Author

Stephen Baker

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Same name, identified by ORCID

Biology Disciplines

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Genomics· 3 Microbiology· 2

Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 5 Organism:human· 3 Organism:bacteria (other)· 2 Approach:experimental assay· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Research Focus:chromatin & epigenetic regulation· 1 Approach:deep learning· 1

Frequent Co-Authors

Kathryn E Holt· 3 shared Duy Pham ThanhiD· 2 shared Guy Thwaites· 2 shared Hao Chung TheiD· 2 shared Maia A Rabaa· 2 shared To Nguyen Thi NguyeniD· 2 shared Alan Elena· 1 shared Alejandra M Abdala· 1 shared

Activity by Year

2014-2016 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersMicrobiology

Kathryn E Holt

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection

My V.T. Phan, Pham Hong Anh, Nguyen Van Cuong, Bas B. Oude Munnink, Lia van der Hoek, Phuc Tran My, Tue Ngo Tri, Juliet E. Bryant, Stephen Baker, Guy Thwaites, Mark Woolhouse, Paul Kellam, Maia A Rabaa, Matthew L Cotten

The paper uses deep sequencing to analyze human and porcine stool samples, revealing rotavirus diversity and potential zoonotic transmission in Vietnam.

bioRxiv · Jun 14, 2016Genomics

Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate

Duy Pham Thanh, Ha Thanh Tuyen, To Nguyen Thi Nguyen, Hao Chung The, Ryan R Wick, Guy Thwaites, Stephen Baker, Kathryn E Holt

The paper identifies an inactive mcr-1 gene on a plasmid in a 2008 Vietnamese Shigella sonnei isolate, which becomes active under colistin exposure.

Journal of Antimicrobial Chemotherapy · May 30, 2016Peer-reviewedMicrobiology

Whole genome sequencing identifies independent outbreaks of Shigellosis in 2010 and 2011 in La Pampa Province, Argentina

Isabel Chinen, Marcelo Galas, Ezequiel Tuduri, Maria Rosa Viñas, Carolina Carbonari, Anabella Della Gaspera, Daniela Nápoli, David M Aanensen, Silvia Argimón, Nicholas R Thomson, Darren Hughes, Stephen Baker, Caterina Guzmán-Verri, Matthew TG Holden, Alejandra M Abdala, , Josefina Campos

The paper uses whole genome sequencing to confirm two independent Shigella sonnei outbreaks in Argentina and identifies genetic differences between the strains.

bioRxiv · Apr 28, 2016 · PreprintGenomics

South Asia as a reservoir for the global spread of ciprofloxacin resistant Shigella sonnei

Hao Chung The, Maia A Rabaa, Duy Pham Thanh, Niall De Lappe, Martin Cormican, Benjamin P Howden, Sonam Wangchuk, Ladaporn Bodhidatta, Carl Jeffries, To Nguyen Thi Nguyen, Duong Vu Thuy, Corinne N Thompson, Nguyen Phu Huong Lan, Phat Voong Vinh, Tuyen Ha Thanh, , Stephen Baker

This study identifies South Asia as the primary source of ciprofloxacin-resistant Shigella sonnei, showing a single clonal emergence event driving global spread.

bioRxiv · Feb 25, 2016Microbiology

Extensive capsule locus variation and large-scale genomic recombination within the Klebsiella pneumoniae clonal complex 258/11.

Kelly L Wyres, Claire Gorrie, David J Edwards, Heiman FL Wertheim, Li Yang Hsu, Nguyen Van Kinh, Ruth Zadoks, Stephen Baker, Kathryn E Holt

This study identifies extensive capsule locus variation and large-scale genomic recombination in K. pneumoniae CC258/11, expanding the complex to include ST395 and revealing 11 distinct cps loci.

bioRxiv · Oct 27, 2014Genomics