Author

James Qu

Broad Institute

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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Genomics· 4 Epidemiology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Assay:whole-genome sequencing· 4 Research Focus:phylogenetics / evolution· 3 Organism:human· 2 Research Focus:variant calling· 2 Organism:virus· 2 Assay:metagenomics· 1

Frequent Co-Authors

Andreas GnirkeiD· 3 shared Christian B. Matranga· 3 shared Daniel J. ParkiD· 3 shared Hayden C. MetskyiD· 3 shared Pardis Christine SabetiiD· 3 shared Sandra SmoleiD· 3 shared Scott HenniganiD· 3 shared Shirlee WohliD· 3 shared

Activity by Year

2017-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersGenomics

Andreas GnirkeORCID

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Author profile →

5 papers

Recent·Most cited

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

Rauf Salamzade, Abigail L. Manson, Bruce J. Walker, Thea Brennan-Krohn, Colin J. Worby, Peijun Ma, Lorrie L. He, Terrance Shea, James Qu, Sinéad B. Chapman, Whitney Howe, Sarah Young, Jenna I. Wurster, Mary Louise Delaney, Sanjat Kanjilal, , Ashlee M. Earl

The paper develops a method to trace horizontal gene transfer and persistence of carbapenem resistance genes across bacterial species using genomic data from clinical isolates.

Genome Medicine · Apr 4, 2022Peer-reviewedGenomics

Co-circulating mumps lineages at multiple geographic scales

Shirlee Wohl, Hayden C. Metsky, Stephen F. Schaffner, Anne L Piantadosi, Meagan Burns, Joseph A. Lewnard, Bridget Chak, Lydia Andreyevna Krasilnikova, Katherine J. Siddle, Christian B. Matranga, Bettina Bankamp, Scott Hennigan, Brandon Sabina, Elizabeth H. Byrne, Rebecca J. McNall, , Pardis Christine Sabeti

The paper analyzes mumps virus circulation in the US using genomic data to show multiple co-circulating lineages and transmission patterns, but finds no evidence of vaccine escape variants.

PLoS Biology · Feb 11, 2020Peer-reviewedGenomics

Capturing diverse microbial sequence with comprehensive and scalable probe design

Hayden C. Metsky, Katherine J. Siddle, Adrianne D. Gladden, James Qu, David K. Yang, Patrick Brehio, Andrew Goldfarb, Anne L Piantadosi, Shirlee Wohl, Amber Carter, Aaron E. Lin, Kayla G. Barnes, Damien C. Tully, Björn Corleis, Scott Hennigan, , Christian B. Matranga

The paper introduces CATCH, a method for designing compact and scalable probe sets to enhance metagenomic sequencing sensitivity, demonstrating improved viral genome recovery and diversity preservation.

Nature Biotechnology · Feb 1, 2019Peer-reviewedGenomics

Genome sequencing reveals Zika virus diversity and spread in the Americas

Hayden C. Metsky, Christian B. Matranga, Shirlee Wohl, Stephen F. Schaffner, Catherine A. Freije, Sarah M. Winnicki, Kendra L. West, James Qu, Mary Lynn Baniecki, Adrianne D. Gladden, Aaron E. Lin, Christopher H. Tomkins-Tinch, Simon H. Ye, Daniel J. Park, Cynthia Y. Luo, , Pardis Christine Sabeti

This study sequenced 110 Zika virus genomes from 10 countries, revealing rapid expansion in Brazil, multiple introductions into other regions, and undetected circulation before confirmed cases.

Nature · May 23, 2017Peer-reviewedGenomics

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic.

Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J Tatem, Guy Baele, Nuno Faria, Daniel Park, Jason Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah Caddy, Matt Cotten, Jonathan Dambrozio, Simon Dellicour, , Georgios

This study analyzes 1600 Ebola virus genomes to show viral spread followed a gravity model, with cross-border transmission before border closures contributing to an international epidemic.

Nature · Apr 12, 2017Peer-reviewedEpidemiology