developing new molecular methods (selected publications)

 

 


Domcke, Hill, Cusanovich, Daza et al. A human cell atlas of fetal chromatin accessibility. Science (2020)
PMID: 33184180
(with Cusanovich & Trapnell Labs)
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Cao et al. Sci-fate characterizes the dynamics of gene expression in single cells. Nature Biotechnology (2020)
PMID: 32284584
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Yin et al. High-Throughput Single-Cell Sequencing with Linear Amplification. Molecular Cell (2019)
PMID: 31495564
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Alexander et al. Concurrent genome and epigenome editing by CRISPR-mediated sequence replacement. BMC Biology (2019)
PMID: 31739790
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Kircher, Xiong, Martin, Schubach et al. Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nature Communications (2019)
PMID: 31395865
(with Ahituv and Kircher Labs)
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Chen et al. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. Nucleic Acids Research (2019)
PMID: 31165867
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Ramani et al. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell Reports (2019)
PMID: 30811994
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Cao, Spielmann et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature (2019)
PMID: 30787437
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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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Matreyek, Starita et al. Multiplex assessment of protein variant abundance by massively parallel sequencing. Nature Genetics (2018)
PMID: 29785012
(with 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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Snyder et al. Haplotype-resolved genome sequencing: experimental methods and applications. Nature Reviews Genetics (2015)
PMID: 25948246
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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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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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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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