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140 Publications
2020 | Research Data | IST-REx-ID: 7383 | 
Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. IST Austria, 2020, doi:10.15479/AT:ISTA:7383.
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2020 | Preprint | IST-REx-ID: 7463 |
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, doi:10.1101/2020.02.03.930966.
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2020 | Journal Article | IST-REx-ID: 7490 |
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 |
Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Biological Systems.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/848374.
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2020 | Journal Article | IST-REx-ID: 7569 |
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 | 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 | Journal Article | IST-REx-ID: 7656 |
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 |
Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.
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2020 | Preprint | IST-REx-ID: 7675 |
Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.
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2020 | Research Data | IST-REx-ID: 8930 |
Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” IST Austria, 2020, doi:10.15479/AT:ISTA:8930.
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2020 | Journal Article | IST-REx-ID: 8955 |
Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology, vol. 11, 558070, Frontiers, 2020, doi:10.3389/fphys.2020.558070.
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2020 | Journal Article | IST-REx-ID: 9000 |
Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:10.1073/pnas.2006731117.
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2019 | Journal Article | IST-REx-ID: 196 |
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: 7422 |
Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867.
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2019 | Preprint | IST-REx-ID: 7552 |
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 |
Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.
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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: 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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2019 | Journal Article | IST-REx-ID: 6046 |
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 |
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 |
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 |
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 |
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 |
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 |
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 | Journal Article | IST-REx-ID: 7103 |
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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2018 | Journal Article | IST-REx-ID: 281 |
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: 292 |
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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2018 | Journal Article | IST-REx-ID: 19 |
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: 543 |
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 | Research Data | IST-REx-ID: 5584 |
Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. IST Austria, 2018, doi:10.15479/AT:ISTA:98.
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2018 | Research Data | IST-REx-ID: 5587 |
De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria, 2018, doi:10.15479/AT:ISTA:62.
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2018 | Journal Article | IST-REx-ID: 607 |
Bod’ová, Katarína, 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: 161 |
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: 406 |
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: 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: 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 |
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 |
Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.
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2018 | Journal Article | IST-REx-ID: 316 |
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: 67 |
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 | Research Data | IST-REx-ID: 5585 |
Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. IST Austria, 2018, doi:10.15479/AT:ISTA:108.
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2017 | Journal Article | IST-REx-ID: 823 |
Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.
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2017 | Journal Article | IST-REx-ID: 2016 |
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: 720 |
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 |
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 Gašper Tkačik. “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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2017 | Journal Article | IST-REx-ID: 735
Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell, vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:10.1016/j.devcel.2017.09.014.
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2017 | Journal Article | IST-REx-ID: 548 |
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 | Research Data | IST-REx-ID: 5560 |
Bergmiller, Tobias, et al. Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity. IST Austria, 2017, doi:doi:10.15479/AT:ISTA:53.
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