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Items: 1 to 50 of 302

1.

The Rhododendron genome and chromosomal organization provide insight into shared whole genome duplications across the heath family (Ericaceae).

Soza VL, Lindsley D, Waalkes A, Ramage E, Patwardhan RP, Burton JN, Adey A, Kumar A, Qiu R, Shendure J, Hall B.

Genome Biol Evol. 2019 Nov 8. pii: evz245. doi: 10.1093/gbe/evz245. [Epub ahead of print]

PMID:
31702783
2.

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

Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF.

Genome Biol. 2019 Nov 4;20(1):223. doi: 10.1186/s13059-019-1845-6.

3.

Voices in methods development.

Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW Jr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X.

Nat Methods. 2019 Oct;16(10):945-951. doi: 10.1038/s41592-019-0585-6. No abstract available.

PMID:
31562479
4.

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

Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z.

Methods. 2019 Sep 16. pii: S1046-2023(18)30475-4. doi: 10.1016/j.ymeth.2019.09.012. [Epub ahead of print]

PMID:
31536770
5.

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

Kim S, Shendure J.

Mol Cell. 2019 Oct 17;76(2):306-319. doi: 10.1016/j.molcel.2019.08.010. Epub 2019 Sep 11. Review.

PMID:
31521504
6.

Supervised classification enables rapid annotation of cell atlases.

Pliner HA, Shendure J, Trapnell C.

Nat Methods. 2019 Oct;16(10):983-986. doi: 10.1038/s41592-019-0535-3. Epub 2019 Sep 9.

PMID:
31501545
7.

High-Throughput Single-Cell Sequencing with Linear Amplification.

Yin Y, Jiang Y, Lam KG, Berletch JB, Disteche CM, Noble WS, Steemers FJ, Camerini-Otero RD, Adey AC, Shendure J.

Mol Cell. 2019 Aug 28. pii: S1097-2765(19)30618-5. doi: 10.1016/j.molcel.2019.08.002. [Epub ahead of print]

PMID:
31495564
8.

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

McFaline-Figueroa JL, Hill AJ, Qiu X, Jackson D, Shendure J, Trapnell C.

Nat Genet. 2019 Sep;51(9):1389-1398. doi: 10.1038/s41588-019-0489-5. Epub 2019 Sep 2.

PMID:
31477929
9.

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.

10.

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 Sep 2;218(9):2919-2944. doi: 10.1083/jcb.201902117. Epub 2019 Aug 8.

PMID:
31395619
11.

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 Sep 5;47(15):7989-8003. doi: 10.1093/nar/gkz487.

12.

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.

13.

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
14.

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 Sep;40(9):1280-1291. doi: 10.1002/humu.23797. Epub 2019 Jun 23.

PMID:
31106481
15.

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.

16.

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.

17.

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
18.

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.

19.

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 Sep;42(5):993-997. doi: 10.1002/jimd.12091. Epub 2019 Apr 16.

PMID:
30945312
20.

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
21.

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
22.

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.

23.

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.

24.

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.

25.

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
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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
44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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