Gasper Tkacik

Tkacik Group

114 Publications

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[114]
2025 | Published | Journal Article | IST-REx-ID: 18850 | OA
Chromatin enables precise and scalable gene regulation with factors of limited specificity
M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 122 (2025).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[113]
2025 | Published | Journal Article | IST-REx-ID: 18849 | OA
Deriving a genetic regulatory network from an optimization principle
T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 122 (2025).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[112]
2025 | Research Data | IST-REx-ID: 19294 | OA
Data for "Pulsatile basal gene expression as a fitness determinant in bacteria"
K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, C.C. Guet, (2025).
[Published Version] View | Files available | DOI
 
[111]
2025 | Published | Journal Article | IST-REx-ID: 19453 | OA
Learning reshapes the hippocampal representation hierarchy
H.S.C. Chiossi, M. Nardin, G. Tkačik, J.L. Csicsvari, Proceedings of the National Academy of Sciences 122 (2025).
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[110]
2024 | Published | Journal Article | IST-REx-ID: 18902 | OA
Assessing the precision of morphogen gradients in neural tube development
M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe, A. Kicheva, Nature Communications 15 (2024).
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[109]
2024 | Epub ahead of print | Journal Article | IST-REx-ID: 18936 | OA
Linking molecular mechanisms to their evolutionary consequences: a primer
R. Grah, C.C. Guet, G. Tkačik, M. Lagator, Genetics (2024).
[Published Version] View | DOI | Download Published Version (ext.)
 
[108]
2024 | Published | Journal Article | IST-REx-ID: 17123 | OA
Information content and optimization of self-organized developmental systems
D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences 121 (2024).
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[107]
2024 | Published | Journal Article | IST-REx-ID: 18525 | OA
Quantitative omnigenic model discovers interpretable genome-wide associations
N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).
[Published Version] View | Files available | DOI
 
[106]
2023 | Published | Journal Article | IST-REx-ID: 13127 | OA
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).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[105]
2023 | Published | Journal Article | IST-REx-ID: 14515 | OA
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).
[Published Version] View | Files available | DOI | arXiv
 
[104]
2023 | Published | Journal Article | IST-REx-ID: 12762 | OA
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.
[Published Version] View | Files available | DOI | arXiv
 
[103]
2023 | Published | Journal Article | IST-REx-ID: 14656 | OA
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.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[102]
2022 | Published | Journal Article | IST-REx-ID: 12156 | OA
Eukaryotic gene regulation at equilibrium, or non?
B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).
[Published Version] View | Files available | DOI
 
[101]
2022 | Published | Journal Article | IST-REx-ID: 12332 | OA
Efficient coding theory of dynamic attentional modulation
W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.
[Published Version] View | Files available | DOI | WoS
 
[100]
2022 | Published | Journal Article | IST-REx-ID: 10736 | OA
Predicting bacterial promoter function and evolution from random sequences
M. Lagator, S. Sarikas, M. Steinrück, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[99]
2022 | Published | Journal Article | IST-REx-ID: 12081 | OA
Accumulation and maintenance of information in evolution
M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[98]
2021 | Submitted | Preprint | IST-REx-ID: 10579 | OA
Token-driven totally asymmetric simple exclusion process
B. Kavcic, G. Tkačik, ArXiv (n.d.).
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[97]
2021 | Published | Journal Article | IST-REx-ID: 8997 | OA
Minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
[Published Version] View | Files available | DOI | WoS
 
[96]
2021 | Published | Journal Article | IST-REx-ID: 9226 | OA
The many bits of positional information
G. Tkačik, T. Gregor, Development 148 (2021).
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[95]
2021 | Published | Journal Article | IST-REx-ID: 9362 | OA
Inferring the function performed by a recurrent neural network
M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[94]
2021 | Submitted | Preprint | IST-REx-ID: 10912 | OA
Quantifying the coexistence of neuronal oscillations and avalanches
F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, (n.d.).
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[93]
2021 | Published | Journal Article | IST-REx-ID: 7553 | OA
Statistical analysis and optimality of neural systems
W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS
 
[92]
2021 | Draft | Preprint | IST-REx-ID: 10077 | OA
The structure of hippocampal CA1 interactions optimizes spatial coding across experience
M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[91]
2020 | Published | Preprint | IST-REx-ID: 7675 | OA
Normative models of enhancer function
R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[90]
2020 | Published | Journal Article | IST-REx-ID: 8698 | OA
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.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[89]
2020 | Published | Journal Article | IST-REx-ID: 9000 | OA
Nonequilibrium models of optimal enhancer function
R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2020 | Published | Journal Article | IST-REx-ID: 7656 | OA
Clustering of neural activity: A design principle for population codes
M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[87]
2020 | Published | Journal Article | IST-REx-ID: 7652 | OA
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] View | Files available | DOI | WoS
 
[86]
2020 | Published | Journal Article | IST-REx-ID: 8250 | OA
Mechanisms of drug interactions between translation-inhibiting antibiotics
B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).
[Published Version] View | Files available | DOI | WoS
 
[85]
2020 | Published | Preprint | IST-REx-ID: 7673 | OA
A minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[84]
2019 | Published | Journal Article | IST-REx-ID: 6900 | OA
Estimating information in time-varying signals
S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[83]
2019 | Research Data Reference | IST-REx-ID: 9786
Supporting text and results
J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).
[Published Version] View | Files available | DOI
 
[82]
2019 | Published | Journal Article | IST-REx-ID: 5945 | OA
Optimal decoding of cellular identities in a genetic network
M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.
[Published Version] View | Files available | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[81]
2019 | Submitted | Preprint | IST-REx-ID: 7552 | OA
Action at a distance in transcriptional regulation
W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).
[Preprint] View | Download Preprint (ext.) | arXiv
 
[80]
2019 | Published | Journal Article | IST-REx-ID: 6784 | OA
Molecular noise of innate immunity shapes bacteria-phage ecologies
J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019).
[Published Version] View | Files available | DOI | WoS
 
[79]
2019 | Published | Conference Paper | IST-REx-ID: 7606 | OA
A tight upper bound on mutual information
M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | arXiv
 
[78]
2018 | Published | Journal Article | IST-REx-ID: 406 | OA
Probabilistic models of individual and collective animal behavior
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).
[Submitted Version] View | Files available | DOI | WoS
 
[77]
2018 | Published | Journal Article | IST-REx-ID: 281 | OA
Distributed and dynamic intracellular organization of extracellular information
A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | PubMed | Europe PMC
 
[76]
2018 | Research Data Reference | IST-REx-ID: 9831
Implementation of the inference method in Matlab
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
[Published Version] View | Files available | DOI
 
[75]
2018 | Published | Journal Article | IST-REx-ID: 292 | OA
Nonlinear decoding of a complex movie from the mammalian retina
V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational Biology 14 (2018).
[Published Version] View | Files available | DOI | WoS
 
[74]
2018 | Published | Journal Article | IST-REx-ID: 31 | OA
Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons
U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018).
[Preprint] View | DOI | Download Preprint (ext.) | WoS
 
[73]
2018 | Published | Journal Article | IST-REx-ID: 543 | OA
Toward a unified theory of efficient, predictive, and sparse coding
M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS
 
[72]
2018 | Research Data | IST-REx-ID: 5584 | OA
Nonlinear decoding of a complex movie from the mammalian retina
S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).
[Published Version] View | Files available | DOI
 
[71]
2018 | Research Data | IST-REx-ID: 5587 | OA
Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH"
D. De Martino, G. Tkačik, (2018).
[Published Version] View | Files available | DOI
 
[70]
2018 | Published | Journal Article | IST-REx-ID: 161 | OA
Statistical mechanics for metabolic networks during steady state growth
D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).
[Published Version] View | Files available | DOI | WoS
 
[69]
2018 | Published | Journal Article | IST-REx-ID: 67 | OA
Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.
[Submitted Version] View | Files available | DOI | WoS
 
[68]
2018 | Research Data | IST-REx-ID: 5585 | OA
Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).
[Published Version] View | Files available | DOI
 
[67]
2017 | Published | Journal Article | IST-REx-ID: 955 | OA
Evolution of new regulatory functions on biophysically realistic fitness landscapes
T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).
[Published Version] View | Files available | DOI | WoS
 
[66]
2017 | Research Data Reference | IST-REx-ID: 9709 | OA
Data from: Error-robust modes of the retinal population code
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[65]
2017 | Published | Journal Article | IST-REx-ID: 943 | OA
Decoding of position in the developing neural tube from antiparallel morphogen gradients
M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[64]
2017 | Published | Journal Article | IST-REx-ID: 1104 | OA
Multiplexed computations in retinal ganglion cells of a single type
S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017).
[Published Version] View | Files available | DOI | WoS
 
[63]
2017 | Research Data | IST-REx-ID: 5560 | OA
Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity
T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, (2017).
[Published Version] View | Files available | DOI
 
[62]
2017 | Research Data | IST-REx-ID: 5562 | OA
Multi-electrode array recording from salamander retinal ganglion cells
O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).
[Published Version] View | Files available | DOI
 
[61]
2017 | Published | Journal Article | IST-REx-ID: 613 | OA
Shaping bacterial population behavior through computer interfaced control of individual cells
R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).
[Published Version] View | Files available | DOI
 
[60]
2017 | Published | Journal Article | IST-REx-ID: 665
Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity
T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.
View | Files available | DOI
 
[59]
2017 | Published | Journal Article | IST-REx-ID: 720 | OA
Probabilistic models for neural populations that naturally capture global coupling and criticality
J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).
[Published Version] View | Files available | DOI
 
[58]
2017 | Published | Journal Article | IST-REx-ID: 725 | OA
Discrete modes of social information processing predict individual behavior of fish in a group
R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[57]
2017 | Published | Journal Article | IST-REx-ID: 730
Maximum entropy models as a tool for building precise neural controls
C. Savin, G. Tkačik, Current Opinion in Neurobiology 46 (2017) 120–126.
View | DOI | WoS
 
[56]
2016 | Published | Journal Article | IST-REx-ID: 1358 | OA
Intrinsic limits to gene regulation by global crosstalk
T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).
[Published Version] View | Files available | DOI
 
[55]
2016 | Research Data Reference | IST-REx-ID: 9869
Error bound on an estimator of position
P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
[Published Version] View | Files available | DOI
 
[54]
2016 | Research Data Reference | IST-REx-ID: 9870
Computation of positional information in an Ising model
P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
[Published Version] View | Files available | DOI
 
[53]
2016 | Research Data Reference | IST-REx-ID: 9871
Computation of positional information in a discrete morphogen field
P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
[Published Version] View | Files available | DOI
 
[52]
2016 | Published | Journal Article | IST-REx-ID: 1420 | OA
A general approximation for the dynamics of quantitative traits
K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[51]
2016 | Published | Conference Paper | IST-REx-ID: 1082 | OA
Relevant sparse codes with variational information bottleneck
M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.
[Preprint] View | Files available | Download Preprint (ext.)
 
[50]
2016 | Published | Conference Paper | IST-REx-ID: 1105
Estimating nonlinear neural response functions using GP priors and Kronecker methods
C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.
View | Download None (ext.)
 
[49]
2016 | Published | Journal Article | IST-REx-ID: 1171
Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.
G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.
View | DOI
 
[48]
2016 | Published | Journal Article | IST-REx-ID: 1197 | OA
Error-robust modes of the retinal population code
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).
[Published Version] View | Files available | DOI
 
[47]
2016 | Published | Journal Article | IST-REx-ID: 1242 | OA
Extending the dynamic range of transcription factor action by translational regulation
T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).
[Preprint] View | DOI | Download Preprint (ext.)
 
[46]
2016 | Published | Journal Article | IST-REx-ID: 1248 | OA
Information processing in living systems
G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.
[Preprint] View | DOI | Download Preprint (ext.)
 
[45]
2016 | Published | Journal Article | IST-REx-ID: 1270 | OA
Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information
P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).
[Published Version] View | Files available | DOI
 
[44]
2015 | Published | Journal Article | IST-REx-ID: 1576 | OA
Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[43]
2015 | Published | Journal Article | IST-REx-ID: 1666 | OA
Dynamics of transcription factor binding site evolution
M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).
[Published Version] View | Files available | DOI
 
[42]
2015 | Research Data Reference | IST-REx-ID: 9712
Other fitness models for comparison & for interacting TFBSs
M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).
[Published Version] View | Files available | DOI
 
[41]
2015 | Published | Journal Article | IST-REx-ID: 1697 | OA
High accuracy decoding of dynamical motion from a large retinal population
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015).
[Published Version] View | Files available | DOI
 
[40]
2015 | Published | Journal Article | IST-REx-ID: 1701 | OA
Thermodynamics and signatures of criticality in a network of neurons
G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[39]
2015 | Published | Journal Article | IST-REx-ID: 1885 | OA
Positional information, positional error, and readout precision in morphogenesis: A mathematical framework
G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.
[Preprint] View | DOI | Download Preprint (ext.)
 
[38]
2015 | Published | Journal Article | IST-REx-ID: 1940 | OA
Optimizing information flow in small genetic networks. IV. Spatial coupling
T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
[Preprint] View | DOI | Download Preprint (ext.)
 
[37]
2014 | Published | Journal Article | IST-REx-ID: 3263 | OA
Adaptation to changes in higher-order stimulus statistics in the salamander retina
G. Tkačik, A. Ghosh, E. Schneidman, R. Segev, PLoS One 9 (2014).
[Published Version] View | Files available | DOI
 
[36]
2014 | Research Data Reference | IST-REx-ID: 9752 | OA
Data from: Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[35]
2014 | Published | Journal Article | IST-REx-ID: 2257 | OA
Searching for collective behavior in a large network of sensory neurons
G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[34]
2014 | Published | Journal Article | IST-REx-ID: 1886 | OA
Variance predicts salience in central sensory processing
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).
[Published Version] View | Files available | DOI
 
[33]
2014 | Published | Journal Article | IST-REx-ID: 2231 | OA
Noise and information transmission in promoters with multiple internal states
G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[32]
2013 | Published | Journal Article | IST-REx-ID: 3261 | OA
Positional information, in bits
J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[31]
2013 | Published | Journal Article | IST-REx-ID: 2850 | OA
The simplest maximum entropy model for collective behavior in a neural network
G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[30]
2013 | Published | Journal Article | IST-REx-ID: 2851
A simple method for estimating the entropy of neural activity
M. Berry, G. Tkačik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
View | DOI
 
[29]
2013 | Published | Journal Article | IST-REx-ID: 2277 | OA
Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, PLoS Computational Biology 9 (2013).
[Published Version] View | Files available | DOI
 
[28]
2013 | Published | Journal Article | IST-REx-ID: 2818 | OA
Learning quadratic receptive fields from neural responses to natural stimuli
K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[27]
2013 | Published | Journal Article | IST-REx-ID: 2863 | OA
Stimulus-dependent maximum entropy models of neural population codes
E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).
[Published Version] View | Files available | DOI
 
[26]
2013 | Published | Journal Article | IST-REx-ID: 2913 | OA
Retinal metric: a stimulus distance measure derived from population neural responses
G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).
[Preprint] View | DOI | Download Preprint (ext.)
 
[25]
2013 | Published | Journal Article | IST-REx-ID: 2914 | OA
Statistical thermodynamics of natural images
G. Stephens, T. Mora, G. Tkačik, W. Bialek, Physical Review Letters 110 (2013).
[Published Version] View | Files available | DOI | arXiv
 
[24]
2012 | Published | Journal Article | IST-REx-ID: 3262 | OA
Optimizing information flow in small genetic networks. III. A self-interacting gene
G. Tkačik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 85 (2012).
[Preprint] View | DOI | Download Preprint (ext.)
 
[23]
2011 | Published | Journal Article | IST-REx-ID: 3276 | OA
Fast, scalable, Bayesian spike identification for multi-electrode arrays
J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson, PLoS One 6 (2011).
View | Files available | DOI
 
[22]
2011 | Published | Journal Article | IST-REx-ID: 3374 | OA
Information transmission in genetic regulatory networks a review
G. Tkačik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).
[Submitted Version] View | DOI | Download Submitted Version (ext.)
 
[21]
2011 | Published | Journal Article | IST-REx-ID: 3384 | OA
Natural images from the birthplace of the human eye
G. Tkačik, P. Garrigan, C. Ratliff, G. Milcinski, J. Klein, L. Seyfarth, P. Sterling, D. Brainard, V. Balasubramanian, PLoS One 6 (2011).
[Published Version] View | Files available | DOI
 
[20]
2011 | Published | Journal Article | IST-REx-ID: 3401
The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source
S. Little, G. Tkačik, T. Kneeland, E. Wieschaus, T. Gregor, PLoS Biology 9 (2011).
View | DOI
 
[19]
2010 | Published | Conference Paper | IST-REx-ID: 3430 | OA
Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics
G. Tkačik, in:, Elsevier, 2010.
View | Download (ext.)
 
[18]
2010 | Published | Journal Article | IST-REx-ID: 3735
Local statistics in natural scenes predict the saliency of synthetic textures
G. Tkačik, J. Prentice, J. Victor, V. Balasubramanian, PNAS 107 (2010) 18149–18154.
View | DOI | Download (ext.)
 
[17]
2010 | Published | Journal Article | IST-REx-ID: 3736
Optimal population coding by noisy spiking neurons
G. Tkačik, J. Prentice, V. Balasubramanian, E. Schneidman, PNAS 107 (2010) 14419–14424.
View | DOI | Download (ext.)
 
[16]
2010 | Published | Journal Article | IST-REx-ID: 3738
Optimizing information flow in small genetic networks. II. Feed-forward interactions
A. Walczak, G. Tkačik, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 81 (2010).
View | DOI | Download (ext.)
 
[15]
2010 | Published | Preprint | IST-REx-ID: 3743 | OA
From statistical mechanics to information theory: understanding biophysical information-processing systems
G. Tkačik, ArXiv q-MN (2010) 1–52.
View | Download (ext.)
 
[14]
2009 | Published | Preprint | IST-REx-ID: 3732 | OA
Spin glass models for a network of real neurons
G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv q-NC (2009).
View | Download (ext.)
 
[13]
2009 | Published | Journal Article | IST-REx-ID: 3733
The dynamics of adaptation on correlated fitness landscapes
S. Kryazhimskiy, G. Tkačik, J. Plotkin, PNAS 106 (2009) 18638–18643.
View | DOI | Download (ext.)
 
[12]
2009 | Published | Journal Article | IST-REx-ID: 3737
Optimizing information flow in small genetic networks
G. Tkačik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 80 (2009).
View | DOI | Download (ext.)
 
[11]
2009 | Published | Journal Article | IST-REx-ID: 3745
Diffusion, dimensionality, and noise in transcriptional regulation
G. Tkačik, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 79 (2009).
View | DOI
 
[10]
2009 | Published | Book Chapter | IST-REx-ID: 3747
Cell Biology: Networks, regulation, pathways
G. Tkačik, W. Bialek, in:, R. Meyers (Ed.), Encyclopedia of Complexity and Systems Science, Springer, 2009, pp. 719–741.
View | DOI
 
[9]
2008 | Published | Journal Article | IST-REx-ID: 3734 | OA
The role of input noise in transcriptional regulation
G. Tkačik, T. Gregor, W. Bialek, PLoS One 3 (2008).
View | DOI | Download (ext.)
 
[8]
2008 | Published | Journal Article | IST-REx-ID: 3739
Information capacity of genetic regulatory elements
G. Tkačik, C. Callan, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 78 (2008).
View | DOI
 
[7]
2008 | Published | Journal Article | IST-REx-ID: 3740 | OA
Information flow and optimization in transcriptional regulation
G. Tkačik, C. Callan, W. Bialek, PNAS 105 (2008) 12265–12270.
View | DOI | Download (ext.)
 
[6]
2008 | Published | Journal Article | IST-REx-ID: 3744 | OA
Decoding spike timing: The differential reverse-correlation method
G. Tkačik, M. Magnasco, Biosystems 93 (2008) 90–100.
View | DOI | Download (ext.)
 
[5]
2007 | Published | Journal Article | IST-REx-ID: 3731
Precise physical models of protein-DNA interaction from high-throughput data
J. Kinney, G. Tkačik, C. Callan, PNAS 104 (2007) 501–506.
View | DOI | Download (ext.)
 
[4]
2007 | Published | Preprint | IST-REx-ID: 3742 | OA
Faster solutions of the inverse pairwise Ising problem
T. Broderick, M. Dudik, G. Tkačik, R. Schapire, W. Bialek, ArXiv q-QM (2007).
View | Download (ext.)
 
[3]
2006 | Published | Preprint | IST-REx-ID: 3431 | OA
Ising models for networks of real neurons
G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4.
View | Download (ext.)
 
[2]
2005 | Published | Journal Article | IST-REx-ID: 3741 | OA
Information-based clustering
N. Slonim, G. Atwal, G. Tkačik, W. Bialek, PNAS 102 (2005) 18297–18302.
View | DOI | Download (ext.)
 
[1]
2005 | Published | Preprint | IST-REx-ID: 3746 | OA
Estimating mutual information and multi-information in large networks
N. Slonim, G. Atwal, G. Tkačik, W. Bialek, ArXiv (2005) 1–11.
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114 Publications

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[114]
2025 | Published | Journal Article | IST-REx-ID: 18850 | OA
Chromatin enables precise and scalable gene regulation with factors of limited specificity
M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 122 (2025).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[113]
2025 | Published | Journal Article | IST-REx-ID: 18849 | OA
Deriving a genetic regulatory network from an optimization principle
T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 122 (2025).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[112]
2025 | Research Data | IST-REx-ID: 19294 | OA
Data for "Pulsatile basal gene expression as a fitness determinant in bacteria"
K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, C.C. Guet, (2025).
[Published Version] View | Files available | DOI
 
[111]
2025 | Published | Journal Article | IST-REx-ID: 19453 | OA
Learning reshapes the hippocampal representation hierarchy
H.S.C. Chiossi, M. Nardin, G. Tkačik, J.L. Csicsvari, Proceedings of the National Academy of Sciences 122 (2025).
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[110]
2024 | Published | Journal Article | IST-REx-ID: 18902 | OA
Assessing the precision of morphogen gradients in neural tube development
M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe, A. Kicheva, Nature Communications 15 (2024).
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[109]
2024 | Epub ahead of print | Journal Article | IST-REx-ID: 18936 | OA
Linking molecular mechanisms to their evolutionary consequences: a primer
R. Grah, C.C. Guet, G. Tkačik, M. Lagator, Genetics (2024).
[Published Version] View | DOI | Download Published Version (ext.)
 
[108]
2024 | Published | Journal Article | IST-REx-ID: 17123 | OA
Information content and optimization of self-organized developmental systems
D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences 121 (2024).
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[107]
2024 | Published | Journal Article | IST-REx-ID: 18525 | OA
Quantitative omnigenic model discovers interpretable genome-wide associations
N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).
[Published Version] View | Files available | DOI
 
[106]
2023 | Published | Journal Article | IST-REx-ID: 13127 | OA
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).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[105]
2023 | Published | Journal Article | IST-REx-ID: 14515 | OA
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).
[Published Version] View | Files available | DOI | arXiv
 
[104]
2023 | Published | Journal Article | IST-REx-ID: 12762 | OA
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.
[Published Version] View | Files available | DOI | arXiv
 
[103]
2023 | Published | Journal Article | IST-REx-ID: 14656 | OA
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.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[102]
2022 | Published | Journal Article | IST-REx-ID: 12156 | OA
Eukaryotic gene regulation at equilibrium, or non?
B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).
[Published Version] View | Files available | DOI
 
[101]
2022 | Published | Journal Article | IST-REx-ID: 12332 | OA
Efficient coding theory of dynamic attentional modulation
W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.
[Published Version] View | Files available | DOI | WoS
 
[100]
2022 | Published | Journal Article | IST-REx-ID: 10736 | OA
Predicting bacterial promoter function and evolution from random sequences
M. Lagator, S. Sarikas, M. Steinrück, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[99]
2022 | Published | Journal Article | IST-REx-ID: 12081 | OA
Accumulation and maintenance of information in evolution
M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[98]
2021 | Submitted | Preprint | IST-REx-ID: 10579 | OA
Token-driven totally asymmetric simple exclusion process
B. Kavcic, G. Tkačik, ArXiv (n.d.).
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[97]
2021 | Published | Journal Article | IST-REx-ID: 8997 | OA
Minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
[Published Version] View | Files available | DOI | WoS
 
[96]
2021 | Published | Journal Article | IST-REx-ID: 9226 | OA
The many bits of positional information
G. Tkačik, T. Gregor, Development 148 (2021).
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[95]
2021 | Published | Journal Article | IST-REx-ID: 9362 | OA
Inferring the function performed by a recurrent neural network
M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[94]
2021 | Submitted | Preprint | IST-REx-ID: 10912 | OA
Quantifying the coexistence of neuronal oscillations and avalanches
F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, (n.d.).
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[93]
2021 | Published | Journal Article | IST-REx-ID: 7553 | OA
Statistical analysis and optimality of neural systems
W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS
 
[92]
2021 | Draft | Preprint | IST-REx-ID: 10077 | OA
The structure of hippocampal CA1 interactions optimizes spatial coding across experience
M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[91]
2020 | Published | Preprint | IST-REx-ID: 7675 | OA
Normative models of enhancer function
R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[90]
2020 | Published | Journal Article | IST-REx-ID: 8698 | OA
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.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[89]
2020 | Published | Journal Article | IST-REx-ID: 9000 | OA
Nonequilibrium models of optimal enhancer function
R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2020 | Published | Journal Article | IST-REx-ID: 7656 | OA
Clustering of neural activity: A design principle for population codes
M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[87]
2020 | Published | Journal Article | IST-REx-ID: 7652 | OA
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] View | Files available | DOI | WoS
 
[86]
2020 | Published | Journal Article | IST-REx-ID: 8250 | OA
Mechanisms of drug interactions between translation-inhibiting antibiotics
B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).
[Published Version] View | Files available | DOI | WoS
 
[85]
2020 | Published | Preprint | IST-REx-ID: 7673 | OA
A minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[84]
2019 | Published | Journal Article | IST-REx-ID: 6900 | OA
Estimating information in time-varying signals
S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[83]
2019 | Research Data Reference | IST-REx-ID: 9786
Supporting text and results
J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).
[Published Version] View | Files available | DOI
 
[82]
2019 | Published | Journal Article | IST-REx-ID: 5945 | OA
Optimal decoding of cellular identities in a genetic network
M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.
[Published Version] View | Files available | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[81]
2019 | Submitted | Preprint | IST-REx-ID: 7552 | OA
Action at a distance in transcriptional regulation
W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).
[Preprint] View | Download Preprint (ext.) | arXiv
 
[80]
2019 | Published | Journal Article | IST-REx-ID: 6784 | OA
Molecular noise of innate immunity shapes bacteria-phage ecologies
J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019).
[Published Version] View | Files available | DOI | WoS
 
[79]
2019 | Published | Conference Paper | IST-REx-ID: 7606 | OA
A tight upper bound on mutual information
M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | arXiv
 
[78]
2018 | Published | Journal Article | IST-REx-ID: 406 | OA
Probabilistic models of individual and collective animal behavior
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).
[Submitted Version] View | Files available | DOI | WoS
 
[77]
2018 | Published | Journal Article | IST-REx-ID: 281 | OA
Distributed and dynamic intracellular organization of extracellular information
A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.
[Preprint] View | Files available | DOI | Download Preprint (ext.) | WoS | PubMed | Europe PMC
 
[76]
2018 | Research Data Reference | IST-REx-ID: 9831
Implementation of the inference method in Matlab
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
[Published Version] View | Files available | DOI
 
[75]
2018 | Published | Journal Article | IST-REx-ID: 292 | OA
Nonlinear decoding of a complex movie from the mammalian retina
V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational Biology 14 (2018).
[Published Version] View | Files available | DOI | WoS
 
[74]
2018 | Published | Journal Article | IST-REx-ID: 31 | OA
Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons
U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018).
[Preprint] View | DOI | Download Preprint (ext.) | WoS
 
[73]
2018 | Published | Journal Article | IST-REx-ID: 543 | OA
Toward a unified theory of efficient, predictive, and sparse coding
M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS
 
[72]
2018 | Research Data | IST-REx-ID: 5584 | OA
Nonlinear decoding of a complex movie from the mammalian retina
S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).
[Published Version] View | Files available | DOI
 
[71]
2018 | Research Data | IST-REx-ID: 5587 | OA
Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH"
D. De Martino, G. Tkačik, (2018).
[Published Version] View | Files available | DOI
 
[70]
2018 | Published | Journal Article | IST-REx-ID: 161 | OA
Statistical mechanics for metabolic networks during steady state growth
D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).
[Published Version] View | Files available | DOI | WoS
 
[69]
2018 | Published | Journal Article | IST-REx-ID: 67 | OA
Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.
[Submitted Version] View | Files available | DOI | WoS
 
[68]
2018 | Research Data | IST-REx-ID: 5585 | OA
Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).
[Published Version] View | Files available | DOI
 
[67]
2017 | Published | Journal Article | IST-REx-ID: 955 | OA
Evolution of new regulatory functions on biophysically realistic fitness landscapes
T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).
[Published Version] View | Files available | DOI | WoS
 
[66]
2017 | Research Data Reference | IST-REx-ID: 9709 | OA
Data from: Error-robust modes of the retinal population code
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[65]
2017 | Published | Journal Article | IST-REx-ID: 943 | OA
Decoding of position in the developing neural tube from antiparallel morphogen gradients
M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[64]
2017 | Published | Journal Article | IST-REx-ID: 1104 | OA
Multiplexed computations in retinal ganglion cells of a single type
S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017).
[Published Version] View | Files available | DOI | WoS
 
[63]
2017 | Research Data | IST-REx-ID: 5560 | OA
Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity
T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, (2017).
[Published Version] View | Files available | DOI
 
[62]
2017 | Research Data | IST-REx-ID: 5562 | OA
Multi-electrode array recording from salamander retinal ganglion cells
O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).
[Published Version] View | Files available | DOI
 
[61]
2017 | Published | Journal Article | IST-REx-ID: 613 | OA
Shaping bacterial population behavior through computer interfaced control of individual cells
R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).
[Published Version] View | Files available | DOI
 
[60]
2017 | Published | Journal Article | IST-REx-ID: 665
Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity
T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.
View | Files available | DOI
 
[59]
2017 | Published | Journal Article | IST-REx-ID: 720 | OA
Probabilistic models for neural populations that naturally capture global coupling and criticality
J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).
[Published Version] View | Files available | DOI
 
[58]
2017 | Published | Journal Article | IST-REx-ID: 725 | OA
Discrete modes of social information processing predict individual behavior of fish in a group
R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[57]
2017 | Published | Journal Article | IST-REx-ID: 730
Maximum entropy models as a tool for building precise neural controls
C. Savin, G. Tkačik, Current Opinion in Neurobiology 46 (2017) 120–126.
View | DOI | WoS
 
[56]
2016 | Published | Journal Article | IST-REx-ID: 1358 | OA
Intrinsic limits to gene regulation by global crosstalk
T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).
[Published Version] View | Files available | DOI
 
[55]
2016 | Research Data Reference | IST-REx-ID: 9869
Error bound on an estimator of position
P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
[Published Version] View | Files available | DOI
 
[54]
2016 | Research Data Reference | IST-REx-ID: 9870
Computation of positional information in an Ising model
P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
[Published Version] View | Files available | DOI
 
[53]
2016 | Research Data Reference | IST-REx-ID: 9871
Computation of positional information in a discrete morphogen field
P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
[Published Version] View | Files available | DOI
 
[52]
2016 | Published | Journal Article | IST-REx-ID: 1420 | OA
A general approximation for the dynamics of quantitative traits
K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[51]
2016 | Published | Conference Paper | IST-REx-ID: 1082 | OA
Relevant sparse codes with variational information bottleneck
M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.
[Preprint] View | Files available | Download Preprint (ext.)
 
[50]
2016 | Published | Conference Paper | IST-REx-ID: 1105
Estimating nonlinear neural response functions using GP priors and Kronecker methods
C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.
View | Download None (ext.)
 
[49]
2016 | Published | Journal Article | IST-REx-ID: 1171
Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.
G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.
View | DOI
 
[48]
2016 | Published | Journal Article | IST-REx-ID: 1197 | OA
Error-robust modes of the retinal population code
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).
[Published Version] View | Files available | DOI
 
[47]
2016 | Published | Journal Article | IST-REx-ID: 1242 | OA
Extending the dynamic range of transcription factor action by translational regulation
T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).
[Preprint] View | DOI | Download Preprint (ext.)
 
[46]
2016 | Published | Journal Article | IST-REx-ID: 1248 | OA
Information processing in living systems
G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.
[Preprint] View | DOI | Download Preprint (ext.)
 
[45]
2016 | Published | Journal Article | IST-REx-ID: 1270 | OA
Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information
P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).
[Published Version] View | Files available | DOI
 
[44]
2015 | Published | Journal Article | IST-REx-ID: 1576 | OA
Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[43]
2015 | Published | Journal Article | IST-REx-ID: 1666 | OA
Dynamics of transcription factor binding site evolution
M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).
[Published Version] View | Files available | DOI
 
[42]
2015 | Research Data Reference | IST-REx-ID: 9712
Other fitness models for comparison & for interacting TFBSs
M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).
[Published Version] View | Files available | DOI
 
[41]
2015 | Published | Journal Article | IST-REx-ID: 1697 | OA
High accuracy decoding of dynamical motion from a large retinal population
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015).
[Published Version] View | Files available | DOI
 
[40]
2015 | Published | Journal Article | IST-REx-ID: 1701 | OA
Thermodynamics and signatures of criticality in a network of neurons
G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[39]
2015 | Published | Journal Article | IST-REx-ID: 1885 | OA
Positional information, positional error, and readout precision in morphogenesis: A mathematical framework
G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.
[Preprint] View | DOI | Download Preprint (ext.)
 
[38]
2015 | Published | Journal Article | IST-REx-ID: 1940 | OA
Optimizing information flow in small genetic networks. IV. Spatial coupling
T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
[Preprint] View | DOI | Download Preprint (ext.)
 
[37]
2014 | Published | Journal Article | IST-REx-ID: 3263 | OA
Adaptation to changes in higher-order stimulus statistics in the salamander retina
G. Tkačik, A. Ghosh, E. Schneidman, R. Segev, PLoS One 9 (2014).
[Published Version] View | Files available | DOI
 
[36]
2014 | Research Data Reference | IST-REx-ID: 9752 | OA
Data from: Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[35]
2014 | Published | Journal Article | IST-REx-ID: 2257 | OA
Searching for collective behavior in a large network of sensory neurons
G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[34]
2014 | Published | Journal Article | IST-REx-ID: 1886 | OA
Variance predicts salience in central sensory processing
A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).
[Published Version] View | Files available | DOI
 
[33]
2014 | Published | Journal Article | IST-REx-ID: 2231 | OA
Noise and information transmission in promoters with multiple internal states
G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[32]
2013 | Published | Journal Article | IST-REx-ID: 3261 | OA
Positional information, in bits
J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[31]
2013 | Published | Journal Article | IST-REx-ID: 2850 | OA
The simplest maximum entropy model for collective behavior in a neural network
G. Tkačik, O. Marre, T. Mora, D. Amodei, M. Berry, W. Bialek, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[30]
2013 | Published | Journal Article | IST-REx-ID: 2851
A simple method for estimating the entropy of neural activity
M. Berry, G. Tkačik, J. Dubuis, O. Marre, R. Da Silveira, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).
View | DOI
 
[29]
2013 | Published | Journal Article | IST-REx-ID: 2277 | OA
Transformation of stimulus correlations by the retina
K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, PLoS Computational Biology 9 (2013).
[Published Version] View | Files available | DOI
 
[28]
2013 | Published | Journal Article | IST-REx-ID: 2818 | OA
Learning quadratic receptive fields from neural responses to natural stimuli
K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 
[27]
2013 | Published | Journal Article | IST-REx-ID: 2863 | OA
Stimulus-dependent maximum entropy models of neural population codes
E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational Biology 9 (2013).
[Published Version] View | Files available | DOI
 
[26]
2013 | Published | Journal Article | IST-REx-ID: 2913 | OA
Retinal metric: a stimulus distance measure derived from population neural responses
G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).
[Preprint] View | DOI | Download Preprint (ext.)
 
[25]
2013 | Published | Journal Article | IST-REx-ID: 2914 | OA
Statistical thermodynamics of natural images
G. Stephens, T. Mora, G. Tkačik, W. Bialek, Physical Review Letters 110 (2013).
[Published Version] View | Files available | DOI | arXiv
 
[24]
2012 | Published | Journal Article | IST-REx-ID: 3262 | OA
Optimizing information flow in small genetic networks. III. A self-interacting gene
G. Tkačik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 85 (2012).
[Preprint] View | DOI | Download Preprint (ext.)
 
[23]
2011 | Published | Journal Article | IST-REx-ID: 3276 | OA
Fast, scalable, Bayesian spike identification for multi-electrode arrays
J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson, PLoS One 6 (2011).
View | Files available | DOI
 
[22]
2011 | Published | Journal Article | IST-REx-ID: 3374 | OA
Information transmission in genetic regulatory networks a review
G. Tkačik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).
[Submitted Version] View | DOI | Download Submitted Version (ext.)
 
[21]
2011 | Published | Journal Article | IST-REx-ID: 3384 | OA
Natural images from the birthplace of the human eye
G. Tkačik, P. Garrigan, C. Ratliff, G. Milcinski, J. Klein, L. Seyfarth, P. Sterling, D. Brainard, V. Balasubramanian, PLoS One 6 (2011).
[Published Version] View | Files available | DOI
 
[20]
2011 | Published | Journal Article | IST-REx-ID: 3401
The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source
S. Little, G. Tkačik, T. Kneeland, E. Wieschaus, T. Gregor, PLoS Biology 9 (2011).
View | DOI
 
[19]
2010 | Published | Conference Paper | IST-REx-ID: 3430 | OA
Lecture notes for 2010 summer school on Quantitative Evolutionary and Comparative Genomics
G. Tkačik, in:, Elsevier, 2010.
View | Download (ext.)
 
[18]
2010 | Published | Journal Article | IST-REx-ID: 3735
Local statistics in natural scenes predict the saliency of synthetic textures
G. Tkačik, J. Prentice, J. Victor, V. Balasubramanian, PNAS 107 (2010) 18149–18154.
View | DOI | Download (ext.)
 
[17]
2010 | Published | Journal Article | IST-REx-ID: 3736
Optimal population coding by noisy spiking neurons
G. Tkačik, J. Prentice, V. Balasubramanian, E. Schneidman, PNAS 107 (2010) 14419–14424.
View | DOI | Download (ext.)
 
[16]
2010 | Published | Journal Article | IST-REx-ID: 3738
Optimizing information flow in small genetic networks. II. Feed-forward interactions
A. Walczak, G. Tkačik, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 81 (2010).
View | DOI | Download (ext.)
 
[15]
2010 | Published | Preprint | IST-REx-ID: 3743 | OA
From statistical mechanics to information theory: understanding biophysical information-processing systems
G. Tkačik, ArXiv q-MN (2010) 1–52.
View | Download (ext.)
 
[14]
2009 | Published | Preprint | IST-REx-ID: 3732 | OA
Spin glass models for a network of real neurons
G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv q-NC (2009).
View | Download (ext.)
 
[13]
2009 | Published | Journal Article | IST-REx-ID: 3733
The dynamics of adaptation on correlated fitness landscapes
S. Kryazhimskiy, G. Tkačik, J. Plotkin, PNAS 106 (2009) 18638–18643.
View | DOI | Download (ext.)
 
[12]
2009 | Published | Journal Article | IST-REx-ID: 3737
Optimizing information flow in small genetic networks
G. Tkačik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 80 (2009).
View | DOI | Download (ext.)
 
[11]
2009 | Published | Journal Article | IST-REx-ID: 3745
Diffusion, dimensionality, and noise in transcriptional regulation
G. Tkačik, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 79 (2009).
View | DOI
 
[10]
2009 | Published | Book Chapter | IST-REx-ID: 3747
Cell Biology: Networks, regulation, pathways
G. Tkačik, W. Bialek, in:, R. Meyers (Ed.), Encyclopedia of Complexity and Systems Science, Springer, 2009, pp. 719–741.
View | DOI
 
[9]
2008 | Published | Journal Article | IST-REx-ID: 3734 | OA
The role of input noise in transcriptional regulation
G. Tkačik, T. Gregor, W. Bialek, PLoS One 3 (2008).
View | DOI | Download (ext.)
 
[8]
2008 | Published | Journal Article | IST-REx-ID: 3739
Information capacity of genetic regulatory elements
G. Tkačik, C. Callan, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 78 (2008).
View | DOI
 
[7]
2008 | Published | Journal Article | IST-REx-ID: 3740 | OA
Information flow and optimization in transcriptional regulation
G. Tkačik, C. Callan, W. Bialek, PNAS 105 (2008) 12265–12270.
View | DOI | Download (ext.)
 
[6]
2008 | Published | Journal Article | IST-REx-ID: 3744 | OA
Decoding spike timing: The differential reverse-correlation method
G. Tkačik, M. Magnasco, Biosystems 93 (2008) 90–100.
View | DOI | Download (ext.)
 
[5]
2007 | Published | Journal Article | IST-REx-ID: 3731
Precise physical models of protein-DNA interaction from high-throughput data
J. Kinney, G. Tkačik, C. Callan, PNAS 104 (2007) 501–506.
View | DOI | Download (ext.)
 
[4]
2007 | Published | Preprint | IST-REx-ID: 3742 | OA
Faster solutions of the inverse pairwise Ising problem
T. Broderick, M. Dudik, G. Tkačik, R. Schapire, W. Bialek, ArXiv q-QM (2007).
View | Download (ext.)
 
[3]
2006 | Published | Preprint | IST-REx-ID: 3431 | OA
Ising models for networks of real neurons
G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4.
View | Download (ext.)
 
[2]
2005 | Published | Journal Article | IST-REx-ID: 3741 | OA
Information-based clustering
N. Slonim, G. Atwal, G. Tkačik, W. Bialek, PNAS 102 (2005) 18297–18302.
View | DOI | Download (ext.)
 
[1]
2005 | Published | Preprint | IST-REx-ID: 3746 | OA
Estimating mutual information and multi-information in large networks
N. Slonim, G. Atwal, G. Tkačik, W. Bialek, ArXiv (2005) 1–11.
View | Download (ext.)
 
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