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J. Zook · SciRah

Researcher profile · Semantic Scholar

J. Zook

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J. Zook — researcher profile on SciRah

h-index: 48
Works: 169
Citations: 15K

Most-cited papers

The complete sequence of a human genome
S. Nurk, S. Koren, A. Rhie, Mikko Rautiainen +96 more
2021bioRxiv2,660 citations Open access
Semantic Scholar
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
A. Wenger, P. Peluso, W. Rowell, Pi-Chuan Chang +24 more
2019Nature Biotechnology1,596 citations Open access
Semantic Scholar
A draft human pangenome reference
Wen-Wei Liao, Mobin Asri, Jana Ebler, D. Doerr +115 more
2022bioRxiv983 citations Open access
Semantic Scholar
Complete genomic and epigenetic maps of human centromeres
Nicolas Altemose, G. Logsdon, Andrey V. Bzikadze, Pragya Sidhwani +55 more
2021bioRxiv529 citations Open access
Semantic Scholar
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness +28 more
2020Nature Biotechnology446 citations Open access
Semantic Scholar
The complete sequence of a human Y chromosome
A. Rhie, S. Nurk, Monika Cechova, S. Hoyt +83 more
2023bioRxiv443 citations Open access
Semantic Scholar
A robust benchmark for detection of germline large deletions and insertions
J. Zook, N. Hansen, N. Olson, Lesley M. Chapman +46 more
2020Nature Biotechnology377 citations Open access
Semantic Scholar
Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes
P. Krusche, L. Trigg, P. Boutros, C. Mason +13 more
2019Nature Biotechnology371 citations Open access
Semantic Scholar
A complete reference genome improves analysis of human genetic variation
S. Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche +29 more
2021bioRxiv334 citations Open access
Semantic Scholar
An open resource for accurately benchmarking small variant and reference calls
J. Zook, Jennifer McDaniel, N. Olson, Justin Wagner +10 more
2019Nature Biotechnology319 citations Open access
Semantic Scholar
Curated variation benchmarks for challenging medically-relevant autosomal genes
Justin Wagner, N. Olson, Lindsay Harris, Jennifer McDaniel +33 more
2022Nature Biotechnology214 citations Open access
Semantic Scholar
Benchmarking challenging small variants with linked and long reads
Justin Wagner, N. Olson, Lindsay Harris, Jennifer H. McDaniel +38 more
2020bioRxiv194 citations Open access
Semantic Scholar
Semi-automated assembly of high-quality diploid human reference genomes
E. Jarvis, G. Formenti, A. Rhie, A. Guarracino +79 more
2022Nature185 citations Open access
Semantic Scholar
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
N. Olson, Justin Wagner, Jennifer McDaniel, Sarah Stephens +69 more
2020bioRxiv185 citations Open access
Semantic Scholar
Variant calling and benchmarking in an era of complete human genome sequences
N. Olson, Justin Wagner, Nathan Dwarshuis, K. Miga +3 more
2023Nature reviews genetics135 citations
Semantic Scholar
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Ann M. Mc Cartney, Kishwar Shafin, Michael Alonge, Andrey V. Bzikadze +16 more
2021Nature Methods133 citations Open access
Semantic Scholar
Chromosome-scale, haplotype-resolved assembly of human genomes
Shilpa Garg, A. Fungtammasan, Andrew Carroll, Michael F. Chou +18 more
2020Nature Biotechnology124 citations Open access
Semantic Scholar
Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
J. Foox, S. Tighe, C. Nicolet, J. Zook +23 more
2021Nature Biotechnology114 citations Open access
Semantic Scholar
Recombination between heterologous human acrocentric chromosomes
A. Guarracino, S. Buonaiuto, L. G. de Lima, Tamara A. Potapova +119 more
2023bioRxiv112 citations Open access
Semantic Scholar
One 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
S. Lincoln, T. Hambuch, J. Zook, S. Bristow +22 more
2020Genetics in Medicine85 citations Open access
Semantic Scholar
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
J. Gustafson, Sophia B. Gibson, N. Damaraju, M. Zalusky +43 more
2024Genome Research81 citations Open access
Semantic Scholar
A diploid assembly-based benchmark for variants in the major histocompatibility complex
C. Chin, Justin Wagner, Q. Zeng, Erik Garrison +22 more
2019Nature Communications77 citations Open access
Semantic Scholar
A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing—Detected Variants with an Orthogonal Method in Clinical Genetic Testing
S. Lincoln, R. Truty, Chiao-Feng Lin, J. Zook +6 more
2019Journal of Molecular Diagnostics71 citations Open access
Semantic Scholar
Analysis and benchmarking of small and large genomic variants across tandem repeats
A. English, E. Dolzhenko, Helyaneh Ziaei Jam, Sean Mckenzie +10 more
2024Nature Biotechnology67 citations Open access
Semantic Scholar
Efficient chromosome-scale haplotype-resolved assembly of human genomes
S. Garg, A. Fungtammasan, Andrew Carroll, Michael F. Chou +18 more
2019bioRxiv65 citations Open access
Semantic Scholar
Highly-accurate long-read sequencing improves variant detection and assembly of a human genome
A. Wenger, P. Peluso, W. Rowell, Pi-Chuan Chang +24 more
2019bioRxiv62 citations Open access
Semantic Scholar
A robust benchmark for germline structural variant detection
J. Zook, N. Hansen, N. Olson, Lesley M. Chapman +46 more
2019bioRxiv59 citations Open access
Semantic Scholar
A complete diploid human genome benchmark for personalized genomics
Nancy F. Hansen, Nathan Dwarshuis, Hyun Joo Ji, A. Rhie +61 more
2025bioRxiv56 citations
Semantic Scholar
Assembly and annotation of an Ashkenazi human reference genome
Alaina Shumate, A. Zimin, Rachel M. Sherman, D. Puiu +6 more
2020bioRxiv54 citations Open access
Semantic Scholar
Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes
Chen-Shan Chin, S. Behera, A. Khalak, F. Sedlazeck +3 more
2023Nature Methods48 citations Open access
Semantic Scholar
Reproducible integration of multiple sequencing datasets to form high-confidence SNP, indel, and reference calls for five human genome reference materials
J. Zook, Jennifer McDaniel, H. Parikh, Haynes Heaton +8 more
2018bioRxiv48 citations Open access
Semantic Scholar
Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation
J. Gustafson, S. Gibson, N. Damaraju, M. Zalusky +43 more
2024medRxiv45 citations Open access
Semantic Scholar
Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit
Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness +26 more
2019bioRxiv44 citations Open access
Semantic Scholar
The GIAB genomic stratifications resource for human reference genomes
Nathan Dwarshuis, D. Kalra, Jennifer H. McDaniel, P. Sanio +10 more
2024Nature Communications43 citations Open access
Semantic Scholar
The Platinum Pedigree: A long-read benchmark for genetic variants
Z. Kronenberg, Cillian Nolan, D. Porubsky, T. Mokveld +30 more
2024bioRxiv41 citations Open access
Semantic Scholar
The GIAB genomic stratifications resource for human reference genomes
Nathan Dwarshuis, D. Kalra, Jennifer McDaniel, P. Sanio +10 more
2023bioRxiv40 citations Open access
Semantic Scholar
Assessing reproducibility of inherited variants detected with short-read whole genome sequencing
Bohu Pan, Luyao Ren, Vitor Onuchic, Meijian Guan +51 more
2022Genome Biology36 citations Open access
Semantic Scholar
Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes
Peter Krusche, L. Trigg, P. Boutros, Christopher E. Mason +12 more
2018bioRxiv32 citations Open access
Semantic Scholar
Publisher Correction: Modeling neural tube development by differentiation of human embryonic stem cells in a microfluidic WNT gradient
J. Zook, N. Hansen, N. Olson, Lesley M. Chapman +46 more
2020Nature Biotechnology30 citations Open access
Semantic Scholar
FixItFelix: improving genomic analysis by fixing reference errors
S. Behera, J. LeFaive, P. Orchard, M. Mahmoud +8 more
2023Genome Biology27 citations Open access
Semantic Scholar
LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads
Helyaneh Ziaei Jam, J. Zook, Sara Javadzadeh, Jonghun Park +2 more
2024Genome Biology26 citations Open access
Semantic Scholar
Recommendations 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.
E. Duncavage, J. Coleman, M. D. de Baca, Sabah Kadri +6 more
2022Journal of Molecular Diagnostics24 citations Open access
Semantic Scholar
Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes
Justin Wagner, N. Olson, Lindsay Harris, Jennifer McDaniel +33 more
2021bioRxiv23 citations Open access
Semantic Scholar
Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings.
I. Lubin, N. Aziz, L. Babb, D. Ballinger +20 more
2017Journal of Molecular Diagnostics23 citations Open access
Semantic Scholar
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair
Jennifer H. McDaniel, V. Patel, Nathan D. Olson, Hua-Jun He +81 more
2025Scientific Data22 citations Open access
Semantic Scholar
Unraveling the hidden complexity of cancer through long-read sequencing
Qiuhui Li, A. Keskus, Justin Wagner, M. Izydorczyk +6 more
2025Genome Research16 citations Open access
Semantic Scholar
A strategy for building and using a human reference pangenome
Bastien Llamas, Giuseppe Narzisi, Valerie A. Schneider, P. Audano +36 more
2019F1000Research16 citations Open access
Semantic Scholar
Tools for annotation and comparison of structural variation
F. Sedlazeck, Andi Dhroso, D. Bodian, J. Paschall +2 more
2017F1000Research16 citations Open access
Semantic Scholar
Determining Performance Metrics for Targeted Next Generation Sequencing Panels Using Reference Materials
M. Cleveland, J. Zook, M. Salit, P. Vallone
2018Journal of Molecular Diagnostics15 citations Open access
Semantic Scholar
An interlaboratory study of complex variant detection
S. Lincoln, J. Zook, S. Chowdhury, S. Mahamdallie +18 more
2017bioRxiv13 citations Open access
Semantic Scholar

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