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182 Publications


2017 | Journal Article | IST-REx-ID: 548 | OA
D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” Physical Review E, vol. 96, no. 6. American Physical Society, 2017.
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2017 | Journal Article | IST-REx-ID: 1007 | OA
M. Lang and E. Sontag, “Zeros of nonlinear systems with input invariances,” Automatica, vol. 81C. International Federation of Automatic Control, pp. 46–55, 2017.
[Published Version] View | Files available | DOI | WoS
 

2017 | Research Data | IST-REx-ID: 5562 | OA
O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017.
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2017 | Research Data | IST-REx-ID: 5560 | OA
T. Bergmiller et al., “Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science and Technology Austria, 2017.
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2017 | Journal Article | IST-REx-ID: 665
T. Bergmiller et al., “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science, vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315, 2017.
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2017 | Journal Article | IST-REx-ID: 735
V. Barone et al., “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” Developmental Cell, vol. 43, no. 2. Cell Press, pp. 198–211, 2017.
View | Files available | DOI | WoS
 

2016 | Conference Paper | IST-REx-ID: 1082 | OA
M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.
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2016 | Conference Paper | IST-REx-ID: 1105
C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.
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2016 | Journal Article | IST-REx-ID: 1170
M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society for Industrial and Applied Mathematics , pp. B988–B1008, 2016.
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2016 | Journal Article | IST-REx-ID: 1171
G. Tkačik, “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.,” Physics of Life Reviews, vol. 17. Elsevier, pp. 166–167, 2016.
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2016 | Journal Article | IST-REx-ID: 1188 | OA
D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.
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2016 | Journal Article | IST-REx-ID: 1203 | OA
F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” Journal of Clinical Microbiology, vol. 54, no. 12. American Society for Microbiology, pp. 3010–3017, 2016.
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2016 | Conference Paper | IST-REx-ID: 1214
G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea, 2016, vol. 2016–November.
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2016 | Conference Paper | IST-REx-ID: 1220 | OA
G. Mikić, A. Stoll, J. Bevirt, R. Grah, and M. Moore, “Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency,” presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA, 2016, pp. 1–19.
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2016 | Journal Article | IST-REx-ID: 1242 | OA
T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American Institute of Physics, 2016.
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2016 | Journal Article | IST-REx-ID: 1244 | OA
P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” PNAS, vol. 113, no. 7. National Academy of Sciences, pp. 1811–1816, 2016.
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2016 | Journal Article | IST-REx-ID: 1248 | OA
G. Tkačik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016.
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2016 | Journal Article | IST-REx-ID: 1260 | OA
D. De Martino, “The dual of the space of interactions in neural network models,” International Journal of Modern Physics C, vol. 27, no. 6. World Scientific Publishing, 2016.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 

2016 | Journal Article | IST-REx-ID: 1266 | OA
M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” eLife, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016.
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2016 | Journal Article | IST-REx-ID: 1290 | OA
L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” Nature Chemical Biology, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.
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2016 | Conference Paper | IST-REx-ID: 1320
M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential operators,” presented at the ACC: American Control Conference, Boston, MA, USA, 2016, vol. 2016–July.
[Preprint] View | Files available | DOI
 

2016 | Journal Article | IST-REx-ID: 1332 | OA
R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
[Published Version] View | Files available | DOI
 

2016 | Journal Article | IST-REx-ID: 1342 | OA
M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016.
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2016 | Journal Article | IST-REx-ID: 1394 | OA
D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016.
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2016 | Journal Article | IST-REx-ID: 1420 | OA
K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 

2016 | Journal Article | IST-REx-ID: 1485 | OA
D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” Physical Biology, vol. 13, no. 1. IOP Publishing Ltd., 2016.
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2016 | Journal Article | IST-REx-ID: 1148
C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” Biosystems, vol. 149. Elsevier, pp. 15–25, 2016.
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2016 | Conference Paper | IST-REx-ID: 8094 | OA
G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in Proceedings of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp. 142–143.
[Published Version] View | Files available | DOI
 

2016 | Journal Article | IST-REx-ID: 1197 | OA
J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11. Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 

2016 | Conference Paper | IST-REx-ID: 948
T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.
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2016 | Journal Article | IST-REx-ID: 1270 | OA
P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9. Public Library of Science, 2016.
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2016 | Research Data Reference | IST-REx-ID: 9870
P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 

2016 | Research Data Reference | IST-REx-ID: 9869
P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 

2016 | Research Data Reference | IST-REx-ID: 9871
P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.
[Published Version] View | Files available | DOI
 

2016 | Thesis | IST-REx-ID: 1128 | OA
G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016.
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2016 | Journal Article | IST-REx-ID: 1358 | OA
T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
[Published Version] View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 10794 | OA
F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” Frontiers in Environmental Science, vol. 3. Frontiers, 2015.
[Published Version] View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1539 | OA
J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” Journal of Chemical Physics, vol. 143, no. 24. American Institute of Physics, 2015.
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2015 | Journal Article | IST-REx-ID: 1538 | OA
J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2015 | Journal Article | IST-REx-ID: 1564 | OA
M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.
[Published Version] View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1570 | OA
R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2015 | Conference Paper | IST-REx-ID: 1658
S. Bogomolov, T. A. Henzinger, A. Podelski, J. Ruess, and C. Schilling, “Adaptive moment closure for parameter inference of biochemical reaction networks,” vol. 9308. Springer, pp. 77–89, 2015.
View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1697 | OA
O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7. Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1701 | OA
G. Tkačik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2015 | Journal Article | IST-REx-ID: 1861
J. Ruess and J. Lygeros, “Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015.
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2015 | Journal Article | IST-REx-ID: 1885 | OA
G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.
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2015 | Journal Article | IST-REx-ID: 1940 | OA
T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.
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2015 | Research Data Reference | IST-REx-ID: 9718
T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.
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2015 | Journal Article | IST-REx-ID: 1827 | OA
T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015.
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2015 | Research Data Reference | IST-REx-ID: 9773
T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.
[Published Version] View | Files available | DOI
 

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