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168 Publications

2022 | Journal Article | IST-REx-ID: 10736 | OA
Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.64543
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2022 | Preprint | IST-REx-ID: 10821 | OA
Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2022). Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.03.03.482657
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2022 | Journal Article | IST-REx-ID: 11638 | OA
Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., & Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.4.023240
View | Files available | DOI | arXiv
 
2022 | Journal Article | IST-REx-ID: 10530 | OA
Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2021.12.006
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2021 | Journal Article | IST-REx-ID: 7463 | OA
Lombardi, F., Shriki, O., Herrmann, H. J., & de Arcangelis, L. (2021). Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. Elsevier. https://doi.org/10.1016/j.neucom.2020.05.126
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2021 | Journal Article | IST-REx-ID: 7553 | OA
Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020
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2021 | Preprint | IST-REx-ID: 10579 | OA
Kavcic, B., & Tkačik, G. (n.d.). On token-driven totally asymmetric simple exclusion process. arXiv.
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2021 | Preprint | IST-REx-ID: 10912 | OA
Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (n.d.). Quantifying the coexistence of neuronal oscillations and avalanches. arXiv. https://doi.org/10.48550/ARXIV.2108.06686
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2021 | Journal Article | IST-REx-ID: 8997 | OA
Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008529
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2021 | Journal Article | IST-REx-ID: 9283 | OA
Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., & Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.65993
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2021 | Journal Article | IST-REx-ID: 9362 | OA
Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed by a recurrent neural network. PLoS ONE. https://doi.org/10.1371/journal.pone.0248940
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2021 | Journal Article | IST-REx-ID: 9439 | OA
Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0
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2021 | Journal Article | IST-REx-ID: 9822 | OA
Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850
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2021 | Journal Article | IST-REx-ID: 9828 | OA
Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899
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2021 | Journal Article | IST-REx-ID: 9226 | OA
Tkačik, G., & Gregor, T. (2021). The many bits of positional information. Development. The Company of Biologists. https://doi.org/10.1242/dev.176065
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2021 | Preprint | IST-REx-ID: 10077 | OA
Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602
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2021 | Journal Article | IST-REx-ID: 10535 | OA
Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661
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2020 | Journal Article | IST-REx-ID: 8084 | OA
Lombardi, F., Gómez-Extremera, M., Bernaola-Galván, P., Vetrivelan, R., Saper, C. B., Scammell, T. E., & Ivanov, P. C. (2020). 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. Society for Neuroscience. https://doi.org/10.1523/jneurosci.1278-19.2019
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2020 | Research Data | IST-REx-ID: 8097 | OA
Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” IST Austria. https://doi.org/10.15479/AT:ISTA:8097
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2020 | Journal Article | IST-REx-ID: 8105 | OA
Lombardi, F., Wang, J. W. J. L., Zhang, X., & Ivanov, P. C. (2020). 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. EDP Sciences. https://doi.org/10.1051/epjconf/202023000005
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2020 | Thesis | IST-REx-ID: 8155 | OA
Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. IST Austria. https://doi.org/10.15479/AT:ISTA:8155
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2020 | Research Data | IST-REx-ID: 7383 | OA
Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. IST Austria. https://doi.org/10.15479/AT:ISTA:7383
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2020 | Journal Article | IST-REx-ID: 7490 | OA
Narasimhan, M., Johnson, A. J., Prizak, R., Kaufmann, W., Tan, S., Casillas Perez, B. E., & Friml, J. (2020). Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.52067
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2020 | Journal Article | IST-REx-ID: 7569 | OA
Grah, R., & Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642
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2020 | Journal Article | IST-REx-ID: 7656 | OA
Berry, M. J., & Tkačik, G. (2020). Clustering of neural activity: A design principle for population codes. Frontiers in Computational Neuroscience. Frontiers. https://doi.org/10.3389/fncom.2020.00020
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2020 | Preprint | IST-REx-ID: 7675 | OA
Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.08.029405
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2020 | Journal Article | IST-REx-ID: 8698 | OA
Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117
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2020 | Research Data | IST-REx-ID: 8930 | OA
Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” IST Austria. https://doi.org/10.15479/AT:ISTA:8930
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2020 | Journal Article | IST-REx-ID: 8955 | OA
Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., & Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. Frontiers in Physiology. Frontiers. https://doi.org/10.3389/fphys.2020.558070
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2020 | Journal Article | IST-REx-ID: 9000 | OA
Grah, R., Zoller, B., & Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2006731117
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2020 | Research Data Reference | IST-REx-ID: 9776
Grah, R., & Friedlander, T. (2020). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s001
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2020 | Research Data Reference | IST-REx-ID: 9777
Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002
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2020 | Research Data Reference | IST-REx-ID: 9779
Grah, R., & Friedlander, T. (2020). Distribution of crosstalk values. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s003
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2020 | Thesis | IST-REx-ID: 8657 | OA
Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics to genetics and physiology. IST Austria. https://doi.org/10.15479/AT:ISTA:8657
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2020 | Journal Article | IST-REx-ID: 8250 | OA
Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17734-z
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2020 | Preprint | IST-REx-ID: 7673 | OA
Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.18.047886
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2020 | Journal Article | IST-REx-ID: 7652 | OA
Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-020-1132-7
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2019 | Journal Article | IST-REx-ID: 5817 | OA
Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c8sm01956h
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2019 | Journal Article | IST-REx-ID: 5945 | OA
Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.01.007
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2019 | Journal Article | IST-REx-ID: 6046 | OA
Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and precision of complex stress responses in individual bacteria. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.20188470
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2019 | Journal Article | IST-REx-ID: 6049 | OA
De Martino, D. (2019). Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/aaf2dd
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2019 | Thesis | IST-REx-ID: 6071 | OA
Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. IST Austria. https://doi.org/10.15479/at:ista:th6071
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2019 | Journal Article | IST-REx-ID: 7103 | OA
Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLOS Computational Biology. PLoS. https://doi.org/10.1371/journal.pcbi.1007268
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2019 | Journal Article | IST-REx-ID: 7422 | OA
Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5064867
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2019 | Preprint | IST-REx-ID: 7552 | OA
Bialek, W., Gregor, T., & Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. arXiv:1912.08579. ArXiv.
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2019 | Conference Paper | IST-REx-ID: 7606 | OA
Hledik, M., Sokolowski, T. R., & Tkačik, G. (2019). A tight upper bound on mutual information. In IEEE Information Theory Workshop, ITW 2019. Visby, Sweden: IEEE. https://doi.org/10.1109/ITW44776.2019.8989292
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2019 | Journal Article | IST-REx-ID: 6090 | OA
Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. APS. https://doi.org/10.1103/PhysRevE.99.022423
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2019 | Thesis | IST-REx-ID: 6473 | OA
Cepeda Humerez, S. A. (2019). Estimating information flow in single cells. IST Austria. https://doi.org/10.15479/AT:ISTA:6473
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2019 | Journal Article | IST-REx-ID: 6784 | OA
Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168
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2019 | Journal Article | IST-REx-ID: 6900 | OA
Cepeda Humerez, S. A., Ruess, J., & Tkačik, G. (2019). Estimating information in time-varying signals. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007290
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