GT
Gasper Tkacik
q-bio.MNq-bio.NCModels, Geneticphysics.bio-phModels, Neurologicalneurosciencecond-mat.stat-mechGene Regulatory NetworksGene Expression RegulationModels, Biological
On Valency
published · living versionsW_6uv2jkb5·v1 · currentpublished
Thermodynamics for a network of neurons: Signatures of criticality
with Thierry Mora, Olivier Marre, Dario Amodei, Michael J. Berry +1
1 version
Preprints & journals
169 papers in the corpus · 2006–2026Stable and robust differentiation programs are predominantly irreversible10.64898/2026.07.30.741799v1 · Mani, S., Tkacik, G.2026 · 0 citationsbioRxiv
Nonlocal Decoding of Positional and Correlational Information during Development.42537083 · Zhang, Alex Chen Yi, Hoyos, Pablo Mateu, Brückner, David et al.2026 · 0 citationsPhysical review letters. 2026;137(3):038401
Long-term evolution of regulatory DNA sequences. Part 1: simulations on global, biophysically-realistic genotype-phenotype maps.42107304 · Mascolo, Elia, Borbély, Réka, Herrera-Álvarez, Santiago et al.2026 · 0 citationsCurrent opinion in genetics & development. 2026;99:102483
Long-term evolution of regulatory DNA sequences. Part 2: theory and future challenges.41985221 · Mascolo, Elia, Borbély, Réka, Borst, Noa O et al.2026 · 1 citationCurrent opinion in genetics & development. 2026;98:102472
Invariant nonequilibrium dynamics in gene regulation optimize information flow.42406962 · Zoller, Benjamin, Bénichou, Alexis, Gregor, Thomas et al.2026 · 0 citationsProceedings of the National Academy of Sciences of the United States of America. 2026;123(28):e2524855123
Intrinsic Population Dynamics are a Neuronal Substrate for Visual Attention10.64898/2026.06.02.729565v1 · Schmidt, F. H., Mlynarski, W., Georges, A. et al.2026 · 0 citationsbioRxiv
The scaling behavior of hippocampal activity in sleep/rest predicts spatial memory performance10.64898/2026.03.11.711043v2 · Zivadinovic, P., Lombardi, F., Dupret, D. et al.2026 · 0 citationsbioRxiv
Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges2601.21480v1 · Elia Mascolo, R'eka Borb'ely, Noa Ottilie Borst et al.2026 · 1 citationarXiv
Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype-phenotype maps2601.19681v1 · Elia Mascolo, R'eka Borb'ely, Santiago Herrera-'Alvarez et al.2026 · 0 citationsarXiv
Nonlocal decoding of positional and correlational information during development2512.20536v1 · Alex Chen Yi Zhang, Pablo Mateu Hoyos, David Bruckner et al.2025 · 0 citationsarXiv
Invariant non-equilibrium dynamics of transcriptional regulation optimize information flow.40709307 · Zoller, Benjamin, Bénichou, Alexis, Gregor, Thomas et al.2025 · 0 citationsArXiv. 2025
Invariant non-equilibrium dynamics of transcriptional regulation optimize information flow2507.12395v1 · Benjamin Zoller, Alexis B'enichou, Thomas Gregor et al.2025 · 0 citationsarXiv
Token-driven totally asymmetric simple exclusion processes.40533952 · Kavčič, Bor, Tkačik, Gašper2025 · 2 citationsPhysical review. E. 2025;111(5-1):054122
Evolution and information content of optimal gene regulatory architectures10.1101/2025.06.10.657849v1 · Barton, N. H., Tkacik, G.2025 · 2 citationsbioRxiv
Regulatory architectures optimized for rapid evolution of gene expression10.1101/2025.06.10.658850v1 · Borbely, R., Tkacik, G.2025 · 1 citationbioRxiv
Eukaryotic gene regulation at equilibrium, or non?36590072 · Zoller, Benjamin, Gregor, Thomas, Tkačik, Gašper2025 · 37 citationsCurrent opinion in systems biology. 2022;31
Pulsatile basal gene expression as a fitness determinant in bacteria.40193613 · Jain, K, Hauschild, R, Bochkareva, O O et al.2025 · 4 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(15):e2413709122
Learning reshapes the hippocampal representation hierarchy.40063792 · Chiossi, Heloisa S C, Nardin, Michele, Tkačik, Gašper et al.2025 · 7 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(11):e2417025122
Information Processing in Biochemical Networks.39929539 · Tkačik, Gašper, Wolde, Pieter Rein Ten2025 · 26 citationsAnnual review of biophysics. 2025;54(1):249-274
Linking molecular mechanisms to their evolutionary consequences: a primer.39601269 · Grah, Rok, Guet, Calin C, Tkačik, Gasper et al.2025 · 5 citationsGenetics. 2025;229(2)
Thermodynamics for a network of neurons: Signatures of criticality1407.5946v1 · Gasper Tkacik, Thierry Mora, Olivier Marre et al.2014 · 23 citationsProceedings of the National Academy of Sciences (USA)112, 11508-11513 (2015)on Valency
Token-driven totally asymmetric simple exclusion process2112.13558v3 · Bor Kavcic, Gasper Tkacik2021 · 1 citationarXiv
Chromatin enables precise and scalable gene regulation with factors of limited specificity.39793086 · Perkins, Mindy Liu, Crocker, Justin, Tkačik, Gašper2025 · 12 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(1):e2411887121
Deriving a genetic regulatory network from an optimization principle.39752518 · Sokolowski, Thomas R, Gregor, Thomas, Bialek, William et al.2025 · 26 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(1):e2402925121
Quantitative omnigenic model discovers interpretable genome-wide associations.39441639 · Ružičková, Natália, Hledík, Michal, Tkačik, Gašper2024 · 10 citationsProceedings of the National Academy of Sciences of the United States of America. 2024;121(44):e2402340121
Pulsatile basal gene expression as a fitness determinant in bacteria10.1101/2024.09.30.615870v1 · Jain, K., Hauschild, R., Bochkareva, O. O. et al.2024 · 4 citationsbioRxiv
Quantitative omnigenic model discovers interpretable genome-wide associations10.1101/2024.02.01.578486v2 · Ruzickova, N., Hledik, M., Tkacik, G.2024 · 10 citationsbioRxiv
Learning reshapes the hippocampal representation hierarchy10.1101/2024.08.21.608911v1 · Chiossi, H. S. C., Nardin, M., Tkacik, G. et al.2024 · 7 citationsbioRxiv
Linking Molecular Mechanisms to their Evolutionary Consequences: a primer10.1101/2024.07.18.604043v1 · Grah, R., Guet, C. C., Tkacik, G. et al.2024 · 5 citationsbioRxiv
Chromatin enables precise and scalable gene regulation with factors of limited specificity10.1101/2024.06.13.598840v1 · Perkins, M. L., Crocker, J., Tkacik, G.2024 · 12 citationsbioRxiv
Information content and optimization of self-organized developmental systems.38819997 · Brückner, David B, Tkačik, Gašper2024 · 24 citationsProceedings of the National Academy of Sciences of the United States of America. 2024;121(23):e2322326121
Clustering of Neural Activity: A Design Principle for Population Codes.32231528 · Berry, Michael J, Tkačik, Gašper2024 · 15 citationsFrontiers in computational neuroscience. 2020;14:20
Assessing the precision of morphogen gradients in neural tube development.38302459 · Zagorski, Marcin, Brandenberg, Nathalie, Lutolf, Matthias et al.2024 · 6 citationsNature communications. 2024;15(1):929
Optimal decoding of information from a genetic network1612.08084v1 · Mariela D. Petkova, Gasper Tkacik, William Bialek et al.2016 · 215 citationsCell 176, 844 (2019)
Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain.38177880 · Lombardi, Fabrizio, Pepić, Selver, Shriki, Oren et al.2024 · 45 citationsNature computational science. 2023;3(3):254-263
Information content and optimization of self-organized developmental systems2312.05895v2 · David B. Bruckner, Gasper Tkacik2023 · 24 citationsarXiv
Deriving a genetic regulatory network from an optimization principle2302.05680v2 · Thomas R Sokolowski, Thomas Gregor, William Bialek et al.2023 · 26 citationsarXiv
The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.37758476 · Nardin, Michele, Csicsvari, Jozsef, Tkačik, Gašper et al.2023 · 11 citationsThe Journal of neuroscience : the official journal of the Society for Neuroscience. 2023;43(48):8140-8156
Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories2203.03461v2 · Manuel Reinhardt, Gasper Tkacik, Pieter Rein ten Wolde2022 · 20 citationsPhys. Rev. X 13 (2023) 041017
Dynamic pathogen detection and social feedback shape collective hygiene in ants.37270641 · Casillas-Pérez, Barbara, Boďová, Katarína, Grasse, Anna V et al.2023 · 14 citationsNature communications. 2023;14(1):3232
Efficient coding theory of dynamic attentional modulation.36542662 · Młynarski, Wiktor, Tkačik, Gašper2023 · 18 citationsPLoS biology. 2022;20(12):e3001889
Accumulation and maintenance of information in evolution.36037343 · Hledík, Michal, Barton, Nick, Tkačik, Gašper2022 · 29 citationsProceedings of the National Academy of Sciences of the United States of America. 2022;119(36):e2123152119
Statistical modeling of adaptive neural networks explains coexistence of avalanches and oscillations in resting human brain2108.06686v2 · Fabrizio Lombardi, Selver Pepi'c, Oren Shriki et al.2021 · 1 citationarXiv
Accumulation and maintenance of information in evolution10.1101/2021.12.23.473971v2 · Hledik, M., Barton, N. H., Tkacik, G.2021 · 29 citationsbioRxiv
Discrete modes of social information processing predict individual behavior of fish in a group1703.03065v1 · Roy Harpaz, Gasper Tkacik, Elad Schneidman2017 · 56 citationsarXivon Valency
Limited specificity of molecular interactions incurs an environment-dependent fitness cost in bacteria10.1101/2021.10.20.465141v1 · Igler, C., Fourcade, C., Waldminghaus, T. et al.2021 · 2 citationsbioRxiv
Eukaryotic gene regulation at equilibrium, or non?2110.06214v1 · Benjamin Zoller, Thomas Gregor, Gasper Tkacik2021 · 37 citationsarXiv
The structure of hippocampal CA1 interactions optimizes spatial coding across experience10.1101/2021.09.28.460602v1 · Nardin, M., Csicsvari, J., Tkacik, G. et al.2021 · 11 citationsbioRxiv
Inferring the function performed by a recurrent neural network.33857170 · Chalk, Matthew, Tkacik, Gasper, Marre, Olivier2021 · 8 citationsPloS one. 2021;16(4):e0248940
Minimal biophysical model of combined antibiotic action.33411759 · Kavčič, Bor, Tkačik, Gašper, Bollenbach, Tobias2021 · 13 citationsPLoS computational biology. 2021;17(1):e1008529
Career total: 172 works. 169 are in this corpus.Showing the 50 most recent.
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