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86 Publications

2020 | Journal Article | IST-REx-ID: 7652
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 4, no. 4 (2020): 612–25. https://doi.org/10.1038/s41559-020-1132-7.
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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 16, no. 2 (2020): e1007642. https://doi.org/10.1371/journal.pcbi.1007642.
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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: 7383
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 | Preprint | IST-REx-ID: 7675   OA
Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020.
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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 10 (2019). https://doi.org/10.3389/fmicb.2019.01171.
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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 10, no. 1 (2019). https://doi.org/10.1038/s41467-019-09974-5.
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2019 | Thesis | IST-REx-ID: 6371
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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2019 | Journal Article | IST-REx-ID: 138   OA
Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics 65, no. 1 (2019): 133–38. https://doi.org/10.1007/s00294-018-0879-8.
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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: 6784   OA
Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology 15, no. 7 (2019). https://doi.org/10.1371/journal.pcbi.1007168.
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2019 | Research Data | IST-REx-ID: 7016
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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2018 | Journal Article | IST-REx-ID: 67   OA
Igler, Claudia, Mato Lagator, Gasper Tkacik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution 2, no. 10 (2018): 1633–43. https://doi.org/10.1038/s41559-018-0651-y.
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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 16, no. 8 (2018). https://doi.org/10.1371/journal.pbio.2005971.
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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: 19   OA
Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution 35, no. 11 (2018): 2669–84. https://doi.org/10.1093/molbev/msy163.
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2018 | Preprint | IST-REx-ID: 196   OA
Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” ArXiv. ArXiv, 2018.
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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 1771 (2018): 183–202. https://doi.org/10.1007/978-1-4939-7792-5_15.
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2018 | Thesis | IST-REx-ID: 26
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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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 80, no. 5 (2018): 1604–33. https://doi.org/10.1007/s00453-017-0369-2.
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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 2, no. 2 (2018): 359–66. https://doi.org/10.1038/s41559-017-0424-z.
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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 268 (2018): 40–52. https://doi.org/10.1016/j.jbiotec.2018.01.008.
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2018 | Journal Article | IST-REx-ID: 161
De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gasper Tkacik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications 9, no. 1 (2018). https://doi.org/10.1038/s41467-018-05417-9.
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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 9, no. 1 (2018). https://doi.org/10.1038/s41467-018-04342-1.
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2018 | Journal Article | IST-REx-ID: 438
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 46, no. 6 (2018): 2918–31. https://doi.org/10.1093/nar/gky079.
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2018 | Research Data | IST-REx-ID: 5585
Igler, Claudia, Mato Lagator, Gasper Tkacik, 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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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 104, no. 1 (2017): 16–31. https://doi.org/10.1111/mmi.13597.
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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 13, no. 12 (2017). https://doi.org/10.1098/rsbl.2017.0646.
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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 2017, no. 9 (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 6 (2017). https://doi.org/10.7554/eLife.23136.
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2017 | Journal Article | IST-REx-ID: 1351
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 54, no. 8 (2017): 765–87. https://doi.org/10.1007/s00236-016-0278-x.
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2017 | Thesis | IST-REx-ID: 202
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: 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 6 (2017). https://doi.org/10.7554/eLife.25192.
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2017 | Journal Article | IST-REx-ID: 613   OA
Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gasper Tkacik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications 8, no. 1 (2017). https://doi.org/10.1038/s41467-017-01683-1.
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2017 | Journal Article | IST-REx-ID: 1028
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 56, no. 16 (2017): 4608–11. https://doi.org/10.1002/anie.201611998.
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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 6 (2017). https://doi.org/10.7554/eLife.28921.
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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: 538   OA
Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie 129, no. 16 (2017): 4679–82. https://doi.org/10.1002/ange.201611998.
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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 43, no. 2 (2017): 198–211. https://doi.org/10.1016/j.devcel.2017.09.014.
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2017 | Journal Article | IST-REx-ID: 696
Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology 13, no. 7 (2017). https://doi.org/10.1371/journal.pcbi.1005609.
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2017 | Journal Article | IST-REx-ID: 704
Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife 6 (2017). https://doi.org/10.7554/eLife.25100.
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2017 | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gasper Tkacik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science 356, no. 6335 (2017): 311–15. https://doi.org/10.1126/science.aaf4762.
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2017 | Research Data | IST-REx-ID: 5560
Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gasper Tkacik, 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 | Journal Article | IST-REx-ID: 1007   OA
Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” Automatica 81C (2017): 46–55. https://doi.org/10.1016/j.automatica.2017.03.030.
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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 78, no. 2 (2017): 681–713. https://doi.org/10.1007/s00453-016-0212-1.
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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 13, no. 12 (2017). https://doi.org/10.1371/journal.pgen.1007122.
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2016 | Journal Article | IST-REx-ID: 1008
Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” ACS Synthetic Biology 5, no. 10 (2016): 1098–1107. https://doi.org/10.1021/acssynbio.6b00013.
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2016 | Journal Article | IST-REx-ID: 1250   OA
Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” PLoS Genetics 12, no. 4 (2016). https://doi.org/10.1371/journal.pgen.1005974.
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2016 | Conference Paper | IST-REx-ID: 1320
Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,” Vol. 2016–July. IEEE, 2016. https://doi.org/10.1109/ACC.2016.7526722.
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2016 | Journal Article | IST-REx-ID: 1332   OA
Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications 7 (2016). https://doi.org/10.1038/ncomms10333.
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