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

 

 


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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Gasperini et al. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell (2019)
PMID: 30612741
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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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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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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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Klein et al. Functional characterization of enhancer evolution in the primate lineage. Genome Biology (2018)
PMID: 30045748
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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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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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Neveling, Mensenkamp et al. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clinical Chemistry (2017)
PMID: 27974384
(with Nelen, Hoischen Labs)
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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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Ramani et al. Massively multiplex single-cell Hi-C. Nature Methods (2017)
PMID: 28135255
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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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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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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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Underhill et al. Fragment Length of Circulating Tumor DNA. PLoS Genetics (2016)
PMID: 27428049
(with Underhill 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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Klein et al. Multiplex pairwise assembly of array-derived DNA oligonucleotides. Nucleic Acids Research (2015)
PMID: 26553805
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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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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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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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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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Findlay, Boyle et al. Saturation editing of genomic regions by multiplex homology-directed repair. Nature (2014)
PMID: 25141179
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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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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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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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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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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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Schwartz et al. Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules. Nature Methods (2012)
PMID: 22886093
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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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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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Adey & Shendure. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Research (2012)
PMID: 22466172
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Kumar et al. Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. PNAS (2011)
PMID: 21949389
(with Nelson 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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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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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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Ng et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature (2009)
PMID: 19684571
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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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