Publications by authors named "Jay Shendure"

100Publications

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

Nat Methods 2020 Nov 12;17(11):1083-1091. Epub 2020 Oct 12.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1038/s41592-020-0965-yDOI Listing
November 2020

Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks.

Cell Rep 2020 05;31(7):107663

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.107663DOI Listing
May 2020

Suppressor mutations in -null mice implicate the DNA damage response in Rett syndrome pathology.

Genome Res 2020 04 21;30(4):540-552. Epub 2020 Apr 21.

Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.

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http://dx.doi.org/10.1101/gr.258400.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197480PMC
April 2020

Sci-fate characterizes the dynamics of gene expression in single cells.

Nat Biotechnol 2020 08 13;38(8):980-988. Epub 2020 Apr 13.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1038/s41587-020-0480-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7416490PMC
August 2020

Towards a comprehensive catalogue of validated and target-linked human enhancers.

Nat Rev Genet 2020 05 27;21(5):292-310. Epub 2020 Jan 27.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1038/s41576-019-0209-0DOI Listing
May 2020

Concurrent genome and epigenome editing by CRISPR-mediated sequence replacement.

BMC Biol 2019 11 18;17(1):90. Epub 2019 Nov 18.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1186/s12915-019-0711-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862751PMC
November 2019

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

Genome Biol 2019 11 4;20(1):223. Epub 2019 Nov 4.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.

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http://dx.doi.org/10.1186/s13059-019-1845-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6827219PMC
November 2019

Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells.

Methods 2020 01 16;170:61-68. Epub 2019 Sep 16.

Division of Hematology, University of Washington School of Medicine, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2019.09.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6949367PMC
January 2020

Mechanisms of Interplay between Transcription Factors and the 3D Genome.

Mol Cell 2019 10 11;76(2):306-319. Epub 2019 Sep 11.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.08.010DOI Listing
October 2019

Supervised classification enables rapid annotation of cell atlases.

Nat Methods 2019 10 9;16(10):983-986. Epub 2019 Sep 9.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1038/s41592-019-0535-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6791524PMC
October 2019

High-Throughput Single-Cell Sequencing with Linear Amplification.

Mol Cell 2019 11 5;76(4):676-690.e10. Epub 2019 Sep 5.

Department of Genome Sciences, University of Washington, Seattle, WA, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874760PMC
November 2019

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

Nat Commun 2019 08 8;10(1):3583. Epub 2019 Aug 8.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.

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http://dx.doi.org/10.1038/s41467-019-11526-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687891PMC
August 2019

Functional testing of thousands of osteoarthritis-associated variants for regulatory activity.

Nat Commun 2019 06 4;10(1):2434. Epub 2019 Jun 4.

Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.

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http://dx.doi.org/10.1038/s41467-019-10439-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547687PMC
June 2019

Expanding the single-cell genomics toolkit.

Nat Genet 2019 06;51(6):931-932

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1038/s41588-019-0429-4DOI Listing
June 2019

A combination of transcription factors mediates inducible interchromosomal contacts.

Elife 2019 05 13;8. Epub 2019 May 13.

Department of Genome Sciences, University of Washington, Seattle, United States.

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http://dx.doi.org/10.7554/eLife.42499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6548505PMC
May 2019

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

Nature 2019 Apr;568(7752):E11

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/s41586-019-1120-8DOI Listing
April 2019

Genomic Medicine-Progress, Pitfalls, and Promise.

Cell 2019 03;177(1):45-57

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1016/j.cell.2019.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6531313PMC
March 2019

High Sensitivity Profiling of Chromatin Structure by MNase-SSP.

Cell Rep 2019 02;26(9):2465-2476.e4

Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582983PMC
February 2019

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

Cell 2019 01 3;176(1-2):377-390.e19. Epub 2019 Jan 3.

Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98105, USA; Howard Hughes Medical Institute, Seattle, WA 98105, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183155
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http://dx.doi.org/10.1016/j.cell.2018.11.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690346PMC
January 2019

Condensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence.

Mol Cell 2019 02 27;73(3):533-546.e4. Epub 2018 Dec 27.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.11.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368455PMC
February 2019

CADD: predicting the deleteriousness of variants throughout the human genome.

Nucleic Acids Res 2019 01;47(D1):D886-D894

Berlin Institute of Health (BIH), 10178 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gky1016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323892PMC
January 2019

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

N Engl J Med 2018 10 26;379(15):1403-1415. Epub 2018 Sep 26.

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http://dx.doi.org/10.1056/NEJMoa1800474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6121966PMC
October 2018

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

Am J Hum Genet 2018 10 12;103(4):498-508. Epub 2018 Sep 12.

Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, USA; Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297183024
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http://dx.doi.org/10.1016/j.ajhg.2018.07.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174279PMC
October 2018

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

Mol Cell 2018 09 2;71(5):858-871.e8. Epub 2018 Aug 2.

Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.06.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582963PMC
September 2018

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Cell 2018 08 2;174(5):1309-1324.e18. Epub 2018 Aug 2.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.06.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158300PMC
August 2018

Functional characterization of enhancer evolution in the primate lineage.

Genome Biol 2018 07 25;19(1):99. Epub 2018 Jul 25.

Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.

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http://dx.doi.org/10.1186/s13059-018-1473-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060477PMC
July 2018

FlashFry: a fast and flexible tool for large-scale CRISPR target design.

BMC Biol 2018 07 5;16(1):74. Epub 2018 Jul 5.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1186/s12915-018-0545-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6033233PMC
July 2018

Highly scalable generation of DNA methylation profiles in single cells.

Nat Biotechnol 2018 06 9;36(5):428-431. Epub 2018 Apr 9.

Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA.

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http://dx.doi.org/10.1038/nbt.4112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938134PMC
June 2018

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.

Nat Biotechnol 2018 06 28;36(5):442-450. Epub 2018 Mar 28.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.4103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938111PMC
June 2018

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

Methods 2018 06 31;142:59-73. Epub 2018 Jan 31.

Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Division of Hematology, Department of Medicine, University of Washington, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2018.01.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993575PMC
June 2018

Identifying Novel Enhancer Elements with CRISPR-Based Screens.

ACS Chem Biol 2018 02 10;13(2):326-332. Epub 2018 Jan 10.

Department of Genome Sciences, University of Washington , Seattle, Washington 98195, United States.

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http://dx.doi.org/10.1021/acschembio.7b00778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218247PMC
February 2018

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

Cell Syst 2018 Jan 6;6(1):116-124.e3. Epub 2017 Dec 6.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24054712173049
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http://dx.doi.org/10.1016/j.cels.2017.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799033PMC
January 2018

Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing.

Methods Mol Biol 2018 ;1708:105-122

Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.

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http://link.springer.com/10.1007/978-1-4939-7481-8_6
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http://dx.doi.org/10.1007/978-1-4939-7481-8_6DOI Listing
July 2018

De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability.

Authors:
Sébastien Küry Geeske M van Woerden Thomas Besnard Martina Proietti Onori Xénia Latypova Meghan C Towne Megan T Cho Trine E Prescott Melissa A Ploeg Stephan Sanders Holly A F Stessman Aurora Pujol Ben Distel Laurie A Robak Jonathan A Bernstein Anne-Sophie Denommé-Pichon Gaëtan Lesca Elizabeth A Sellars Jonathan Berg Wilfrid Carré Øyvind Løvold Busk Bregje W M van Bon Jeff L Waugh Matthew Deardorff George E Hoganson Katherine B Bosanko Diana S Johnson Tabib Dabir Øystein Lunde Holla Ajoy Sarkar Kristian Tveten Julitta de Bellescize Geir J Braathen Paulien A Terhal Dorothy K Grange Arie van Haeringen Christina Lam Ghayda Mirzaa Jennifer Burton Elizabeth J Bhoj Jessica Douglas Avni B Santani Addie I Nesbitt Katherine L Helbig Marisa V Andrews Amber Begtrup Sha Tang Koen L I van Gassen Jane Juusola Kimberly Foss Gregory M Enns Ute Moog Katrin Hinderhofer Nagarajan Paramasivam Sharyn Lincoln Brandon H Kusako Pierre Lindenbaum Eric Charpentier Catherine B Nowak Elouan Cherot Thomas Simonet Claudia A L Ruivenkamp Sihoun Hahn Catherine A Brownstein Fan Xia Sébastien Schmitt Wallid Deb Dominique Bonneau Mathilde Nizon Delphine Quinquis Jamel Chelly Gabrielle Rudolf Damien Sanlaville Philippe Parent Brigitte Gilbert-Dussardier Annick Toutain Vernon R Sutton Jenny Thies Lisenka E L M Peart-Vissers Pierre Boisseau Marie Vincent Andreas M Grabrucker Christèle Dubourg Wen-Hann Tan Nienke E Verbeek Martin Granzow Gijs W E Santen Jay Shendure Bertrand Isidor Laurent Pasquier Richard Redon Yaping Yang Matthew W State Tjitske Kleefstra Benjamin Cogné Slavé Petrovski Kyle Retterer Evan E Eichler Jill A Rosenfeld Pankaj B Agrawal Stéphane Bézieau Sylvie Odent Ype Elgersma Sandra Mercier

Am J Hum Genet 2017 Nov;101(5):768-788

CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes Cedex 1, France.

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http://dx.doi.org/10.1016/j.ajhg.2017.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673671PMC
November 2017

DNA sequencing at 40: past, present and future.

Nature 2017 10 11;550(7676):345-353. Epub 2017 Oct 11.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nature24286DOI Listing
October 2017

The 4D nucleome project.

Nature 2017 09;549(7671):219-226

Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature23884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617335PMC
September 2017

Variant Interpretation: Functional Assays to the Rescue.

Am J Hum Genet 2017 Sep;101(3):315-325

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.07.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590843PMC
September 2017

Encephalopathy caused by novel mutations in the CMP-sialic acid transporter, SLC35A1.

Am J Med Genet A 2017 Nov 29;173(11):2906-2911. Epub 2017 Aug 29.

Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.

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http://doi.wiley.com/10.1002/ajmg.a.38412
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http://dx.doi.org/10.1002/ajmg.a.38412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5650519PMC
November 2017

CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions.

Am J Hum Genet 2017 Aug 14;101(2):192-205. Epub 2017 Jul 14.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297173024
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http://dx.doi.org/10.1016/j.ajhg.2017.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544381PMC
August 2017

The dynamic three-dimensional organization of the diploid yeast genome.

Elife 2017 05 24;6. Epub 2017 May 24.

Department of Genome Sciences, University of Washington, Seattle, United States.

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http://dx.doi.org/10.7554/eLife.23623DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5476426PMC
May 2017

Quantification of differential gene expression by multiplexed targeted resequencing of cDNA.

Nat Commun 2017 05 5;8:15190. Epub 2017 May 5.

Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/ncomms15190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5424154PMC
May 2017

Massively multiplex single-cell Hi-C.

Nat Methods 2017 03 30;14(3):263-266. Epub 2017 Jan 30.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nmeth.4155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330809PMC
March 2017

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

Methods Mol Biol 2017 ;1492:95-106

Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA.

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http://dx.doi.org/10.1007/978-1-4939-6442-0_6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484527PMC
January 2018

Classification and characterization of microsatellite instability across 18 cancer types.

Nat Med 2016 11 3;22(11):1342-1350. Epub 2016 Oct 3.

Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nm.4191DOI Listing
November 2016

Genome evolution in the allotetraploid frog Xenopus laevis.

Nature 2016 10;538(7625):336-343

University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.

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http://dx.doi.org/10.1038/nature19840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313049PMC
October 2016