Jay Shendure

发表

CADD: predicting the deleteriousness of variants throughout the human genome

Gregory M. Cooper, Philipp Rentzsch, Daniela Witten, 2018, Nucleic Acids Res..

Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation

Jay Shendure, Hannah Gelman, Jennifer N. Dines, 2019, Genome Medicine.

Unsupervised manifold alignment for single-cell multi-omics data

William Stafford Noble, He Fang, Jay Shendure, 2020, BCB.

A systematic evaluation of the design and context dependencies of massively parallel reporter assays

Jay Shendure, Martin Kircher, Vikram Agarwal, 2020, Nature Methods.

Massively multiplex single-cell Hi-C by combinatorial indexing

Jay Shendure, Vijay Ramani, Zhijun Duan, 2017 .

Supervised classification enables rapid annotation of cell atlases

Cole Trapnell, Jay Shendure, Hannah A. Pliner, 2019, Nature Methods.

Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies

William Stafford Noble, Jie Liu, Jay Shendure, 2017, Scientific Reports.

Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs).

Jay Shendure, Stuart Cantsilieris, Holly A Stessman, 2017, Methods in molecular biology.

A Three-Dimensional Model of the Yeast Genome

William Stafford Noble, Yoo Jung Kim, Jay Shendure, 2011, RECOMB.

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

William Stafford Noble, Ferhat Ay, Jay Shendure, 2017, bioRxiv.

Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data.

Jay Shendure, Vanessa E. Gray, Vanessa E Gray, 2017, Cell systems.

Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data

Jie Liu, William Stafford Noble, Jay Shendure, 2019, bioRxiv.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Inanç Birol, Dominique Lavenier, Hamidreza Chitsaz, 2013, GigaScience.

Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

Nir Yosef, Jingjing Zhao, Anat Kreimer, 2020, Nature Protocols.

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

Frederick P. Roth, Jay Shendure, Alan F. Rubin, 2019, Genome Biology.

Understanding Spatial Genome Organization: Methods and Insights

Jay Shendure, Vijay Ramani, Zhi-jun Duan, 2016, Genom. Proteom. Bioinform..

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

Michael T. McManus, Gregory M. Cooper, Jay Shendure, 2016 .

Identification of foreign gene sequences by transcript filtering against the human genome

Jay Shendure, George M. Church, David M. Tanenbaum, 2002, Nature Genetics.

Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules

Jay Shendure, Choli Lee, J. Shendure, 2012, Nature Methods.

megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering

David Baker, Jay Shendure, Barry L. Stoddard, 2013, Nucleic acids research.

Rare-variant extensions of the transmission disequilibrium test: application to autism exome sequence data.

Jay Shendure, Deborah A Nickerson, Gao T. Wang, 2014, American journal of human genetics.

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

Trevor Bedford, Karthik Gangavarapu, Jay Shendure, 2020, Science.

Adaptive Gene Amplification As an Intermediate Step in the Expansion of Virus Host Range

Jay Shendure, Greg Brennan, J. Kitzman, 2014, PLoS pathogens.

Computational comparison of two draft sequences of the human genome

Martha L. Bulyk, Jay Shendure, George M. Church, 2001, Nature.

High-resolution comparative analysis of great ape genomes

David Haussler, Fred H. Gage, Andy Wing Chun Pang, 2018, Science.

Functional Testing of Thousands of Osteoarthritis-Associated Variants for Regulatory Activity

Jay Shendure, Aidan Keith, John Loughlin, 2018 .

Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing

Cole Trapnell, Jay Shendure, Duanchen Sun, 2017, bioRxiv.

Cryptic transmission of SARS-CoV-2 in Washington state

Trevor Bedford, Jeffrey S. Duchin, Deborah A. Nickerson, 2020, Science.

Parallel, tag-directed assembly of locally derived short sequence reads

Jay Shendure, Choli Lee, Emily H Turner, 2010, Nature Methods.

Genome interrupted: sequencing of prostate cancer reveals the importance of chromosomal rearrangements

Jay Shendure, J. Shendure, P. Nelson, 2011, Genome Medicine.

Decoding long nanopore sequencing reads of natural DNA

Jay Shendure, Brian C. Ross, Andrew C. Adey, 2014, Nature Biotechnology.

A multiplexed homology-directed DNA repair assay reveals the impact of ~1,700 BRCA1 variants on protein function

Jay Shendure, Jeffrey D. Parvin, Lea M. Starita, 2018, bioRxiv.

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations

Jay Shendure, Arend Sidow, Michael J Bamshad, 2010, Nature Methods.

MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals

Jay Shendure, Evan E Eichler, Peter H. Sudmant, 2014, bioRxiv.

Multiplex pairwise assembly of array-derived DNA oligonucleotides

David Baker, Jay Shendure, Marc J. Lajoie, 2015, Nucleic acids research.

Multiplex amplification of large sets of human exons

Jay Shendure, Bin Xie, George M Church, 2007, Nature Methods.

Rapid and accurate large-scale genotyping of duplicated genes and discovery of novel sites of interlocus gene conversion

Jay Shendure, Francesca Antonacci, John Huddleston, 2013, Nature Methods.

A brief history of human disease genetics

Mark I. McCarthy, Heidi L. Rehm, Jay Shendure, 2020, Nature.

TGFB2 loss of function mutations cause familial thoracic aortic aneurysms and acute aortic dissections associated with mild systemic features of the Marfan syndrome

Jay Shendure, Mathilde Varret, Catherine Boileau, 2012, Nature Genetics.

Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia

Jay Shendure, Jonathan C. Cohen, Helen H. Hobbs, 2010, Human molecular genetics.

Fragment Length of Circulating Tumor DNA

Noah C Welker, Jay Shendure, Daniel N. Baker, 2016, PLoS genetics.

The dynamic three-dimensional organization of the diploid yeast genome

William Stafford Noble, Jay Shendure, William S Noble, 2016, bioRxiv.

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay

Nir Yosef, Anat Kreimer, Jay Shendure, 2019, Human mutation.

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

Cole Trapnell, Jay Shendure, Jacob M. Schreiber, 2019, Cell.

Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube

Jay Shendure, Mostafa Ronaghi, Natalie Morrell, 2017, Nature Biotechnology.

Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer

Hamid Bolouri, Jay Shendure, Min Fang, 2016 .

Methods for genomic partitioning.

Jay Shendure, Deborah A Nickerson, Emily H Turner, 2009, Annual review of genomics and human genetics.

Estimating human mutation rate using autozygosity in a founder population

Jay Shendure, Evan E. Eichler, Laura Vives, 2012, Nature Genetics.

A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function.

Jay Shendure, Stanley Fields, Justin Gullingsrud, 2018, American journal of human genetics.

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

Cole Trapnell, Jay Shendure, Andrew J. Hill, 2019, Nature Genetics.

Nanopore Sequencing of the phi X 174 genome

Jay Shendure, Brian C. Ross, Jens H. Gundlach, 2014 .

Predicting mRNA abundance directly from genomic sequence using deep convolutional neural networks

Jay Shendure, Vikram Agarwal, J. Shendure, 2018, bioRxiv.

Long-read sequence assembly of the gorilla genome

David Haussler, Joel Armstrong, Benedict Paten, 2016, Science.

Digital genotyping and haplotyping with polymerase colonies

David E. Housman, Jay Shendure, George M. Church, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee.

Arcadi Navarro, Jay Shendure, Can Alkan, 2011, Genome research.

Computational discovery of sense-antisense transcription in the human and mouse genomes

Jay Shendure, George M Church, J. Shendure, 2002, Genome Biology.

Genome-Scale Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn-seq

Jay Shendure, J. Shendure, L. Gallagher, 2011, mBio.

Dynamic reorganization of nuclear architecture during human cardiogenesis

William Stafford Noble, Jay Shendure, Charles E. Murry, 2017, bioRxiv.

Classification and characterization of microsatellite instability across 18 cancer types

Jay Shendure, Colin C Pritchard, Stephen J Salipante, 2016, Nature Medicine.

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

Wei Chen, William Stafford Noble, Jay Shendure, 2018 .

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

Jay Shendure, Deborah A Nickerson, Choli Lee, 2012, Nature Genetics.

Characterizing the temporal dynamics of gene expression in single cells with sci-fate

Cole Trapnell, Wei Zhou, Jay Shendure, 2019, bioRxiv.

Massively parallel exon capture and library-free resequencing across 16 genomes

Jay Shendure, Deborah A Nickerson, Choli Lee, 2009, Nature Methods.

Long-range polony haplotyping of individual human chromosome molecules

Jay Shendure, George M Church, Robi D Mitra, 2006, Nature Genetics.

Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers

Stephen J. Salipante, Deborah A. Nickerson, Jay Shendure, 2011, Proceedings of the National Academy of Sciences.

Publisher Correction: DNA sequencing at 40: past, present and future

Jay Shendure, George M. Church, Walter Gilbert, 2019, Nature.

A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes.

William Stafford Noble, Jay Shendure, Mirela Andronescu, 2012, Methods.

Tagmentation-based whole-genome bisulfite sequencing

Roland Eils, Volker Hovestadt, Jay Shendure, 2013, Nature Protocols.

Saturation mutagenesis of disease-associated regulatory elements

Jay Shendure, Martin Kircher, Joseph F. Costello, 2018 .

Capturing native long-range contiguity by in situ library construction and optical sequencing

Jay Shendure, Choli Lee, Andrew C. Adey, 2012, Proceedings of the National Academy of Sciences.

Polony DNA Sequencing

Jay Shendure, George M Church, George M. Church, 2006, Current protocols in molecular biology.

Whole genome prediction for preimplantation genetic diagnosis

Jay Shendure, Matthew Rabinowitz, Matthew W. Snyder, 2015, Genome Medicine.

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

Jay Shendure, Choli Lee, Andrew C. Adey, 2013, Nature.

Disruptive CHD8 Mutations Define a Subtype of Autism Early in Development

Jay Shendure, Serafino Buono, Hilde Peeters, 2014, Cell.

Saturation Editing of Genomic Regions by Multiplex Homology-Directed Repair

Jay Shendure, Evan A. Boyle, J. Shendure, 2014, Nature.

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

Stephen J. Salipante, Jay Shendure, Choli Lee, 2015, PLoS genetics.

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

Jay Shendure, Choli Lee, Dana Pe'er, 2009, Nature Biotechnology.

Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders

Anuj Srivastava, Anuradha Lakshminarayana, Jay Shendure, 2015, Genome research.

The cis-regulatory dynamics of embryonic development at single cell resolution

Cole Trapnell, Jay Shendure, Xiaojie Qiu, 2017 .

Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer

Ming Yu, Colin C. Pritchard, Stephen J. Salipante, 2014, Nature Communications.

Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection.

Jay Shendure, Renee D. George, Graham McVicker, 2011, Genome research.

Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections

Stephen J. Salipante, Jay Shendure, Connor McCoy, 2013, PloS one.

Haploinsufficiency of SF3B4, a component of the pre-mRNA spliceosomal complex, causes Nager syndrome.

Jay Shendure, Michael J Bamshad, Deborah A Nickerson, 2012, American journal of human genetics.

Noninvasive Whole-Genome Sequencing of a Human Fetus

Jay Shendure, Matthew W. Snyder, Jeffrey C. Murray, 2012, Science Translational Medicine.

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

Jay Shendure, Colin C Pritchard, Stephen J Salipante, 2013, Genome research.

Fluorescent in situ sequencing on polymerase colonies.

Jay Shendure, George M Church, Robi D Mitra, 2003, Analytical biochemistry.

Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting.

Jay Shendure, Robert B Darnell, Christina S Leslie, 2012, Molecular cell.

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

Georg Seelig, Jay Shendure, J. Shendure, 2015, Cell.

What Is Your Conceptual Definition of "Cell Type" in the Context of a Mature Organism?

Hans Clevers, Emma Lundberg, Cole Trapnell, 2017, Cell systems.

DNA Sequencing Predicts 1st-Line Tuberculosis Drug Susceptibility Profiles

Phelim Bradley, Zamin Iqbal, Baoli Zhu, 2018, The New England journal of medicine.

Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains

Jay Shendure, Stephen J Salipante, Matthew W. Snyder, 2015, Genome research.

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

Jay Shendure, Martin Kircher, Max Schubach, 2019, Nature Communications.

Next generation sequence analysis for mitochondrial disorders

Jay Shendure, Emily H Turner, Si Houn Hahn, 2009, Genome Medicine.

A general framework for estimating the relative pathogenicity of human genetic variants

Gregory M. Cooper, Jay Shendure, Martin Kircher, 2014 .

Poxviruses Deploy Genomic Accordions to Adapt Rapidly against Host Antiviral Defenses

Jay Shendure, Nels C. Elde, J. Kitzman, 2012, Cell.