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Items: 1 to 50 of 90

1.

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements.

Tycko J, Wainberg M, Marinov GK, Ursu O, Hess GT, Ego BK, Aradhana, Li A, Truong A, Trevino AE, Spees K, Yao D, Kaplow IM, Greenside PG, Morgens DW, Phanstiel DH, Snyder MP, Bintu L, Greenleaf WJ, Kundaje A, Bassik MC.

Nat Commun. 2019 Sep 6;10(1):4063. doi: 10.1038/s41467-019-11955-7.

2.

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion.

Satpathy AT, Granja JM, Yost KE, Qi Y, Meschi F, McDermott GP, Olsen BN, Mumbach MR, Pierce SE, Corces MR, Shah P, Bell JC, Jhutty D, Nemec CM, Wang J, Wang L, Yin Y, Giresi PG, Chang ALS, Zheng GXY, Greenleaf WJ, Chang HY.

Nat Biotechnol. 2019 Aug;37(8):925-936. doi: 10.1038/s41587-019-0206-z. Epub 2019 Aug 2.

PMID:
31375813
3.

Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation.

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

Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):16847-16855. doi: 10.1073/pnas.1901530116. Epub 2019 Aug 2.

PMID:
31375637
4.

Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions.

Ghosh RP, Shi Q, Yang L, Reddick MP, Nikitina T, Zhurkin VB, Fordyce P, Stasevich TJ, Chang HY, Greenleaf WJ, Liphardt JT.

Nat Commun. 2019 Jul 19;10(1):3221. doi: 10.1038/s41467-019-11118-8.

5.

High-Throughput Analysis Reveals Rules for Target RNA Binding and Cleavage by AGO2.

Becker WR, Ober-Reynolds B, Jouravleva K, Jolly SM, Zamore PD, Greenleaf WJ.

Mol Cell. 2019 Aug 22;75(4):741-755.e11. doi: 10.1016/j.molcel.2019.06.012. Epub 2019 Jul 16.

PMID:
31324449
6.

Epigenetic signature of PD-1+ TCF1+ CD8 T cells that act as resource cells during chronic viral infection and respond to PD-1 blockade.

Jadhav RR, Im SJ, Hu B, Hashimoto M, Li P, Lin JX, Leonard WJ, Greenleaf WJ, Ahmed R, Goronzy JJ.

Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14113-14118. doi: 10.1073/pnas.1903520116. Epub 2019 Jun 21.

7.

HiChIRP reveals RNA-associated chromosome conformation.

Mumbach MR, Granja JM, Flynn RA, Roake CM, Satpathy AT, Rubin AJ, Qi Y, Jiang Z, Shams S, Louie BH, Guo JK, Gennert DG, Corces MR, Khavari PA, Atianand MK, Artandi SE, Fitzgerald KA, Greenleaf WJ, Chang HY.

Nat Methods. 2019 Jun;16(6):489-492. doi: 10.1038/s41592-019-0407-x. Epub 2019 May 27.

8.

A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins.

Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D.

Mol Cell. 2019 Jun 6;74(5):966-981.e18. doi: 10.1016/j.molcel.2019.04.012. Epub 2019 May 8.

PMID:
31078383
9.

Blind tests of RNA-protein binding affinity prediction.

Kappel K, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D, Das R.

Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8336-8341. doi: 10.1073/pnas.1819047116. Epub 2019 Apr 8.

PMID:
30962376
10.

Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2.

Becker WR, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D.

RNA. 2019 Jun;25(6):702-712. doi: 10.1261/rna.068585.118. Epub 2019 Mar 26.

PMID:
30914482
11.

Large-Scale, Quantitative Protein Assays on a High-Throughput DNA Sequencing Chip.

Layton CJ, McMahon PL, Greenleaf WJ.

Mol Cell. 2019 Mar 7;73(5):1075-1082.e4. doi: 10.1016/j.molcel.2019.02.019.

PMID:
30849388
12.

Chromatin accessibility and the regulatory epigenome.

Klemm SL, Shipony Z, Greenleaf WJ.

Nat Rev Genet. 2019 Apr;20(4):207-220. doi: 10.1038/s41576-018-0089-8. Review.

PMID:
30675018
13.

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.

Rubin AJ, Parker KR, Satpathy AT, Qi Y, Wu B, Ong AJ, Mumbach MR, Ji AL, Kim DS, Cho SW, Zarnegar BJ, Greenleaf WJ, Chang HY, Khavari PA.

Cell. 2019 Jan 10;176(1-2):361-376.e17. doi: 10.1016/j.cell.2018.11.022. Epub 2018 Dec 20.

PMID:
30580963
14.

High-resolution mapping of cancer cell networks using co-functional interactions.

Boyle EA, Pritchard JK, Greenleaf WJ.

Mol Syst Biol. 2018 Dec 20;14(12):e8594. doi: 10.15252/msb.20188594.

15.

Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules.

Zviran A, Mor N, Rais Y, Gingold H, Peles S, Chomsky E, Viukov S, Buenrostro JD, Scognamiglio R, Weinberger L, Manor YS, Krupalnik V, Zerbib M, Hezroni H, Jaitin DA, Larastiaso D, Gilad S, Benjamin S, Gafni O, Mousa A, Ayyash M, Sheban D, Bayerl J, Aguilera-Castrejon A, Massarwa R, Maza I, Hanna S, Stelzer Y, Ulitsky I, Greenleaf WJ, Tanay A, Trumpp A, Amit I, Pilpel Y, Novershtern N, Hanna JH.

Cell Stem Cell. 2019 Feb 7;24(2):328-341.e9. doi: 10.1016/j.stem.2018.11.014. Epub 2018 Dec 13.

PMID:
30554962
16.

Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens.

Haney MS, Bohlen CJ, Morgens DW, Ousey JA, Barkal AA, Tsui CK, Ego BK, Levin R, Kamber RA, Collins H, Tucker A, Li A, Vorselen D, Labitigan L, Crane E, Boyle E, Jiang L, Chan J, Rincón E, Greenleaf WJ, Li B, Snyder MP, Weissman IL, Theriot JA, Collins SR, Barres BA, Bassik MC.

Nat Genet. 2018 Dec;50(12):1716-1727. doi: 10.1038/s41588-018-0254-1. Epub 2018 Nov 5.

17.

Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity.

Chen X, Litzenburger UM, Wei Y, Schep AN, LaGory EL, Choudhry H, Giaccia AJ, Greenleaf WJ, Chang HY.

Nat Commun. 2018 Nov 2;9(1):4590. doi: 10.1038/s41467-018-07115-y.

18.

The chromatin accessibility landscape of primary human cancers.

Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network, Greenleaf WJ, Chang HY.

Science. 2018 Oct 26;362(6413). pii: eaav1898. doi: 10.1126/science.aav1898.

19.

Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers.

Denny SK, Greenleaf WJ.

Cold Spring Harb Perspect Biol. 2018 Oct 15. pii: a032300. doi: 10.1101/cshperspect.a032300. [Epub ahead of print]

PMID:
30322887
20.

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 Oct;8(10):1316-1331. doi: 10.1158/2159-8290.CD-17-0987. Epub 2018 Sep 18.

PMID:
30228179
21.

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 Sep 26;7(3):310-322.e4. doi: 10.1016/j.cels.2018.07.007. Epub 2018 Aug 22.

PMID:
30145115
22.

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.

23.

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.

24.

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.

25.

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
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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
44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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