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J

Justin M. Zook

national institute of standards and technology

54H-index
229Paper Count
1.8WCitation Count
Published Papers 62
Publication Date
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Harmonizing standards and resources for the medical genome
errNature
IF48.5
err2026-07-01
err0
PREAI
errEuan A. Ashley; Ash A. Alizadeh; Hanae Armitage; Ami S. Bhatt; Yair Blumenfeld; Andrew Carroll; R. Martin Chavez; Petros Giannikopoulos; Megan E. Grove; Meghan C. Halley; Kiran Khush; Niall J. Lennon; Samantha Maragh; Alexander Marson; Benedict Paten; Adam M. Phillippy; Matthew H. Porteus; Heidi L. Rehm; Bradley R. Ringeisen; Julia Salzman; Valerie A. Schneider; Fritz J. Sedlazeck; Lars M. Steinmetz; Fyodor D. Urnov; Stacia K. Wyman; Justin M. Zook; Lloyd B. Minor; Jennifer A. Doudna
errShare
errSave
Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers
errCell Genomics
IF9
err2026-04-01
err0
errOAAI
errDaniels, Camille A.; Abdulkadir, Adetola A.; Cleveland, Megan H.; McDaniel, Jennifer H.; Jaspez, David; Rubio-Rodrnguez, Luis Alberto; Munoz-Barrera, Adrian; Lorenzo-Salazar, Jose Miguel; Flores, Carlos; Yoo, Byunggil; Sahraeian, Sayed Mohammad Ebrahim; Wang, Yina; Rossi, Massimiliano; Visvanath, Arun; Murray, Lisa; Chen, Wei-Ting; Catreux, Severine; Han, James; Mehio, Rami; Parnaby, Gavin; Carroll, Andrew; Chang, Pi-Chuan; Shafin, Kishwar; Cook, Daniel; Kolesnikov, Alexey; Brambrink, Lucas; Mootor, Mohammed Faizal Eeman; Patel, Yash; Yamaguchi, Takafumi N.; Boutros, Paul C.; Sienkiewicz, Karolina; Foox, Jonathan; Mason, Christopher E.; Lajoie, Bryan R.; Ruiz-Perez, Carlos A.; Kruglyak, Semyon; Zook, Justin M.; Olson, Nathan D.
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Correction: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair
errScientific Data
IF6.9
err2025-08-08
err0
errOAAI
errJennifer H. McDaniel; Vaidehi Patel; Nathan D. Olson; Hua-Jun He; Zhiyong He; Kenneth D. Cole; Alexander A. Gooden; Anthony Schmitt; Kristin Sikkink; Fritz J. Sedlazeck; Harsha Doddapaneni; Shalini N. Jhangiani; Donna M. Muzny; Marie-Claude Gingras; Heer Mehta; Sairam Behera; Luis F. Paulin; Alex R. Hastie; Hung-Chun Yu; Victor Weigman; Alison Rojas; Katie Kennedy; Jamie Remington; Isai Salas-González; Mitch Sudkamp; Kelly Wiseman; Bryan R. Lajoie; Shawn Levy; Miten Jain; Stuart Akeson; Giuseppe Narzisi; Zoe Steinsnyder; Catherine Reeves; Jennifer Shelton; Sarah B. Kingan; Christine Lambert; Primo Baybayan; Aaron M. Wenger; Ian J. McLaughlin; Aaron Adamson; Christopher Kingsley; Melanie Wescott; Young Kim; Benedict Paten; Jimin Park; Ivo Violich; Karen H. Miga; Joshua Gardner; Brandy McNulty; Gail L. Rosen; Rajiv McCoy; Francesco Brundu; Erfan Sayyari; Konrad Scheffler; Sean Truong; Severine Catreux; Lesley Chapman Hannah; Doron Lipson; Hila Benjamin; Nika Iremadze; Ilya Soifer; Gat Krieger; Stephen Eacker; Mary Wood; Erin Cross; Greg Husar; Stephen Gross; Michael Vernich; Mikhail Kolmogorov; Tanveer Ahmad; Ayse G. Keskus; Asher Bryant; Francoise Thibaud-Nissen; Jonathan Trow; Jacqueline Proszynski; Jeremy Wain Hirschberg; Krista Ryon; Christopher E. Mason; Mital S. Bhakta; J. Zachary Sanborn; Elizabeth M. Munding; Justin Wagner; Chunlin Xiao; Andrew S. Liss; Justin M. Zook
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errSave
The Platinum Pedigree: a long-read benchmark for genetic variants
errNature Methods
IF32.1
err2025-08-04
err0
errOAAI
errZev Kronenberg; Cillian Nolan; David Porubsky; Tom Mokveld; William J. Rowell; Sangjin Lee; Egor Dolzhenko; Pi-Chuan Chang; James M. Holt; Christopher T. Saunders; Nathan D. Olson; Cody J. Steely; Sean McGee; Andrea Guarracino; Nidhi Koundinya; William T. Harvey; W. Scott Watkins; Katherine M. Munson; Kendra Hoekzema; Khi Pin Chua; Xiao Chen; Cairbre Fanslow; Christine Lambert; Harriet Dashnow; Erik Garrison; Joshua D. Smith; Peter M. Lansdorp; Justin M. Zook; Andrew Carroll; Lynn B. Jorde; Deborah W. Neklason; Aaron R. Quinlan; Evan E. Eichler; Michael A. Eberle
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errSave
Interlaboratory assessment of candidate reference materials for lentiviral vector copy number and integration site measurements
errMOLECULAR THERAPY METHODS & CLINICAL DEVELOPMENT
IF4.7
err2025-06-01
err0
errOAAI
errHua-Jun He; Zhiyong He; Steven P. Lund; Laure Turner; Yongjun Fan; Yu Qiu; David C. Corney; Boro Dropulic; Rimas Orentas; Oxana Slessareva; Priscilla Welch; Katie Dungca; Ellen Stelloo; Gabrielle Dijksteel; Harma Feitsma; Sana Ahmed-Seghir; Rostyslav Makarenko; Engin Altunlu; Daniëlle Steenmans; Jan Spanholtz; Monica Raimo; Shai Senderovich; Barbara S. Paugh; Chieh-Yuan Li; Benjamin Schroeder; Alexandra S. Whale; Dilek Yener; Carole A. Foy; Shareef Nahas; Feng Tu; Michael Sheldon; Yan Ding; Jennifer Kandell; Uma Lakshmipathy; Jennifer H. McDaniel; Justin M. Zook; Sierra Miller; Samantha Maragh; Simona Patange; Mahir Mohiuddin; Alessandro Tona; Kenneth D. Cole; Sheng Lin-Gibson
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errSave
The GIAB genomic stratifications resource for human reference genomes
errNATURE COMMUNICATIONS
IF15.7
err2024-10-19
err0
errOAAI
errDwarshuis, Nathan; Kalra, Divya; McDaniel, Jennifer; Sanio, Philippe; Jerez, Pilar Alvarez; Jadhav, Bharati; Huang, Wenyu (Eddy); Mondal, Rajarshi; Busby, Ben; Olson, Nathan D.; Sedlazeck, Fritz J.; Wagner, Justin; Majidian, Sina; Zook, Justin M.
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errSave
StratoMod: predicting sequencing and variant calling errors with interpretable machine learning
errCOMMUNICATIONS BIOLOGY
IF5.1
err2024-10-13
err1
errOAAI
errDwarshuis, Nathan; Tonner, Peter; Olson, Nathan D.; Sedlazeck, Fritz J.; Wagner, Justin; Zook, Justin M.
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errSave
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
errGENOME RESEARCH
IF5.5
err2024-10-02
err7
PREAI
errGustafson, Jonas A.; Gibson, Sophia B.; Damaraju, Nikhita; Zalusky, Miranda P. G.; Hoekzema, Kendra; Twesigomwe, David; Yang, Lei; Snead, Anthony A.; Richmond, Phillip A.; De Coster, Wouter; Olson, Nathan D.; Guarracino, Andrea; Li, Qiuhui; Miller, Angela L.; Goffena, Joy; Anderson, Zachary B.; Storz, Sophie H. R.; Ward, Sydney A.; Sinha, Maisha; Gonzaga-Jauregui, Claudia; Clarke, Wayne E.; Basile, Anna O.; Corvelo, Andre; Reeves, Catherine; Helland, Adrienne; Musunuri, Rajeeva Lochan; Revsine, Mahler; Patterson, Karynne E.; Paschal, Cate R.; Zakarian, Christina; Goodwin, Sara; Jensen, Tanner D.; Robb, Esther; McCombie, William Richard; Sedlazeck, Fritz J.; Zook, Justin M.; Montgomery, Stephen B.; Garrison, Erik; Kolmogorov, Mikhail; Schatz, Michael C.; McLaughlin Jr, Richard N.; Dashnow, Harriet; Zody, Michael C.; Loose, Matt; Jain, Miten; Eichler, Evan E.; Miller, Danny E.
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errSave
Jointly benchmarking small and structural variant calls with vcfdist
errGENOME BIOLOGY
IF9.4
err2024-10-02
err0
errOAAI
errDunn, Tim; Zook, Justin M.; Holt, James M.; Narayanasamy, Satish
errShare
errSave
LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads
errGENOME BIOLOGY
IF9.4
err2024-07-04
err3
errOAAI
errJam, Helyaneh Ziaei; Zook, Justin M.; Javadzadeh, Sara; Park, Jonghun; Sehgal, Aarushi; Gymrek, Melissa
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errSave
Analysis and benchmarking of small and large genomic variants across tandem repeats
errNATURE BIOTECHNOLOGY
IF41.7
err2024-04-26
err5
PREAI
errEnglish, Adam C.; Dolzhenko, Egor; Jam, Helyaneh Ziaei; Mckenzie, Sean K.; Olson, Nathan D.; De Coster, Wouter; Park, Jonghun; Gu, Bida; Wagner, Justin; Eberle, Michael A.; Gymrek, Melissa; Chaisson, Mark J. P.; Zook, Justin M.; Sedlazeck, Fritz J.
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errSave
Continued analysis of extensive data towards Genome in a Bottle benchmarks for a new tumor normal pair
errCANCER RESEARCH
IF16.6
err2024-03-22
err0
PREAI
errWagner, Justin; McDaniel, Jennifer; Rosen, Gail L.; Olson, Nathan D.; Patel, Vaidehi; Xiao, Chunlin; Liss, Andrew; Zook, Justin
errShare
errSave
Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes
errNATURE METHODS
IF32.1
err2023-06-26
err11
errOAAI
errChin, Chen-Shan; Behera, Sairam; Khalak, Asif; Sedlazeck, Fritz J.; Sudmant, Peter H.; Wagner, Justin; Zook, Justin M.
errShare
errSave
Pangenome graph construction from genome alignments with Minigraph-Cactus
errNATURE BIOTECHNOLOGY
IF41.7
err2023-05-10
err49
errOAAI
errHickey, Glenn; Monlong, Jean; Ebler, Jana; Novak, Adam M.; Eizenga, Jordan M.; Gao, Yan; Marschall, Tobias; Li, Heng; Paten, Benedict; Abel, Haley J.; Antonacci-Fulton, Lucinda L.; Asri, Mobin; Baid, Gunjan; Baker, Carl A.; Belyaeva, Anastasiya; Billis, Konstantinos; Bourque, Guillaume; Buonaiuto, Silvia; Carroll, Andrew; Chaisson, Mark J. P.; Chang, Pi-Chuan; Chang, Xian H.; Cheng, Haoyu; Chu, Justin; Cody, Sarah; Colonna, Vincenza; Cook, Daniel E.; Cook-Deegan, Robert M.; Cornejo, Omar E.; Diekhans, Mark; Doerr, Daniel; Ebert, Peter; Ebler, Jana; Eichler, Evan E.; Eizenga, Jordan M.; Fairley, Susan; Fedrigo, Olivier; Felsenfeld, Adam L.; Feng, Xiaowen; Fischer, Christian; Flicek, Paul; Formenti, Giulio; Frankish, Adam; Fulton, Robert S.; Gao, Yan; Garg, Shilpa; Garrison, Erik; Garrison, Nanibaa' A.; Giron, Carlos Garcia; Green, Richard E.; Groza, Cristian; Guarracino, Andrea; Haggerty, Leanne; Hall, Ira M.; Harvey, William T.; Haukness, Marina; Haussler, David; Heumos, Simon; Hickey, Glenn; Hoekzema, Kendra; Hourlier, Thibaut; Howe, Kerstin; Jain, Miten; Jarvis, Erich D.; Ji, Hanlee P.; Kenny, Eimear E.; Koenig, Barbara A.; Kolesnikov, Alexey; Korbel, Jan O.; Kordosky, Jennifer; Koren, Sergey; Lee, HoJoon; Lewis, Alexandra P.; Liao, Wen-Wei; Lu, Shuangjia; Lu, Tsung-Yu; Lucas, Julian K.; Hugo, Magalhaes; Santiago, Marco-Sola; Marijon, Pierre; Markello, Charles; Marschall, Tobias; Martin, Fergal J.; McCartney, Ann; McDaniel, Jennifer; Miga, Karen H.; Mitchell, Matthew W.; Monlong, Jean; Mountcastle, Jacquelyn; Munson, Katherine M.; Mwaniki, Moses Njagi; Nattestad, Maria; Novak, Adam M.; Nurk, Sergey; Olsen, Hugh E.; Olson, Nathan D.; Pesout, Trevor; Phillippy, Adam M.; Popejoy, Alice B.; Porubsky, David; Prins, Pjotr; Puiu, Daniela; Rautiainen, Mikko; Regier, Allison A.; Rhie, Arang; Sacco, Samuel; Sanders, Ashley D.; Schneider, Valerie A.; Schultz, Baergen, I; Shafin, Kishwar; Sibbesen, Jonas A.; Siren, Jouni; Smith, Michael W.; Sofia, Heidi J.; Abou Tayoun, Ahmad N.; Thibaud-Nissen, Francoise; Tomlinson, Chad; Tricomi, Francesca Floriana; Villani, Flavia; Vollger, Mitchell R.; Wagner, Justin; Walenz, Brian; Wang, Ting; Wood, Jonathan M. D.; Zimin, Aleksey, V; Zook, Justin M.
errShare
errSave
Variant calling and benchmarking in an era of complete human genome sequences
errNATURE REVIEWS GENETICS
IF52
err2023-04-14
err34
PREAI
errOlson, Nathan D.; Wagner, Justin; Dwarshuis, Nathan; Miga, Karen H.; Sedlazeck, Fritz J.; Salit, Marc; Zook, Justin M.
errShare
errSave
Sequencing a new broadly-consented tumor/normal cell line for a Genome in a Bottle Benchmark
errCANCER RESEARCH
IF16.6
err2023-04-04
err0
PREAI
errRosen, Gail; Wagner, Justin; Liss, Andrew; Zook, Justin
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errSave
FixItFelix: improving genomic analysis by fixing reference errors
errGENOME BIOLOGY
IF9.4
err2023-02-21
err6
errOAAI
errBehera, Sairam; LeFaive, Jonathon; Orchard, Peter; Mahmoud, Medhat; Paulin, Luis F.; Farek, Jesse; Soto, Daniela C.; Parker, Stephen C. J.; Smith, Albert V.; Dennis, Megan Y.; Zook, Justin M.; Sedlazeck, Fritz J.
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errSave
Recommendations for the Use of in Silico Approaches for Next-Generation Sequencing Bioinformatic Pipeline Validation
errJOURNAL OF MOLECULAR DIAGNOSTICS
IF3.4
err2023-01-01
err12
errOAAI
errDuncavage, Eric J.; Coleman, Joshua F.; Baca, Monica E. de; Kadri, Sabah; Leon, Annette; Routbort, Mark; Roy, Somak; Suarez, Carlos J.; Vanderbilt, Chad; Zook, Justin M.
errShare
errSave
Benchmarking challenging small variants with linked and long reads
errCELL GENOMICS
IF9
err2022-05-01
err51
errOAAI
errWagner, Justin; Olson, Nathan D.; Harris, Lindsay; Khan, Ziad; Farek, Jesse; Mahmoud, Medhat; Stankovic, Ana; Kovacevic, Vladimir; Yoo, Byunggil; Miller, Neil; Rosenfeld, Jeffrey A.; Ni, Bohan; Zarate, Samantha; Kirsche, Melanie; Aganezov, Sergey; Schatz, Michael C.; Narzisi, Giuseppe; Byrska-Bishop, Marta; Clarke, Wayne; Evani, Uday S.; Markello, Charles; Shafin, Kishwar; Zhou, Xin; Sidow, Arend; Bansal, Vikas; Ebert, Peter; Marschall, Tobias; Lansdorp, Peter; Hanlon, Vincent; Mattsson, Carl-Adam; Barrio, Alvaro Martinez; Fiddes, Ian T.; Xiao, Chunlin; Fungtammasan, Arkarachai; Chin, Chen-Shan; Wenger, Aaron M.; Rowell, William J.; Sedlazeck, Fritz J.; Carroll, Andrew; Salit, Marc; Zook, Justin M.
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errSave
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
errNATURE METHODS
IF32.1
err2022-03-31
err48
errOAAI
errCartney, Ann M. Mc; Shafin, Kishwar; Alonge, Michael; Bzikadze, Andrey, V; Formenti, Giulio; Fungtammasan, Arkarachai; Howe, Kerstin; Jain, Chirag; Koren, Sergey; Logsdon, Glennis A.; Miga, Karen H.; Mikheenko, Alla; Paten, Benedict; Shumate, Alaina; Soto, Daniela C.; Sovic, Ivan; Wood, Jonathan Md; Zook, Justin M.; Phillippy, Adam M.; Rhie, Arang
errShare
errSave

Research Directions

No research directions
Co-authors
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