massively parallel functional genomics (selected publications)

 

 


Chardon, McDiarmid et al. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. Nature Communications (2024)
PMID: 39294132
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Klein, Agarwal, Inoue, Keith et al. A systematic evaluation of the design and context dependencies of massively parallel reporter assays. Nature Methods (2020)
PMID: 33046894
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Gordon, Inoue, Martin, Schubach et al. lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature Protocols (2020)
PMID: 32641802
(with Ahituv and Kircher Labs)
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Srivatsan, McFaline-Figueroa, Ramani et al. Massively multiplex chemical transcriptomics at single-cell resolution. Science (2020)
PMID: 31806696
(with Trapnell Lab)
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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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Klein, Keith et al. Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nature Communications (2019)
PMID: 31164647
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Kim, Dunham, Shendure. A combination of transcription factors mediates inducible interchromosomal contacts. eLife (2019)
PMID: 31081754
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Findlay et al. Accurate classification of BRCA1 variants with saturation genome editing. Nature (2018)
PMID: 30209399
(with Starita Lab)
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Klein et al. Functional characterization of enhancer evolution in the primate lineage. Genome Biology (2018)
PMID: 30045748
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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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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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Inoue, Kircher et al. A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Research (2017)
PMID: 27831498
(with Ahituv Lab)
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Fields, Shendure. Massively Parallel Genetics. Genetics (2016)
PMID: 27270695
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Starita, Shendure, Fields et al. Massively Parallel Functional Analysis of BRCA1 RING Domain Variants. Genetics (2015)
PMID: 25823446
(with Fields 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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Smith, Taher L et al. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nature Genetics (2013)
PMID: 23892608
(with Ahituv, Ovcharenko Labs)
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Patwardhan, Hiatt et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nature Biotechnology (2012)
PMID: 22371081
(with Pennacchio, Ahituv Labs)
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