Jay Shendure



  1. McKenna A, Findlay G, Gagnon J, Horwitz M, Schier A, Shendure J. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science. 2016;353:aaf7907 pubmed publisher
    ..In future analyses, genome editing of synthetic target arrays for lineage tracing (GESTALT) can be used to generate large-scale maps of cell lineage in multicellular systems for normal development and disease. ..
  2. Shendure J, Fields S. Massively Parallel Genetics. Genetics. 2016;203:617-9 pubmed publisher
    ..These studies will help establish the disease risk of both observed and potential genetic variants and to overcome the problem of "variants of uncertain significance." ..
  3. Shendure J, Findlay G, Snyder M. Genomic Medicine-Progress, Pitfalls, and Promise. Cell. 2019;177:45-57 pubmed publisher
  4. Ramani V, Qiu R, Shendure J. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell Rep. 2019;26:2465-2476.e4 pubmed publisher
    ..Looking forward, we anticipate that single stranded protocol (SSP) adaptations of any protein-DNA interaction mapping technique (e.g., ChIP-exo and CUT&RUN) will enhance the information content of the resulting data. ..
  5. Cao J, Spielmann M, Qiu X, Huang X, Ibrahim D, Hill A, et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature. 2019;566:496-502 pubmed publisher
    ..We explore the dynamics of gene expression within cell types and trajectories over time, including focused analyses of the apical ectodermal ridge, limb mesenchyme and skeletal muscle. ..
  6. Gasperini M, Hill A, McFaline Figueroa J, Martin B, Kim S, Zhang M, et al. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell. 2019;176:377-390.e19 pubmed publisher
    ..This framework will facilitate the large-scale mapping of enhancer-gene regulatory interactions, a critical yet largely uncharted component of the cis-regulatory landscape of the human genome. ..
  7. Findlay G, Daza R, Martin B, Zhang M, Leith A, Gasperini M, et al. Accurate classification of BRCA1 variants with saturation genome editing. Nature. 2018;562:217-222 pubmed publisher
  8. Cusanovich D, Hill A, Aghamirzaie D, Daza R, Pliner H, Berletch J, et al. A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. Cell. 2018;174:1309-1324.e18 pubmed publisher
    ..These data define the in vivo landscape of the regulatory genome for common mammalian cell types at single-cell resolution. ..
  9. Pliner H, Packer J, McFaline Figueroa J, Cusanovich D, Daza R, Aghamirzaie D, et al. Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. Mol Cell. 2018;71:858-871.e8 pubmed publisher
    ..Our strategy can be applied to dissect the architecture, sequence determinants, and mechanisms of cis-regulation on a genome-wide scale. ..

More Information


  1. Cusanovich D, Daza R, Adey A, Pliner H, Christiansen L, Gunderson K, et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015;348:910-4 pubmed publisher
    ..We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas. ..
  2. Klein J, Keith A, Agarwal V, Durham T, Shendure J. Functional characterization of enhancer evolution in the primate lineage. Genome Biol. 2018;19:99 pubmed publisher
    ..We use these data to quantify the relationship between sequence and functional divergence, and to identify CpG deamination as a potentially important force in driving changes in enhancer activity during primate evolution. ..
  3. Hause R, Shendure J. Genetic variation meets replication origins. Cell. 2014;159:973-974 pubmed publisher
    ..These so-called rtQTLs represent a new form of quantitative trait loci that may influence gene dosage and mutational frequency and provide mechanistic insights into the regulation of DNA replication. ..
  4. Ramani V, Shendure J. Smash and DASH with Cas9. Genome Biol. 2016;17:42 pubmed publisher
    ..It seems plausible that the in vitro use of CRISPR/Cas9 has unrealized potential to revolutionize the practice of molecular biology well beyond genome editing. ..
  5. Gasperini M, Findlay G, McKenna A, Milbank J, Lee C, Zhang M, et al. CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions. Am J Hum Genet. 2017;101:192-205 pubmed publisher
    ..Further application of ScanDel could shed light on the role of regulatory mutations in disease at other loci while also facilitating a deeper understanding of endogenous gene regulation. ..
  6. Snyder M, Kircher M, Hill A, Daza R, Shendure J. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. Cell. 2016;164:57-68 pubmed publisher
    ..Since this strategy does not rely on genetic differences to distinguish between contributing tissues, it may enable the noninvasive monitoring of a much broader set of clinical conditions than currently possible. ..
  7. Yang F, Deng X, Ma W, Berletch J, Rabaia N, Wei G, et al. The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biol. 2015;16:52 pubmed publisher
    ..The X-linked lncRNA Firre helps to position the inactive X chromosome near the nucleolus and to preserve one of its main epigenetic features. ..
  8. Adey A, Kitzman J, Burton J, Daza R, Kumar A, Christiansen L, et al. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res. 2014;24:2041-9 pubmed publisher
    ..Finally, we demonstrate CPT-seq as a means of anchoring unplaced novel human contigs to the reference genome as well as for detecting misassembled sequences. ..