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

 

 


Calderon, Blecher-Gonen, Huang, Secchia et al. The continuum of Drosophila embryonic development at single-cell resolution. Science (2022)
PMID: 35926038
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Choi, Chen et al. Precise genomic deletions using paired prime editing. Nature Biotechnology (2022)
PMID: 34650269
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Qiu et al. Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nature Genetics (2022)
PMID: 35288709
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Srivatsan, Regier et al. Embryo-scale, single-cell spatial transcriptomics. Science (2021)
PMID: 34210887
(with Trapnell Lab)
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Srivatsan et al. SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing. Clinical Chemistry (2021)
PMID: 32511368
(with Seattle Flu Study)
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Cao et al. A human cell atlas of fetal gene expression. Science (2020)
PMID: 33184181
(with Trapnell Lab)
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Domcke, Hill, Daza et al. A human cell atlas of fetal chromatin accessibility. Science (2020)
PMID: 33184180
(with Cusanovich & Trapnell Labs)
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Bedford, Greninger,Roychoudhury, Starita, Famulare et al. Cryptic transmission of SARS-CoV-2 in Washington state. Science (2020)
PMID: 32511596
(with Seattle Flu Study)
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Chu et al. Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform. New England Journal of Medicine (2020)
PMID: 32356944
(with Seattle Flu Study)
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Agarwal & Shendure. Predicting mRNA abundance directly from genomic sequence using deep convolutional neural networks. Cell Reports (2020)
PMID: 32433972
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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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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, McKenna, Schrieber 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, Keith 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
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(with Kircher 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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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
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(with Trapnell Lab)

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
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(with Schier Lab)

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
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(with Rostomily Lab)

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
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(with Ahituv, Ovcharenko Labs)

 

 


Schwartz et al. Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules. Nature Methods (2012)
PMID: 22886093
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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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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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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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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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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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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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Turner et al. Massively parallel exon capture and library-free resequencing across 16 genomes. Nature Methods (2009)
PMID: 19349981
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