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Items: 23

1.

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques.

Petrovic J, Zhou Y, Fasolino M, Goldman N, Schwartz GW, Mumbach MR, Nguyen SC, Rome KS, Sela Y, Zapataro Z, Blacklow SC, Kruhlak MJ, Shi J, Aster JC, Joyce EF, Little SC, Vahedi G, Pear WS, Faryabi RB.

Mol Cell. 2019 Feb 5. pii: S1097-2765(19)30006-1. doi: 10.1016/j.molcel.2019.01.006. [Epub ahead of print]

PMID:
30745086
2.

A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells.

Van Gool F, Nguyen MLT, Mumbach MR, Satpathy AT, Rosenthal WL, Giacometti S, Le DT, Liu W, Brusko TM, Anderson MS, Rudensky AY, Marson A, Chang HY, Bluestone JA.

Immunity. 2019 Feb 19;50(2):362-377.e6. doi: 10.1016/j.immuni.2018.12.016. Epub 2019 Jan 29.

PMID:
30709738
3.

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
4.

Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment.

Pattison JM, Melo SP, Piekos SN, Torkelson JL, Bashkirova E, Mumbach MR, Rajasingh C, Zhen HH, Li L, Liaw E, Alber D, Rubin AJ, Shankar G, Bao X, Chang HY, Khavari PA, Oro AE.

Nat Genet. 2018 Dec;50(12):1658-1665. doi: 10.1038/s41588-018-0263-0. Epub 2018 Nov 5.

PMID:
30397335
5.

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.

6.

Enhancer Connectome Nominates Target Genes of Inherited Risk Variants from Inflammatory Skin Disorders.

Jeng MY, Mumbach MR, Granja JM, Satpathy AT, Chang HY, Chang ALS.

J Invest Dermatol. 2019 Mar;139(3):605-614. doi: 10.1016/j.jid.2018.09.011. Epub 2018 Oct 10.

7.

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
8.

Expression of the transcription factor ZBTB46 distinguishes human histiocytic disorders of classical dendritic cell origin.

Satpathy AT, Brown RA, Gomulia E, Briseño CG, Mumbach MR, Pan Z, Murphy KM, Natkunam Y, Chang HY, Kim J.

Mod Pathol. 2018 Sep;31(9):1479-1486. doi: 10.1038/s41379-018-0052-4. Epub 2018 May 9.

9.

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element.

Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY.

Cell. 2018 May 31;173(6):1398-1412.e22. doi: 10.1016/j.cell.2018.03.068. Epub 2018 May 3.

PMID:
29731168
10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE.

Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY.

Nat Protoc. 2016 Feb;11(2):273-90. doi: 10.1038/nprot.2016.011. Epub 2016 Jan 14.

17.

Shade avoidance components and pathways in adult plants revealed by phenotypic profiling.

Nozue K, Tat AV, Kumar Devisetty U, Robinson M, Mumbach MR, Ichihashi Y, Lekkala S, Maloof JN.

PLoS Genet. 2015 Apr 15;11(4):e1004953. doi: 10.1371/journal.pgen.1004953. eCollection 2015 Apr.

18.

Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.

Jovanovic M, Rooney MS, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A.

Science. 2015 Mar 6;347(6226):1259038. doi: 10.1126/science.1259038. Epub 2015 Feb 12.

19.

Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.

Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A.

Cell. 2014 Sep 25;159(1):148-162. doi: 10.1016/j.cell.2014.08.028. Epub 2014 Sep 11.

20.

Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.

Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A.

Cell Rep. 2014 Jul 10;8(1):284-96. doi: 10.1016/j.celrep.2014.05.048. Epub 2014 Jun 26.

21.

High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.

Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A.

Cell. 2013 Dec 5;155(6):1409-21. doi: 10.1016/j.cell.2013.10.047. Epub 2013 Nov 21.

22.

Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs.

Edelheit S, Schwartz S, Mumbach MR, Wurtzel O, Sorek R.

PLoS Genet. 2013 Jun;9(6):e1003602. doi: 10.1371/journal.pgen.1003602. Epub 2013 Jun 27.

23.

LeafJ: an ImageJ plugin for semi-automated leaf shape measurement.

Maloof JN, Nozue K, Mumbach MR, Palmer CM.

J Vis Exp. 2013 Jan 21;(71). pii: 50028. doi: 10.3791/50028.

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