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88 Publications

2020 | Research Data | IST-REx-ID: 7383 | OA
R. Grah, Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. IST Austria, 2020.
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2020 | Journal Article | IST-REx-ID: 7569 | OA
R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” PLOS Computational Biology, vol. 16, no. 2, 2020.
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2020 | Journal Article | IST-REx-ID: 7652
I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4, pp. 612–625, 2020.
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2020 | Preprint | IST-REx-ID: 7675 | OA
R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
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2020 | Thesis | IST-REx-ID: 7680
S. Kainrath, Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. IST Austria, 2020.
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2020 | Thesis | IST-REx-ID: 8155 | OA
R. Grah, Gene regulation across scales – how biophysical constraints shape evolution. IST Austria, 2020.
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2020 | Book Chapter | IST-REx-ID: 8173
S. Kainrath and H. L. Janovjak, “Design and application of light-regulated receptor tyrosine kinases,” in Photoswitching Proteins, vol. 2173, D. Niopek, Ed. Springer Nature, 2020, pp. 233–246.
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2019 | Conference Paper | IST-REx-ID: 7147
C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in 17th International Conference on Computational Methods in Systems Biology, Trieste, Italy, 2019, vol. 11773, pp. 155–187.
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2019 | Thesis | IST-REx-ID: 6371 | OA
C. Igler, On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. IST Austria, 2019.
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2019 | Journal Article | IST-REx-ID: 6465 | OA
H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, and M. Fussenegger, “A modular degron library for synthetic circuits in mammalian cells,” Nature Communications, vol. 10, no. 1, 2019.
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2019 | Journal Article | IST-REx-ID: 6717 | OA
C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision,” Frontiers in Microbiology, vol. 10, 2019.
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2019 | Journal Article | IST-REx-ID: 6784 | OA
J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7, 2019.
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2019 | Research Data | IST-REx-ID: 7016 | OA
I. Tomanek, Data for the paper “Gene amplification as a form of population-level gene expression regulation.” IST Austria, 2019.
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2019 | Journal Article | IST-REx-ID: 196 | OA
M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings of the National Academy of Sciences, vol. 116, no. 8, pp. 2821–2830, 2019.
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2019 | Journal Article | IST-REx-ID: 138 | OA
N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system,” Current Genetics, vol. 65, no. 1, pp. 133–138, 2019.
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2018 | Thesis | IST-REx-ID: 26 | OA
M. Steinrück, The influence of sequence context on the evolution of bacterial gene expression. IST Austria, 2018.
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2018 | Journal Article | IST-REx-ID: 723 | OA
P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5, pp. 1604–1633, 2018.
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2018 | Journal Article | IST-REx-ID: 438 | OA
N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” Nucleic Acids Research, vol. 46, no. 6, pp. 2918–2931, 2018.
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2018 | Journal Article | IST-REx-ID: 457
M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2, pp. 359–366, 2018.
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2018 | Journal Article | IST-REx-ID: 503
K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” Journal of Biotechnology, vol. 268, pp. 40–52, 2018.
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2018 | Research Data | IST-REx-ID: 5569 | OA
T. Bergmiller and N. Nikolic, Time-lapse microscopy data. IST Austria, 2018.
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2018 | Research Data | IST-REx-ID: 5585 | OA
C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. IST Austria, 2018.
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2018 | Journal Article | IST-REx-ID: 5984 | OA
M. Morri et al., “Optical functionalization of human class A orphan G-protein-coupled receptors,” Nature Communications, vol. 9, no. 1, 2018.
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2018 | Journal Article | IST-REx-ID: 305
P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771, pp. 183–202, 2018.
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2018 | Journal Article | IST-REx-ID: 67 | OA
C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10, pp. 1633–1643, 2018.
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2018 | Journal Article | IST-REx-ID: 161 | OA
D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1, 2018.
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2018 | Journal Article | IST-REx-ID: 19 | OA
A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” Molecular Biology and Evolution, vol. 35, no. 11, pp. 2669–2684, 2018.
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2018 | Journal Article | IST-REx-ID: 82 | OA
W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8, 2018.
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2017 | Thesis | IST-REx-ID: 202 | OA
M. Pleska, Biology of restriction-modification systems at the single-cell and population level. IST Austria, 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, pp. 198–211, 2017.
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2017 | Journal Article | IST-REx-ID: 538 | OA
S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” Angewandte Chemie, vol. 129, no. 16, pp. 4679–4682, 2017.
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2017 | Journal Article | IST-REx-ID: 541 | OA
N. Nikolic et al., “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no. 12, 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. IST Austria, 2017.
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2017 | Research Data | IST-REx-ID: 5564 | OA
M. Steinrück and C. C. Guet, Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.” IST Austria, 2017.
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2017 | Journal Article | IST-REx-ID: 561
M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” Biology Letters, vol. 13, no. 12, 2017.
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2017 | Journal Article | IST-REx-ID: 570 | OA
M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6, 2017.
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2017 | Journal Article | IST-REx-ID: 613 | OA
R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1, 2017.
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2017 | Journal Article | IST-REx-ID: 624 | OA
N. Nikolic, Z. Didara, and I. Moll, “MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations,” PeerJ, vol. 2017, no. 9, 2017.
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2017 | Journal Article | IST-REx-ID: 655 | OA
T. Renault et al., “Bacterial flagella grow through an injection diffusion mechanism,” eLife, vol. 6, 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, pp. 311–315, 2017.
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2017 | Journal Article | IST-REx-ID: 696 | OA
M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7, 2017.
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2017 | Journal Article | IST-REx-ID: 704 | OA
M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” eLife, vol. 6, 2017.
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2017 | Journal Article | IST-REx-ID: 954 | OA
M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6, 2017.
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2017 | Journal Article | IST-REx-ID: 1336 | OA
T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” Algorithmica, vol. 78, no. 2, pp. 681–713, 2017.
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2017 | Journal Article | IST-REx-ID: 1351 | OA
M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8, pp. 765–787, 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, pp. 46–55, 2017.
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2017 | Journal Article | IST-REx-ID: 1028 | OA
S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie - International Edition, vol. 56, no. 16, pp. 4608–4611, 2017.
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2017 | Journal Article | IST-REx-ID: 1084
C. Fang et al., “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology, vol. 104, no. 1, pp. 16–31, 2017.
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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 | Conference Paper | IST-REx-ID: 1234 | OA
P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands, 2016, vol. 9636, pp. 112–129.
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