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160 Publications

2021 | Journal Article | IST-REx-ID: 8997 | OA
Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology, vol. 17, e1008529, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008529.
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2021 | Journal Article | IST-REx-ID: 9226
Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development, vol. 148, no. 2, dev176065, The Company of Biologists, 2021, doi:10.1242/dev.176065.
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2021 | Journal Article | IST-REx-ID: 9283 | OA
Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife, vol. 10, e65993, eLife Sciences Publications, 2021, doi:10.7554/elife.65993.
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2021 | Journal Article | IST-REx-ID: 9362 | OA
Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE, vol. 16, no. 4 April, e0248940, 2021, doi:10.1371/journal.pone.0248940.
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2021 | Journal Article | 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.” Neurocomputing, Elsevier, doi:10.1016/j.neucom.2020.05.126.
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2021 | Journal Article | IST-REx-ID: 7553 | OA
Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.
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2021 | Journal Article | IST-REx-ID: 9822 | OA
Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850.
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2021 | Preprint | IST-REx-ID: 10077 | OA
Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602.
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2021 | Journal Article | IST-REx-ID: 9439 | OA
Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0.
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2021 | Journal Article | IST-REx-ID: 9828 | OA
Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.
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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 | Research Data | IST-REx-ID: 8097 | OA
Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” IST Austria, 2020, doi:10.15479/AT:ISTA:8097.
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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 | 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: 8698 | OA
Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117.
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2020 | Research Data | IST-REx-ID: 7383 | OA
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 | 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 | 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: 7675 | OA
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 | OA
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 | OA
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 | OA
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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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 | Research Data Reference | IST-REx-ID: 9779
Grah, Rok, and Tamar Friedlander. Distribution of Crosstalk Values. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s003.
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2020 | Research Data Reference | IST-REx-ID: 9776
Grah, Rok, and Tamar Friedlander. Supporting Information. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s001.
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2020 | Research Data Reference | IST-REx-ID: 9777
Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002.
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2020 | Thesis | IST-REx-ID: 8657 | OA
Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology. IST Austria, 2020, doi:10.15479/AT:ISTA:8657.
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2020 | Journal Article | IST-REx-ID: 7652 | OA
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: 8250 | OA
Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020, doi:10.1038/s41467-020-17734-z.
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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, doi:10.1101/2020.04.18.047886.
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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: 7422 | OA
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 | 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, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.
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2019 | Journal Article | IST-REx-ID: 5817 | OA
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 | OA
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 | 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: 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 | 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: 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 | Research Data Reference | IST-REx-ID: 9786
Ruess, Jakob, et al. Supporting Text and Results. Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.
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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: 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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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: 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 | Research Data | IST-REx-ID: 5584 | OA
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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