featured research articles (work led or co-led by our lab)

 

 


Starita et al. A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function. AJHG (2018)
PMID: 30219179
(with Parvin Lab)
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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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Cusanovich, Hill et al. A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. Cell (2018)
PMID: 30078704
(with Trapnell 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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McKenna & Shendure. FlashFry: a fast and flexible tool for large-scale CRISPR target design. BMC Biology (2018)
PMID: 29976198
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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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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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Kim et al. The dynamic three-dimensional organization of the diploid yeast genome. eLIFE (2017)
PMID: 28537556
(with Dunham 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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Hause et al. Classification and characterization of microsatellite instability across 18 cancer types. Nature Medicine (2016)
PMID: 27694933
(with Salipante Lab)
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Ramani et al. Massively multiplex single-cell Hi-C. Nature Methods (2017)
PMID: 28135255
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Kumar, Coleman et al. Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer. Nature Medicine (2016)
PMID: 26928463
(with Nelson Lab)
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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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Underhill et al. Fragment Length of Circulating Tumor DNA. PLoS Genetics (2016)
PMID: 27428049
(with Underhill 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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Fairfield et al. Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders. Genome Research (2015)
PMID: 25917818
(with Reinholdt Lab)
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Roach et al. A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota.PLoS Genetics (2015)
PMID: 26230489
(with Salipante Lab)
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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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Kumar, Ryan et al. Whole genome prediction for preimplantation genetic diagnosis. Genome Medicine (2015)
PMID: 26019723
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Snyder, Simmons et al. Copy-Number Variation and False Positive Prenatal Aneuploidy Screening Results. New England Journal of Medicine (2015)
PMID: 25830323
(with Gammill Lab)
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Kumar et al. Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes. Genome Biology (2014)
PMID: 25608559
(with Rostomily Lab)
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Findlay, Boyle et al. Saturation editing of genomic regions by multiplex homology-directed repair. Nature (2014)
PMID: 25141179
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Adey et al. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Research (2014)
PMID: 25327137
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Iossifov, O'Roak, Sanders, Ronemus et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature (2014)
PMID: 25363768
(with Wigler, State, Eichler Labs)
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Schwartz, Roach et al. Primate evolution of the recombination regulator PRDM9. Nature Communications (2014)
PMID: 25001002
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Kircher, Witten et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nature Genetics (2014)
PMID: 24487276
(with Witten, Cooper Labs)
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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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Adey, Burton, Kitzman et al. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature (2013)
PMID: 23925245
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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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O'Roak et al. Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders. Science (2012)
PMID: 23160955
(with Eichler Lab)
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Schwartz et al. Capturing native long-range contiguity by in situ library construction and optical sequencing. PNAS (2012)
PMID: 23112150
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Kitzman et al. Noninvasive whole-genome sequencing of a human fetus. Science Translational Medicine (2012)
PMID: 22674554
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O'Roak et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature (2012)
PMID: 22495309
(with Eichler Lab)
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Adey & Shendure. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Research (2012)
PMID: 22466172
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George et al. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Research (2011)
PMID: 21795384
(with Thomas Lab)
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Kitzman et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotechnology (2011)
PMID: 21170042
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O'Roak et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nature Genetics (2011)
PMID: 21572417
(with Eichler Lab)
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Ng, Bigham et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nature Genetics (2010)
PMID: 20711175
(with Bamshad Lab)
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Ng, Buckingham et al. Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics (2010)
PMID: 19915526
(with Bamshad Lab)
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Patwardhan et al. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nature Biotechnology (2009)
PMID: 19915551
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Vasta V et al. Next generation sequence analysis for mitochondrial disorders. Genome Medicine (2009)
PMID: 19852779
(with Hahn 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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