Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 71

1.

Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin.

Yang D, Denny SK, Greenside PG, Chaikovsky AC, Brady JJ, Ouadah Y, Granja JM, Jahchan NS, Lim JS, Kwok S, Kong CS, Berghoff AS, Schmitt A, Reinhardt HC, Park KS, Preusser M, Kundaje A, Greenleaf WJ, Sage J, Winslow MM.

Cancer Discov. 2018 Sep 18. doi: 10.1158/2159-8290.CD-17-0987. [Epub ahead of print]

PMID:
30228179
2.

A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas.

Arda HE, Tsai J, Rosli YR, Giresi P, Bottino R, Greenleaf WJ, Chang HY, Kim SK.

Cell Syst. 2018 Aug 10. pii: S2405-4712(18)30315-6. doi: 10.1016/j.cels.2018.07.007. [Epub ahead of print]

PMID:
30145115
3.

Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency.

Mor N, Rais Y, Sheban D, Peles S, Aguilera-Castrejon A, Zviran A, Elinger D, Viukov S, Geula S, Krupalnik V, Zerbib M, Chomsky E, Lasman L, Shani T, Bayerl J, Gafni O, Hanna S, Buenrostro JD, Hagai T, Masika H, Vainorius G, Bergman Y, Greenleaf WJ, Esteban MA, Elling U, Levin Y, Massarwa R, Merbl Y, Novershtern N, Hanna JH.

Cell Stem Cell. 2018 Sep 6;23(3):412-425.e10. doi: 10.1016/j.stem.2018.07.004. Epub 2018 Aug 16.

PMID:
30122475
4.

High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding.

Denny SK, Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ.

Cell. 2018 Jul 12;174(2):377-390.e20. doi: 10.1016/j.cell.2018.05.038. Epub 2018 Jun 28.

PMID:
29961580
5.

Unsupervised clustering and epigenetic classification of single cells.

Zamanighomi M, Lin Z, Daley T, Chen X, Duren Z, Schep A, Greenleaf WJ, Wong WH.

Nat Commun. 2018 Jun 20;9(1):2410. doi: 10.1038/s41467-018-04629-3.

6.

Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation.

Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A.

Nature. 2018 Jul;559(7715):E13. doi: 10.1038/s41586-018-0227-7.

PMID:
29899441
7.

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.

Buenrostro JD, Corces MR, Lareau CA, Wu B, Schep AN, Aryee MJ, Majeti R, Chang HY, Greenleaf WJ.

Cell. 2018 May 31;173(6):1535-1548.e16. doi: 10.1016/j.cell.2018.03.074. Epub 2018 Apr 26.

PMID:
29706549
8.

Transcript-indexed ATAC-seq for precision immune profiling.

Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, Granja JM, Lareau CA, Li R, Qi Y, Parker KR, Mumbach MR, Serratelli WS, Gennert DG, Schep AN, Corces MR, Khodadoust MS, Kim YH, Khavari PA, Greenleaf WJ, Davis MM, Chang HY.

Nat Med. 2018 May;24(5):580-590. doi: 10.1038/s41591-018-0008-8. Epub 2018 Apr 23.

PMID:
29686426
9.

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts.

Bell JC, Jukam D, Teran NA, Risca VI, Smith OK, Johnson WL, Skotheim JM, Greenleaf WJ, Straight AF.

Elife. 2018 Apr 12;7. pii: e27024. doi: 10.7554/eLife.27024.

10.

Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery.

Aggeli D, Karas VO, Sinnott-Armstrong NA, Varghese V, Shafer RW, Greenleaf WJ, Sherlock G.

Nucleic Acids Res. 2018 Apr 20;46(7):e42. doi: 10.1093/nar/gky022.

11.

INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division.

Gowans GJ, Schep AN, Wong KM, King DA, Greenleaf WJ, Morrison AJ.

Cell Rep. 2018 Jan 16;22(3):611-623. doi: 10.1016/j.celrep.2017.12.079.

12.

Rapid chromatin repression by Aire provides precise control of immune tolerance.

Koh AS, Miller EL, Buenrostro JD, Moskowitz DM, Wang J, Greenleaf WJ, Chang HY, Crabtree GR.

Nat Immunol. 2018 Feb;19(2):162-172. doi: 10.1038/s41590-017-0032-8. Epub 2018 Jan 15.

13.

A Public Database of Immersive VR Videos with Corresponding Ratings of Arousal, Valence, and Correlations between Head Movements and Self Report Measures.

Li BJ, Bailenson JN, Pines A, Greenleaf WJ, Williams LM.

Front Psychol. 2017 Dec 5;8:2116. doi: 10.3389/fpsyg.2017.02116. eCollection 2017.

14.

Origin and differentiation of human memory CD8 T cells after vaccination.

Akondy RS, Fitch M, Edupuganti S, Yang S, Kissick HT, Li KW, Youngblood BA, Abdelsamed HA, McGuire DJ, Cohen KW, Alexe G, Nagar S, McCausland MM, Gupta S, Tata P, Haining WN, McElrath MJ, Zhang D, Hu B, Greenleaf WJ, Goronzy JJ, Mulligan MJ, Hellerstein M, Ahmed R.

Nature. 2017 Dec 21;552(7685):362-367. doi: 10.1038/nature24633. Epub 2017 Dec 13.

15.

Challenges and recommendations for epigenomics in precision health.

Carter AC, Chang HY, Church G, Dombkowski A, Ecker JR, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill D, Ko J, Kohane I, Kundaje A, Palmer M, Snyder MP, Tung J, Urban A, Vidal M, Wong W.

Nat Biotechnol. 2017 Dec 8;35(12):1128-1132. doi: 10.1038/nbt.4030. No abstract available.

16.

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans.

Daugherty AC, Yeo RW, Buenrostro JD, Greenleaf WJ, Kundaje A, Brunet A.

Genome Res. 2017 Dec;27(12):2096-2107. doi: 10.1101/gr.226233.117. Epub 2017 Nov 15.

17.

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.

Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY.

Nat Genet. 2017 Nov;49(11):1602-1612. doi: 10.1038/ng.3963. Epub 2017 Sep 25.

18.

Discovery of stimulation-responsive immune enhancers with CRISPR activation.

Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A.

Nature. 2017 Sep 7;549(7670):111-115. doi: 10.1038/nature23875. Epub 2017 Aug 30. Erratum in: Nature. 2018 Jul;559(7715):E13.

19.

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY.

Nat Methods. 2017 Oct;14(10):959-962. doi: 10.1038/nmeth.4396. Epub 2017 Aug 28.

20.

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.

Schep AN, Wu B, Buenrostro JD, Greenleaf WJ.

Nat Methods. 2017 Oct;14(10):975-978. doi: 10.1038/nmeth.4401. Epub 2017 Aug 21.

21.

Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.

Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, Snyder M, Chang HY, Fraser P, Khavari PA.

Nat Genet. 2017 Oct;49(10):1522-1528. doi: 10.1038/ng.3935. Epub 2017 Aug 14.

22.

Open Chromatin Profiling in hiPSC-Derived Neurons Prioritizes Functional Noncoding Psychiatric Risk Variants and Highlights Neurodevelopmental Loci.

Forrest MP, Zhang H, Moy W, McGowan H, Leites C, Dionisio LE, Xu Z, Shi J, Sanders AR, Greenleaf WJ, Cowan CA, Pang ZP, Gejman PV, Penzes P, Duan J.

Cell Stem Cell. 2017 Sep 7;21(3):305-318.e8. doi: 10.1016/j.stem.2017.07.008. Epub 2017 Aug 10.

23.

Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors.

Qu K, Zaba LC, Satpathy AT, Giresi PG, Li R, Jin Y, Armstrong R, Jin C, Schmitt N, Rahbar Z, Ueno H, Greenleaf WJ, Kim YH, Chang HY.

Cancer Cell. 2017 Jul 10;32(1):27-41.e4. doi: 10.1016/j.ccell.2017.05.008. Epub 2017 Jun 15.

24.

Corrigendum: Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells.

Xu J, Carter AC, Gendrel AV, Attia M, Loftus J, Greenleaf WJ, Tibshirani R, Heard E, Chang HY.

Nat Genet. 2017 May 26;49(6):970. doi: 10.1038/ng0617-970a. No abstract available.

PMID:
28546577
25.

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding.

Boyle EA, Andreasson JOL, Chircus LM, Sternberg SH, Wu MJ, Guegler CK, Doudna JA, Greenleaf WJ.

Proc Natl Acad Sci U S A. 2017 May 23;114(21):5461-5466. doi: 10.1073/pnas.1700557114. Epub 2017 May 11.

26.

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens.

Morgens DW, Wainberg M, Boyle EA, Ursu O, Araya CL, Tsui CK, Haney MS, Hess GT, Han K, Jeng EE, Li A, Snyder MP, Greenleaf WJ, Kundaje A, Bassik MC.

Nat Commun. 2017 May 5;8:15178. doi: 10.1038/ncomms15178.

27.

Epigenomics of human CD8 T cell differentiation and aging.

Moskowitz DM, Zhang DW, Hu B, Le Saux S, Yanes RE, Ye Z, Buenrostro JD, Weyand CM, Greenleaf WJ, Goronzy JJ.

Sci Immunol. 2017 Feb;2(8). pii: eaag0192. doi: 10.1126/sciimmunol.aag0192. Epub 2017 Feb 17.

28.

Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome.

She R, Chakravarty AK, Layton CJ, Chircus LM, Andreasson JO, Damaraju N, McMahon PL, Buenrostro JD, Jarosz DF, Greenleaf WJ.

Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):3619-3624. doi: 10.1073/pnas.1618370114. Epub 2017 Mar 21.

29.

TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin.

Miller EL, Hargreaves DC, Kadoch C, Chang CY, Calarco JP, Hodges C, Buenrostro JD, Cui K, Greenleaf WJ, Zhao K, Crabtree GR.

Nat Struct Mol Biol. 2017 Apr;24(4):344-352. doi: 10.1038/nsmb.3384. Epub 2017 Feb 27.

30.

Single-cell epigenomic variability reveals functional cancer heterogeneity.

Litzenburger UM, Buenrostro JD, Wu B, Shen Y, Sheffield NC, Kathiria A, Greenleaf WJ, Chang HY.

Genome Biol. 2017 Jan 24;18(1):15. doi: 10.1186/s13059-016-1133-7.

31.

Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells.

Xu J, Carter AC, Gendrel AV, Attia M, Loftus J, Greenleaf WJ, Tibshirani R, Heard E, Chang HY.

Nat Genet. 2017 Mar;49(3):377-386. doi: 10.1038/ng.3769. Epub 2017 Jan 23. Erratum in: Nat Genet. 2017 May 26;49(6):970.

32.

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping.

Risca VI, Denny SK, Straight AF, Greenleaf WJ.

Nature. 2017 Jan 12;541(7636):237-241. doi: 10.1038/nature20781. Epub 2016 Dec 26.

33.

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.

Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY.

Nat Methods. 2016 Dec;13(12):1013-1020. doi: 10.1038/nmeth.4031. Epub 2016 Oct 17.

34.

HiChIP: efficient and sensitive analysis of protein-directed genome architecture.

Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, Chang HY.

Nat Methods. 2016 Nov;13(11):919-922. doi: 10.1038/nmeth.3999. Epub 2016 Sep 19.

35.

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution.

Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY.

Nat Genet. 2016 Oct;48(10):1193-203. doi: 10.1038/ng.3646. Epub 2016 Aug 15.

36.

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility.

Denny SK, Yang D, Chuang CH, Brady JJ, Lim JS, GrĂ¼ner BM, Chiou SH, Schep AN, Baral J, Hamard C, Antoine M, Wislez M, Kong CS, Connolly AJ, Park KS, Sage J, Greenleaf WJ, Winslow MM.

Cell. 2016 Jul 14;166(2):328-342. doi: 10.1016/j.cell.2016.05.052. Epub 2016 Jun 30.

37.

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations.

Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WJ.

Nat Genet. 2016 Feb;48(2):117-25. doi: 10.1038/ng.3471. Epub 2015 Dec 21.

38.

Beyond the Linear Genome: Paired-End Sequencing as a Biophysical Tool.

Risca VI, Greenleaf WJ.

Trends Cell Biol. 2015 Dec;25(12):716-719. doi: 10.1016/j.tcb.2015.08.004. Epub 2015 Oct 1.

39.

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.

Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ.

Genome Res. 2015 Nov;25(11):1757-70. doi: 10.1101/gr.192294.115. Epub 2015 Aug 27.

40.

Individuality and variation of personal regulomes in primary human T cells.

Qu K, Zaba LC, Giresi PG, Li R, Longmire M, Kim YH, Greenleaf WJ, Chang HY.

Cell Syst. 2015 Jul 29;1(1):51-61.

41.

Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors.

Maza I, Caspi I, Zviran A, Chomsky E, Rais Y, Viukov S, Geula S, Buenrostro JD, Weinberger L, Krupalnik V, Hanna S, Zerbib M, Dutton JR, Greenleaf WJ, Massarwa R, Novershtern N, Hanna JH.

Nat Biotechnol. 2015 Jul;33(7):769-74. doi: 10.1038/nbt.3270. Epub 2015 Jun 22.

42.

Single-cell chromatin accessibility reveals principles of regulatory variation.

Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ.

Nature. 2015 Jul 23;523(7561):486-90. doi: 10.1038/nature14590. Epub 2015 Jun 17.

43.

Unraveling the 3D genome: genomics tools for multiscale exploration.

Risca VI, Greenleaf WJ.

Trends Genet. 2015 Jul;31(7):357-72. doi: 10.1016/j.tig.2015.03.010. Epub 2015 Apr 14. Review.

44.

ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.

Buenrostro JD, Wu B, Chang HY, Greenleaf WJ.

Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-9. doi: 10.1002/0471142727.mb2129s109.

45.

Assaying the epigenome in limited numbers of cells.

Greenleaf WJ.

Methods. 2015 Jan 15;72:51-6. doi: 10.1016/j.ymeth.2014.10.010. Epub 2014 Oct 22. Review.

46.

The future of sequencing: convergence of intelligent design and market Darwinism.

Greenleaf WJ, Sidow A.

Genome Biol. 2014 Mar 25;15(3):303. doi: 10.1186/gb4168.

47.

A conditional system to specifically link disruption of protein-coding function with reporter expression in mice.

Chiou SH, Kim-Kiselak C, Risca VI, Heimann MK, Chuang CH, Burds AA, Greenleaf WJ, Jacks TE, Feldser DM, Winslow MM.

Cell Rep. 2014 Jun 26;7(6):2078-86. doi: 10.1016/j.celrep.2014.05.031. Epub 2014 Jun 12.

48.

A pause sequence enriched at translation start sites drives transcription dynamics in vivo.

Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ, Landick R, Weissman JS.

Science. 2014 May 30;344(6187):1042-7. doi: 10.1126/science.1251871. Epub 2014 May 1.

49.

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes.

Buenrostro JD, Araya CL, Chircus LM, Layton CJ, Chang HY, Snyder MP, Greenleaf WJ.

Nat Biotechnol. 2014 Jun;32(6):562-8. doi: 10.1038/nbt.2880. Epub 2014 Apr 13.

50.

Exome sequencing identifies a DNAJB6 mutation in a family with dominantly-inherited limb-girdle muscular dystrophy.

Couthouis J, Raphael AR, Siskind C, Findlay AR, Buenrostro JD, Greenleaf WJ, Vogel H, Day JW, Flanigan KM, Gitler AD.

Neuromuscul Disord. 2014 May;24(5):431-5. doi: 10.1016/j.nmd.2014.01.014. Epub 2014 Feb 10.

Supplemental Content

Loading ...
Support Center