Author

J. Kavanagh

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

Biology Disciplines

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Microbiology· 4

Signature Assays, Organisms & Methods

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Organism:human· 3 Research Focus:variant calling· 3 Research Focus:differential expression· 2 Approach:experimental assay· 2 Assay:long-read sequencing· 2 Assay:metagenomics· 2 Organism:bacteria (other)· 1 Approach:deep learning· 1

Frequent Co-Authors

D. W. Crook· 3 shared L. Barker· 3 shared N. D. Sanderson· 3 shared A. S. Walker· 2 shared D. W. Eyre· 2 shared J. Swann· 2 shared M. Andersson· 2 shared S. Hoosdally· 2 shared

Activity by Year

2019-2021 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 38 mutual co-author links

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3 shared papersMicrobiology

D. W. Crook

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Author profile →

4 papers

Recent·Most cited

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

L. P. Shaw, K. K. Chau, J. Kavanagh, M. AbuOun, E. Stubberfield, H. S. Gweon, L. Barker, G. Rodger, M. J. Bowes, A. T. M. Hubbard, H. Pickford, J. Swann, D. Gilson, R. P. Smith, S. J. Hoosdally, , REHAB consortium

The paper analyzes the pangenome dynamics of Enterobacteriaceae from environmental sources, finding that plasmids carry more AMR genes and are influenced by niche and geography rather than phylogeny.

Science Advances · Apr 9, 2021Peer-reviewedMicrobiology

Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples

T. L. Street, L. Barker, N. D. Sanderson, J. Kavanagh, S. Hoosdally, K. Cole, R. Newnham, M. Selvaratnam, M. Andersson, M. Llewelyn, J. O'Grady, D. W. Crook, D. W. Eyre

This study optimizes DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae directly from urine samples to enable culture-free whole-genome reconstruction.

Journal of Clinical Microbiology · Feb 24, 2020Peer-reviewedMicrobiology

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

N. D. Sanderson, J. Swann, L. Barker, J. Kavanagh, S. Hoosdally, D. Crook, the GonFast Investigators Group, T. L. Street, D. W. Eyre

This study develops a workflow for high-precision variant and antimicrobial resistance calling from metagenomic Nanopore sequencing of Neisseria gonorrhoeae.

bioRxiv · Feb 7, 2020Microbiology

Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples

K. Lewandowski, Y. Xu, S. T. Pullan, D. Foster, N. D. Sanderson, A. Vaughan, M. Morgan, N. Bright, J. Kavanagh, R. T. Vipond, M. W. Carroll, A. C. Marriott, K. E. Gooch, M. Andersson, K. Jeffery, , P. C. Matthews

This study uses metagenomic Nanopore sequencing to detect influenza virus in clinical respiratory samples, achieving high sensitivity and complete genome sequencing.

bioRxiv · Jun 19, 2019Microbiology