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125 Publications

2020 | Preprint | IST-REx-ID: 7463 | OA
Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” BioRxiv, Cold Spring Harbor Laboratory, 2020.
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2020 | Journal Article | IST-REx-ID: 7490 | OA
Narasimhan, Madhumitha, et al. “Evolutionarily Unique Mechanistic Framework of Clathrin-Mediated Endocytosis in Plants.” ELife, vol. 9, e52067, eLife Sciences Publications, 2020, doi:10.7554/eLife.52067.
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2020 | Preprint | IST-REx-ID: 7553 | OA
Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Biological Systems.” BioRxiv, Cold Spring Harbor Laboratory.
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2020 | Journal Article | IST-REx-ID: 7656 | OA
Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design Principle for Population Codes.” Frontiers in Computational Neuroscience, vol. 14, 20, Frontiers, 2020, doi:10.3389/fncom.2020.00020.
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2020 | Preprint | IST-REx-ID: 7673 | OA
Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, Cold Spring Harbor Laboratory, 2020.
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2020 | Journal Article | IST-REx-ID: 8105 | OA
Lombardi, Fabrizio, et al. “Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.” EPJ Web of Conferences, vol. 230, 00005, EDP Sciences, 2020, doi:10.1051/epjconf/202023000005.
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2020 | Journal Article | IST-REx-ID: 8084 | OA
Lombardi, Fabrizio, et al. “Critical Dynamics and Coupling in Bursts of Cortical Rhythms Indicate Non-Homeostatic Mechanism for Sleep-Stage Transitions and Dual Role of VLPO Neurons in Both Sleep and Wake.” Journal of Neuroscience, vol. 40, no. 1, Society for Neuroscience, 2020, pp. 171–90, doi:10.1523/jneurosci.1278-19.2019.
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2020 | Journal Article | IST-REx-ID: 7569 | OA
Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.
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2020 | Thesis | IST-REx-ID: 8155 | OA
Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. IST Austria, 2020, doi:10.15479/AT:ISTA:8155.
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2020 | Journal Article | IST-REx-ID: 7652
Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.
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2020 | Preprint | IST-REx-ID: 7675 | OA
Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020.
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2019 | Journal Article | IST-REx-ID: 5817
Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h.
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2019 | Journal Article | IST-REx-ID: 6046 | OA
Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology, vol. 15, no. 2, e8470, Embo Press, 2019, doi:10.15252/msb.20188470.
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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, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:10.1088/1751-8121/aaf2dd.
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2019 | Thesis | IST-REx-ID: 6071 | OA
Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. IST Austria, 2019, doi:10.15479/at:ista:th6071.
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2019 | Journal Article | IST-REx-ID: 6090 | OA
Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, APS, 2019, doi:10.1103/PhysRevE.99.022423.
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2019 | Thesis | IST-REx-ID: 6473 | OA
Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells. IST Austria, 2019, doi:10.15479/AT:ISTA:6473.
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2019 | Journal Article | IST-REx-ID: 6784 | OA
Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.
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2019 | Journal Article | IST-REx-ID: 6900 | OA
Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:10.1371/journal.pcbi.1007290.
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2019 | Preprint | IST-REx-ID: 7083 | OA
Kavcic, Bor, et al. “Mechanistic Origin of Drug Interactions between Translation-Inhibiting Antibiotics.” BioRxiv, Cold Spring Harbor Laboratory.
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2019 | Journal Article | IST-REx-ID: 7103 | OA
Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLOS Computational Biology, vol. 15, no. 11, e1007268, PLoS, 2019, doi:10.1371/journal.pcbi.1007268.
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2019 | Journal Article | IST-REx-ID: 7422 | OA
Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of Chemical Physics, vol. 150, no. 5, AIP Publishing, 2019, p. 054108, doi:10.1063/1.5064867.
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2019 | Preprint | IST-REx-ID: 7552 | OA
Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579, ArXiv.
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2019 | Conference Paper | IST-REx-ID: 7606 | OA
Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE Information Theory Workshop, ITW 2019, IEEE, 2019, p. 8989292, doi:10.1109/ITW44776.2019.8989292.
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2019 | Journal Article | IST-REx-ID: 196 | OA
Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences, vol. 116, no. 8, National Academy of Sciences, 2019, pp. 2821–30, doi:10.1073/pnas.1812015116.
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2019 | Journal Article | IST-REx-ID: 5945
Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.
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2018 | Journal Article | IST-REx-ID: 19 | OA
Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11, NLM , 2018, pp. 2669–84, doi:10.1093/molbev/msy163.
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2018 | Journal Article | IST-REx-ID: 281 | OA
Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.
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2018 | Journal Article | IST-REx-ID: 457
Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z.
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2018 | Journal Article | IST-REx-ID: 543 | OA
Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.
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2018 | Journal Article | IST-REx-ID: 607 | OA
Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.
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2018 | Journal Article | IST-REx-ID: 67 | OA
Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.
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2018 | Journal Article | IST-REx-ID: 305
Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp. 183–202, doi: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, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596.
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2018 | Journal Article | IST-REx-ID: 31 | OA
Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, American Physical Society, 2018, p. 042410, doi:10.1103/PhysRevE.98.042410.
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2018 | Journal Article | IST-REx-ID: 406 | OA
Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.
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2018 | Journal Article | IST-REx-ID: 161 | OA
De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.
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2018 | Journal Article | IST-REx-ID: 316 | OA
Bod’ová, Katarína, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.
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2018 | Journal Article | IST-REx-ID: 292 | OA
Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.
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2017 | Journal Article | IST-REx-ID: 2016 | OA
Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal of Statistics, vol. 44, no. 2, Wiley-Blackwell, 2017, pp. 285–306, doi:10.1111/sjos.12251.
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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, vol. 96, no. 6, 060401, American Physiological Society, 2017, doi:10.1103/PhysRevE.96.060401.
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2017 | Journal Article | IST-REx-ID: 613 | OA
Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi: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. 7846789, IEEE, 2017, doi: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, vol. 11, no. MAR, 00008, Frontiers Research Foundation, 2017, doi:10.3389/fnbot.2017.00008.
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2017 | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:10.1126/science.aaf4762.
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2017 | Journal Article | IST-REx-ID: 666 | OA
Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001.
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2017 | Journal Article | IST-REx-ID: 680 | OA
Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational Biology, vol. 13, no. 6, e1005582, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005582.
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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, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.
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2017 | Journal Article | IST-REx-ID: 725 | OA
Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.
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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, vol. 46, Elsevier, 2017, pp. 120–26, doi:10.1016/j.conb.2017.08.001.
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