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Justin Zook (Fed)

Co-Leader, Biomarker and Genomic Sciences Group

Dr. Justin Zook is co-leading the Genome in a Bottle Consortium’s work developing authoritatively characterized human genomes to benchmark sequencing methods. He developed methods to compare and integrate whole genome DNA sequencing data from multiple platforms and sequencing runs to characterize the first whole human genome Reference Materials.  He is now leading the GIAB Analysis Team work combining short, linked, and long read sequencing technologies to characterize structural variation and challenging regions of the genome.  He co-led the variants team in the Telomere-to-Telomere Consortium demonstrating the utility of the first complete human genome. He was an Informatics Representative to the Association for Molecular Pathology Clinical Practice Committee, and he chaired the Global Alliance for Genomics and Health Benchmarking Team, which published best practices for benchmarking genome sequencing results in 2019. He has co-authored >60 papers, including in Science, Nature Biotechnology, Nature Methods, JAMA, and Cell Genomics, and he wrote a blog about the inspiration for his NIST work.  

Research Opportunities

NIST-NRC Postdoctoral Fellowship: 2-year fellowship at NIST, US citizens only, ~$72,000 salary plus benefits, relocation expenses included, application deadlines are Feb. 1 and Aug. 1, requires 10 page research proposal, contact me if interested in writing a proposal on a bioinformatics genomics research project. We have opportunities posted for metrology in Cancer GenomicsDiploid AssemblyEpigenomics and TranscriptomicsBiological Data Science/Machine Learning, and Precision Medicine.

For additional job opportunities in genome bioinformatics, including for non-US citizens, contact me at my email address in the panel to the right.


    Department of Commerce Gold Award
    Presidential Early Career Award for Scientists and Engineers (PECASE)
    NIST Judson C. French Award
    Council for Chemical Research Rising Star Award
    NIST/NRC Postdoctoral Research Fellowship
    NSF Graduate Research Fellowship


    FixItFelix: improving genomic analysis by fixing reference errors

    Sairam Behera, Jonathan LeFaive, Peter Orchard, Justin Zook, Fritz Sedlazeck
    The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions

    Semi-automated assembly of high-quality diploid human reference genomes

    Erich Jarvis, Giulio Formenti, Jennifer McDaniel, Nathanael David Olson, Justin Wagner, Justin Zook, Kerstin Howe, Karen Miga
    The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it

    Benchmarking challenging small variants with linked and long reads

    Justin Wagner, Nathanael David Olson, Lindsay Harris, Marc L. Salit, Fritz Sedlazeck, Chunlin Xiao, Justin Zook
    Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use

    Complete genomic and epigenetic maps of human centromeres

    Nicolas Altemose, Glennis Logsdon, Andrey Bzikadze, Pragya Sidhwani, Sasha Langley, Gina Caldas, Justin Zook, Ivan Alexandrov, Karen Miga
    Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their

    A complete reference genome improves analysis of human genetic variation

    Sergey Aganezov, Stephanie Yan, Daniela Soto, Melanie Kirsche, Samantha Zarate, Justin Wagner, Jennifer McDaniel, Nathanael David Olson, Rajiv McCoy, Megan Dennis, Justin Zook, Michael Schatz
    Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and
    Created September 24, 2019, Updated December 8, 2022