Sergio Arredondo-Alonso

Affiliations
  • Department of Biostatistics, University of Oslo, 0372 Blindern, Norway.
  • Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom.

Publications (14)

Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe.

Genome research
Avec: Gerry Tonkin-Hill , Rebecca A Gladstone , Anna K Pöntinen , Sergio Arredondo-Alonso , Stephen D Bentley , Jukka Corander

Evolutionary and functional history of the Escherichia coli K1 capsule.

Nature communications
Avec: Sergio Arredondo-Alonso , George Blundell-Hunter , Zuyi Fu , Rebecca A Gladstone , Alfred Fillol-Salom , Jessica Loraine , Elaine Cloutman-Green , Pål J Johnsen , Ørjan Samuelsen , Anna K Pöntinen , François Cléon , Susana Chavez-Bueno , Miguel A De la Cruz , Miguel A Ares , Manivanh Vongsouvath , Agnieszka Chmielarczyk , Carolyne Horner , Nigel Klein , Alan McNally , Joice N Reis , José R Penadés , Nicholas R Thomson , Jukka Corander , Peter W Taylor , Alex J McCarthy

Detecting co-selection through excess linkage disequilibrium in bacterial genomes.

NAR genomics and bioinformatics
Avec: Sudaraka Mallawaarachchi , Gerry Tonkin-Hill , Anna K Pöntinen , Jessica K Calland , Rebecca A Gladstone , Sergio Arredondo-Alonso , Neil MacAlasdair , Harry A Thorpe , Janetta Top , Samuel K Sheppard , David Balding , Nicholas J Croucher , Jukka Corander

A high-throughput multiplexing and selection strategy to complete bacterial genomes.

GigaScience
Avec: Sergio Arredondo-Alonso , Anna K Pöntinen , François Cléon , Rebecca A Gladstone , Anita C Schürch , Pål J Johnsen , Ørjan Samuelsen , Jukka Corander

Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals.

Genome medicine
Avec: Sergio Arredondo-Alonso , Janetta Top , Jukka Corander , Rob J L Willems , Anita C Schürch

PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in

Microbial genomics
Avec: Julian A Paganini , Jesse J Kerkvliet , Lisa Vader , Nienke L Plantinga , Rodrigo Meneses , Jukka Corander , Rob J L Willems , Sergio Arredondo-Alonso , Anita C Schürch

Conditionally essential genes for survival during starvation in Enterococcus faecium E745.

BMC genomics
Avec: Vincent de Maat , Sergio Arredondo-Alonso , Rob J L Willems , Willem van Schaik

Recovering

Microorganisms
Avec: Julian A Paganini , Nienke L Plantinga , Sergio Arredondo-Alonso , Rob J L Willems , Anita C Schürch

Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study.

The Lancet. Microbe
Avec: Harry A Thorpe , Maiju Pesonen , Marta Corbella , Henri Pesonen , Stefano Gaiarsa , Christine J Boinett , Gerry Tonkin-Hill , Tommi Mäklin , Anna K Pöntinen , Neil MacAlasdair , Rebecca A Gladstone , Sergio Arredondo-Alonso , Teemu Kallonen , Dorota Jamrozy , Stephanie W Lo , Chrispin Chaguza , Grace A Blackwell , Antti Honkela , Anita C Schürch , Rob J L Willems , Cristina Merla , Greta Petazzoni , Edward J Feil , Patrizia Cambieri , Nicholas R Thomson , Stephen D Bentley , Davide Sassera , Jukka Corander

Mge-cluster: a reference-free approach for typing bacterial plasmids.

NAR genomics and bioinformatics
Avec: Sergio Arredondo-Alonso , Rebecca A Gladstone , Anna K Pöntinen , João A Gama , Anita C Schürch , Val F Lanza , Pål Jarle Johnsen , Ørjan Samuelsen , Gerry Tonkin-Hill , Jukka Corander

gplas: a comprehensive tool for plasmid analysis using short-read graphs.

Bioinformatics (Oxford, England)
Avec: Sergio Arredondo-Alonso , Martin Bootsma , Yaïr Hein , Malbert R C Rogers , Jukka Corander , Rob J L Willems , Anita C Schürch

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).

The Journal of antimicrobial chemotherapy
Avec: T D Verschuuren , D van Hout , S Arredondo-Alonso , A C Fluit , E A Reuland , J Top , A C Schürch , T Bosch , M J M Bonten , J A J W Kluytmans , R J L Willems

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era.

Nature communications
Avec: Anna K Pöntinen , Janetta Top , Sergio Arredondo-Alonso , Gerry Tonkin-Hill , Ana R Freitas , Carla Novais , Rebecca A Gladstone , Maiju Pesonen , Rodrigo Meneses , Henri Pesonen , John A Lees , Dorota Jamrozy , Stephen D Bentley , Val F Lanza , Carmen Torres , Luisa Peixe , Teresa M Coque , Julian Parkhill , Anita C Schürch , Rob J L Willems , Jukka Corander

Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs.

Genome research
Avec: Juri Kuronen , Samuel T Horsfield , Anna K Pöntinen , Sudaraka Mallawaarachchi , Sergio Arredondo-Alonso , Harry Thorpe , Rebecca A Gladstone , Rob J L Willems , Stephen D Bentley , Nicholas J Croucher , Johan Pensar , John A Lees , Gerry Tonkin-Hill , Jukka Corander

Réseau de co-auteurs

Jukka Corander 11 collaborations
Rebecca A Gladstone 8 collaborations
Anna K Pöntinen 8 collaborations
Anita C Schürch 8 collaborations
Rob J L Willems 8 collaborations
Gerry Tonkin-Hill 6 collaborations
Stephen D Bentley 4 collaborations
Ørjan Samuelsen 3 collaborations
Janetta Top 3 collaborations
Pål J Johnsen 2 collaborations
François Cléon 2 collaborations
Nicholas R Thomson 2 collaborations
Sudaraka Mallawaarachchi 2 collaborations
Neil MacAlasdair 2 collaborations
Harry A Thorpe 2 collaborations
Nicholas J Croucher 2 collaborations
Julian A Paganini 2 collaborations
Nienke L Plantinga 2 collaborations
Rodrigo Meneses 2 collaborations
Maiju Pesonen 2 collaborations
Henri Pesonen 2 collaborations
Dorota Jamrozy 2 collaborations
Val F Lanza 2 collaborations
John A Lees 2 collaborations
George Blundell-Hunter 1 collaboration
Zuyi Fu 1 collaboration
Alfred Fillol-Salom 1 collaboration
Jessica Loraine 1 collaboration
Elaine Cloutman-Green 1 collaboration
Susana Chavez-Bueno 1 collaboration
Miguel A De la Cruz 1 collaboration
Miguel A Ares 1 collaboration
Manivanh Vongsouvath 1 collaboration
Agnieszka Chmielarczyk 1 collaboration
Carolyne Horner 1 collaboration
Nigel Klein 1 collaboration
Alan McNally 1 collaboration
Joice N Reis 1 collaboration
José R Penadés 1 collaboration
Peter W Taylor 1 collaboration
Alex J McCarthy 1 collaboration
Jessica K Calland 1 collaboration
Samuel K Sheppard 1 collaboration
David Balding 1 collaboration
Jesse J Kerkvliet 1 collaboration
Lisa Vader 1 collaboration
Vincent de Maat 1 collaboration
Willem van Schaik 1 collaboration
Marta Corbella 1 collaboration
Stefano Gaiarsa 1 collaboration
Christine J Boinett 1 collaboration
Tommi Mäklin 1 collaboration
Teemu Kallonen 1 collaboration
Stephanie W Lo 1 collaboration
Chrispin Chaguza 1 collaboration
Grace A Blackwell 1 collaboration
Antti Honkela 1 collaboration
Cristina Merla 1 collaboration
Greta Petazzoni 1 collaboration
Edward J Feil 1 collaboration
Patrizia Cambieri 1 collaboration
Davide Sassera 1 collaboration
João A Gama 1 collaboration
Pål Jarle Johnsen 1 collaboration
Martin Bootsma 1 collaboration
Yaïr Hein 1 collaboration
Malbert R C Rogers 1 collaboration
T D Verschuuren 1 collaboration
D van Hout 1 collaboration
S Arredondo-Alonso 1 collaboration
A C Fluit 1 collaboration
E A Reuland 1 collaboration
J Top 1 collaboration
A C Schürch 1 collaboration
T Bosch 1 collaboration
M J M Bonten 1 collaboration
J A J W Kluytmans 1 collaboration
R J L Willems 1 collaboration
Ana R Freitas 1 collaboration
Carla Novais 1 collaboration
Carmen Torres 1 collaboration
Luisa Peixe 1 collaboration
Teresa M Coque 1 collaboration
Julian Parkhill 1 collaboration
Juri Kuronen 1 collaboration
Samuel T Horsfield 1 collaboration
Harry Thorpe 1 collaboration
Johan Pensar 1 collaboration