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

 

 


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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Klein et al. Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nature Communications (2019)
PMID: 31164647
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Ramani et al. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell (2019)
PMID: 30811994
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Cao, Spielmann et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature (2019)
PMID: 30787437
(with Trapnell Lab)
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Rentzsch et al. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Research (2019)
PMID: 30371827
(with Kircher Lab)
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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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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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Pliner et al. Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. Molecular Cell (2018)
PMID: 30078726
(with Trapnell Lab)
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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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Cusanovich, Reddington, Garfield et al. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature (2018)
PMID: 29539636
(with Furlong 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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Kim et al. The dynamic three-dimensional organization of the diploid yeast genome. eLIFE (2017)
PMID: 28537556
(with Dunham Lab)
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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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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, Cusanovich et al. Mapping 3D genome architecture through in situ DNase Hi-C. Nature Protocols (2016)
PMID: 27685100
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Snyder, Kircher et al. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. Cell (2016)
PMID: 26771485
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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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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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Starita et al. Massively Parallel Functional Analysis of BRCA1 RING Domain Variants. Genetics (2015)
PMID: 25823446
(with Fields 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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Kitzman, Starita et al. Massively parallel single-amino-acid mutagenesis. Nature Methods (2015)
PMID: 25559584
(with Fields 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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O'Roak, Stessman et al. Recurrent de novo mutations implicate novel genes underlying simplex autism risk. Nature Communications (2014)
PMID: 25418537
(with Eichler 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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Salipante, Roach et al. Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains. Genome Research (2014)
PMID: 25373147
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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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Burton, Liachko et al. Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps. G3 (2014)
PMID: 24855317
(with Dunham Lab)
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Schwartz, Roach et al. Primate evolution of the recombination regulator PRDM9. Nature Communications (2014)
PMID: 25001002
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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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Burton et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology (2013)
PMID: 24185095
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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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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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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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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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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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Hiatt, Patwardhan et al. Parallel, tag-directed assembly of locally derived short sequence reads. Nature Methods (2010)
PMID: 20081835
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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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Turner et al. Massively parallel exon capture and library-free resequencing across 16 genomes. Nature Methods (2009)
PMID: 19349981
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