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Davidovi, Anela, Remy P Chait, Gregory Batt, and Jakob Ruess. “Parameter Inference for Stochastic Biochemical Models from Perturbation Experiments Parallelised at the Single Cell Level.”https://doi.org/10.1371/journal.pcbi.1009950__PLoS Computational Biology. Public Library of Science, 2022.https://doi.org/10.1371/journal.pcbi.1009950 .
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Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.”https://doi.org/10.1186/s13104-022-06061-9__BMC Research Notes. Springer Nature, 2022.https://doi.org/10.1186/s13104-022-06061-9 .
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Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gasper Tkadik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.”https://doi.org/10.7554/eLife.64543__ELife. eLife Sciences Publications, 2022.https://doi.org/10.7554/eLife.64543 .
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Römhild, Roderich, Mark Tobias Bollenbach, and Dan I. Andersson. “The Physiology and Genetics of Bacterial Responses to Antibiotic Combinations.”https://doi.org/10.1038/s41579-022-00700-5__Nature Reviews Microbiology. Springer Nature, 2022.https://doi.org/10.1038/s41579-022-00700-5 .
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Glover, Georgina, Margaritis Voliotis, Urszula apiska, Brandon M. Invergo, Darren Soanes, Paul O’Neill, Karen Moore, et al. “Nutrient and Salt Depletion Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.”https://doi.org/10.1038/s42003-022-03336-6__Communications Biology. Springer Nature, 2022.https://doi.org/10.1038/s42003-022-03336-6 .
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Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to C.”https://doi.org/10.7554/eLife.78995__ELife. eLife Sciences Publications, 2022.https://doi.org/10.7554/eLife.78995 .
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Tomanek, Isabella, and Calin C Guet. “Adaptation Dynamics between Copynumber and Point Mutations.”https://doi.org/10.7554/ELIFE.82240__ELife. eLife Sciences Publications, 2022.https://doi.org/10.7554/ELIFE.82240 .
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Tomanek, Isabella, and Calin C Guet. “Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose.”https://doi.org/10.5061/dryad.rfj6q57ds__Dryad, 2022.https://doi.org/10.5061/dryad.rfj6q57ds .
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Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.”https://doi.org/10.1371/journal.ppat.1009172__PLoS Pathogens. Public Library of Science, 2021.https://doi.org/10.1371/journal.ppat.1009172 .
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Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.”https://doi.org/10.1016/j.tcs.2021.05.023__Theoretical Computer Science. Elsevier, 2021.https://doi.org/10.1016/j.tcs.2021.05.023 .
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Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.”https://doi.org/10.1021/acsami.1c09850__ACS Applied Materials and Interfaces. American Chemical Society, 2021.https://doi.org/10.1021/acsami.1c09850 .
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Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.”https://doi.org/10.7554/elife.68876__ELife. eLife Sciences Publications, 2021.https://doi.org/10.7554/elife.68876 .
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Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.”https://doi.org/10.1093/protein/gzab025__Protein Engineering, Design and Selection. Oxford University Press, 2021.https://doi.org/10.1093/protein/gzab025 .
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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.”https://doi.org/10.7554/elife.65993__ELife. eLife Sciences Publications, 2021.https://doi.org/10.7554/elife.65993 .
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Le, Dai, Ekaterina Krasnopeeva, Faris Sinjab, Teuta Pilizota, and Minsu Kim. “Active Efflux Leads to Heterogeneous Dissipation of Proton Motive Force by Protonophores in Bacteria.”https://doi.org/10.1128/mbio.00676-21__MBio. American Society for Microbiology, 2021.https://doi.org/10.1128/mbio.00676-21 .
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Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.”https://doi.org/10.15479/at:ista:10307__Institute of Science and Technology Austria, 2021.https://doi.org/10.15479/at:ista:10307 .
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Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to C.”https://doi.org/10.1101/2021.10.18.464770__BioRxiv. Cold Spring Harbor Laboratory, n.d.https://doi.org/10.1101/2021.10.18.464770 .
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Kainrath, Stephanie, and Harald L Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.”https://doi.org/10.1007/978-1-0716-0755-8_16__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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Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.”https://doi.org/10.15479/AT:ISTA:8155__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:8155 .
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Grah, Rok, Benjamin Zoller, and Gasper Tkadik. “Normative Models of Enhancer Function.”https://doi.org/10.1101/2020.04.08.029405__BioRxiv. Cold Spring Harbor Laboratory, 2020.https://doi.org/10.1101/2020.04.08.029405 .
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Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.”https://doi.org/10.1371/journal.pcbi.1007642__PLOS Computational Biology. Public Library of Science, 2020.https://doi.org/10.1371/journal.pcbi.1007642 .
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Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’”https://doi.org/10.15479/AT:ISTA:8951__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:8951 .
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Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.”https://doi.org/10.15479/AT:ISTA:7383__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:7383 .
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DOI: 10.15479/AT:ISTA:7383

Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.”https://doi.org/10.15479/AT:ISTA:7680__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:7680 .
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DOI: 10.15479/AT:ISTA:7680

Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gasper Tkadik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.”https://doi.org/10.1038/s41559-020-1132-7__Nature Ecology &; Evolution. Springer Nature, 2020.https://doi.org/10.1038/s41559-020-1132-7 .
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Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.”https://doi.org/10.15479/AT:ISTA:8653__Institute of Science and Technology Austria, 2020.https://doi.org/10.15479/AT:ISTA:8653 .
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DOI: 10.15479/AT:ISTA:8653

Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.”https://doi.org/10.1038/s41467-019-09974-5__Nature Communications. Springer Nature, 2019.https://doi.org/10.1038/s41467-019-09974-5 .
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Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.”https://doi.org/10.3389/fmicb.2019.01171__Frontiers in Microbiology. Frontiers, 2019.https://doi.org/10.3389/fmicb.2019.01171 .
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Ruess, Jakob, Maros Pleska, Calin C Guet, and Gasper Tkadik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.”https://doi.org/10.1371/journal.pcbi.1007168__PLoS Computational Biology. Public Library of Science, 2019.https://doi.org/10.1371/journal.pcbi.1007168 .
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Ruess, Jakob, Maros Pleska, Calin C Guet, and Gasper Tkadik. “Supporting Text and Results.”https://doi.org/10.1371/journal.pcbi.1007168.s001__Public Library of Science, 2019.https://doi.org/10.1371/journal.pcbi.1007168.s001 .
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DOI: 10.1371/journal.pcbi.1007168.s001

Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.”https://doi.org/10.1007/978-3-030-31304-3_9__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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Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.”https://doi.org/10.1007/s00294-018-0879-8__Current Genetics. Springer, 2019.https://doi.org/10.1007/s00294-018-0879-8 .
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Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.”https://doi.org/10.1073/pnas.1812015116__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019.https://doi.org/10.1073/pnas.1812015116 .
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DOI: 10.1073/pnas.1812015116
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PMID:  30728300
arXiv: 1806.10823

Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’”https://doi.org/10.15479/AT:ISTA:7016__Institute of Science and Technology Austria, 2019.https://doi.org/10.15479/AT:ISTA:7016 .
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Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.”https://doi.org/10.15479/AT:ISTA:6371__Institute of Science and Technology Austria, 2019.https://doi.org/10.15479/AT:ISTA:6371 .
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Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.”https://doi.org/10.1007/978-1-4939-7792-5_15__Methods in Molecular Biology. Springer, 2018.https://doi.org/10.1007/978-1-4939-7792-5_15 .
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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.”https://doi.org/10.1007/s00453-017-0369-2__Algorithmica. Springer, 2018.https://doi.org/10.1007/s00453-017-0369-2 .
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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.”https://doi.org/10.1016/j.jbiotec.2018.01.008__Journal of Biotechnology. Elsevier, 2018.https://doi.org/10.1016/j.jbiotec.2018.01.008 .
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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.”https://doi.org/10.1371/journal.pbio.2005971__PLoS Biology. Public Library of Science, 2018.https://doi.org/10.1371/journal.pbio.2005971 .
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DOI: 10.1371/journal.pbio.2005971
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Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.”https://doi.org/10.1371/journal.pbio.2005971.s008__Public Library of Science, 2018.https://doi.org/10.1371/journal.pbio.2005971.s008 .
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Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.”https://doi.org/10.1038/s41559-017-0424-z__Nature Ecology and Evolution. Springer Nature, 2018.https://doi.org/10.1038/s41559-017-0424-z .
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DOI: 10.1038/s41559-017-0424-z
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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.”https://doi.org/10.1038/s41467-018-04342-1__Nature Communications. Springer Nature, 2018.https://doi.org/10.1038/s41467-018-04342-1 .
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Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.”https://doi.org/10.1093/molbev/msy163__Molecular Biology and Evolution. Oxford University Press, 2018.https://doi.org/10.1093/molbev/msy163 .
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DOI: 10.1093/molbev/msy163
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PMID: 30169679

Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.”https://doi.org/10.1093/nar/gky079__Nucleic Acids Research. Oxford University Press, 2018.https://doi.org/10.1093/nar/gky079 .
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Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.”https://doi.org/10.15479/AT:ISTA:74__Institute of Science and Technology Austria, 2018.https://doi.org/10.15479/AT:ISTA:74 .
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De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gasper Tkadik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.”https://doi.org/10.1038/s41467-018-05417-9__Nature Communications. Springer Nature, 2018.https://doi.org/10.1038/s41467-018-05417-9 .
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Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.”https://doi.org/10.15479/AT:ISTA:th1059__Institute of Science and Technology Austria, 2018.https://doi.org/10.15479/AT:ISTA:th1059 .
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DOI: 10.15479/AT:ISTA:th1059

Igler, Claudia, Mato Lagator, Gasper Tkadik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.”https://doi.org/10.1038/s41559-018-0651-y__Nature Ecology and Evolution. Nature Publishing Group, 2018.https://doi.org/10.1038/s41559-018-0651-y .
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Igler, Claudia, Mato Lagator, Gasper Tkadik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.”https://doi.org/10.15479/AT:ISTA:108__Institute of Science and Technology Austria, 2018.https://doi.org/10.15479/AT:ISTA:108 .
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