| Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches AC Schürch, S Arredondo-Alonso, RJL Willems, RV Goering Clinical microbiology and infection 24 (4), 350-354, 2018 | 469 | 2018 |
| On the (im) possibility of reconstructing plasmids from whole-genome short-read sequencing data S Arredondo-Alonso, RJ Willems, W Van Schaik, AC Schürch Microbial genomics 3 (10), e000128, 2017 | 271 | 2017 |
| mlplasmids: A user-friendly tool to predict plasmid-and chromosome-derived sequences for single species S Arredondo-Alonso, MRC Rogers, JC Braat, TD Verschuuren, J Top, ... Microbial genomics 4 (11), e000224, 2018 | 148 | 2018 |
| Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium S Arredondo-Alonso, J Top, A McNally, S Puranen, M Pesonen, J Pensar, ... MBio 11 (1), 10.1128/mbio. 03284-19, 2020 | 119 | 2020 |
| Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era AK Pöntinen, J Top, S Arredondo-Alonso, G Tonkin-Hill, AR Freitas, ... Nature communications 12 (1), 1523, 2021 | 107 | 2021 |
| Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals S Arredondo-Alonso, J Top, J Corander, RJL Willems, AC Schürch Genome medicine 13, 1-18, 2021 | 35 | 2021 |
| Comparative genomics of ESBL-producing Escherichia coli (ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes … TD Verschuuren, D Van Hout, S Arredondo-Alonso, AC Fluit, EA Reuland, ... Journal of Antimicrobial Chemotherapy 76 (4), 901-908, 2021 | 21 | 2021 |
| Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe G Tonkin-Hill, RA Gladstone, AK Pöntinen, S Arredondo-Alonso, ... Genome Research 33 (1), 129-140, 2023 | 19 | 2023 |
| gplas: a comprehensive tool for plasmid analysis using short-read graphs S Arredondo-Alonso, M Bootsma, Y Hein, MRC Rogers, J Corander, ... Bioinformatics 36 (12), 3874-3876, 2020 | 19 | 2020 |
| A high-throughput multiplexing and selection strategy to complete bacterial genomes S Arredondo-Alonso, AK Pöntinen, F Cléon, RA Gladstone, AC Schürch, ... Gigascience 10 (12), giab079, 2021 | 16 | 2021 |
| Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium J Top, S Arredondo-Alonso, AC Schürch, S Puranen, M Pesonen, ... Microbial genomics 6 (12), e000488, 2020 | 16 | 2020 |
| Conditionally essential genes for survival during starvation in Enterococcus faecium E745 V de Maat, S Arredondo-Alonso, RJL Willems, W van Schaik BMC genomics 21, 1-11, 2020 | 15 | 2020 |
| Evolutionary and functional history of the Escherichia coli K1 capsule S Arredondo-Alonso, G Blundell-Hunter, Z Fu, RA Gladstone, ... Nature Communications 14 (1), 3294, 2023 | 14 | 2023 |
| Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data JA Paganini, NL Plantinga, S Arredondo-Alonso, RJL Willems, ... Microorganisms 9 (8), 1613, 2021 | 14 | 2021 |
| Mge-cluster: a reference-free approach for typing bacterial plasmids S Arredondo-Alonso, RA Gladstone, AK Pöntinen, JA Gama, AC Schürch, ... NAR genomics and bioinformatics 5 (3), lqad066, 2023 | 7* | 2023 |
| The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection C Chaguza, AK Pöntinen, J Top, S Arredondo-Alonso, AR Freitas, ... Microbiology spectrum 11 (6), e00201-23, 2023 | 2 | 2023 |
| Escherichia coliplasmidome maps the game of clones S Arredondo-Alonso, AK Pöntinen, JA Gama, RA Gladstone, K Harms, ... | 2 | 2023 |
| Functional characterization of a gene cluster responsible for inositol catabolism associated with hospital-adapted isolates of Enterococcus faecium J Top, J Baan, A Bisschop, S Arredondo-Alonso, W van Schaik, ... Microbiology 167 (9), 001085, 2021 | 2 | 2021 |
| Detecting co-selection through excess linkage disequilibrium in bacterial genomes S Mallawaarachchi, G Tonkin-Hill, AK Pöntinen, JK Calland, ... NAR Genomics and Bioinformatics 6 (2), 2024 | 1 | 2024 |
| Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study HA Thorpe, M Pesonen, M Corbella, H Pesonen, S Gaiarsa, CJ Boinett, ... The Lancet Microbe, 2024 | | 2024 |
