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Author Details

Justin M Zook
National Institute of Standards and Technology
2005
60
30
PMIDPaper TitleJournal TitlePublished Year
36244574Recommendations for the Use of in Silico Approaches for Next-Generation Sequencing Bioinformatic Pipeline Validation: A Joint Report of the Association for Molecular Pathology, Association for Pathology Informatics, and College of American Pathologists.J Mol Diagn2023
37961319Benchmarking of small and large variants across tandem repeats.bioRxiv2023
37612512The complete sequence of a human Y chromosome.Nature2023
37059810Variant calling and benchmarking in an era of complete human genome sequences.Nat Rev Genet2023
37365340Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes.Nat Methods2023
36810122FixItFelix: improving genomic analysis by fixing reference errors.Genome Biol2023
34980216Assessing reproducibility of inherited variants detected with short-read whole genome sequencing.Genome Biol2022
35720974PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.Cell Genom2022
35361931Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.Nat Methods2022
35357935A complete reference genome improves analysis of human genetic variation.Science2022
35132260Curated variation benchmarks for challenging medically relevant autosomal genes.Nat Biotechnol2022
33288905Chromosome-scale, haplotype-resolved assembly of human genomes.Nat Biotechnol2021
34635840Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.Nat Biotechnol2021
34504351Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.Nat Biotechnol2021
34007000One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation.Genet Med2021
34283192Challenges of Accuracy in Germline Clinical Sequencing Data.JAMA2021
32487205Assembly and annotation of an Ashkenazi human reference genome.Genome Biol2020
32686750Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.Nat Biotechnol2020
32699374Author Correction: A robust benchmark for detection of germline large deletions and insertions.Nat Biotechnol2020
32541955A robust benchmark for detection of germline large deletions and insertions.Nat Biotechnol2020
32559231A crowdsourced set of curated structural variants for the human genome.PLoS Comput Biol2020
30610921A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing.J Mol Diagn2019
31406327Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.Nat Biotechnol2019
31201313High-coverage, long-read sequencing of Han Chinese trio reference samples.Sci Data2019
30899106Author Correction: Best practices for benchmarking germline small-variant calls in human genomes.Nat Biotechnol2019
30864325CrowdVariant: a crowdsourcing approach to classify copy number variants.Pac Symp Biocomput2019
30858580Best practices for benchmarking germline small-variant calls in human genomes.Nat Biotechnol2019
30936564An open resource for accurately benchmarking small variant and reference calls.Nat Biotechnol2019
29959024Determining Performance Metrics for Targeted Next-Generation Sequencing Panels Using Reference Materials.J Mol Diagn2018
28714986Genome-wide reconstruction of complex structural variants using read clouds.Nat Methods2017
28315672Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings.J Mol Diagn2017
29123647Tools for annotation and comparison of structural variation.F1000Res2017
28924496Challenging a bioinformatic tool's ability to detect microbial contaminants using <i>in silico</i> whole genome sequencing data.PeerJ2017
27099173A research roadmap for next-generation sequencing informatics.Sci Transl Med2016
27271295Extensive sequencing of seven human genomes to characterize benchmark reference materials.Sci Data2016
27578503Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships.Ann Lab Med2016
26935931PEPR: pipelines for evaluating prokaryotic references.Anal Bioanal Chem2016
26772178svclassify: a method to establish benchmark structural variant calls.BMC Genomics2016
26932475Medical implications of technical accuracy in genome sequencing.Genome Med2016
25711446An analytical framework for optimizing variant discovery from personal genomes.Nat Commun2015
26269718Achieving high-sensitivity for clinical applications using augmented exome sequencing.Genome Med2015
26286809svviz: a read viewer for validating structural variants.Bioinformatics2015
27135909Advancing Benchmarks for Genome Sequencing.Cell Syst2015
27077030International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons.Biomol Detect Quantif2015
26154004Good laboratory practice for clinical next-generation sequencing informatics pipelines.Nat Biotechnol2015
26217378Best practices for evaluating single nucleotide variant calling methods for microbial genomics.Front Genet2015
24531798Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.Nat Biotechnol2014
22859977Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing.PLoS One2012
23138292Assuring the quality of next-generation sequencing in clinical laboratory practice.Nat Biotechnol2012
21142841Stable nanoparticle aggregates/agglomerates of different sizes and the effect of their size on hemolytic cytotoxicity.Nanotoxicology2011
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Collaborators

Marc Salit
Stanford University
Co-authored papers 27
Fritz J Sedlazeck
Baylor College of Medicine
Co-authored papers 17
Nathan D Olson
National Institute of Standards and Technology
Co-authored papers 16
Chunlin Xiao
Chongqing Aier Eye Hospital
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Christopher E Mason
Feil Family Brain and Mind Research Institute.
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Stanford University
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Rebecca Truty
Invitae Corporation
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DNAnexus Inc.
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Birgit Funke
Partners Healthcare Center for Personalized Genetic Medicine
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Mark J P Chaisson
University of Southern California
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Heidi L Rehm
The Broad Institute of MIT and Harvard
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Noah Alexander
David Geffen School of Medicine, university of california los angeles
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Joyce Lee
Co-authored papers 4
Paul C Boutros
University of California los angeles
Co-authored papers 4
Arend Sidow
Co-authored papers 4
Zivana Tezak
Center for Devices and Radiological Health
Co-authored papers 4
Benedict Paten
UC Santa Cruz Genomics Institute, University of California
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Len Trigg
Co-authored papers 4
Nancy F Hansen
National Human Genome Research Institute, National Institutes of Health
Co-authored papers 4
Ira M Lubin
Centers for Disease Control and Prevention
Co-authored papers 3
Euan A Ashley
Stanford University
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Release 1.2