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182 Publications


2017 | Journal Article | IST-REx-ID: 548 | OA
De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6), 060401.
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2017 | Journal Article | IST-REx-ID: 1007 | OA
Lang M, Sontag E. 2017. Zeros of nonlinear systems with input invariances. Automatica. 81C, 46–55.
[Published Version] View | Files available | DOI | WoS
 

2017 | Research Data | IST-REx-ID: 5562 | OA
Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode array recording from salamander retinal ganglion cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:61.
[Published Version] View | Files available | DOI
 

2017 | Research Data | IST-REx-ID: 5560 | OA
Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:53.
[Published Version] View | Files available | DOI
 

2017 | Journal Article | IST-REx-ID: 665
Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.
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2017 | Journal Article | IST-REx-ID: 735
Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211.
View | Files available | DOI | WoS
 

2016 | Conference Paper | IST-REx-ID: 1082 | OA
Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.
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2016 | Conference Paper | IST-REx-ID: 1105
Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618.
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2016 | Journal Article | IST-REx-ID: 1170
Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.
[Submitted Version] View | Files available | DOI
 

2016 | Journal Article | IST-REx-ID: 1171
Tkačik G. 2016. 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. 17, 166–167.
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2016 | Journal Article | IST-REx-ID: 1188 | OA
De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.
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2016 | Journal Article | IST-REx-ID: 1203 | OA
Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017.
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2016 | Conference Paper | IST-REx-ID: 1214
Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International Conference on Intelligent Robots and Systems IROS vol. 2016–November, 7759138.
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2016 | Conference Paper | IST-REx-ID: 1220 | OA
Mikić G, Stoll A, Bevirt J, Grah R, Moore M. 2016. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. AIAA: Aviation Technology, Integration, and Operations Conference, 1–19.
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2016 | Journal Article | IST-REx-ID: 1242 | OA
Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.
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2016 | Journal Article | IST-REx-ID: 1244 | OA
Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.
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2016 | Journal Article | IST-REx-ID: 1248 | OA
Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117.
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2016 | Journal Article | IST-REx-ID: 1260 | OA
De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 

2016 | Journal Article | IST-REx-ID: 1266 | OA
Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.
[Published Version] View | Files available | DOI
 

2016 | Journal Article | IST-REx-ID: 1290 | OA
Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904.
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2016 | Conference Paper | IST-REx-ID: 1320
Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July, 7526722.
[Preprint] View | Files available | DOI
 

2016 | Journal Article | IST-REx-ID: 1332 | OA
Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333.
[Published Version] View | Files available | DOI
 

2016 | Journal Article | IST-REx-ID: 1342 | OA
Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304), 1147–1151.
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2016 | Journal Article | IST-REx-ID: 1394 | OA
De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 13(3), 036005.
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2016 | Journal Article | IST-REx-ID: 1420 | OA
Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.
[Preprint] View | DOI | Download Preprint (ext.) | arXiv
 

2016 | Journal Article | IST-REx-ID: 1485 | OA
De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003.
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2016 | Journal Article | IST-REx-ID: 1148
Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25.
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2016 | Conference Paper | IST-REx-ID: 8094 | OA
Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.
[Published Version] View | Files available | DOI
 

2016 | Journal Article | IST-REx-ID: 1197 | OA
Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.
[Published Version] View | Files available | DOI
 

2016 | Conference Paper | IST-REx-ID: 948
Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.
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2016 | Journal Article | IST-REx-ID: 1270 | OA
Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 11(9), e0163628.
[Published Version] View | Files available | DOI
 

2016 | Research Data Reference | IST-REx-ID: 9870
Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, 10.1371/journal.pone.0163628.s002.
[Published Version] View | Files available | DOI
 

2016 | Research Data Reference | IST-REx-ID: 9869
Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, 10.1371/journal.pone.0163628.s001.
[Published Version] View | Files available | DOI
 

2016 | Research Data Reference | IST-REx-ID: 9871
Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science, 10.1371/journal.pone.0163628.s003.
[Published Version] View | Files available | DOI
 

2016 | Thesis | IST-REx-ID: 1128 | OA
Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.
[Published Version] View | Files available
 

2016 | Journal Article | IST-REx-ID: 1358 | OA
Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.
[Published Version] View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 10794 | OA
Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.
[Published Version] View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1539 | OA
Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103.
[Published Version] View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1538 | OA
Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2015 | Journal Article | IST-REx-ID: 1564 | OA
Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.
[Published Version] View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1570 | OA
Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

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

2015 | Journal Article | IST-REx-ID: 1697 | OA
Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. 2015. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 11(7), e1004304.
[Published Version] View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1701 | OA
Tkačik G, Mora T, Marre O, Amodei D, Palmer S, Berry Ii M, Bialek W. 2015. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 112(37), 11508–11513.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 

2015 | Journal Article | IST-REx-ID: 1861
Ruess J, Lygeros J. 2015. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 25(2), 8.
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2015 | Journal Article | IST-REx-ID: 1885 | OA
Tkačik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 199(1), 39–59.
[Preprint] View | DOI | Download Preprint (ext.)
 

2015 | Journal Article | IST-REx-ID: 1940 | OA
Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6), 062710.
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2015 | Research Data Reference | IST-REx-ID: 9718
Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, 10.1371/journal.pcbi.1004055.s001.
[Published Version] View | Files available | DOI
 

2015 | Journal Article | IST-REx-ID: 1827 | OA
Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).
[Published Version] View | Files available | DOI
 

2015 | Research Data Reference | IST-REx-ID: 9773
Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002.
[Published Version] View | Files available | DOI
 

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