developing new molecular methods (selected publications)

 

 


Chen, Choi et al. Symbolic recording of signalling and cis-regulatory element activity to DNA. Nature (2024)
PMID:
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Liao, Choi, Shendure. Molecular recording using DNA Typewriter. Nature Protocols (2024)
PMID: 38844553
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Martin et al. Optimized single-nucleus transcriptional profiling by combinatorial indexing. Nature Protocols (2022)
PMID: 36261634
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Choi et al. A time-resolved, multi-symbol molecular recorder via sequential genome editing. Nature (2022)
PMID: 35794474
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Srivatsan, Regier et al. Embryo-scale, single-cell spatial transcriptomics. Science (2021)
PMID: 34210887
(with Trapnell and Stevens Labs)
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Simeonov et al. Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states. Cancer Cell (2021)
PMID: 34115987
(with Lengner and McKenna 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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Srivatsan et al. Massively multiplex chemical transcriptomics at single-cell resolution. Science (2020)
PMID: 31806696
(with Trapnell Lab)
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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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Pliner et al. Supervised classification enables rapid annotation of cell atlases. Nature Methods (2019)
PMID: 31501545
(with Trapnell Lab)
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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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Kim et al. A combination of transcription factors mediates inducible interchromosomal contacts. eLife (2019)
PMID: 31081754
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Cao, Spielmann et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature (2019)
PMID: 30787437
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Gasperini et al. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell (2019)
PMID: 30612741
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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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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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Ramani et al. Massively multiplex single-cell Hi-C. Nature Methods (2017)
PMID: 28135255
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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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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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Klein et al. Multiplex pairwise assembly of array-derived DNA oligonucleotides. Nucleic Acids Research (2015)
PMID: 26553805
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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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Schwartz et al. Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules. Nature Methods (2012)
PMID: 22886093
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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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Turner et al. Massively parallel exon capture and library-free resequencing across 16 genomes. Nature Methods (2009)
PMID: 19349981
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