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Items: 1 to 50 of 294

1.

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

Kircher M, Xiong C, Martin B, Schubach M, Inoue F, Bell RJA, Costello JF, Shendure J, Ahituv N.

Nat Commun. 2019 Aug 8;10(1):3583. doi: 10.1038/s41467-019-11526-w.

2.

Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy.

Bertero A, Fields PA, Smith AST, Leonard A, Beussman K, Sniadecki NJ, Kim DH, Tse HF, Pabon L, Shendure J, Noble WS, Murry CE.

J Cell Biol. 2019 Aug 8. pii: jcb.201902117. doi: 10.1083/jcb.201902117. [Epub ahead of print]

PMID:
31395619
3.

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

Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J.

Nucleic Acids Res. 2019 Jun 5. pii: gkz487. doi: 10.1093/nar/gkz487. [Epub ahead of print]

PMID:
31165867
4.

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

Klein JC, Keith A, Rice SJ, Shepherd C, Agarwal V, Loughlin J, Shendure J.

Nat Commun. 2019 Jun 4;10(1):2434. doi: 10.1038/s41467-019-10439-y.

5.

Expanding the single-cell genomics toolkit.

Minkina A, Shendure J.

Nat Genet. 2019 Jun;51(6):931-932. doi: 10.1038/s41588-019-0429-4. No abstract available.

PMID:
31152159
6.

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

Shigaki D, Adato O, Adhikari AN, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar DD, Schubach M, Xiong C, Yan Z, Boyle AP, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, Beer MA.

Hum Mutat. 2019 May 20. doi: 10.1002/humu.23797. [Epub ahead of print]

PMID:
31106481
7.

GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions.

Farhat MR, Freschi L, Calderon R, Ioerger T, Snyder M, Meehan CJ, de Jong B, Rigouts L, Sloutsky A, Kaur D, Sunyaev S, van Soolingen D, Shendure J, Sacchettini J, Murray M.

Nat Commun. 2019 May 13;10(1):2128. doi: 10.1038/s41467-019-10110-6.

8.

A combination of transcription factors mediates inducible interchromosomal contacts.

Kim S, Dunham MJ, Shendure J.

Elife. 2019 May 13;8. pii: e42499. doi: 10.7554/eLife.42499.

9.

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

Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH.

Nature. 2019 Apr;568(7752):E11. doi: 10.1038/s41586-019-1120-8.

PMID:
30948799
10.

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory.

Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE.

Nat Commun. 2019 Apr 4;10(1):1538. doi: 10.1038/s41467-019-09483-5.

11.

Mutations in the translocon-associated protein complex subunit SSR3 cause a novel congenital disorder of glycosylation.

Ng BG, Lourenço CM, Losfeld ME, Buckingham KJ, Kircher M, Nickerson DA, Shendure J, Bamshad MJ; University of Washington Center for Mendelian Genomics, Freeze HH.

J Inherit Metab Dis. 2019 Apr 3. doi: 10.1002/jimd.12091. [Epub ahead of print]

PMID:
30945312
12.

Genomic Medicine-Progress, Pitfalls, and Promise.

Shendure J, Findlay GM, Snyder MW.

Cell. 2019 Mar 21;177(1):45-57. doi: 10.1016/j.cell.2019.02.003. Review.

PMID:
30901547
13.

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

Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J.

Cell. 2019 Mar 7;176(6):1516. doi: 10.1016/j.cell.2019.02.027. No abstract available.

PMID:
30849375
14.

High Sensitivity Profiling of Chromatin Structure by MNase-SSP.

Ramani V, Qiu R, Shendure J.

Cell Rep. 2019 Feb 26;26(9):2465-2476.e4. doi: 10.1016/j.celrep.2019.02.007.

15.

The single-cell transcriptional landscape of mammalian organogenesis.

Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J.

Nature. 2019 Feb;566(7745):496-502. doi: 10.1038/s41586-019-0969-x. Epub 2019 Feb 20.

16.

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

Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J.

Cell. 2019 Jan 10;176(1-2):377-390.e19. doi: 10.1016/j.cell.2018.11.029. Epub 2019 Jan 3. Erratum in: Cell. 2019 Mar 7;176(6):1516.

17.

Condensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence.

Swygert SG, Kim S, Wu X, Fu T, Hsieh TH, Rando OJ, Eisenman RN, Shendure J, McKnight JN, Tsukiyama T.

Mol Cell. 2019 Feb 7;73(3):533-546.e4. doi: 10.1016/j.molcel.2018.11.020. Epub 2018 Dec 27.

PMID:
30595435
18.

New insights into structural features and optimal detection of circulating tumor DNA determined by single-strand DNA analysis.

Sanchez C, Snyder MW, Tanos R, Shendure J, Thierry AR.

NPJ Genom Med. 2018 Nov 23;3:31. doi: 10.1038/s41525-018-0069-0. eCollection 2018.

19.

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

Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M.

Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894. doi: 10.1093/nar/gky1016.

20.

Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History.

Liu S, Huang S, Chen F, Zhao L, Yuan Y, Francis SS, Fang L, Li Z, Lin L, Liu R, Zhang Y, Xu H, Li S, Zhou Y, Davies RW, Liu Q, Walters RG, Lin K, Ju J, Korneliussen T, Yang MA, Fu Q, Wang J, Zhou L, Krogh A, Zhang H, Wang W, Chen Z, Cai Z, Yin Y, Yang H, Mao M, Shendure J, Wang J, Albrechtsen A, Jin X, Nielsen R, Xu X.

Cell. 2018 Oct 4;175(2):347-359.e14. doi: 10.1016/j.cell.2018.08.016.

PMID:
30290141
21.

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

CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B.

N Engl J Med. 2018 Oct 11;379(15):1403-1415. doi: 10.1056/NEJMoa1800474. Epub 2018 Sep 26.

22.

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

Starita LM, Islam MM, Banerjee T, Adamovich AI, Gullingsrud J, Fields S, Shendure J, Parvin JD.

Am J Hum Genet. 2018 Oct 4;103(4):498-508. doi: 10.1016/j.ajhg.2018.07.016. Epub 2018 Sep 12.

23.

Accurate classification of BRCA1 variants with saturation genome editing.

Findlay GM, Daza RM, Martin B, Zhang MD, Leith AP, Gasperini M, Janizek JD, Huang X, Starita LM, Shendure J.

Nature. 2018 Oct;562(7726):217-222. doi: 10.1038/s41586-018-0461-z. Epub 2018 Sep 12.

24.

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J.

Science. 2018 Sep 28;361(6409):1380-1385. doi: 10.1126/science.aau0730. Epub 2018 Aug 30.

25.

DPAGT1 Deficiency with Encephalopathy (DPAGT1-CDG): Clinical and Genetic Description of 11 New Patients.

Ng BG, Underhill HR, Palm L, Bengtson P, Rozet JM, Gerber S, Munnich A, Zanlonghi X, Stevens CA, Kircher M, Nickerson DA, Buckingham KJ, Josephson KD, Shendure J, Bamshad MJ; University of Washington Center for Mendelian Genomics, Freeze HH, Eklund EA.

JIMD Rep. 2019;44:85-92. doi: 10.1007/8904_2018_128. Epub 2018 Aug 17.

26.

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

Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C.

Mol Cell. 2018 Sep 6;71(5):858-871.e8. doi: 10.1016/j.molcel.2018.06.044. Epub 2018 Aug 2.

27.

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

Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J.

Cell. 2018 Aug 23;174(5):1309-1324.e18. doi: 10.1016/j.cell.2018.06.052. Epub 2018 Aug 2.

28.

Functional characterization of enhancer evolution in the primate lineage.

Klein JC, Keith A, Agarwal V, Durham T, Shendure J.

Genome Biol. 2018 Jul 25;19(1):99. doi: 10.1186/s13059-018-1473-6.

29.

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

McKenna A, Shendure J.

BMC Biol. 2018 Jul 5;16(1):74. doi: 10.1186/s12915-018-0545-0.

30.

High-resolution comparative analysis of great ape genomes.

Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE.

Science. 2018 Jun 8;360(6393). pii: eaar6343. doi: 10.1126/science.aar6343.

31.

Multiplex assessment of protein variant abundance by massively parallel sequencing.

Matreyek KA, Starita LM, Stephany JJ, Martin B, Chiasson MA, Gray VE, Kircher M, Khechaduri A, Dines JN, Hause RJ, Bhatia S, Evans WE, Relling MV, Yang W, Shendure J, Fowler DM.

Nat Genet. 2018 Jun;50(6):874-882. doi: 10.1038/s41588-018-0122-z. Epub 2018 May 21.

32.

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

Inoue F, Kircher M, Martin B, Cooper GM, Witten DM, McManus MT, Ahituv N, Shendure J.

Genome Res. 2018 May;28(5):766.3. doi: 10.1101/gr.237321.118. No abstract available.

33.

Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.

Bonora G, Deng X, Fang H, Ramani V, Qiu R, Berletch JB, Filippova GN, Duan Z, Shendure J, Noble WS, Disteche CM.

Nat Commun. 2018 Apr 13;9(1):1445. doi: 10.1038/s41467-018-03694-y.

34.

Highly scalable generation of DNA methylation profiles in single cells.

Mulqueen RM, Pokholok D, Norberg SJ, Torkenczy KA, Fields AJ, Sun D, Sinnamon JR, Shendure J, Trapnell C, O'Roak BJ, Xia Z, Steemers FJ, Adey AC.

Nat Biotechnol. 2018 Jun;36(5):428-431. doi: 10.1038/nbt.4112. Epub 2018 Apr 9.

35.

Corrigendum: Classification and characterization of microsatellite instability across 18 cancer types.

Hause RJ, Pritchard CC, Shendure J, Salipante SJ.

Nat Med. 2018 Apr 10;24(4):525. doi: 10.1038/nm0418-525a.

PMID:
29634692
36.

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

Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF.

Nat Biotechnol. 2018 Jun;36(5):442-450. doi: 10.1038/nbt.4103. Epub 2018 Mar 28.

37.

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

Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM.

Nature. 2018 Mar 22;555(7697):538-542. doi: 10.1038/nature25981. Epub 2018 Mar 14.

38.

On the design of CRISPR-based single-cell molecular screens.

Hill AJ, McFaline-Figueroa JL, Starita LM, Gasperini MJ, Matreyek KA, Packer J, Jackson D, Shendure J, Trapnell C.

Nat Methods. 2018 Apr;15(4):271-274. doi: 10.1038/nmeth.4604. Epub 2018 Feb 19.

39.

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

Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z.

Methods. 2018 Jun 1;142:59-73. doi: 10.1016/j.ymeth.2018.01.014. Epub 2018 Jan 31.

40.

Identifying Novel Enhancer Elements with CRISPR-Based Screens.

Klein JC, Chen W, Gasperini M, Shendure J.

ACS Chem Biol. 2018 Feb 16;13(2):326-332. doi: 10.1021/acschembio.7b00778. Epub 2018 Jan 10. Review.

41.

Novel approach to genetic analysis and results in 3000 hemophilia patients enrolled in the My Life, Our Future initiative.

Johnsen JM, Fletcher SN, Huston H, Roberge S, Martin BK, Kircher M, Josephson NC, Shendure J, Ruuska S, Koerper MA, Morales J, Pierce GF, Aschman DJ, Konkle BA.

Blood Adv. 2017 May 18;1(13):824-834. doi: 10.1182/bloodadvances.2016002923. eCollection 2017 May 23.

42.

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

Gray VE, Hause RJ, Luebeck J, Shendure J, Fowler DM.

Cell Syst. 2018 Jan 24;6(1):116-124.e3. doi: 10.1016/j.cels.2017.11.003. Epub 2017 Dec 6.

43.

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

Weichenhan D, Wang Q, Adey A, Wolf S, Shendure J, Eils R, Plass C.

Methods Mol Biol. 2018;1708:105-122. doi: 10.1007/978-1-4939-7481-8_6.

PMID:
29224141
44.

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

Liu J, Halloran JT, Bilmes JA, Daza RM, Lee C, Mahen EM, Prunkard D, Song C, Blau S, Dorschner MO, Gadi VK, Shendure J, Blau CA, Noble WS.

Sci Rep. 2017 Dec 5;7(1):16943. doi: 10.1038/s41598-017-16813-4.

45.

Corrigendum: The 4D nucleome project.

Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S; 4D Nucleome Network.

Nature. 2017 Dec 14;552(7684):278. doi: 10.1038/nature24667. Epub 2017 Nov 22.

PMID:
29168505
46.

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

Küry S, van Woerden GM, Besnard T, Proietti Onori M, Latypova X, Towne MC, Cho MT, Prescott TE, Ploeg MA, Sanders S, Stessman HAF, Pujol A, Distel B, Robak LA, Bernstein JA, Denommé-Pichon AS, Lesca G, Sellars EA, Berg J, Carré W, Busk ØL, van Bon BWM, Waugh JL, Deardorff M, Hoganson GE, Bosanko KB, Johnson DS, Dabir T, Holla ØL, Sarkar A, Tveten K, de Bellescize J, Braathen GJ, Terhal PA, Grange DK, van Haeringen A, Lam C, Mirzaa G, Burton J, Bhoj EJ, Douglas J, Santani AB, Nesbitt AI, Helbig KL, Andrews MV, Begtrup A, Tang S, van Gassen KLI, Juusola J, Foss K, Enns GM, Moog U, Hinderhofer K, Paramasivam N, Lincoln S, Kusako BH, Lindenbaum P, Charpentier E, Nowak CB, Cherot E, Simonet T, Ruivenkamp CAL, Hahn S, Brownstein CA, Xia F, Schmitt S, Deb W, Bonneau D, Nizon M, Quinquis D, Chelly J, Rudolf G, Sanlaville D, Parent P, Gilbert-Dussardier B, Toutain A, Sutton VR, Thies J, Peart-Vissers LELM, Boisseau P, Vincent M, Grabrucker AM, Dubourg C; Undiagnosed Diseases Network, Tan WH, Verbeek NE, Granzow M, Santen GWE, Shendure J, Isidor B, Pasquier L, Redon R, Yang Y, State MW, Kleefstra T, Cogné B; GEM HUGO; Deciphering Developmental Disorders Study, Petrovski S, Retterer K, Eichler EE, Rosenfeld JA, Agrawal PB, Bézieau S, Odent S, Elgersma Y, Mercier S.

Am J Hum Genet. 2017 Nov 2;101(5):768-788. doi: 10.1016/j.ajhg.2017.10.003.

47.

DNA sequencing at 40: past, present and future.

Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH.

Nature. 2017 Oct 19;550(7676):345-353. doi: 10.1038/nature24286. Epub 2017 Oct 11. Review. Erratum in: Nature. 2019 Apr;568(7752):E11.

PMID:
29019985
48.

Corrigendum: Classification and characterization of microsatellite instability across 18 cancer types.

Hause RJ, Pritchard CC, Shendure J, Salipante SJ.

Nat Med. 2017 Oct 6;23(10):1241. doi: 10.1038/nm1017-1241a.

PMID:
28985213
49.

The 4D nucleome project.

Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S; 4D Nucleome Network.

Nature. 2017 Sep 13;549(7671):219-226. doi: 10.1038/nature23884. Erratum in: Nature. 2017 Nov 22;:.

50.

Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C.

Smukowski Heil C, Burton JN, Liachko I, Friedrich A, Hanson NA, Morris CL, Schacherer J, Shendure J, Thomas JH, Dunham MJ.

Yeast. 2018 Jan;35(1):71-84. doi: 10.1002/yea.3280. Epub 2017 Oct 19.

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