Genome Sequencing Technologies

(selected publications)

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2021

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing (opens in new tab)

Srivatsan et al. SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing.

Clinical Chemistry (2021)

PMID: 32511368 (opens in new tab) | PDF (opens in new tab)

(with Seattle Flu Study)

2019

High-Throughput Single-Cell Sequencing with Linear Amplification (opens in new tab)

Yin et al. High-Throughput Single-Cell Sequencing with Linear Amplification.

Molecular Cell (2019)

PMID: 31495564 (opens in new tab) | PDF (opens in new tab)

2017

DNA sequencing at 40: past, present and future (opens in new tab)

Shendure et al. DNA sequencing at 40: past, present and future.

Nature (2017)

PMID: 29019985 (opens in new tab) | PDF (opens in new tab)

2015

Haplotype-resolved genome sequencing: experimental methods and applications (opens in new tab)

Snyder et al. Haplotype-resolved genome sequencing: experimental methods and applications.

Nature Reviews Genetics (2015)

PMID: 25948246 (opens in new tab) | PDF (opens in new tab)

2014

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity (opens in new tab)

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

Genome Research (2014)

PMID: 25327137 (opens in new tab) | PDF (opens in new tab)

Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps (opens in new tab)

Burton, Liachko et al. Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps.

G3 (2014)

PMID: 24855317 (opens in new tab) | PDF (opens in new tab)

(with Dunham Lab)

2013

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line (opens in new tab)

Adey, Burton, Kitzman et al. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line.

Nature (2013)

PMID: 23925245 (opens in new tab) | PDF (opens in new tab)

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions (opens in new tab)

Burton et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.

Nature Biotechnology (2013)

PMID: 24185095 (opens in new tab) | PDF (opens in new tab)

2012

Capturing native long-range contiguity by in situ library construction and optical sequencing (opens in new tab)

Schwartz et al. Capturing native long-range contiguity by in situ library construction and optical sequencing.

PNAS (2012)

PMID: 23112150 (opens in new tab) | PDF (opens in new tab)

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing (opens in new tab)

Adey, Shendure. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing.

Genome Research (2012)

PMID: 22466172 (opens in new tab) | PDF (opens in new tab)

Noninvasive whole-genome sequencing of a human fetus (opens in new tab)

Kitzman et al. Noninvasive whole-genome sequencing of a human fetus.

Science Translational Medicine (2012)

PMID: 22674554 (opens in new tab) | PDF (opens in new tab)

2011

Haplotype-resolved genome sequencing of a Gujarati Indian individual (opens in new tab)

Kitzman et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual.

Nature Biotechnology (2011)

PMID: 21170042 (opens in new tab) | PDF (opens in new tab)

2010

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition (opens in new tab)

Adey, Morrison, Asan, Xun et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.

Genome Biology (2010)

PMID: 21143862 (opens in new tab) | PDF (opens in new tab)

(with Zhang Lab)

Parallel, tag-directed assembly of locally derived short sequence reads (opens in new tab)

Hiatt, Patwardhan et al. Parallel, tag-directed assembly of locally derived short sequence reads.

Nature Methods (2010)

PMID: 20081835 (opens in new tab) | PDF (opens in new tab)

2009

Targeted capture and massively parallel sequencing of 12 human exomes (opens in new tab)

Ng et al. Targeted capture and massively parallel sequencing of 12 human exomes.

Nature (2009)

PMID: 19684571 (opens in new tab) | PDF (opens in new tab)

Massively parallel exon capture and library-free resequencing across 16 genomes (opens in new tab)

Turner et al. Massively parallel exon capture and library-free resequencing across 16 genomes.

Nature Methods (2009)

PMID: 19349981 (opens in new tab) | PDF (opens in new tab)

2008

Next generation DNA sequencing (opens in new tab)

Shendure, Ji. Next generation DNA sequencing.

Nature Biotechnology (2008)

PMID: 18846087 (opens in new tab) | PDF (opens in new tab)

2005

Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome (opens in new tab)

Shendure, Porreca et al. Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome.

Science (2005)

PMID: 16081699 (opens in new tab) | PDF (opens in new tab)

(in Church Lab)