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86 Publications

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 | 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, p. e1007642, 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 | Research Data | IST-REx-ID: 7383
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 | 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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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: 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 | Thesis | IST-REx-ID: 6371
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: 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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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 | 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
I. Tomanek, Data for the paper “Gene amplification as a form of population-level gene expression regulation.” IST Austria, 2019.
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2018 | Journal Article | IST-REx-ID: 67   OA
C. Igler, M. Lagator, G. Tkacik, 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: 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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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 | 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 | Preprint | IST-REx-ID: 196   OA
M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” ArXiv. ArXiv, 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 | Thesis | IST-REx-ID: 26
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: 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 | Journal Article | IST-REx-ID: 161
D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkacik, “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: 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: 438
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 | Research Data | IST-REx-ID: 5585
C. Igler, M. Lagator, G. Tkacik, 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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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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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: 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: 1351
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 | Thesis | IST-REx-ID: 202
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: 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: 613   OA
R. P. Chait, J. Ruess, T. Bergmiller, G. Tkacik, 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: 1028
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: 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 | 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: 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: 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: 696
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
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: 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 | Research Data | IST-REx-ID: 5560
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 | 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: 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: 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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2016 | Journal Article | IST-REx-ID: 1008
R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” ACS Synthetic Biology, vol. 5, no. 10, pp. 1098–1107, 2016.
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2016 | Journal Article | IST-REx-ID: 1250   OA
A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Genetic manipulation of glycogen allocation affects replicative lifespan in E coli,” PLoS Genetics, vol. 12, no. 4, 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.
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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, 2016.
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