developing new molecular methods (selected publications)


Gasperini et al. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell (2019)
PMID: 30612741
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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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Hill, McFaline-Figueroa et al. On the design of CRISPR-based single-cell molecular screens. Nature Methods (2018)
PMID: 29457792
(with Trapnell 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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Gasperini, Findlay et al. CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions. AJHG (2017)
PMID: 28712454
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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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Klein et al. Multiplex pairwise assembly of array-derived DNA oligonucleotides. Nucleic Acids Research (2015)
PMID: 26553805
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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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Snyder et al. Haplotype-resolved genome sequencing: experimental methods and applications. Nature Reviews Genetics (2015)
PMID: 25948246
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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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Hiatt et al. Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation. Genome Research (2013)
PMID: 23382536
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Shendure & Lieberman-Aiden. The expanding scope of DNA sequencing. Nature Biotechnology (2012)
PMID: 23138308
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Schwartz et al. Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules. Nature Methods (2012)
PMID: 22886093
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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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Turner et al. Massively parallel exon capture and library-free resequencing across 16 genomes. Nature Methods (2009)
PMID: 19349981
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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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