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121 Publications

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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2020 | Preprint | IST-REx-ID: 7463   OA View | Download (ext.)
 
2020 | Journal Article | IST-REx-ID: 7569   OA
The relation between crosstalk and gene regulation form revisited
R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020) e1007642.
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2020 | Journal Article | IST-REx-ID: 7490   OA
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) e52067.
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2020 | Preprint | IST-REx-ID: 7553   OA
Statistical analysis and optimality of biological systems
W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, BioRxiv (n.d.).
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2020 | Preprint | IST-REx-ID: 7673   OA
A minimal biophysical model of combined antibiotic action
B. Kavcic, G. Tkačik, T. Bollenbach, BioRxiv (2020).
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2020 | 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) 20.
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2020 | Preprint | IST-REx-ID: 7675   OA
Normative models of enhancer function
R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).
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2019 | Journal Article | IST-REx-ID: 6046   OA
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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2019 | Journal Article | IST-REx-ID: 7103   OA
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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2019 | Preprint | IST-REx-ID: 7083   OA
Mechanistic origin of drug interactions between translation-inhibiting antibiotics
B. Kavcic, G. Tkačik, T. Bollenbach, BioRxiv (n.d.).
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2019 | Preprint | IST-REx-ID: 7552   OA
Action at a distance in transcriptional regulation
W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).
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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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2019 | Thesis | IST-REx-ID: 6473
Estimating information flow in single cells
S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, IST Austria, 2019.
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2019 | Journal Article | IST-REx-ID: 6049   OA
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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2019 | 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).
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2019 | Journal Article | IST-REx-ID: 5945
Optimal decoding of cellular identities in a genetic network
M.D. Petkova, G. Tkacik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.
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2019 | Journal Article | IST-REx-ID: 7422   OA
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) 054108.
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2019 | 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.
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2019 | Journal Article | IST-REx-ID: 6090   OA
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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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, IST Austria, 2019.
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2019 | 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, p. 8989292.
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2018 | Journal Article | IST-REx-ID: 543   OA
Toward a unified theory of efficient, predictive, and sparse coding
M.J. Chalk, O. Marre, G. Tkacik, PNAS 115 (2018) 186–191.
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2018 | 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. Tkacik, O. Marre, T. Mora, Physical Review E 98 (2018) 042410.
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2018 | Journal Article | IST-REx-ID: 67   OA
Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkacik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.
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2018 | Journal Article | IST-REx-ID: 607   OA
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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2018 | Journal Article | IST-REx-ID: 316   OA
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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2018 | Journal Article | IST-REx-ID: 19   OA
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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2018 | Preprint | IST-REx-ID: 196   OA
Harmonic dynamics of the Abelian sandpile
M. Lang, M. Shkolnikov, ArXiv (2018).
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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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2018 | 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. Tkacik, PLoS One 13 (2018).
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2018 | 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. Tkacik, PLoS Computational Biology 14 (2018) e1006057.
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2018 | Journal Article | IST-REx-ID: 306   OA View | Files available | DOI
 
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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2018 | 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. Tkacik, P. Swain, PNAS 115 (2018) 6088–6093.
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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. Tkacik, Nature Communications 9 (2018).
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2017 | Journal Article | IST-REx-ID: 725   OA
Discrete modes of social information processing predict individual behavior of fish in a group
R. Harpaz, G. Tkacik, E. Schneidman, PNAS 114 (2017) 10149–10154.
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2017 | 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. Tkacik, O. Marre, Nature Communications 8 (2017).
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2017 | Journal Article | IST-REx-ID: 720   OA View | Files available | DOI
 
2017 | Journal Article | IST-REx-ID: 548   OA View | DOI | Download (ext.)
 
2017 | Journal Article | IST-REx-ID: 947   OA
Quantifying the entropic cost of cellular growth control
D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).
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2017 | Journal Article | IST-REx-ID: 959   OA
Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics
D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95 (2017) 062419.
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2017 | 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. Tkacik, C.C. Guet, Nature Communications 8 (2017).
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2017 | Conference Paper | IST-REx-ID: 652 View | DOI
 
2017 | Journal Article | IST-REx-ID: 823   OA
Phase transitions in integer linear problems
S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).
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2017 | Journal Article | IST-REx-ID: 993   OA
Subsampling scaling
A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).
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2017 | 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. Tkacik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.
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2017 | 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. Tkacik, Nature Communications 8 (2017).
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2017 | Journal Article | IST-REx-ID: 658   OA
Self organized behavior generation for musculoskeletal robots
R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).
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2017 | Journal Article | IST-REx-ID: 2016
Exact goodness-of-fit testing for the Ising model
A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.
View | Files available | DOI | Download (ext.) | arXiv
 

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