, no. 6, World Scientific Publishing, 2016, p. 1650067, doi:10.1142/S0129183116500674.
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2016 | Journal Article | IST-REx-ID: 1266 | OA
Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife, vol. 5, no. 2016JULY, e13824, eLife Sciences Publications, 2016, doi:10.7554/eLife.13824.
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2016 | Journal Article | IST-REx-ID: 1270 | OA
Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.
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2016 | Journal Article | IST-REx-ID: 1290 | OA
Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi: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, 7526722, IEEE, 2016, doi:10.1109/ACC.2016.7526722.
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2016 | Journal Article | IST-REx-ID: 1332 | OA
Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications, vol. 7, 10333, Nature Publishing Group, 2016, doi:10.1038/ncomms10333.
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2016 | Journal Article | IST-REx-ID: 1342 | OA
Baym, Michael, et al. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1147–51, doi:10.1126/science.aag0822.
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2016 | Journal Article | IST-REx-ID: 1358 | OA
Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.
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2016 | Journal Article | IST-REx-ID: 1394 | OA
De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology, vol. 13, no. 3, 036005, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/3/036005.
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2016 | Journal Article | IST-REx-ID: 1420 | OA
Bod’ová, Katarína, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi: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, vol. 13, no. 1, 016003, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/1/016003.
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2016 | Conference Paper | IST-REx-ID: 1082 | OA
Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems, 2016, pp. 1965–73.
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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. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18.
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2016 | Journal Article | IST-REx-ID: 1148
Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Biosystems, vol. 149, Elsevier, 2016, pp. 15–25, doi: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, vol. 38, no. 6, Society for Industrial and Applied Mathematics , 2016, pp. B988–1008, doi: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, vol. 17, Elsevier, 2016, pp. 166–67, doi: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, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi: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, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112.
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2015 | Journal Article | IST-REx-ID: 1576 | OA
Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi: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, vol. 17, no. 10, Multidisciplinary Digital Publishing Institute, 2015, pp. 7266–97, doi:10.3390/e17107266.
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2015 | Conference Paper | IST-REx-ID: 1658
Bogomolov, Sergiy, et al. Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks. Vol. 9308, Springer, 2015, pp. 77–89, doi:10.1007/978-3-319-23401-4_8.
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2015 | Journal Article | IST-REx-ID: 1666 | OA
Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
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2015 | Journal Article | IST-REx-ID: 1697 | OA
Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304.
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2015 | Journal Article | IST-REx-ID: 1701 | OA
Tkacik, Gasper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112.
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2015 | Journal Article | IST-REx-ID: 1827 | OA
Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi: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, vol. 25, no. 2, 8, ACM, 2015, doi:10.1145/2688906.
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2015 | Journal Article | IST-REx-ID: 1885 | OA
Tkacik, Gasper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi: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, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.062710.
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2015 | Journal Article | IST-REx-ID: 1538 | OA
Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi: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, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi: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, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.
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2014 | Journal Article | IST-REx-ID: 2257 | OA
Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408.
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2014 | Journal Article | IST-REx-ID: 537 | OA
Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi: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. Vol. 3, no. January, Neural Information Processing Systems, 2014, pp. 2024–32.
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2014 | Journal Article | IST-REx-ID: 1886 | OA
Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.
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2014 | Journal Article | IST-REx-ID: 1896 | OA
Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.
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2014 | Journal Article | IST-REx-ID: 1909 | OA
Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207.
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2014 | Journal Article | IST-REx-ID: 1928
Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology, vol. 360, Elsevier, 2014, pp. 149–62, doi: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, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057.
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2014 | Journal Article | IST-REx-ID: 3263 | OA
Tkačik, Gašper, et al. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” PLoS One, vol. 9, no. 1, e85841, Public Library of Science, 2014, doi:10.1371/journal.pone.0085841.
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2013 | Journal Article | IST-REx-ID: 2277 | OA
Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003344.
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