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167 Publications

2022 | Journal Article | IST-REx-ID: 10736 | OA
M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.
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2022 | Preprint | IST-REx-ID: 10821 | OA
F. Lombardi et al., “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” bioRxiv. Cold Spring Harbor Laboratory, 2022.
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2021 | Journal Article | IST-REx-ID: 7463 | OA
F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches,” Neurocomputing, vol. 461. Elsevier, pp. 657–666, 2021.
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2021 | Journal Article | IST-REx-ID: 7553 | OA
W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.
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2021 | Preprint | IST-REx-ID: 10579 | OA
B. Kavcic and G. Tkačik, “On token-driven totally asymmetric simple exclusion process,” arXiv. .
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2021 | Preprint | IST-REx-ID: 10912 | OA
F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Quantifying the coexistence of neuronal oscillations and avalanches.” arXiv.
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2021 | Journal Article | IST-REx-ID: 8997 | OA
B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” PLOS Computational Biology, vol. 17. Public Library of Science, 2021.
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2021 | Journal Article | IST-REx-ID: 9283 | OA
A. A. Nagy-Staron et al., “Local genetic context shapes the function of a gene regulatory network,” eLife, vol. 10. eLife Sciences Publications, 2021.
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2021 | Preprint | IST-REx-ID: 10077 | OA
M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory.
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2021 | Journal Article | IST-REx-ID: 10530 | OA
T. Zisis et al., “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” Biophysical Journal. Elsevier, 2021.
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2021 | Journal Article | IST-REx-ID: 9362 | OA
M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4 April. 2021.
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2021 | Journal Article | IST-REx-ID: 9439 | OA
W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.
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2021 | Journal Article | IST-REx-ID: 9822 | OA
T. Zisis 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, pp. 35545–35560, 2021.
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2021 | Journal Article | IST-REx-ID: 9828 | OA
M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,” IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical and Electronics Engineers, pp. 4039–4054, 2021.
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2021 | Journal Article | IST-REx-ID: 10535 | OA
K. Bod’ová, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” PLoS Computational Biology, vol. 17, no. 12. Public Library of Science, 2021.
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2021 | Journal Article | IST-REx-ID: 9226 | OA
G. Tkačik and T. Gregor, “The many bits of positional information,” Development, vol. 148, no. 2. The Company of Biologists, 2021.
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2020 | Journal Article | IST-REx-ID: 8084 | OA
F. Lombardi 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, pp. 171–190, 2020.
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2020 | Research Data | IST-REx-ID: 8097 | OA
B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” IST Austria, 2020.
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2020 | Journal Article | IST-REx-ID: 8105 | OA
F. Lombardi, J. W. J. L. Wang, X. Zhang, and P. C. Ivanov, “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. EDP Sciences, 2020.
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2020 | Thesis | IST-REx-ID: 8155 | OA
R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” IST Austria, 2020.
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2020 | Research Data | IST-REx-ID: 7383 | OA
R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” IST Austria, 2020.
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2020 | Journal Article | IST-REx-ID: 7490 | OA
M. Narasimhan et al., “Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants,” eLife, vol. 9. eLife Sciences Publications, 2020.
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2020 | Journal Article | IST-REx-ID: 7569 | OA
R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library of Science, 2020.
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2020 | Journal Article | IST-REx-ID: 7656 | OA
M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle for population codes,” Frontiers in Computational Neuroscience, vol. 14. Frontiers, 2020.
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2020 | Preprint | IST-REx-ID: 7675 | OA
R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
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2020 | Journal Article | IST-REx-ID: 8698 | OA
O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “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, pp. 25066–25073, 2020.
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2020 | Research Data | IST-REx-ID: 8930 | OA
B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” IST Austria, 2020.
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2020 | Journal Article | IST-REx-ID: 8955 | OA
R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” Frontiers in Physiology, vol. 11. Frontiers, 2020.
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2020 | Journal Article | IST-REx-ID: 9000 | OA
R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” PNAS, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.
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2020 | Research Data Reference | IST-REx-ID: 9776
R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020.
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2020 | Research Data Reference | IST-REx-ID: 9777
R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.
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2020 | Research Data Reference | IST-REx-ID: 9779
R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library of Science, 2020.
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2020 | Thesis | IST-REx-ID: 8657 | OA
B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” IST Austria, 2020.
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2020 | Journal Article | IST-REx-ID: 8250 | OA
B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020.
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2020 | Preprint | IST-REx-ID: 7673 | OA
B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
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2020 | Journal Article | IST-REx-ID: 7652 | OA
I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.
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2019 | Journal Article | IST-REx-ID: 5817 | OA
B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019.
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2019 | Journal Article | IST-REx-ID: 5945 | OA
M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019.
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2019 | Journal Article | IST-REx-ID: 6046 | OA
K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision of complex stress responses in individual bacteria,” Molecular systems biology, vol. 15, no. 2. Embo Press, 2019.
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2019 | Journal Article | IST-REx-ID: 6049 | OA
D. De Martino, “Feedback-induced self-oscillations in large interacting systems subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4. IOP Publishing, 2019.
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2019 | Thesis | IST-REx-ID: 6071 | OA
R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” IST Austria, 2019.
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2019 | Journal Article | IST-REx-ID: 7103 | OA
J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “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. PLoS, 2019.
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2019 | Journal Article | IST-REx-ID: 7422 | OA
T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.
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2019 | Preprint | IST-REx-ID: 7552 | OA
W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” arXiv:1912.08579. ArXiv.
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2019 | Conference Paper | IST-REx-ID: 7606 | OA
M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden, 2019.
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2019 | Journal Article | IST-REx-ID: 6090 | OA
M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. APS, 2019.
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2019 | Thesis | IST-REx-ID: 6473 | OA
S. A. Cepeda Humerez, “Estimating information flow in single cells,” IST Austria, 2019.
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2019 | Journal Article | IST-REx-ID: 6784 | OA
J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.
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2019 | Journal Article | IST-REx-ID: 6900 | OA
S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” PLoS computational biology, vol. 15, no. 9. Public Library of Science, p. e1007290, 2019.
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2019 | Research Data Reference | IST-REx-ID: 9786
J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.” Public Library of Science, 2019.
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