J
John R. Tyson
Researcher at University of British Columbia
Publications - 46
Citations - 4780
John R. Tyson is an academic researcher from University of British Columbia. The author has contributed to research in topics: Nanopore sequencing & Minion. The author has an hindex of 21, co-authored 36 publications receiving 3745 citations. Previous affiliations of John R. Tyson include BC Centre for Disease Control & University of Manchester.
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Journal ArticleDOI
Nanopore sequencing and assembly of a human genome with ultra-long reads
Miten Jain,Sergey Koren,Karen H. Miga,Josh Quick,Arthur C Rand,Thomas A Sasani,John R. Tyson,Andrew D Beggs,Alexander T. Dilthey,Ian T. Fiddes,Sunir Malla,Hannah Marriott,Tom Nieto,Justin O'Grady,Hugh E. Olsen,Brent S. Pedersen,Arang Rhie,Hollian Richardson,Aaron R. Quinlan,Terrance P. Snutch,Louise Tee,Benedict Paten,Adam M. Phillippy,Jared T. Simpson,Jared T. Simpson,Nicholas J. Loman,Matthew Loose +26 more
TL;DR: Ultra-long reads enabled assembly and phasing of the 4-Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length, and closure of gaps in the reference human genome assembly GRCh38.
Journal ArticleDOI
Nanopore native RNA sequencing of a human poly(A) transcriptome.
Rachael E. Workman,Alison D. Tang,Paul S. Tang,Miten Jain,John R. Tyson,Roham Razaghi,Philip C. Zuzarte,Timothy Gilpatrick,Alexander Payne,Joshua Quick,Norah Sadowski,Nadine Holmes,Jaqueline Goes de Jesus,Karen Jones,Cameron M. Soulette,Terrance P. Snutch,Nicholas J. Loman,Benedict Paten,Matthew Loose,Jared T. Simpson,Jared T. Simpson,Hugh E. Olsen,Angela N. Brooks,Mark Akeson,Winston Timp +24 more
TL;DR: This study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions to identify 33,984 plausible RNA isoforms and describes strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes.
Journal ArticleDOI
Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans.
Sheldon J. McKay,Robert C. Johnsen,Jaswinder Khattra,Jennifer Asano,David L. Baillie,Susanna Y. Chan,N. Dube,L. Fang,Barbara Goszczynski,E. Ha,E. Halfnight,R. Hollebakken,P. Huang,Kineta Hung,Victor L. Jensen,Steven J.M. Jones,H. Kai,Dion Tik Shun Li,A. Mah,Marco A. Marra,James D. McGhee,R. Newbury,Anatoli Timofeyevich Pouzyrev,Donald L. Riddle,Erik L. L. Sonnhammer,H. Tian,D. Tu,John R. Tyson,G. P. Vatcher,Adam Warner,Kim Wong,Zhongying Zhao,Donald G. Moerman +32 more
TL;DR: The ultimate goal is not only to describe detailed gene expression profiles, but also to gain a greater understanding of the organization of gene regulatory networks and to determine how they control cell function during development and differentiation in C. elegans.
Posted ContentDOI
Nanopore sequencing and assembly of a human genome with ultra-long reads
Miten Jain,Sergey Koren,Josh Quick,Arthur C Rand,Thomas A Sasani,John R. Tyson,Andrew D Beggs,Alexander T. Dilthey,Ian T. Fiddes,Sunir Malla,Hannah Marriott,Karen H. Miga,Tom Nieto,Justin O'Grady,Hugh E. Olsen,Brent S. Pedersen,Arang Rhie,Hollian Richardson,Aaron R. Quinlan,Terrance P. Snutch,Louise Tee,Benedict Paten,Adam M. Phillippy,Jared T. Simpson,Nicholas J. Loman,Matthew Loose +25 more
TL;DR: Modelling the repeat structure of the human genome predicts extraordinarily contiguous assemblies may be possible using nanopore reads alone, and it is found that adding an additional 5×-coverage of ‘ultra-long’ reads more than doubled the assembly contiguity.
Posted ContentDOI
Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore
John R. Tyson,Phillip James,David Stoddart,Natalie Sparks,Arthur Wickenhagen,Grant Hall,Ji Hyun Choi,Hope R. Lapointe,Kimia Kamelian,Andrew D. Smith,Natalie Prystajecky,Ian Goodfellow,Sam J. Wilson,Richard Harrigan,Terrance P. Snutch,Nicholas J. Loman,Joshua Quick +16 more
TL;DR: An updated primer scheme with 22 additional primers to improve genome coverage and cost savings which bring the reagent cost down to £10 per sample making it practical for individual labs to sequence thousands of SARS-CoV-2 genomes to support national and international genomic epidemiology efforts.