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165 Publications
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: 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.
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: 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 | 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: 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: 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: 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 | 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: 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 | 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 | 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: 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: 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: 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: 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.
2017 | Journal Article | IST-REx-ID: 823 |
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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S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).
2017 | Journal Article | IST-REx-ID: 548 |
Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes
D. De Martino, Physical Review E 96 (2017).
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D. De Martino, Physical Review E 96 (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 | 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.
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C. Savin, G. Tkačik, Current Opinion in Neurobiology 46 (2017) 120–126.
2017 | Journal Article | IST-REx-ID: 1104 |
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).
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S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017).
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: 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.
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T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.
2017 | Journal Article | IST-REx-ID: 666 |
Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment
K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.
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K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.
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 | Journal Article | IST-REx-ID: 1007 |
Zeros of nonlinear systems with input invariances
M. Lang, E. Sontag, Automatica 81C (2017) 46–55.
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M. Lang, E. Sontag, Automatica 81C (2017) 46–55.
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.
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A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.
2017 | Journal Article | IST-REx-ID: 943 |
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.
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M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.
2017 | Journal Article | IST-REx-ID: 947 |
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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D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).
2017 | Journal Article | IST-REx-ID: 955 |
Evolution of new regulatory functions on biophysically realistic fitness landscapes
T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).
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T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).
2017 | Journal Article | IST-REx-ID: 959 |
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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D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95 (2017) 062419.
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).
2017 | Journal Article | IST-REx-ID: 993 |
Subsampling scaling
A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).
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A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).
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: 735
An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate
V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.
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V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.
2016 | Conference Paper | IST-REx-ID: 8094 |
Self-organized control of an tendon driven arm by differential extrinsic plasticity
G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.
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G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.
2016 | Conference Paper | IST-REx-ID: 1082 |
Relevant sparse codes with variational information bottleneck
M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.
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M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.
2016 | 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.
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C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.
2016 | Thesis | IST-REx-ID: 1128 |
Studying the complexities of transcriptional regulation
G. Rieckh, Studying the Complexities of Transcriptional Regulation, IST Austria, 2016.
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G. Rieckh, Studying the Complexities of Transcriptional Regulation, IST Austria, 2016.
2016 | Journal Article | IST-REx-ID: 1148
Adaptive moment closure for parameter inference of biochemical reaction networks
C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.
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C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.
2016 | Journal Article | IST-REx-ID: 1170
Modular parameter identification of biomolecular networks
M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.
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M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.
2016 | 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.
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G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.
2016 | Journal Article | IST-REx-ID: 1188 |
Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth
D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).
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D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).
2016 | Journal Article | IST-REx-ID: 1203 |
Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination
F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.
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F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.
2016 | Conference Paper | IST-REx-ID: 1214
Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm
G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016.
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G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016.
2016 | Conference Paper | IST-REx-ID: 1220 |
Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency
G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.
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G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.