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M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.
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B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkadik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” Nature Communications, vol. 14. Springer Nature, 2023.
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F. Lombardi, S. Pepic, O. Shriki, G. Tkadik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023.
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M. Reinhardt, G. Tkadik, and P. R. Ten Wolde, “Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories,” Physical Review X, vol. 13, no. 4. American Physical Society, 2023.
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M. Nardin, J. L. Csicsvari, G. Tkadik, and C. Savin, “The structure of hippocampal C interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023.
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S. Scarpetta et al., “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” iScience, vol. 26, no. 10. Elsevier, p. 107840, 2023.
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S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in European Journal of Public Health, 2023, vol. 33, no. Supplement_2.
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F. Lombardi et al., “Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state,” Cell Reports, vol. 42, no. 10. Elsevier, 2023.
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F. Lombardi et al., “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” bioRxiv. Cold Spring Harbor Laboratory, 2022.
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V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,” Physical Review Research, vol. 4, no. 2. American Physical Society, 2022.
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B. Zoller, T. Gregor, and G. Tkadik, “Eukaryotic gene regulation at equilibrium, or non?,” Current Opinion in Systems Biology, vol. 31, no. 9. Elsevier, 2022.
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T. Zisis et al., “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” Biophysical Journal, vol. 121, no. 1. Elsevier, pp. -60, 2022.
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M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.
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W. F. Mlynarski and G. Tkadik, “Efficient coding theory of dynamic attentional modulation,” PLoS Biology, vol. 20, no. 12. Public Library of Science, p. e3001889, 2022.
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M. Hledik, N. H. Barton, and G. Tkadik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022.
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K. Bodova, 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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F. Lombardi, S. Pepic, O. Shriki, G. Tkadik, and D. De Martino, “Quantifying the coexistence of neuronal oscillations and avalanches.” arXiv.
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B. Kavcic and G. Tkadik, “Token-driven totally asymmetric simple exclusion process,” arXiv. .
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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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G. Tkadik and T. Gregor, “The many bits of positional information,” Development, vol. 148, no. 2. The Company of Biologists, 2021.
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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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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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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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arXiv: 2102.04832

M. J. Chalk, G. Tkadik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of Science, 2021.
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B. Kavcic, G. Tkadik, 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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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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W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkadik, “Statistical analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.
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M. Nardin, J. L. Csicsvari, G. Tkadik, and C. Savin, “The structure of hippocampal C interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory.
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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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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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R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library of Science, 2020.
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R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020.
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M. J. Berry and G. Tkadik, “Clustering of neural activity: A design principle for population codes,” Frontiers in Computational Neuroscience, vol. 14. Frontiers, 2020.
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O. Maoz, G. Tkadik, 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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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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R. Grah, B. Zoller, and G. Tkadik, “Nonequilibrium models of optimal enhancer function,” PNAS, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.
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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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R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.
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R. Grah, B. Zoller, and G. Tkadik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
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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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R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.
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B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020.
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B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.
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R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.
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B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.
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B. Kavcic, G. Tkadik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020.
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B. Kavcic, G. Tkadik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
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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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W. Bialek, T. Gregor, and G. Tkadik, “Action at a distance in transcriptional regulation,” arXiv:1912.08579. ArXiv.
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arXiv: 1912.08579