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133 Publications

2020 | Journal Article | IST-REx-ID: 7652
I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4, pp. 612–625, 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, 2020.
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2020 | Preprint | IST-REx-ID: 7673 | OA
B. Kavcic, G. Tkačik, and T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 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: 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, 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, 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 | 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, 2020.
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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, p. 054108, 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, p. 8989292.
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2019 | Journal Article | IST-REx-ID: 5817
B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” Soft Matter, vol. 15, no. 4, pp. 602–614, 2019.
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2019 | Journal Article | IST-REx-ID: 5945
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, 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, 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, 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: 6090 | OA
M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2, 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, 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, p. e1007290, 2019.
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2019 | Preprint | IST-REx-ID: 7083 | OA
B. Kavcic, G. Tkačik, and T. Bollenbach, “Mechanistic origin of drug interactions between translation-inhibiting antibiotics,” bioRxiv. Cold Spring Harbor Laboratory.
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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, 2019.
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2019 | Journal Article | IST-REx-ID: 196 | OA
M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings of the National Academy of Sciences, vol. 116, no. 8, pp. 2821–2830, 2019.
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2018 | Journal Article | IST-REx-ID: 406 | OA
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3, 2018.
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2018 | Journal Article | IST-REx-ID: 457
M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2, pp. 359–366, 2018.
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2018 | Journal Article | IST-REx-ID: 543 | OA
M. J. Chalk, O. Marre, and G. Tkacik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1, pp. 186–191, 2018.
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2018 | Research Data | IST-REx-ID: 5584 | OA
S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, Nonlinear decoding of a complex movie from the mammalian retina. IST Austria, 2018.
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2018 | Research Data | IST-REx-ID: 5585 | OA
C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. IST Austria, 2018.
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2018 | Research Data | IST-REx-ID: 5587 | OA
D. De Martino and G. Tkačik, Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria, 2018.
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2018 | Journal Article | IST-REx-ID: 607 | OA
K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377, pp. 108–120, 2018.
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2018 | Journal Article | IST-REx-ID: 281 | OA
A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkacik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23, pp. 6088–6093, 2018.
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2018 | Journal Article | IST-REx-ID: 292 | OA
V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5, 2018.
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2018 | Journal Article | IST-REx-ID: 305
P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771, pp. 183–202, 2018.
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2018 | Journal Article | IST-REx-ID: 306 | OA
A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4, 2018.
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2018 | Journal Article | IST-REx-ID: 31 | OA
U. Ferrari, S. Deny, M. J. Chalk, G. Tkacik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4, p. 042410, 2018.
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2018 | Journal Article | IST-REx-ID: 67 | OA
C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10, pp. 1633–1643, 2018.
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2018 | Journal Article | IST-REx-ID: 161 | OA
D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1, 2018.
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2018 | Journal Article | IST-REx-ID: 19 | OA
A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” Molecular Biology and Evolution, vol. 35, no. 11, pp. 2669–2684, 2018.
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2018 | Journal Article | IST-REx-ID: 316 | OA
K. Bod’ová, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3, pp. 861–883, 2018.
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2017 | Journal Article | IST-REx-ID: 2016 | OA
A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” Scandinavian Journal of Statistics, vol. 44, no. 2, pp. 285–306, 2017.
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2017 | Journal Article | IST-REx-ID: 720 | OA
J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9, 2017.
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2017 | Journal Article | IST-REx-ID: 725 | OA
R. Harpaz, G. Tkacik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38, pp. 10149–10154, 2017.
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2017 | Journal Article | IST-REx-ID: 730
C. Savin and G. Tkacik, “Maximum entropy models as a tool for building precise neural controls,” Current Opinion in Neurobiology, vol. 46, pp. 120–126, 2017.
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2017 | Journal Article | IST-REx-ID: 735
V. Barone et al., “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” Developmental Cell, vol. 43, no. 2, pp. 198–211, 2017.
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2017 | Journal Article | IST-REx-ID: 548 | OA
D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” Physical Review E, vol. 96, no. 6, 2017.
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2017 | Research Data | IST-REx-ID: 5560 | OA
T. Bergmiller et al., Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. IST Austria, 2017.
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2017 | Research Data | IST-REx-ID: 5562 | OA
O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, Multi-electrode array recording from salamander retinal ganglion cells. IST Austria, 2017.
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2017 | Journal Article | IST-REx-ID: 613 | OA
R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1, 2017.
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2017 | Conference Paper | IST-REx-ID: 652
R. Der and G. S. Martius, “Dynamical self consistency leads to behavioral development and emergent social interactions in robots,” presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France, 2017.
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