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182 Publications
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.
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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.).
2019 | Journal Article | IST-REx-ID: 5945 |
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.
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| PubMed | Europe PMC
M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.
2019 | Journal Article | IST-REx-ID: 6049 |
Feedback-induced self-oscillations in large interacting systems subjected to phase transitions
D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).
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D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).
2019 | Journal Article | IST-REx-ID: 6046 |
Temporal order and precision of complex stress responses in individual bacteria
K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).
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K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).
2019 | Journal Article | IST-REx-ID: 6784 |
Molecular noise of innate immunity shapes bacteria-phage ecologies
J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019).
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J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019).
2019 | Research Data Reference | IST-REx-ID: 9786
Supporting text and results
J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).
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J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).
2019 | Journal Article | IST-REx-ID: 7422 |
eGFRD in all dimensions
T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019).
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T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019).
2019 | Journal Article | IST-REx-ID: 6900 |
Estimating information in time-varying signals
S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290.
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S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290.
2019 | Journal Article | IST-REx-ID: 196 |
Harmonic dynamics of the Abelian sandpile
M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116 (2019) 2821–2830.
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M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116 (2019) 2821–2830.
2019 | Journal Article | IST-REx-ID: 5817 |
Limiting shapes of confined lipid vesicles
B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.
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B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.
2019 | Thesis | IST-REx-ID: 6473 |
Estimating information flow in single cells
S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.
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S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.
2019 | Thesis | IST-REx-ID: 6071 |
Coevolution of transcription factors and their binding sites in sequence space
R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.
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R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.
2019 | Journal Article | IST-REx-ID: 7103 |
Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture
J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019).
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J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019).
2019 | Journal Article | IST-REx-ID: 6090 |
Receptor crosstalk improves concentration sensing of multiple ligands
M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).
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M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).
2019 | Conference Paper | IST-REx-ID: 7606 |
A tight upper bound on mutual information
M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.
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M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.
2018 | Journal Article | IST-REx-ID: 306 |
An introduction to the maximum entropy approach and its application to inference problems in biology
A. De Martino, D. De Martino, Heliyon 4 (2018).
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A. De Martino, D. De Martino, Heliyon 4 (2018).
2018 | Journal Article | IST-REx-ID: 305
Fabrication and operation of microfluidic hanging drop networks
P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202.
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P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202.
2018 | Journal Article | IST-REx-ID: 281 |
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.
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A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.
2018 | Journal Article | IST-REx-ID: 316 |
Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system
K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.
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K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.
2018 | Research Data Reference | IST-REx-ID: 9813 |
Supplemental material for Bodova et al., 2018
K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).
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K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).
2018 | Journal Article | IST-REx-ID: 406 |
Probabilistic models of individual and collective animal behavior
K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).
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K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).
2018 | Journal Article | IST-REx-ID: 457
Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity
M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.
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M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.
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).
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K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
2018 | Journal Article | IST-REx-ID: 31 |
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).
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U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018).
2018 | Journal Article | IST-REx-ID: 543 |
Toward a unified theory of efficient, predictive, and sparse coding
M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.
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M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.
2018 | Journal Article | IST-REx-ID: 607 |
Well posedness and maximum entropy approximation for the dynamics of quantitative traits
K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.
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K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.
2018 | Journal Article | IST-REx-ID: 19 |
Nonoptimal gene expression creates latent potential for antibiotic resistance
A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.
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A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.
2018 | Journal Article | IST-REx-ID: 292 |
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).
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V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational Biology 14 (2018).
2018 | Research Data | IST-REx-ID: 5584 |
Nonlinear decoding of a complex movie from the mammalian retina
S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).
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S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).
2018 | Journal Article | IST-REx-ID: 161 |
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).
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D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).
2018 | Research Data | IST-REx-ID: 5587 |
Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH"
D. De Martino, G. Tkačik, (2018).
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D. De Martino, G. Tkačik, (2018).
2018 | Journal Article | IST-REx-ID: 67 |
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.
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C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.
2018 | Research Data | IST-REx-ID: 5585 |
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).
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C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).
2017 | Journal Article | IST-REx-ID: 613 |
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).
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R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).
2017 | Conference Paper | IST-REx-ID: 652
Dynamical self consistency leads to behavioral development and emergent social interactions in robots
R. Der, G.S. Martius, in:, IEEE, 2017.
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R. Der, G.S. Martius, in:, IEEE, 2017.
2017 | Journal Article | IST-REx-ID: 658 |
Self organized behavior generation for musculoskeletal robots
R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).
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R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).
2017 | Journal Article | IST-REx-ID: 720 |
Probabilistic models for neural populations that naturally capture global coupling and criticality
J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).
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J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).
2017 | Journal Article | IST-REx-ID: 725 |
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.
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R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.
2017 | Research Data Reference | IST-REx-ID: 9709 |
Data from: Error-robust modes of the retinal population code
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
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J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
2017 | Journal Article | IST-REx-ID: 680 |
Sensory noise predicts divisive reshaping of receptive fields
M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13 (2017).
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M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13 (2017).
2017 | Research Data Reference | IST-REx-ID: 9855
Supplementary appendix
M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).
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M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).