Research output per year
Research output per year
- 1 - 50 out of 235 results
Search results
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2024
Colonization of vancomycin-resistant Enterococcus faecium in human-derived colonic epithelium: Unraveling the transcriptional dynamics of host-enterococcal interactions
Stege, P. B., Beekman, J. M., Hendrickx, A. P. A., Van Eijk, L., Rogers, M. R. C., Suen, S. W. F., Vonk, A. M., Willems, R. J. L. & Paganelli, F. L., 7 May 2024, In: FEMS Microbes. 5, xtae014.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile -
Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements
Kerkvliet, J. J., Bossers, A., Kers, J. G., Meneses, R., Willems, R. & Schürch, A. C., 2024, In: PeerJ. 12, p. e16695 e16695.Research output: Contribution to journal › Article › Academic › peer-review
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Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
Kuronen, J., Horsfield, S. T., Pöntinen, A. K., Mallawaarachchi, S., Arredondo-Alonso, S., Thorpe, H., Gladstone, R. A., Willems, R. J. L., Bentley, S. D., Croucher, N. J., Pensar, J., Lees, J. A., Tonkin-Hill, G. & Corander, J., 20 Aug 2024, In: Genome Research. 34, 7, p. 1081-1088 8 p.Research output: Contribution to journal › Article › Academic › peer-review
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PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli.
Paganini, J. A., Kerkvliet, J. J., Vader, L., Plantinga, N. L., Meneses, R., Corander, J., Willems, R. J. L., Arredondo-Alonso, S. & Schürch, A. C., Feb 2024, In: Microbial genomics. 10, 2, 001193.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile1 Downloads (Pure) -
YajC, a predicted membrane protein, promotes Enterococcus faecium biofilm formation in vitro and in a rat endocarditis model
Top, J., Zhang, X., Hendrickx, A. P. A., Boeren, S., van Schaik, W., Huebner, J., Willems, R. J. L., Leavis, H. L. & Paganelli, F. L., 2024, In: FEMS Microbes. 5, xtae017.Research output: Contribution to journal › Article › Academic › peer-review
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2023
Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone
Boralli, C. M. D. S., Paganini, J. A., Meneses, R. S., Mata, C. P. S. M. D., Leite, E. M. M., Schürch, A. C., Paganelli, F. L., Willems, R. J. L. & Camargo, I. L. B. C., May 2023, In: Antibiotics. 12, 5, 926.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile2 Downloads (Pure) -
Enterococcus spp. from chicken meat collected 20 years apart overcome multiple stresses occurring in the poultry production chain: Antibiotics, copper and acids
Rebelo, A., Duarte, B., Ferreira, C., Mourão, J., Ribeiro, S., Freitas, A. R., Coque, T. M., Willems, R., Corander, J., Peixe, L., Antunes, P. & Novais, C., 2 Jan 2023, In: International Journal of Food Microbiology. 384, 109981.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile1 Citation (Scopus)4 Downloads (Pure) -
Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition
Stege, P. B., Hordijk, J., Sandholt, A. K. S., Zomer, A. L., Viveen, M. C., Rogers, M. R. C., Salomons, M., Wagenaar, J. A., Mughini-Gras, L., Willems, R. J. L. & Paganelli, F. L., 17 Aug 2023, In: Microbiology spectrum. 11, 4, p. 1-14 e0006323.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile4 Downloads (Pure) -
Gut microbiome dynamics in index patients colonized with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales after hospital discharge and their household contacts
Top, J., Verschuuren, T. D., Viveen, M. C., Riccio, M. E., Harbarth, S., Kluytmans, J. A. J. W., Willems, R. J. L. & Paganelli, F. L., 12 Dec 2023, In: Microbiology spectrum. 11, 6, 13 p., e0127523.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile12 Downloads (Pure) -
The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection
Chaguza, C., Pöntinen, A. K., Top, J., Arredondo-Alonso, S., Freitas, A. R., Novais, C., Torres, C., Bentley, S. D., Peixe, L., Coque, T. M., Willems, R. J. L. & Corander, J., 12 Dec 2023, In: Microbiology spectrum. 11, 6, 21 p., e0020123.Research output: Contribution to journal › Article › Academic › peer-review
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Unraveling Enterococcus susceptibility to quaternary ammonium compounds: genes, phenotypes, and the impact of environmental conditions
Oct 2023, In: Microbiology spectrum. 11, 5, 18 p., e0232423.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile15 Downloads (Pure) -
2022
Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial
Reyman, M., van Houten, M. A., Watson, R. L., Chu, M. L. J. N., Arp, K., de Waal, W. J., Schiering, I., Plötz, F. B., Willems, R. J. L., van Schaik, W., Sanders, E. A. M. & Bogaert, D., 16 Feb 2022, In: Nature Communications. 13, 1, p. 1-12 893.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile17 Downloads (Pure) -
Evolution of Chlorhexidine Susceptibility and of the EfrEF Operon among Enterococcus faecalis from Diverse Environments, Clones, and Time Spans
Pereira, A. P., Antunes, P., Willems, R., Corander, J., Coque, T. M., Peixe, L., Freitas, A. R. & Novais, C., 31 Aug 2022, In: Microbiology spectrum. 10, 4, e0117622.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile3 Downloads (Pure) -
External validation of WGS-based antimicrobial susceptibility prediction tools, KOVER-AMR and ResFinder 4.1, for Escherichia coli clinical isolates
Verschuuren, T., Bosch, T., Mascaro, V., Willems, R. & Kluytmans, J., Nov 2022, In: Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. 28, 11, p. 1465-1470 6 p.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile12 Downloads (Pure) -
Impact of long-term dietary habits on the human gut resistome in the Dutch population
Stege, P. B., Hordijk, J., Shetty, S. A., Visser, M., Viveen, M. C., Rogers, M. R. C., Gijsbers, E., Dierikx, C. M., van der Plaats, R. Q. J., van Duijkeren, E., Franz, E., Willems, R. J. L., Fuentes, S. & Paganelli, F. L., 3 Feb 2022, In: Scientific Reports. 12, 1, p. 1-13 1892.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile8 Downloads (Pure) -
Species-Specific Patterns of Gut Metabolic Modules in Dutch Individuals with Different Dietary Habits
Shetty, S. A., Stege, P. B., Hordijk, J., Gijsbers, E., Dierikx, C. M., Van Duijkeren, E., Franz, E., Willems, R. J. L., Paganelli, F. L. & Fuentes, S., Nov 2022, In: mSphere. 7, 6, e0051222.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile9 Downloads (Pure) -
The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis
van Hal, S. J., Willems, R. J. L., Gouliouris, T., Ballard, S. A., Coque, T. M., Hammerum, A. M., Hegstad, K., Pinholt, M., Howden, B. P., Malhotra-Kumar, S., Werner, G., Yanagihara, K., Earl, A. M., Raven, K. E., Corander, J. & Bowden, R., Feb 2022, In: The Lancet Microbe. 3, 2, p. e133-e141Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile1 Citation (Scopus)3 Downloads (Pure) -
2021
Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era
Pöntinen, A. K., Top, J., Arredondo-Alonso, S., Tonkin-Hill, G., Freitas, A. R., Novais, C., Gladstone, R. A., Pesonen, M., Meneses, R., Pesonen, H., Lees, J. A., Jamrozy, D., Bentley, S. D., Lanza, V. F., Torres, C., Peixe, L., Coque, T. M., Parkhill, J., Schürch, A. C., Willems, R. J. L., & 1 others, 9 Mar 2021, In: Nature Communications. 12, 1, 13 p., 1523.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile12 Downloads (Pure) -
Comparative genomics of ESBL-producing Escherichia coli (ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes among human community faecal and extra-intestinal infection isolates in the Netherlands (2014-17)
Verschuuren, T. D., van Hout, D., Arredondo-Alonso, S., Fluit, A. C., Reuland, E. A., Top, J., Schürch, A. C., Bosch, T., Bonten, M. J. M., Kluytmans, J. A. J. W. & Willems, R. J. L., 12 Mar 2021, In: The Journal of antimicrobial chemotherapy. 76, 4, p. 901-908 8 p.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile9 Downloads (Pure) -
Evolution of colistin resistance in the Klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics
Janssen, A. B., Doorduijn, D. J., Mills, G., Rogers, M. R. C., Bonten, M. J. M., Rooijakkers, S. H. M., Willems, R. J. L., Bengoechea, J. A. & van Schaik, W., Jan 2021, In: Antimicrobial Agents and Chemotherapy. 65, 1, p. 1-15 e01958-20.Research output: Contribution to journal › Article › Academic › peer-review
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Functional characterization of a gene cluster responsible for inositol catabolism associated with hospital-adapted isolates of Enterococcus faecium
Top, J., Baan, J., Bisschop, A., Arredondo-Alonso, S., van Schaik, W. & Willems, R. J. L., 1 Sept 2021, In: Microbiology (Reading, England). 167, 9, p. 1-12 001085.Research output: Contribution to journal › Article › Academic › peer-review
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Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals
Arredondo-Alonso, S., Top, J., Corander, J., Willems, R. J. L. & Schürch, A. C., 20 Jan 2021, In: Genome Medicine. 13, 1, p. 1-18 18 p., 9.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile24 Downloads (Pure) -
Recovering escherichia coli plasmids in the absence of long-read sequencing data
Paganini, J. A., Plantinga, N. L., Arredondo-alonso, S., Willems, R. J. L. & Schürch, A. C., 28 Jul 2021, In: Microorganisms. 9, 8, p. 1-20 1613.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile16 Downloads (Pure) -
The global dissemination of hospital clones of Enterococcus faecium
Dec 2021, In: Genome Medicine. 13, 1, 12 p., 52.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile18 Citations (Scopus)21 Downloads (Pure) -
2020
Conditionally essential genes for survival during starvation in Enterococcus faecium E745
de Maat, V., Arredondo-Alonso, S., Willems, R. J. L. & van Schaik, W., 18 Aug 2020, In: BMC Genomics. 21, 1, 11 p., 568.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile4 Downloads (Pure) -
Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content
van Hout, D., Verschuuren, T. D., Bruijning-Verhagen, P. C. J., Bosch, T., Schürch, A. C., Willems, R. J. L., Bonten, M. J. M. & Kluytmans, J. A. J. W., 1 Jan 2020, In: PLoS ONE. 15, 1, p. 1-14 14 p., e0227604.Research output: Contribution to journal › Article › Academic › peer-review
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Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, enterococcus faecium
Top, J., Arredondo-Alonso, S., Schürch, A. C., Puranen, S., Pesonen, M., Pensar, J., Willems, R. J. L. & Corander, J., 2020, In: Microbial genomics. 6, 12, p. 1-8 8 p., 000488.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile6 Downloads (Pure) -
gplas: a comprehensive tool for plasmid analysis using short-read graphs
Arredondo-Alonso, S., Bootsma, M., Hein, Y., Rogers, M. R. C., Corander, J., Willems, R. J. L. & Schürch, A. C., 15 Jun 2020, In: Bioinformatics (Oxford, England). 36, 12, p. 3874-3876 3 p.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile7 Downloads (Pure) -
Low IgA Associated With Oropharyngeal Microbiota Changes and Lung Disease in Primary Antibody Deficiency
Berbers, R. M., Mohamed Hoesein, F. A. A., Ellerbroek, P. M., van Montfrans, J. M., Dalm, V. A. S. H., van Hagen, P. M., Paganelli, F. L., Viveen, M. C., Rogers, M. R. C., de Jong, P. A., Uh, H. W., Willems, R. J. L. & Leavis, H. L., 19 Jun 2020, In: Frontiers in Immunology. 11, 11 p., 1245.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile7 Downloads (Pure) -
Microevolution of acquired colistin resistance in Enterobacteriaceae from ICU patients receiving selective decontamination of the digestive tract
Janssen, A. B., van Hout, D., Bonten, M. J. M., Willems, R. J. L. & van Schaik, W., Nov 2020, In: The Journal of antimicrobial chemotherapy. 75, 11, p. 3135-3143 9 p.Research output: Contribution to journal › Article › Academic › peer-review
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Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli
Apr 2020, In: Nature. 580, 7802, p. 269-273 5 p.Research output: Contribution to journal › Article › Academic › peer-review
1 Citation (Scopus) -
Nonclonal Emergence of Colistin Resistance Associated with Mutations in the BasRS Two-Component System in Escherichia coli Bloodstream Isolates
Janssen, A. B., Bartholomew, T. L., Marciszewska, N. P., Bonten, M. J. M., Willems, R. J. L., Bengoechea, J. A. & van Schaik, W., 1 Mar 2020, In: mSphere. 5, 2, 13 p., e00143-20.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile1 Downloads (Pure) -
Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium
Arredondo-Alonso, S., Top, J., McNally, A., Puranen, S., Pesonen, M., Pensar, J., Marttinen, P., Braat, J. C., Rogers, M. R. C., van Schaik, W., Kaski, S., Willems, R. J. L., Corander, J. & Schürch, A. C., 11 Feb 2020, In: mBio. 11, 1, 17 p., e03284-19.Research output: Contribution to journal › Article › Academic › peer-review
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Whole Genome Sequence Analysis of the First Vancomycin-Resistant Enterococcus faecium Isolates from a Libyan Hospital in Tripoli
Ahmed, M. O., Elramalli, A. K., Baptiste, K. E., Daw, M. A., Zorgani, A., Brouwer, E., Willems, R. J. L. & Top, J., 1 Nov 2020, In: Microbial drug resistance. 26, 11, p. 1390-1398 9 p.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile11 Downloads (Pure) -
2019
Amplified fragment length polymorphism and whole genome sequencing: A comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci
Janes, V. A., Notermans, D. W., Spijkerman, I. J. B., Visser, C. E., Jakobs, M. E., Van Houdt, R., Willems, R. J. L., De Jong, M. D., Schultsz, C. & Matamoros, S., 23 Sept 2019, In: Antimicrobial Resistance and Infection Control. 8, 1, 153.Research output: Contribution to journal › Article › Academic › peer-review
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CRISPR-Cas9-mediated genome editing in vancomycin-resistant Enterococcus faecium
de Maat, V., Stege, P. B., Dedden, M., Hamer, M., van Pijkeren, J. P., Willems, R. J. L. & van Schaik, W., 1 Nov 2019, In: FEMS microbiology letters. 366, 22, fnz 256.Research output: Contribution to journal › Article › Academic › peer-review
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Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization
Bayjanov, J. R., Baan, J., Rogers, M. R. C., Troelstra, A., Willems, R. J. L. & van Schaik, W., 1 Jul 2019, In: Microbial genomics. 5, 7, p. 1-11 000277.Research output: Contribution to journal › Article › Academic › peer-review
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Low-calcium diet in mice leads to reduced gut colonization by Enterococcus faecium
Top, J., Hendrickx, A. P. A., van Ampting, M. T. J., van Limpt, K., Knol, J., van de Kamer, D., Braat, J. C., Viveen, M., Rogers, M. R., Kemperman, H., Willems, R. J. L. & Paganelli, F. L., 1 Dec 2019, In: MicrobiologyOpen. 8, 6 p., e936.Research output: Contribution to journal › Article › Academic › peer-review
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Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species
León-Sampedro, R., del Campo, R., Rodriguez-Baños, M., Lanza, V. F., Pozuelo, M. J., Francés-Cuesta, C., Tedim, A. P., Freitas, A. R., Novais, C., Peixe, L., Willems, R. J. L., Corander, J., González Candelas, F., Baquero, F. & Coque, T. M., Aug 2019, In: Environmental Microbiology. 21, 8, p. 3046-3062 17 p.Research output: Contribution to journal › Article › Academic › peer-review
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Prediction of the intestinal resistome by a three-dimensional structure-based method
Ruppé, E., Ghozlane, A., Tap, J., Pons, N., Alvarez, A. S., Maziers, N., Cuesta, T., Hernando-Amado, S., Clares, I., Martínez, J. L., Coque, T. M., Baquero, F., Lanza, V. F., Máiz, L., Goulenok, T., de Lastours, V., Amor, N., Fantin, B., Wieder, I., Andremont, A., & 16 others, 1 Jan 2019, In: Nature Microbiology. 4, 1, p. 112-123 12 p.Research output: Contribution to journal › Article › Academic › peer-review
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Roux-Y Gastric Bypass and Sleeve Gastrectomy directly change gut microbiota composition independent of surgery type
Paganelli, F. L., Luyer, M., Hazelbag, C. M., Uh, H. W., Rogers, M. R. C., Adriaans, D., Berbers, R. M., Hendrickx, A. P. A., Viveen, M. C., Groot, J. A., Bonten, M. J. M., Fluit, A. C., Willems, R. J. L. & Leavis, H. L., 29 Jul 2019, In: Scientific Reports. 9, 1, 10979.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile39 Citations (Scopus)12 Downloads (Pure) -
2018
Enterococcus faecium TIR-Domain Genes Are Part of a Gene Cluster Which Promotes Bacterial Survival in Blood
Wagner, T. M., Janice, J., Paganelli, F. L., Willems, R. J., Askarian, F., Pedersen, T., Top, J., De Haas, C., Van Strijp, J. A., Johannessen, M. & Hegstad, K., 1 Jan 2018, In: International Journal of Microbiology. 2018, 1435820.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile4 Downloads (Pure) -
Group IIA-secreted phospholipase A2 in human serum kills commensal but not clinical Enterococcus faecium isolates
Paganelli, F. L., Leavis, H. L., He, S., van Sorge, N. M., Payré, C., Lambeau, G., Willems, R. J. L. & Rooijakkers, S. H. M., 1 Aug 2018, In: Infection and Immunity. 86, 8, e00180-18.Research output: Contribution to journal › Article › Academic › peer-review
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Identification of a novel genomic island associated with vand-type vancomycin resistance in six Dutch vancomycin-resistant enterococcus faecium isolates
Top, J., Sinnige, J. C., Brouwer, E. C., Werner, G., Corander, J., Severin, J. A., Jansen, R., Bathoorn, E., Bonten, M. J. M., Rossen, J. W. A. & Willems, R. J. L., 1 Mar 2018, In: Antimicrobial Agents and Chemotherapy. 62, 3, e01793-17.Research output: Contribution to journal › Article › Academic › peer-review
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In-depth resistome analysis by targeted metagenomics
Lanza, V. F., Baquero, F., Martínez, J. L., Ramos-Ruíz, R., González-Zorn, B., Andremont, A., Sánchez-Valenzuela, A., Ehrlich, S. D., Kennedy, S., Ruppé, E., van Schaik, W., Willems, R. J., de la Cruz, F. & Coque, T. M., 1 Jan 2018, In: Microbiome. 6, 1, 11.Research output: Contribution to journal › Article › Academic › peer-review
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Intestinal carriage of ampicillin- and vancomycin-resistant Enterococcus faecium in humans, dogs and cats in the Netherlands
Van den Bunt, G., Top, J., Hordijk, J., De Greeff, S. C., Mughini-Gras, L., Corander, J., van Pelt, W., Bonten, M. J. M., Fluit, A. C. & Willems, R. J. L., 1 Mar 2018, In: Journal of Antimicrobial Chemotherapy. 73, 3, p. 607-614 8 p.Research output: Contribution to journal › Article › Academic › peer-review
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Limited influence of hospital wastewater on the microbiome and resistome of wastewater in a community sewerage system
Buelow, E., Bayjanov, J. R., Majoor, E., Willems, R. J. L., Bonten, M. J. M., Schmitt, H. & van Schaik, W., 1 Jul 2018, In: FEMS Microbiology Ecology. 94, 7, p. 1-9 9 p., fiy087.Research output: Contribution to journal › Article › Academic › peer-review
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mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
Arredondo-Alonso, S., Rogers, M. R. C., Braat, J. C., Verschuuren, T. D., Top, J., Corander, J., Willems, R. J. L. & Schürch, A. C., 1 Nov 2018, In: Microbial genomics. 4, 11, 000224.Research output: Contribution to journal › Article › Academic › peer-review
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Modelling Cryptosporidium infection in human small intestinal and lung organoids
Heo, I., Dutta, D., Schaefer, D. A., Iakobachvili, N., Artegiani, B., Sachs, N., Boonekamp, K. E., Bowden, G., Hendrickx, A. P. A., Willems, R. J. L., Peters, P. J., Riggs, M. W., O'Connor, R. & Clevers, H., 1 Jul 2018, In: Nature Microbiology. 3, 7, p. 814-823 10 p.Research output: Contribution to journal › Article › Academic › peer-review
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Primary murine mucosal response during cephalosporin-induced intestinal colonization by Enterococcus faecium
Hendrickx, A. P. A., van de Kamer, D. & Willems, R. J. L., Oct 2018, In: MicrobiologyOpen. 7, 5, 11 p., e00602.Research output: Contribution to journal › Article › Academic › peer-review
Open AccessFile