| Practical considerations for measuring the effective reproductive number, Rt KM Gostic, L McGough, EB Baskerville, S Abbott, K Joshi, C Tedijanto, ... PLOS Computational Biology 16 (12), e1008409, 2020 | 448 | 2020 |
| Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut E Bakkeren, JS Huisman, SA Fattinger, A Hausmann, M Furter, A Egli, ... Nature 573 (7773), 276-280, 2019 | 190 | 2019 |
| Wastewater-based estimation of the effective reproductive number of SARS-CoV-2 JS Huisman, J Scire, L Caduff, X Fernandez-Cassi, ... Environmental Health Perspectives 130 (5), 057011, 2022 | 115 | 2022 |
| The origin and early spread of SARS-CoV-2 in Europe SA Nadeau, TG Vaughan, J Scire, JS Huisman, T Stadler Proceedings of the National Academy of Sciences 118 (9), e2012008118, 2021 | 99 | 2021 |
| COVID-19 infectivity profile correction P Ashcroft, JS Huisman, S Lehtinen, JA Bouman, CL Althaus, RR Regoes, ... Swiss Medical Weekly 150, 2020 | 87 | 2020 |
| Plasmid-and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo F Benz, JS Huisman, E Bakkeren, JA Herter, T Stadler, M Ackermann, ... The ISME Journal, 1-17, 2020 | 86 | 2020 |
| Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2 JS Huisman, J Scire, DC Angst, J Li, RA Neher, MH Maathuis, ... Elife 11, e71345, 2022 | 68 | 2022 |
| Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements—identification of sources by whole genome sequencing: study protocol for an observational … T Stadler, D Meinel, L Aguilar-Bultet, JS Huisman, R Schindler, A Egli, ... BMJ open 8 (2), e021823, 2018 | 43 | 2018 |
| Quantification of the spread of SARS-CoV-2 variant B. 1.1. 7 in Switzerland C Chen, SA Nadeau, I Topolsky, M Manceau, JS Huisman, KP Jablonski, ... Epidemics 37, 100480, 2021 | 38 | 2021 |
| Evolutionary mechanisms that determine which bacterial genes are carried on plasmids S Lehtinen, JS Huisman, S Bonhoeffer Evolution letters 5 (3), 290-301, 2021 | 29 | 2021 |
| Estimating plasmid conjugation rates: a new computational tool and a critical comparison of methods JS Huisman, F Benz, SJN Duxbury, JAGM de Visser, AR Hall, EAJ Fischer, ... Plasmid, 102627, 2022 | 28* | 2022 |
| Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium E Bakkeren, E Gül, JS Huisman, Y Steiger, A Rocker, WD Hardt, M Diard Nature Communications 13 (1), 1-13, 2022 | 24* | 2022 |
| Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut E Bakkeren, JA Herter, JS Huisman, Y Steiger, E Gül, JPM Newson, ... eLife 10, e69744, 2021 | 14 | 2021 |
| Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases J Pires, JS Huisman, S Bonhoeffer, TP Van Boeckel Microbiology Spectrum 9 (2), e00495-21, 2021 | 13 | 2021 |
| Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases J Pires, JS Huisman, S Bonhoeffer, TP Van Boeckel Journal of Antimicrobial Chemotherapy 77 (3), 646-655, 2022 | 12 | 2022 |
| Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State LM Carroll, JS Huisman, M Wiedmann Scientific Reports 10 (1), 14428, 2020 | 11 | 2020 |
| Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics C Igler, JS Huisman, B Siedentop, S Bonhoeffer, S Lehtinen Philosophical Transactions of the Royal Society B 377 (1842), 20200478, 2022 | 8 | 2022 |
| estimateR: an R package to estimate and monitor the effective reproductive number J Scire, JS Huisman, A Grosu, DC Angst, A Lison, J Li, MH Maathuis, ... BMC bioinformatics 24 (1), 310, 2023 | 5 | 2023 |
| The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies JS Huisman, TG Vaughan, A Egli, S Tschudin-Sutter, T Stadler, ... Philosophical Transactions of the Royal Society B 377 (1861), 20210245, 2022 | 4 | 2022 |
| Guidelines for the estimation and reporting of plasmid conjugation rates O Kosterlitz, JS Huisman Plasmid 126, 102685, 2023 | 3 | 2023 |
Sebastian BonhoefferTheoretical Biology, ETH ZurichVerified email at env.ethz.ch
