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182 Publications
2024 | Journal Article | IST-REx-ID: 14901 | 
Tipping points of space debris in low earth orbit
K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024).
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K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024).
2024 | Thesis | IST-REx-ID: 15020 |
Genetic information and biological optimization
M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.
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M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.
2023 | Journal Article | IST-REx-ID: 13127 |
Dynamic pathogen detection and social feedback shape collective hygiene in ants
B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).
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B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).
2023 | Journal Article | IST-REx-ID: 12762 |
Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain
F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.
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F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.
2023 | Journal Article | IST-REx-ID: 14515 |
Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories
M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).
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M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).
2023 | Journal Article | IST-REx-ID: 14656 |
The structure of hippocampal CA1 interactions optimizes spatial coding across experience
M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.
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M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.
2023 | Journal Article | IST-REx-ID: 12487 |
Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture
S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840.
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S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840.
2023 | Conference Abstract | IST-REx-ID: 14862 |
Complex vaccination strategies prevent the emergence of vaccine resistance
S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.
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S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.
2023 | Journal Article | IST-REx-ID: 14402 |
Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state
F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. De Arcangelis, O. Shriki, Cell Reports 42 (2023).
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F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. De Arcangelis, O. Shriki, Cell Reports 42 (2023).
2022 | Preprint | IST-REx-ID: 10821 |
Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades
F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (2022).
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F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (2022).
2022 | Journal Article | IST-REx-ID: 11638 |
Inferring couplings in networks across order-disorder phase transitions
V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).
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V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).
2022 | Journal Article | IST-REx-ID: 12156 |
Eukaryotic gene regulation at equilibrium, or non?
B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).
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B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).
2022 | Journal Article | IST-REx-ID: 10530 |
Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration
T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.
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T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.
2022 | Journal Article | IST-REx-ID: 10736 |
Predicting bacterial promoter function and evolution from random sequences
M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).
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M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).
2022 | Journal Article | IST-REx-ID: 12332 |
Efficient coding theory of dynamic attentional modulation
W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.
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W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.
2022 | Journal Article | IST-REx-ID: 12081 |
Accumulation and maintenance of information in evolution
M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).
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M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).
2021 | Journal Article | IST-REx-ID: 10535 |
Dynamic maximum entropy provides accurate approximation of structured population dynamics
K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).
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K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).
2021 | Preprint | IST-REx-ID: 10912 |
Quantifying the coexistence of neuronal oscillations and avalanches
F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, (n.d.).
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F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, (n.d.).
2021 | Preprint | IST-REx-ID: 10579 |
Token-driven totally asymmetric simple exclusion process
B. Kavcic, G. Tkačik, ArXiv (n.d.).
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B. Kavcic, G. Tkačik, ArXiv (n.d.).
2021 | Journal Article | IST-REx-ID: 7463 |
Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches
F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.
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F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.
2021 | Journal Article | IST-REx-ID: 9226 |
The many bits of positional information
G. Tkačik, T. Gregor, Development 148 (2021).
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G. Tkačik, T. Gregor, Development 148 (2021).
2021 | Journal Article | IST-REx-ID: 9439 |
Efficient and adaptive sensory codes
W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.
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W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.
2021 | Journal Article | IST-REx-ID: 9822 |
Sequential and switchable patterning for studying cellular processes under spatiotemporal control
T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.
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T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.
2021 | Journal Article | IST-REx-ID: 9828 |
Fast and accurate amplitude demodulation of wideband signals
M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.
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M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.
2021 | Journal Article | IST-REx-ID: 9362 |
Inferring the function performed by a recurrent neural network
M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).
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M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).
2021 | Journal Article | IST-REx-ID: 8997 |
Minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
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B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
2021 | Journal Article | IST-REx-ID: 9283 |
Local genetic context shapes the function of a gene regulatory network
A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).
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A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).
2021 | Journal Article | IST-REx-ID: 7553 |
Statistical analysis and optimality of neural systems
W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.
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W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.
2021 | Preprint | IST-REx-ID: 10077 |
The structure of hippocampal CA1 interactions optimizes spatial coding across experience
M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).
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M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).
2020 | Journal Article | IST-REx-ID: 8105 |
Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality
F. Lombardi, J.W.J.L. Wang, X. Zhang, P.C. Ivanov, EPJ Web of Conferences 230 (2020).
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F. Lombardi, J.W.J.L. Wang, X. Zhang, P.C. Ivanov, EPJ Web of Conferences 230 (2020).
2020 | Journal Article | IST-REx-ID: 7490 |
Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants
M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020).
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M. Narasimhan, A.J. Johnson, R. Prizak, W. Kaufmann, S. Tan, B.E. Casillas Perez, J. Friml, ELife 9 (2020).
2020 | Research Data Reference | IST-REx-ID: 9779
Distribution of crosstalk values
R. Grah, T. Friedlander, (2020).
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R. Grah, T. Friedlander, (2020).
2020 | Research Data Reference | IST-REx-ID: 9776
Supporting information
R. Grah, T. Friedlander, (2020).
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R. Grah, T. Friedlander, (2020).
2020 | Journal Article | IST-REx-ID: 7656 |
Clustering of neural activity: A design principle for population codes
M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).
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M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).
2020 | Journal Article | IST-REx-ID: 8698 |
Learning probabilistic neural representations with randomly connected circuits
O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.
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O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.
2020 | Journal Article | IST-REx-ID: 8955 |
Network physiology of cortico–muscular interactions
R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).
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R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).
2020 | Journal Article | IST-REx-ID: 9000 |
Nonequilibrium models of optimal enhancer function
R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.
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R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.
2020 | Journal Article | IST-REx-ID: 8084 |
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
F. Lombardi, M. Gómez-Extremera, P. Bernaola-Galván, R. Vetrivelan, C.B. Saper, T.E. Scammell, P.C. Ivanov, Journal of Neuroscience 40 (2020) 171–190.
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F. Lombardi, M. Gómez-Extremera, P. Bernaola-Galván, R. Vetrivelan, C.B. Saper, T.E. Scammell, P.C. Ivanov, Journal of Neuroscience 40 (2020) 171–190.
2020 | Thesis | IST-REx-ID: 8155 |
Gene regulation across scales – how biophysical constraints shape evolution
R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.
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R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.
2020 | Preprint | IST-REx-ID: 7675 |
Normative models of enhancer function
R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).
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R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).
2020 | Journal Article | IST-REx-ID: 7569 |
The relation between crosstalk and gene regulation form revisited
R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).
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R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).
2020 | Research Data Reference | IST-REx-ID: 9777 |
Maximizing crosstalk
R. Grah, T. Friedlander, (2020).
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R. Grah, T. Friedlander, (2020).
2020 | Research Data | IST-REx-ID: 8097 |
Analysis scripts and research data for the paper "Mechanisms of drug interactions between translation-inhibiting antibiotics"
B. Kavcic, (2020).
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B. Kavcic, (2020).
2020 | Research Data | IST-REx-ID: 8930 |
Analysis scripts and research data for the paper "Minimal biophysical model of combined antibiotic action"
B. Kavcic, (2020).
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B. Kavcic, (2020).
2020 | Research Data | IST-REx-ID: 7383 |
Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation
R. Grah, (2020).
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R. Grah, (2020).
2020 | Thesis | IST-REx-ID: 8657 |
Perturbations of protein synthesis: from antibiotics to genetics and physiology
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, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.
2020 | Journal Article | IST-REx-ID: 8250 |
Mechanisms of drug interactions between translation-inhibiting antibiotics
B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).
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B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).
2020 | Preprint | IST-REx-ID: 7673 |
A minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).
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B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).
2020 | Journal Article | IST-REx-ID: 7652 |
Gene amplification as a form of population-level gene expression regulation
I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.
[Submitted Version]
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I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.
2019 | Preprint | IST-REx-ID: 7552 |
Action at a distance in transcriptional regulation
W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).
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W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).