developing new molecular methods (selected publications)


Cao et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science (2018)
PMID: 30166440
(with Trapnell Lab)
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Matreyek, Starita et al. Multiplex assessment of protein variant abundance by massively parallel sequencing. Nature Genetics (2018)
PMID: 29785012
w/ Fowler Lab
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Cao, Packer et al. Comprehensive single cell transcriptional profiling of a multicelluar organism by combinatorial indexing. Science (2017)
PMID: 28818938
(with Trapnell, Waterston Labs)
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Ramani et al. Massively multiplex single-cell Hi-C. Nature Methods (2017)
PMID: 28135255
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Ramani, Cusanovich et al. Mapping 3D genome architecture through in situ DNase Hi-C. Nature Protocols (2016)
PMID: 27685100
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McKenna, Findlay, Gagnon et al. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science (2016)
PMID: 27229144
(with Schier Lab)
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Ramani et al. High-throughput determination of RNA structure by proximity ligation. Nature Biotechnology (2015)
PMID: 26237516
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Cusanovich et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science (2015)
PMID: 25953818
(with Trapnell Lab)
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Kitzman, Starita et al. Massively parallel single-amino-acid mutagenesis. Nature Methods (2015)
PMID: 25559584
(with Fields Lab)
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Boyle et al. MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing. Bioinformatics (2014)
PMID: 24867941
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Shendure & Lieberman-Aiden. The expanding scope of DNA sequencing. Nature Biotechnology (2012)
PMID: 23138308
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Adey & Shendure. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Research (2012)
PMID: 22466172
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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
(with Zhang Lab)
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Hiatt, Patwardhan et al. Parallel, tag-directed assembly of locally derived short sequence reads. Nature Methods (2010)
PMID: 20081835
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Porreca, Zhang et al. Multiplex Amplification of Large Sets of Human Exons. Nature Methods (2007)
PMID: 17934468
(in Church Lab)
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