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High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

• Sante Gnerre, Iain Maccallum, +17 authors David B. Jaffe
• Proceedings of the National Academy of Sciences…
• 2011

Massively parallel DNA sequencing technologies are revolutionizing genomics by making it possible to generate billions of relatively short (~100-base) sequence reads at very low cost. Whereas such… (More)

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

• Derek M. Bickhart, Benjamin D. Rosen, +27 authors Timothy P L Smith
• Nature Genetics
• 2017

Adam Phillippy, Curtis Van Tassell, Timothy Smith and colleagues present a new reference genome assembly for the domestic goat using a pipeline that improves contiguity of the assembly by more than… (More)

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

• Andrew C Adey, Joshua N. Burton, +6 authors Jay Shendure
• Nature
• 2013

The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks. This was the first successful attempt to immortalize human-derived cells in vitro. The… (More)

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

• Joshua N. Burton, Ivan Liachko, Maitreya J. Dunham, Jay Shendure
• G3
• 2014

Microbial communities consist of mixed populations of organisms, including unknown species in unknown abundances. These communities are often studied through metagenomic shotgun sequencing, but… (More)

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

• David J. Roach, Joshua N. Burton, +6 authors Diarmaid Hughes
• PLoS genetics
• 2015

Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here,… (More)

Targeted enrichment and high-resolution digital profiling of mitochondrial DNA deletions in human brain

• Sean D. Taylor, Nolan G. Ericson, +4 authors Jason H. Bielas
• Aging cell
• 2014

Due largely to the inability to accurately quantify and characterize de novo deletion events, the mechanisms underpinning the pathogenic expansion of mtDNA deletions in aging and neuromuscular… (More)

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.

• Andrew C Adey, Jacob Otto Kitzman, +8 authors Jay Shendure
• Genome research
• 2014

We describe a method that exploits contiguity preserving transposase sequencing (CPT-seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in vitro means of… (More)

Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes

• Derek M. Bickhart, Benjamin D. Rosen, +26 authors Timothy P L Smith
• 2016

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However,… (More)

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

• Joshua N. Burton, Andrew C Adey, Rupali P. Patwardhan, Ruolan Qiu, Jacob Otto Kitzman, Jay Shendure
• Nature Biotechnology
• 2013

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. To address this… (More)

Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.

• Matthew T. Laurie, Jessica Adams Bertout, Sean D. Taylor, Joshua N. Burton, Jay Shendure, Jason H. Bielas
• BioTechniques
• 2013

Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel… (More)

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