Publications
2025
Scholarly publications
2024
Scholarly publications
2023
Scholarly publications
Wehrens, M., Krah, L. H. J., Towbin, B. D., Hermsen, R., & Tans, S. J. (2023). The interplay between metabolic stochasticity and cAMP-CRP regulation in single E. coli cells. Cell Reports, 42(10), Article 113284. [DOI] [Repository]
2022
Scholarly publications
Wehrens, M., Krah, L., Towbin, B., Hermsen, R., & Tans, S. (2022). The interplay between metabolic stochasticity and regulation in single E. coli cells. (pp. 1-10). bioRxiv. [DOI] [Repository]
Hermsen, R. (2022). Emergent multilevel selection in a simple spatial model of the evolution of altruism. PLoS Computational Biology, 18(10), 1-28. Article e1010612. [DOI] [Repository]
2021
Scholarly publications
Doekes, H. M., & Hermsen, R. (2021). Multiscale selection in spatially structured populations. (pp. 1-30). bioRxiv. [DOI] [Repository]
Hermsen, R. (2021). Emergent multilevel selection in a simple spatial model of the evolution of altruism. (pp. 1-37). bioRxiv. [DOI] [Repository]
Okano, H., Hermsen, R., & Hwa, T. (2021). Hierarchical and simultaneous utilization of carbon substrates: mechanistic insights, physiological roles, and ecological consequences. Current Opinion in Microbiology, 63, 172-178. [DOI] [Repository]
Sheinman, M., Arkhipova, K., Arndt, P. F., Dutilh, B. E., Hermsen, R., & Massip, F. (2021). Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. eLife, 10, Article e62719. [DOI] [Repository]
Krah, L. H. J., & Hermsen, R. (2021). The effect of natural selection on the propagation of protein expression noise to bacterial growth. PLoS Computational Biology, 17(7), Article e1009208. [DOI] [Repository]
Doekes, H. M., Mulder, G. A., & Hermsen, R. (2021). Repeated outbreaks drive the evolution of bacteriophage communication. eLife, 10, 1-33. Article e58410. [DOI] [Repository]
2020
Scholarly publications
de Greef, P. C., Oakes, T., Gerritsen, B., Ismail, M., Heather, J. M., Hermsen, R., Chain, B., & de Boer, R. J. (2020). The naive t-cell receptor repertoire has an extremely broad distribution of clone sizes. eLife, 9, 1-24. Article e49900. [DOI] [Repository]
2019
Scholarly publications
Okano, H., Hermsen, R., Kochanowski, K., & Hwa, T. (2019). Regulation underlying hierarchical and simultaneous utilization of carbon substrates by flux sensors in Escherichia coli. Nature Microbiology, 5(1), 206-2015. [DOI] [Repository]
Doekes, H. M., De Boer, R. J., & Hermsen, R. (2019). Toxin production spontaneously becomes regulated by local cell density in evolving bacterial populations. PLoS Computational Biology, 15(8), Article e1007333. [DOI] [Repository]
2018
Scholarly publications
Kleijn, I. T., Krah, L. H. J., & Hermsen, R. (2018). Noise propagation in an integrated model of bacterial gene expression and growth. PLoS Computational Biology, 14(10), Article e1006386. [DOI] [Repository]
2017
Scholarly publications
Sheinman, M., & Hermsen, R. (2017, Jun 15). Effects of DNA oxidation on the evolution of genomes. bioRxiv. [DOI]
2016
Scholarly publications
Hermsen, R. (2016). The adaptation rate of a quantitative trait in an environmental gradient. Physical Biology, 13(6), Article 065003. [DOI] [Repository]
2015
Scholarly publications
Hermsen, R., Okano, H., You, C., Werner, N., & Hwa, T. (2015). A growth-rate composition formula for the growth of E.coli on co-utilized carbon substrates. Molecular Systems Biology [E], 11(4). [DOI] [Repository]
2013
Scholarly publications
Deris, J. B., Kim, M., Zhang, Z., Okano, H., Hermsen, R., Groisman, E. A., & Hwa, T. (2013). The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria. Science, 342, 1237435.
2012
Scholarly publications
Hermsen, R., Deris, J. B., & Hwa, T. (2012). On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient. Proceedings of the National Academy of Sciences of the United States of America, 109, 10775-10780.
2011
Scholarly publications
Hermsen, R., Erickson, D. W., & Hwa, T. (2011). Speed, sensitivity, and bistability in auto-activating signaling circuits. PLoS Computational Biology, 7, e1002265.
2010
Scholarly publications
Hermsen, R., & Hwa, T. (2010). Sources and Sinks: a stochastic model of evolution in heterogeneous environments. Physical Review Letters, 105(24), 248104.
Hermsen, R., Ursem, B., & ten wolde, P. R. (2010). Combinatorial gene regulation using autoregulation. PLoS Computational Biology, 6(6), Article 1000813. [DOI]
2008
Scholarly publications
Hermsen, R., ten Wolde, P. R., & Teichmann, S. (2008). Chance and necessity in chromosomal gene distributions. Trends in Genetics, 24(5), 216-219. [DOI]
2006
Scholarly publications
Hermsen, R., Tans, S., & ten wolde, P. R. (2006). Transcription regulation by competing transcripion factor modules. PLoS Computational Biology, 2(12), Article e164. [DOI] [Repository]