Author

James M. Holt

Pacific Biosciences (United States)

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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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1 Research Focus:genome assembly· 1 Research Focus:variant effect prediction· 1

Frequent Co-Authors

Christopher T. SaundersiD· 1 shared Corbin D. Jones· 1 shared Egor DolzhenkoiD· 1 shared Jeremy R. Wang· 1 shared Justin M. ZookiD· 1 shared Leonard McMillan· 1 shared Michael A. EberleiD· 1 shared Nathan D. OlsoniD· 1 shared

Activity by Year

2016-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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1 shared paperBioinformatics

Christopher T. SaundersORCID

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Author profile →

2 papers

Recent·Most cited

Aardvark: Sifting through differences in a mound of variants

James M. Holt, Christopher T. Saunders, Egor Dolzhenko, Peter Krusche, Nathan D. Olson, Justin M. Zook, Michael A. Eberle, Zev N. Kronenberg

Aardvark benchmarks genomic variant calling accuracy by comparing haplotype sequences with a basepair score, supporting multiple variant types and outperforming hap.py.

DOAJ (DOAJ: Directory of Open Access Journals) · Jun 1, 2026Peer-reviewedBioinformatics

Improved long read correction for de novo assembly using an FM-index

James M. Holt, Jeremy R. Wang, Corbin D. Jones, Leonard McMillan

The paper introduces a method to correct long read errors using an FM-index and short reads, improving de novo assembly quality.

bioRxiv · Aug 2, 2016 · PreprintBioinformatics