Zobrazeno 1 - 10
of 122
pro vyhledávání: '"Justin M Zook"'
Autor:
Lesley M Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M Watson, Christos Proukakis, Wayne E Clarke, Naoki Nariai, Eric Dawson, Garan Jones, Daniel Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza E Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M Wenger, Marc Salit, Justin M Zook
Publikováno v:
PLoS Computational Biology, Vol 16, Iss 6, p e1007933 (2020)
A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is more c
Externí odkaz:
https://doaj.org/article/b08f9ccca37e4727afc897d6fa521024
Autor:
Nathan Dwarshuis, Divya Kalra, Jennifer McDaniel, Philippe Sanio, Pilar Alvarez Jerez, Bharati Jadhav, Wenyu (Eddy) Huang, Rajarshi Mondal, Ben Busby, Nathan D. Olson, Fritz J. Sedlazeck, Justin Wagner, Sina Majidian, Justin M. Zook
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-13 (2024)
Abstract Despite the growing variety of sequencing and variant-calling tools, no workflow performs equally well across the entire human genome. Understanding context-dependent performance is critical for enabling researchers, clinicians, and develope
Externí odkaz:
https://doaj.org/article/cea87d7d5cfe495988b6700aa70955a2
Autor:
Nathan Dwarshuis, Peter Tonner, Nathan D. Olson, Fritz J. Sedlazeck, Justin Wagner, Justin M. Zook
Publikováno v:
Communications Biology, Vol 7, Iss 1, Pp 1-14 (2024)
Abstract Despite the variety in sequencing platforms, mappers, and variant callers, no single pipeline is optimal across the entire human genome. Therefore, developers, clinicians, and researchers need to make tradeoffs when designing pipelines for t
Externí odkaz:
https://doaj.org/article/3d99428358e546d89f6f8424db3c934d
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-19 (2024)
Abstract In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. First,
Externí odkaz:
https://doaj.org/article/44e1ab55a0da4f72b7c6fb634efec6fa
Autor:
Helyaneh Ziaei Jam, Justin M. Zook, Sara Javadzadeh, Jonghun Park, Aarushi Sehgal, Melissa Gymrek
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-12 (2024)
Abstract Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve tandem repeat analysis
Externí odkaz:
https://doaj.org/article/8a8e020eea6b4c08afb2b6b6214b891d
Autor:
Nathan eOlson, Steven P. Lund, Rebecca E. Colman, Jeffrey T Foster, Jason W Sahl, James M Schupp, Paul eKeim, Jayne B Morrow, Marc L Salit, Justin M Zook
Publikováno v:
Frontiers in Genetics, Vol 6 (2015)
Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequencing
Externí odkaz:
https://doaj.org/article/84c2cbef39ef4b7c8c2ac40928067a76
Publikováno v:
PLoS ONE, Vol 7, Iss 7, p e41356 (2012)
While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cau
Externí odkaz:
https://doaj.org/article/a35ecb62c8ca4ec2a8ace6b4145a01de
Autor:
Sairam Behera, Jonathon LeFaive, Peter Orchard, Medhat Mahmoud, Luis F. Paulin, Jesse Farek, Daniela C. Soto, Stephen C. J. Parker, Albert V. Smith, Megan Y. Dennis, Justin M. Zook, Fritz J. Sedlazeck
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-21 (2023)
Abstract 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. These errors impact the variant calling of 33 protein-coding genes, including 1
Externí odkaz:
https://doaj.org/article/ddf9214ce77c4538831718d8d9803918
Autor:
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, Benedict Paten
Publikováno v:
Nature. 617:312-324
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce56c54eebc15371aabecb5595f996d0
https://doi.org/10.1038/s41586-023-05896-x
https://doi.org/10.1038/s41586-023-05896-x
Autor:
Eric J. Duncavage, Joshua F. Coleman, Monica E. de Baca, Sabah Kadri, Annette Leon, Mark Routbort, Somak Roy, Carlos J. Suarez, Chad Vanderbilt, Justin M. Zook
Publikováno v:
The Journal of Molecular Diagnostics. 25:3-16
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d8ad3beaa94bc0483fe1ad322088cca0
https://doi.org/10.1016/j.jmoldx.2022.09.007
https://doi.org/10.1016/j.jmoldx.2022.09.007