J
Joshua N. Burton
Researcher at University of Washington
Publications - 29
Citations - 4711
Joshua N. Burton is an academic researcher from University of Washington. The author has contributed to research in topics: Genome & Sequence assembly. The author has an hindex of 16, co-authored 29 publications receiving 3946 citations. Previous affiliations of Joshua N. Burton include University of Manchester & University of Utah.
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Journal ArticleDOI
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
Sante Gnerre,Iain MacCallum,Dariusz Przybylski,Filipe J. Ribeiro,Joshua N. Burton,Bruce J. Walker,Ted Sharpe,Giles Hall,Terrance Shea,Sean M. Sykes,Aaron M. Berlin,Daniel Aird,Maura Costello,Riza M. Daza,Louise Williams,Robert Nicol,Andreas Gnirke,Chad Nusbaum,Eric S. Lander,David B. Jaffe +19 more
TL;DR: The development of an algorithm for genome assembly, ALLPATHS-LG, and its application to massively parallel DNA sequence data from the human and mouse genomes, generated on the Illumina platform, have good accuracy, short-range contiguity, long-range connectivity, and coverage of the genome.
Journal ArticleDOI
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
TL;DR: Genomes assembled de novo from short reads are highly fragmented relative to the finished chromosomes of Homo sapiens and key model organisms generated by the Human Genome Project, so genome-wide chromatin interaction data sets, such as those generated by Hi-C, are a rich source of long-range information for assigning, ordering and orienting genomic sequences to chromosomes, including across centromeres.
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Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
Derek M. Bickhart,Benjamin D. Rosen,Sergey Koren,B.L. Sayre,Alex Hastie,Saki Chan,Joyce Lee,Ernest T. Lam,Ivan Liachko,Shawn T. Sullivan,Joshua N. Burton,Heather J. Huson,John C Nystrom,Christy M. Kelley,J.L. Hutchison,Yang Zhou,Yang Zhou,Jiajie Sun,Alessandra Crisà,F. Abel Ponce de León,John C. Schwartz,John A. Hammond,Geoffrey C. Waldbieser,Steven G. Schroeder,George E. Liu,Maitreya J. Dunham,Jay Shendure,Jay Shendure,Tad S. Sonstegard,Adam M. Phillippy,Curtis P. Van Tassell,Timothy P L Smith +31 more
TL;DR: This assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.
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The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
Andrew Adey,Joshua N. Burton,Jacob O. Kitzman,Joseph B. Hiatt,Alexandra P. Lewis,Beth Martin,Ruolan Qiu,Choli Lee,Jay Shendure +8 more
TL;DR: Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis.
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ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
Iain MacCallum,Dariusz Przybylski,Sante Gnerre,Joshua N. Burton,Ilya Shlyakhter,Andreas Gnirke,Joel A. Malek,Joel A. Malek,Kevin McKernan,Swati Ranade,Swati Ranade,Terrance Shea,Louise Williams,Sarah Young,Chad Nusbaum,David B. Jaffe +15 more
TL;DR: Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds.