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92 Publications

2021 | Journal Article | IST-REx-ID: 9046 | OA
Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” PLoS Pathogens. Public Library of Science, 2021. https://doi.org/10.1371/journal.ppat.1009172.
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2021 | Journal Article | IST-REx-ID: 9283 | OA
Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.65993.
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2020 | Thesis | IST-REx-ID: 8155 | OA
Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.
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2020 | Book Chapter | IST-REx-ID: 8173
Kainrath, Stephanie, and Harald L Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.” In Photoswitching Proteins, edited by Dominik Niopek, 2173:233–46. MIMB. Springer Nature, 2020. https://doi.org/10.1007/978-1-0716-0755-8_16.
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2020 | Thesis | IST-REx-ID: 8653
Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.
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2020 | Research Data | IST-REx-ID: 7383 | OA
Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.
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2020 | Journal Article | IST-REx-ID: 7569 | OA
Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.
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2020 | Journal Article | IST-REx-ID: 7652 | OA
Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7.
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2020 | Preprint | IST-REx-ID: 7675 | OA
Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405.
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2020 | Thesis | IST-REx-ID: 7680
Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:7680.
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2020 | Research Data | IST-REx-ID: 8951 | OA
Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.
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2019 | Journal Article | IST-REx-ID: 196 | OA
Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.
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2019 | Conference Paper | IST-REx-ID: 7147
Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In 17th International Conference on Computational Methods in Systems Biology, 11773:155–87. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31304-3_9.
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2019 | Journal Article | IST-REx-ID: 6465 | OA
Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09974-5.
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2019 | Journal Article | IST-REx-ID: 6784 | OA
Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.
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2019 | Research Data | IST-REx-ID: 7016 | OA
Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.
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2019 | Journal Article | IST-REx-ID: 138 | OA
Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics. Springer, 2019. https://doi.org/10.1007/s00294-018-0879-8.
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2019 | Journal Article | IST-REx-ID: 6717 | OA
Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology. Frontiers, 2019. https://doi.org/10.3389/fmicb.2019.01171.
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2019 | Thesis | IST-REx-ID: 6371 | OA
Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.
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2018 | Journal Article | IST-REx-ID: 82 | OA
Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.
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2018 | Journal Article | IST-REx-ID: 19 | OA
Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution. NLM , 2018. https://doi.org/10.1093/molbev/msy163.
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2018 | Journal Article | IST-REx-ID: 723 | OA
Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.
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2018 | Journal Article | IST-REx-ID: 503
Tomasek, Kathrin, Tobias Bergmiller, and Calin 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. Elsevier, 2018. https://doi.org/10.1016/j.jbiotec.2018.01.008.
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2018 | Research Data | IST-REx-ID: 5569 | OA
Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” IST Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.
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2018 | Journal Article | IST-REx-ID: 5984 | OA
Morri, Maurizio, Inmaculada Sanchez-Romero, Alexandra-Madelaine Tichy, Stephanie Kainrath, Elliot J. Gerrard, Priscila Hirschfeld, Jan Schwarz, and Harald L Janovjak. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04342-1.
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2018 | Journal Article | IST-REx-ID: 161 | OA
De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9.
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2018 | Journal Article | IST-REx-ID: 438 | OA
Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.
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2018 | Journal Article | IST-REx-ID: 457
Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0424-z.
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2018 | Journal Article | IST-REx-ID: 305
Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15.
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2018 | Journal Article | IST-REx-ID: 67 | OA
Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution. Nature Publishing Group, 2018. https://doi.org/10.1038/s41559-018-0651-y.
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2018 | Research Data | IST-REx-ID: 5585 | OA
Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” IST Austria, 2018. https://doi.org/10.15479/AT:ISTA:108.
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2018 | Thesis | IST-REx-ID: 26 | OA
Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” IST Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1059.
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2017 | Thesis | IST-REx-ID: 202 | OA
Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” IST Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916.
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2017 | Journal Article | IST-REx-ID: 735
Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.014.
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2017 | Journal Article | IST-REx-ID: 538 | OA
Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.
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2017 | Journal Article | IST-REx-ID: 541 | OA
Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics. Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.
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2017 | Research Data | IST-REx-ID: 5560 | OA
Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.” IST Austria, 2017. https://doi.org/doi:10.15479/AT:ISTA:53.
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2017 | Research Data | IST-REx-ID: 5564 | OA
Steinrück, Magdalena, and Calin C Guet. “Fastq Files for ‘Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.’” IST Austria, 2017. https://doi.org/10.15479/AT:ISTA:65.
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2017 | Journal Article | IST-REx-ID: 561
Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters. Royal Society, The, 2017. https://doi.org/10.1098/rsbl.2017.0646.
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2017 | Journal Article | IST-REx-ID: 570 | OA
Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.
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2017 | Journal Article | IST-REx-ID: 613 | OA
Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01683-1.
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2017 | Journal Article | IST-REx-ID: 624 | OA
Nikolic, Nela, Zrinka Didara, and Isabella Moll. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” PeerJ. PeerJ, 2017. https://doi.org/10.7717/peerj.3830.
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2017 | Journal Article | IST-REx-ID: 655 | OA
Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis, Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.23136.
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2017 | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aaf4762.
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2017 | Journal Article | IST-REx-ID: 1336 | OA
Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica. Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.
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2017 | Journal Article | IST-REx-ID: 1351 | OA
Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.
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2017 | Journal Article | IST-REx-ID: 1007 | OA
Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” Automatica. IFAC, the International Federation of Automatic Control, 2017. https://doi.org/10.1016/j.automatica.2017.03.030.
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2017 | Journal Article | IST-REx-ID: 1028 | OA
Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998.
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2017 | Journal Article | IST-REx-ID: 1084
Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597.
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2017 | Journal Article | IST-REx-ID: 954 | OA
Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.
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