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175 Publications
2023 | Journal Article | IST-REx-ID: 12762 | 
Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023. doi:10.1038/s43588-023-00410-9
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| arXiv
2022 | Journal Article | IST-REx-ID: 10530 |
Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 2022;121(1):P44-60. doi:10.1016/j.bpj.2021.12.006
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2022 | Journal Article | IST-REx-ID: 10736 |
Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543
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2022 | Preprint | IST-REx-ID: 10821 |
Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv. 2022. doi:10.1101/2022.03.03.482657
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2022 | Journal Article | IST-REx-ID: 11638 |
Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 2022;4(2). doi:10.1103/PhysRevResearch.4.023240
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| arXiv
2022 | Journal Article | IST-REx-ID: 12081 |
Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 2022;119(36). doi:10.1073/pnas.2123152119
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2022 | Journal Article | IST-REx-ID: 12156 |
Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 2022;31(9). doi:10.1016/j.coisb.2022.100435
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2022 | Journal Article | IST-REx-ID: 12332 |
Mlynarski WF, Tkačik G. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 2022;20(12):e3001889. doi:10.1371/journal.pbio.3001889
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2022 | Preprint | IST-REx-ID: 12487 |
Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. bioRxiv. doi:10.1101/2022.07.12.499725
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2021 | Journal Article | IST-REx-ID: 10535 |
Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 2021;17(12). doi:10.1371/journal.pcbi.1009661
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| arXiv
2021 | Preprint | IST-REx-ID: 10912 |
Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. doi:10.48550/ARXIV.2108.06686
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| arXiv
2021 | Preprint | IST-REx-ID: 10077 |
Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602
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2021 | Journal Article | IST-REx-ID: 7463 |
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. Neurocomputing. 2021;461:657-666. doi:10.1016/j.neucom.2020.05.126
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2021 | Journal Article | IST-REx-ID: 7553 |
Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020
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2021 | Journal Article | IST-REx-ID: 8997 |
Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529
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2021 | Journal Article | IST-REx-ID: 9226 |
Tkačik G, Gregor T. The many bits of positional information. Development. 2021;148(2). doi:10.1242/dev.176065
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2021 | Journal Article | IST-REx-ID: 9283 |
Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. eLife. 2021;10. doi:10.7554/elife.65993
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2021 | Journal Article | IST-REx-ID: 9439 |
Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0
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2021 | Journal Article | IST-REx-ID: 9362 |
Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4 April). doi:10.1371/journal.pone.0248940
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2021 | Journal Article | IST-REx-ID: 9822 |
Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850
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2021 | Journal Article | IST-REx-ID: 9828 |
Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899
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| arXiv
2021 | Preprint | IST-REx-ID: 10579 |
Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. arXiv. doi:10.48550/arXiv.2112.13558
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| arXiv
2020 | Journal Article | IST-REx-ID: 7490 |
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 | Journal Article | IST-REx-ID: 7656 |
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 | Research Data | IST-REx-ID: 7383 |
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 | Journal Article | IST-REx-ID: 8084 |
Lombardi F, Gómez-Extremera M, Bernaola-Galván P, 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. 2020;40(1):171-190. doi:10.1523/jneurosci.1278-19.2019
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2020 | Research Data | IST-REx-ID: 8097 |
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 |
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 |
Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155
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2020 | Preprint | IST-REx-ID: 7675 |
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 | Journal Article | IST-REx-ID: 8955 |
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 |
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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2020 | Research Data | IST-REx-ID: 8930 |
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 | Research Data Reference | IST-REx-ID: 9776
Grah R, Friedlander T. Supporting information. 2020. doi:10.1371/journal.pcbi.1007642.s001
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2020 | Journal Article | IST-REx-ID: 8698 |
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 | Journal Article | IST-REx-ID: 7569 |
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 | Research Data Reference | IST-REx-ID: 9779
Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:10.1371/journal.pcbi.1007642.s003
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2020 | Research Data Reference | IST-REx-ID: 9777
Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002
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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: 7652 |
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: 8250 |
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 | Preprint | IST-REx-ID: 7673 |
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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2019 | Journal Article | IST-REx-ID: 196 |
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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| arXiv
2019 | Journal Article | IST-REx-ID: 5817 |
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 |
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: 6049 |
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 | Journal Article | IST-REx-ID: 6046 |
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: 6090 |
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 |
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: 6900 |
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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