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

 

 


Qiu, Martin, Welsh et al. A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature (2024)
PMID: 38355799
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Abadie, Clark, Valanparambil et al. Reversible, tunable epigenetic silencing of TCF-1 generates flexibility in the T cell memory decision. Cell (2024)
(with Kueh Lab)
PMID: 38301652
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Chiou, Huang et al. A single-cell multi-omic atlas spanning the adult rhesus macaque brain. Science Advances (2023)
(with Snyder-Mackler and Platt Labs)
PMID: 37824616
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Martin et al. Optimized single-nucleus transcriptional profiling by combinatorial indexing. Nature Protocols (2022)
PMID: 36261634
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Choi et al. A time-resolved, multi-symbol molecular recorder via sequential genome editing. Nature (2022)
PMID: 35794474
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Choi, Chen et al. Precise genomic deletions using paired prime editing. Nature Biotechnology (2022)
PMID: 34650269
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Agarwal, Darwin-Lopez et al. The landscape of alternative polyadenylation in single cells of the developing mouse embryo. Nature Communications (2021)
PMID: 34429411
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Srivatsan, Regier et al. Embryo-scale, single-cell spatial transcriptomics. Science (2021)
PMID: 34210887
(with Trapnell and Stevens Labs)
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Simeonov et al. Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states. Cancer Cell (2021)
PMID: 34115987
(with Lengner and McKenna Labs)
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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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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
(with Ahituv Lab)
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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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Cao et al. Sci-fate characterizes the dynamics of gene expression in single cells. Nature Biotechnology (2020)
PMID: 32284584
(with Trapnell Lab)
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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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Yin et al. High-Throughput Single-Cell Sequencing with Linear Amplification. Molecular Cell (2019)
PMID: 31495564
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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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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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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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Kim et al. A combination of transcription factors mediates inducible interchromosomal contacts. eLife (2019)
PMID: 31081754
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Ramani et al. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell (2019)
PMID: 30811994
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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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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)

 

 


Findlay et al. Accurate classification of BRCA1 variants with saturation genome editing. Nature (2018)
PMID: 30209399
(with Starita 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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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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McKenna & Shendure. FlashFry: a fast and flexible tool for large-scale CRISPR target design. BMC Biology (2018)
PMID: 29976198
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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
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(with Trapnell Lab)

 

 


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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Kim et al. The dynamic three-dimensional organization of the diploid yeast genome. eLIFE (2017)
PMID: 28537556
(with Dunham Lab)
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Neveling, Mensenkamp et al. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clinical Chemistry (2017)
PMID: 27974384
(with Nelen and Hoischen Labs)
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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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Ramani et al. Massively multiplex single-cell Hi-C. Nature Methods (2017)
PMID: 28135255
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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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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
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(with Schier Lab)

 

 


Underhill et al. Fragment Length of Circulating Tumor DNA. PLoS Genetics (2016)
PMID: 27428049
(with Underhill Lab)
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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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Klein et al. Multiplex pairwise assembly of array-derived DNA oligonucleotides. Nucleic Acids Research (2015)
PMID: 26553805
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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
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(with Rostomily Lab)

 

 


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 and 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 and Cooper Labs)
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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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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)
(with Ahituv and Ovcharenko Labs)
PMID: 23892608
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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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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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