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141 Publications

2020 | Research Data | IST-REx-ID: 8097 | OA
Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097
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2020 | Journal Article | IST-REx-ID: 8105 | OA
Lombardi F, Wang JWJL, Zhang X, Ivanov PC. 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. 2020;230. doi:10.1051/epjconf/202023000005
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2020 | Thesis | IST-REx-ID: 8155 | OA
Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155
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2020 | Journal Article | IST-REx-ID: 8250 | OA
Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z
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2020 | Thesis | IST-REx-ID: 8657
Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657
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2020 | Journal Article | IST-REx-ID: 8698 | OA
Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117
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2020 | Research Data | IST-REx-ID: 7383 | OA
Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383
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2020 | Preprint | IST-REx-ID: 7463 | OA
Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. bioRxiv. 2020. doi:10.1101/2020.02.03.930966
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2020 | Journal Article | IST-REx-ID: 7490 | OA
Narasimhan M, Johnson AJ, Prizak R, et al. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife. 2020;9. doi:10.7554/eLife.52067
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2020 | Preprint | IST-REx-ID: 7553 | OA
Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of biological systems. bioRxiv. doi:10.1101/848374
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2020 | Journal Article | IST-REx-ID: 7569 | OA
Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642
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2020 | Journal Article | IST-REx-ID: 7652 | OA
Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7
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2020 | Journal Article | IST-REx-ID: 7656 | OA
Berry MJ, Tkačik G. Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. 2020;14. doi:10.3389/fncom.2020.00020
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2020 | Preprint | IST-REx-ID: 7673 | OA
Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886
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2020 | Preprint | IST-REx-ID: 7675 | OA
Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405
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2020 | Research Data | IST-REx-ID: 8930 | OA
Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930
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2020 | Journal Article | IST-REx-ID: 8955 | OA
Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 2020;11. doi:10.3389/fphys.2020.558070
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2020 | Journal Article | IST-REx-ID: 9000 | OA
Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. PNAS. 2020;117(50):31614-31622. doi:10.1073/pnas.2006731117
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2019 | Journal Article | IST-REx-ID: 196 | OA
Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116
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2019 | Journal Article | IST-REx-ID: 7422 | OA
Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867
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2019 | Preprint | IST-REx-ID: 7552 | OA
Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:191208579.
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2019 | Conference Paper | IST-REx-ID: 7606 | OA
Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information. In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292
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2019 | Journal Article | IST-REx-ID: 5817 | OA
Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h
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2019 | Journal Article | IST-REx-ID: 5945 | OA
Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15. doi:10.1016/j.cell.2019.01.007
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2019 | Journal Article | IST-REx-ID: 6046 | OA
Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 2019;15(2). doi:10.15252/msb.20188470
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2019 | Journal Article | IST-REx-ID: 6049 | OA
De Martino D. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 2019;52(4). doi:10.1088/1751-8121/aaf2dd
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2019 | Thesis | IST-REx-ID: 6071 | OA
Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071
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2019 | Journal Article | IST-REx-ID: 6090 | OA
Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423
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2019 | Thesis | IST-REx-ID: 6473 | OA
Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473
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2019 | Journal Article | IST-REx-ID: 6784 | OA
Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168
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2019 | Journal Article | IST-REx-ID: 6900 | OA
Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. PLoS computational biology. 2019;15(9):e1007290. doi:10.1371/journal.pcbi.1007290
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2019 | Journal Article | IST-REx-ID: 7103 | OA
Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLOS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268
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2018 | Journal Article | IST-REx-ID: 281 | OA
Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115
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2018 | Journal Article | IST-REx-ID: 292 | OA
Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5). doi:10.1371/journal.pcbi.1006057
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2018 | Journal Article | IST-REx-ID: 19 | OA
Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684. doi:10.1093/molbev/msy163
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2018 | Journal Article | IST-REx-ID: 543 | OA
Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115
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2018 | Research Data | IST-REx-ID: 5584 | OA
Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98
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2018 | Research Data | IST-REx-ID: 5587 | OA
De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62
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2018 | Journal Article | IST-REx-ID: 607 | OA
Bod’ová K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015
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2018 | Journal Article | IST-REx-ID: 161 | OA
De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9
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2018 | Journal Article | IST-REx-ID: 406 | OA
Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049
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2018 | Journal Article | IST-REx-ID: 457
Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z
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2018 | Journal Article | IST-REx-ID: 305
Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202. doi:10.1007/978-1-4939-7792-5_15
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2018 | Journal Article | IST-REx-ID: 306 | OA
De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596
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2018 | Journal Article | IST-REx-ID: 31 | OA
Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410
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2018 | Journal Article | IST-REx-ID: 316 | OA
Bod’ová K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748
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2018 | Journal Article | IST-REx-ID: 67 | OA
Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y
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2018 | Research Data | IST-REx-ID: 5585 | OA
Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108
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2017 | Journal Article | IST-REx-ID: 823 | OA
Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017;2017(9). doi:10.1088/1742-5468/aa85c3
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2017 | Journal Article | IST-REx-ID: 2016 | OA
Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306. doi:10.1111/sjos.12251
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