The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection
Chaguza, Chrispin, Pöntinen, Anna K, Top, Janetta, Arredondo-Alonso, Sergio, Freitas, Ana R, Novais, Carla, Torres, Carmen, Bentley, Stephen D, Peixe, Luisa, Coque, Teresa M, Willems, Rob J L, Corander, Jukka
Published in Microbiology spectrum (12.12.2023)
Published in Microbiology spectrum (12.12.2023)
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Journal Article
Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data
Paganini, Julian A, Plantinga, Nienke L, Arredondo-Alonso, Sergio, Willems, Rob J L, Schürch, Anita C
Published in Microorganisms (Basel) (28.07.2021)
Published in Microorganisms (Basel) (28.07.2021)
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Journal Article
On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data
Arredondo-Alonso, Sergio, Willems, Rob J, van Schaik, Willem, Schürch, Anita C
Published in Microbial genomics (01.10.2017)
Published in Microbial genomics (01.10.2017)
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Journal Article
Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era
Pöntinen, Anna K., Top, Janetta, Arredondo-Alonso, Sergio, Tonkin-Hill, Gerry, Freitas, Ana R., Novais, Carla, Gladstone, Rebecca A., Pesonen, Maiju, Meneses, Rodrigo, Pesonen, Henri, Lees, John A., Jamrozy, Dorota, Bentley, Stephen D., Lanza, Val F., Torres, Carmen, Peixe, Luisa, Coque, Teresa M., Parkhill, Julian, Schürch, Anita C., Willems, Rob J. L., Corander, Jukka
Published in Nature communications (09.03.2021)
Published in Nature communications (09.03.2021)
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Journal Article
Conditionally essential genes for survival during starvation in Enterococcus faecium E745
de Maat, Vincent, Arredondo-Alonso, Sergio, Willems, Rob J L, van Schaik, Willem
Published in BMC genomics (18.08.2020)
Published in BMC genomics (18.08.2020)
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Journal Article
mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
Arredondo-Alonso, Sergio, Rogers, Malbert R C, Braat, Johanna C, Verschuuren, Tess D, Top, Janetta, Corander, Jukka, Willems, Rob J L, Schürch, Anita C
Published in Microbial genomics (01.11.2018)
Published in Microbial genomics (01.11.2018)
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Journal Article
Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals
Arredondo-Alonso, Sergio, Top, Janetta, Corander, Jukka, Willems, Rob J L, Schürch, Anita C
Published in Genome medicine (20.01.2021)
Published in Genome medicine (20.01.2021)
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Journal Article
Evolutionary and functional history of the Escherichia coli K1 capsule
Arredondo-Alonso, Sergio, Blundell-Hunter, George, Fu, Zuyi, Gladstone, Rebecca A., Fillol-Salom, Alfred, Loraine, Jessica, Cloutman-Green, Elaine, Johnsen, Pål J., Samuelsen, Ørjan, Pöntinen, Anna K., Cléon, François, Chavez-Bueno, Susana, De la Cruz, Miguel A., Ares, Miguel A., Vongsouvath, Manivanh, Chmielarczyk, Agnieszka, Horner, Carolyne, Klein, Nigel, McNally, Alan, Reis, Joice N., Penadés, José R., Thomson, Nicholas R., Corander, Jukka, Taylor, Peter W., McCarthy, Alex J.
Published in Nature communications (15.06.2023)
Published in Nature communications (15.06.2023)
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Journal Article
A high-throughput multiplexing and selection strategy to complete bacterial genomes
Arredondo-Alonso, Sergio, Pöntinen, Anna K, Cléon, François, Gladstone, Rebecca A, Schürch, Anita C, Johnsen, Pål J, Samuelsen, Ørjan, Corander, Jukka
Published in Gigascience (09.12.2021)
Published in Gigascience (09.12.2021)
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Journal Article
Mge-cluster: a reference-free approach for typing bacterial plasmids
Arredondo-Alonso, Sergio, Gladstone, Rebecca A, Pöntinen, Anna K, Gama, João A, Schürch, Anita C, Lanza, Val F, Johnsen, Pål Jarle, Samuelsen, Ørjan, Tonkin-Hill, Gerry, Corander, Jukka
Published in NAR genomics and bioinformatics (01.09.2023)
Published in NAR genomics and bioinformatics (01.09.2023)
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Journal Article
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
Published in mBio (11.02.2020)
Published in mBio (11.02.2020)
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Journal Article
Functional characterization of a gene cluster responsible for inositol catabolism associated with hospital-adapted isolates of Enterococcus faecium
Top, Janetta, Baan, Jery, Bisschop, Adinda, Arredondo-Alonso, Sergio, van Schaik, Willem, Willems, Rob J L
Published in Microbiology (Society for General Microbiology) (01.09.2021)
Published in Microbiology (Society for General Microbiology) (01.09.2021)
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Journal Article
gplas: a comprehensive tool for plasmid analysis using short-read graphs
Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R C, Corander, Jukka, Willems, Rob J L, Schürch, Anita C
Published in Bioinformatics (01.06.2020)
Published in Bioinformatics (01.06.2020)
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Journal Article
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
Kuronen, Juri, Horsfield, Samuel T, Pöntinen, Anna K, Mallawaarachchi, Sudaraka, Arredondo-Alonso, Sergio, Thorpe, Harry, Gladstone, Rebecca A, Willems, Rob J L, Bentley, Stephen D, Croucher, Nicholas J, Pensar, Johan, Lees, John A, Tonkin-Hill, Gerry, Corander, Jukka
Published in Genome research (01.07.2024)
Published in Genome research (01.07.2024)
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Journal Article
Evolutionary and functional history of the Escherichia coli K1 capsule
Alonso, Sergio Arredondo, Blundell-Hunter, George, Fu, Zuyi, Gladstone, Rebecca Ashley, Fillol-Salom, Alfred, Loraine, Jessica, Cloutman-Green, Elaine, Johnsen, Pål Jarle, Samuelsen, Ørjan, Pöntinen, Anna Kaarina, Cleon, Francois Pierre Alexandre, Chavez-Bueno, Susana, De la Cruz, Miguel A, Ares, Miguel A, Vongsouvath, Manivanh, Chmielarczyk, Agnieszka, Horner, Carolyne, Klein, Nigel, McNally, Alan, Reis, Joice N, Penadés, José R, Thomson, Nicholas R, Corander, Jukka, Taylor, Peter W, McCarthy, Alex J
Published in Nature communications (2023)
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Published in Nature communications (2023)
Journal Article
A high-throughput multiplexing and selection strategy to complete bacterial genomes
Alonso, Sergio Arredondo, Pöntinen, Anna K, Cleon, Francois Pierre Alexandre, Gladstone, Rebecca Ashley, Schürch, Anita C, Johnsen, Pål Jarle, Samuelsen, Ørjan, Corander, Jukka
Published in Gigascience (2021)
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Published in Gigascience (2021)
Journal Article
Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium
Top, Janetta, Arredondo-Alonso, Sergio, Schürch, Anita C, Puranen, Santeri, Pesonen, Maiju, Pensar, Johan, Willems, Rob J L, Corander, Jukka
Published in Microbial genomics (01.12.2020)
Published in Microbial genomics (01.12.2020)
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Journal Article
Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study
Thorpe, Harry A, Pesonen, Maiju, Corbella, Marta, Pesonen, Henri, Gaiarsa, Stefano, Boinett, Christine J, Tonkin-Hill, Gerry, Mäklin, Tommi, Pöntinen, Anna K, MacAlasdair, Neil, Gladstone, Rebecca A, Arredondo-Alonso, Sergio, Kallonen, Teemu, Jamrozy, Dorota, Lo, Stephanie W, Chaguza, Chrispin, Blackwell, Grace A, Honkela, Antti, Schürch, Anita C, Willems, Rob J L, Merla, Cristina, Petazzoni, Greta, Feil, Edward J, Cambieri, Patrizia, Thomson, Nicholas R, Bentley, Stephen D, Sassera, Davide, Corander, Jukka
Published in The Lancet. Microbe (01.10.2024)
Published in The Lancet. Microbe (01.10.2024)
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