Guet, C. C., Bruneaux, L., Oikonomou, P., Aldana, M., &; Cluzel, P. (2023). Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. Frontiers.https://doi.org/10.3389/fmicb.2023.1049255 

Davidovi, A., Chait, R. P., Batt, G., &; Ruess, J. (2022). Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. PLoS Computational Biology. Public Library of Science.https://doi.org/10.1371/journal.pcbi.1009950 

Nikolic, N., Sauert, M., Albanese, T. G., &; Moll, I. (2022). Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. BMC Research Notes. Springer Nature.https://doi.org/10.1186/s13104-022-06061-9 

Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., &; Tkadik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. ELife. eLife Sciences Publications.https://doi.org/10.7554/eLife.64543 

Römhild, R., Bollenbach, M. T., &; Andersson, D. I. (2022). The physiology and genetics of bacterial responses to antibiotic combinations. Nature Reviews Microbiology. Springer Nature.https://doi.org/10.1038/s41579-022-00700-5 

Glover, G., Voliotis, M., apiska, U., Invergo, B. M., Soanes, D., O’Neill, P.,https://doi.org/10.1038/s42003-022-03336-6__Pagliara, S. (2022). Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Communications Biology. Springer Nature.https://doi.org/10.1038/s42003-022-03336-6 

Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &; Sixt, M. K. (2022). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to C. ELife. eLife Sciences Publications.https://doi.org/10.7554/eLife.78995 

Tomanek, I., &; Guet, C. C. (2022). Adaptation dynamics between copynumber and point mutations. ELife. eLife Sciences Publications.https://doi.org/10.7554/ELIFE.82240 

Tomanek, I., &; Guet, C. C. (2022). Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. Dryad.https://doi.org/10.5061/dryad.rfj6q57ds 

Römhild, R., &; Andersson, D. I. (2021). Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. PLoS Pathogens. Public Library of Science.https://doi.org/10.1371/journal.ppat.1009172 

Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., &; Guet, C. C. (2021). Long lived transients in gene regulation. Theoretical Computer Science. Elsevier.https://doi.org/10.1016/j.tcs.2021.05.023 

Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P.,https://doi.org/10.1021/acsami.1c09850__Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society.https://doi.org/10.1021/acsami.1c09850 

Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., &; Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. ELife. eLife Sciences Publications.https://doi.org/10.7554/elife.68876 

Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., &; Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. Oxford University Press.https://doi.org/10.1093/protein/gzab025 

Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., &; Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. ELife. eLife Sciences Publications.https://doi.org/10.7554/elife.65993 

Le, D., Krasnopeeva, E., Sinjab, F., Pilizota, T., &; Kim, M. (2021). Active efflux leads to heterogeneous dissipation of proton motive force by protonophores in bacteria. MBio. American Society for Microbiology.https://doi.org/10.1128/mbio.00676-21 

Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.https://doi.org/10.15479/at:ista:10307 

Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &; Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to C. bioRxiv. Cold Spring Harbor Laboratory.https://doi.org/10.1101/2021.10.18.464770 

Kainrath, S., &; Janovjak, H. L. (2020). Design and application of light-regulated receptor tyrosine kinases. In D. Niopek (Ed.), Photoswitching Proteins (Vol. 2173, pp. 233–246). Springer Nature.https://doi.org/10.1007/978-1-0716-0755-8_16 

Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:8155 

Grah, R., Zoller, B., &; Tkadik, G. (2020). Normative models of enhancer function. bioRxiv. Cold Spring Harbor Laboratory.https://doi.org/10.1101/2020.04.08.029405 

Grah, R., &; Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science.https://doi.org/10.1371/journal.pcbi.1007642 

Nagy-Staron, A. A. (2020). 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.https://doi.org/10.15479/AT:ISTA:8951 

Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:7383 

Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:7680 

Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkadik, G., &; Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology &; Evolution. Springer Nature.https://doi.org/10.1038/s41559-020-1132-7 

Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:8653 

Chassin, H., Müller, M., Tigges, M., Scheller, L., Lang, M., &; Fussenegger, M. (2019). A modular degron library for synthetic circuits in mammalian cells. Nature Communications. Springer Nature.https://doi.org/10.1038/s41467-019-09974-5 

Igler, C., &; Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. Frontiers.https://doi.org/10.3389/fmicb.2019.01171 

Ruess, J., Pleska, M., Guet, C. C., &; Tkadik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. Public Library of Science.https://doi.org/10.1371/journal.pcbi.1007168 

Ruess, J., Pleska, M., Guet, C. C., &; Tkadik, G. (2019). Supporting text and results. Public Library of Science.https://doi.org/10.1371/journal.pcbi.1007168.s001 

Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., &; Sezgin, A. (2019). Transient memory in gene regulation. In 17th International Conference on Computational Methods in Systems Biology (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature.https://doi.org/10.1007/978-3-030-31304-3_9 

Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. Springer.https://doi.org/10.1007/s00294-018-0879-8 

Lang, M., &; Shkolnikov, M. (2019). Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. National Academy of Sciences.https://doi.org/10.1073/pnas.1812015116 

Tomanek, I. (2019). 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.https://doi.org/10.15479/AT:ISTA:7016 

Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:6371 

Misun, P., Birchler, A., Lang, M., Hierlemann, A., &; Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. Springer.https://doi.org/10.1007/978-1-4939-7792-5_15 

Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., &; Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. Springer.https://doi.org/10.1007/s00453-017-0369-2 

Tomasek, K., Bergmiller, T., &; Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. Elsevier.https://doi.org/10.1016/j.jbiotec.2018.01.008 

Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J.,https://doi.org/10.1371/journal.pbio.2005971__Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science.https://doi.org/10.1371/journal.pbio.2005971 

Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J.,https://doi.org/10.1371/journal.pbio.2005971.s008__Levin, B. (2018). Numerical data used in figures. Public Library of Science.https://doi.org/10.1371/journal.pbio.2005971.s008 

Pleska, M., Lang, M., Refardt, D., Levin, B., &; Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. Springer Nature.https://doi.org/10.1038/s41559-017-0424-z 

Morri, M., Sanchez-Romero, I., Tichy, A.-M., Kainrath, S., Gerrard, E. J., Hirschfeld, P.,https://doi.org/10.1038/s41467-018-04342-1__Janovjak, H. L. (2018). Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. Springer Nature.https://doi.org/10.1038/s41467-018-04342-1 

Palmer, A., Chait, R. P., &; Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. Oxford University Press.https://doi.org/10.1093/molbev/msy163 

Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., &; Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. Oxford University Press.https://doi.org/10.1093/nar/gky079 

Bergmiller, T., &; Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:74 

De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., &; Tkadik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications. Springer Nature.https://doi.org/10.1038/s41467-018-05417-9 

Steinrück, M. (2018). The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:th1059 

Igler, C., Lagator, M., Tkadik, G., Bollback, J. P., &; Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. Nature Publishing Group.https://doi.org/10.1038/s41559-018-0651-y 

Igler, C., Lagator, M., Tkadik, G., Bollback, J. P., &; Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria.https://doi.org/10.15479/AT:ISTA:108