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Items: 1 to 50 of 132

1.

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.

2.

Impact of a patient-derived hepatitis C viral RNA genome with a mutated microRNA binding site.

Mata M, Neben S, Majzoub K, Carette J, Ramanathan M, Khavari PA, Sarnow P.

PLoS Pathog. 2019 May 10;15(5):e1007467. doi: 10.1371/journal.ppat.1007467. eCollection 2019 May.

3.

Author Correction: Methods to study RNA-protein interactions.

Ramanathan M, Porter DF, Khavari PA.

Nat Methods. 2019 Apr;16(4):351. doi: 10.1038/s41592-019-0366-2.

PMID:
30850752
4.

Methods to study RNA-protein interactions.

Ramanathan M, Porter DF, Khavari PA.

Nat Methods. 2019 Mar;16(3):225-234. doi: 10.1038/s41592-019-0330-1. Epub 2019 Feb 25. Review. Erratum in: Nat Methods. 2019 Apr;16(4):351.

5.

Profiling of rotavirus 3'UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication.

Ren L, Ding S, Song Y, Li B, Ramanathan M, Co J, Amieva MR, Khavari PA, Greenberg HB.

J Biol Chem. 2019 Apr 12;294(15):5993-6006. doi: 10.1074/jbc.RA118.006004. Epub 2019 Feb 15.

PMID:
30770472
6.

The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2.

Kovalski JR, Bhaduri A, Zehnder AM, Neela PH, Che Y, Wozniak GG, Khavari PA.

Mol Cell. 2019 Feb 21;73(4):830-844.e12. doi: 10.1016/j.molcel.2018.12.001. Epub 2019 Jan 10.

PMID:
30639242
7.

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
8.

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.

9.

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.

10.

RNA-protein interaction detection in living cells.

Ramanathan M, Majzoub K, Rao DS, Neela PH, Zarnegar BJ, Mondal S, Roth JG, Gai H, Kovalski JR, Siprashvili Z, Palmer TD, Carette JE, Khavari PA.

Nat Methods. 2018 Mar;15(3):207-212. doi: 10.1038/nmeth.4601. Epub 2018 Feb 5.

11.

Cancer-Associated Long Noncoding RNA SMRT-2 Controls Epidermal Differentiation.

Lee CS, Mah A, Aros CJ, Lopez-Pajares V, Bhaduri A, Webster DE, Kretz M, Khavari PA.

J Invest Dermatol. 2018 Jun;138(6):1445-1449. doi: 10.1016/j.jid.2018.01.003. Epub 2018 Jan 31. No abstract available.

12.

Research Techniques Made Simple: Emerging Methods to Elucidate Protein Interactions through Spatial Proximity.

Che Y, Khavari PA.

J Invest Dermatol. 2017 Dec;137(12):e197-e203. doi: 10.1016/j.jid.2017.09.028. Review.

13.

The functions and unique features of long intergenic non-coding RNA.

Ransohoff JD, Wei Y, Khavari PA.

Nat Rev Mol Cell Biol. 2018 Mar;19(3):143-157. doi: 10.1038/nrm.2017.104. Epub 2017 Nov 15. Review.

14.

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.

15.

CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue.

Bao X, Siprashvili Z, Zarnegar BJ, Shenoy RM, Rios EJ, Nady N, Qu K, Mah A, Webster DE, Rubin AJ, Wozniak GG, Tao S, Wysocka J, Khavari PA.

Dev Cell. 2017 Oct 23;43(2):227-239.e5. doi: 10.1016/j.devcel.2017.08.021. Epub 2017 Sep 21.

16.

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.

17.

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.

18.

Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer.

Gong X, Siprashvili Z, Eminaga O, Shen Z, Sato Y, Kume H, Homma Y, Ogawa S, Khavari PA, Pollack JR, Brooks JD.

Oncotarget. 2017 Mar 21;8(12):18657-18669. doi: 10.18632/oncotarget.15703.

19.

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.

20.

Factors That May Promote an Effective Local Research Environment.

Wang K, Lee CS, Marinkovich MP, Chang HY, Oro AE, Khavari PA.

J Invest Dermatol. 2016 Aug;136(8):1529-1531. doi: 10.1016/j.jid.2016.04.015. No abstract available.

21.

RAC1 activation drives pathologic interactions between the epidermis and immune cells.

Winge MC, Ohyama B, Dey CN, Boxer LM, Li W, Ehsani-Chimeh N, Truong AK, Wu D, Armstrong AW, Makino T, Davidson M, Starcevic D, Kislat A, Nguyen NT, Hashimoto T, Homey B, Khavari PA, Bradley M, Waterman EA, Marinkovich MP.

J Clin Invest. 2016 Jul 1;126(7):2661-77. doi: 10.1172/JCI85738. Epub 2016 Jun 13.

22.

irCLIP platform for efficient characterization of protein-RNA interactions.

Zarnegar BJ, Flynn RA, Shen Y, Do BT, Chang HY, Khavari PA.

Nat Methods. 2016 Jun;13(6):489-92. doi: 10.1038/nmeth.3840. Epub 2016 Apr 25.

23.

7SK-BAF axis controls pervasive transcription at enhancers.

Flynn RA, Do BT, Rubin AJ, Calo E, Lee B, Kuchelmeister H, Rale M, Chu C, Kool ET, Wysocka J, Khavari PA, Chang HY.

Nat Struct Mol Biol. 2016 Mar;23(3):231-8. doi: 10.1038/nsmb.3176. Epub 2016 Feb 15.

24.

A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63.

Bao X, Rubin AJ, Qu K, Zhang J, Giresi PG, Chang HY, Khavari PA.

Genome Biol. 2015 Dec 18;16:284. doi: 10.1186/s13059-015-0840-9.

25.

Network Analysis Identifies Mitochondrial Regulation of Epidermal Differentiation by MPZL3 and FDXR.

Bhaduri A, Ungewickell A, Boxer LD, Lopez-Pajares V, Zarnegar BJ, Khavari PA.

Dev Cell. 2015 Nov 23;35(4):444-57. doi: 10.1016/j.devcel.2015.10.023.

26.

The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer.

Siprashvili Z, Webster DE, Johnston D, Shenoy RM, Ungewickell AJ, Bhaduri A, Flockhart R, Zarnegar BJ, Che Y, Meschi F, Puglisi JD, Khavari PA.

Nat Genet. 2016 Jan;48(1):53-8. doi: 10.1038/ng.3452. Epub 2015 Nov 23.

27.

CALML5 is a ZNF750- and TINCR-induced protein that binds stratifin to regulate epidermal differentiation.

Sun BK, Boxer LD, Ransohoff JD, Siprashvili Z, Qu K, Lopez-Pajares V, Hollmig ST, Khavari PA.

Genes Dev. 2015 Nov 1;29(21):2225-30. doi: 10.1101/gad.267708.115.

28.

Genomic analysis of mycosis fungoides and S├ęzary syndrome identifies recurrent alterations in TNFR2.

Ungewickell A, Bhaduri A, Rios E, Reuter J, Lee CS, Mah A, Zehnder A, Ohgami R, Kulkarni S, Armstrong R, Weng WK, Gratzinger D, Tavallaee M, Rook A, Snyder M, Kim Y, Khavari PA.

Nat Genet. 2015 Sep;47(9):1056-60. doi: 10.1038/ng.3370. Epub 2015 Aug 10.

29.

A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation.

Lopez-Pajares V, Qu K, Zhang J, Webster DE, Barajas BC, Siprashvili Z, Zarnegar BJ, Boxer LD, Rios EJ, Tao S, Kretz M, Khavari PA.

Dev Cell. 2015 Mar 23;32(6):693-706. doi: 10.1016/j.devcel.2015.01.028.

30.

Advances in skin grafting and treatment of cutaneous wounds.

Sun BK, Siprashvili Z, Khavari PA.

Science. 2014 Nov 21;346(6212):941-5. doi: 10.1126/science.1253836. Review.

PMID:
25414301
31.

Dissecting noncoding and pathogen RNA-protein interactomes.

Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY.

RNA. 2015 Jan;21(1):135-43. doi: 10.1261/rna.047803.114. Epub 2014 Nov 19.

32.

ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes.

Boxer LD, Barajas B, Tao S, Zhang J, Khavari PA.

Genes Dev. 2014 Sep 15;28(18):2013-26. doi: 10.1101/gad.246579.114.

33.

Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma.

Lee CS, Bhaduri A, Mah A, Johnson WL, Ungewickell A, Aros CJ, Nguyen CB, Rios EJ, Siprashvili Z, Straight A, Kim J, Aasi SZ, Khavari PA.

Nat Genet. 2014 Oct;46(10):1060-2. doi: 10.1038/ng.3091. Epub 2014 Sep 7.

34.

Quantitative analysis of mammalian translation initiation sites by FACS-seq.

Noderer WL, Flockhart RJ, Bhaduri A, Diaz de Arce AJ, Zhang J, Khavari PA, Wang CL.

Mol Syst Biol. 2014 Aug 28;10:748. doi: 10.15252/msb.20145136.

35.

Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs.

Zheng GX, Do BT, Webster DE, Khavari PA, Chang HY.

Nat Struct Mol Biol. 2014 Jul;21(7):585-90. doi: 10.1038/nsmb.2842. Epub 2014 Jun 15.

36.

Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition.

Webster DE, Barajas B, Bussat RT, Yan KJ, Neela PH, Flockhart RJ, Kovalski J, Zehnder A, Khavari PA.

Genome Res. 2014 May;24(5):751-60. doi: 10.1101/gr.166231.113. Epub 2014 Jan 17.

37.

Activating HRAS mutation in nevus spilus.

Sarin KY, McNiff JM, Kwok S, Kim J, Khavari PA.

J Invest Dermatol. 2014 Jun;134(6):1766-1768. doi: 10.1038/jid.2014.6. Epub 2014 Jan 3. No abstract available.

38.

Activating HRAS mutation in agminated Spitz nevi arising in a nevus spilus.

Sarin KY, Sun BK, Bangs CD, Cherry A, Swetter SM, Kim J, Khavari PA.

JAMA Dermatol. 2013 Sep;149(9):1077-81. doi: 10.1001/jamadermatol.2013.4745.

PMID:
23884457
39.

IQGAP1 scaffold-kinase interaction blockade selectively targets RAS-MAP kinase-driven tumors.

Jameson KL, Mazur PK, Zehnder AM, Zhang J, Zarnegar B, Sage J, Khavari PA.

Nat Med. 2013 May;19(5):626-630. doi: 10.1038/nm.3165. Epub 2013 Apr 21.

40.

ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent induction of KLF4.

Bao X, Tang J, Lopez-Pajares V, Tao S, Qu K, Crabtree GR, Khavari PA.

Cell Stem Cell. 2013 Feb 7;12(2):193-203. doi: 10.1016/j.stem.2012.12.014.

41.

Control of somatic tissue differentiation by the long non-coding RNA TINCR.

Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA.

Nature. 2013 Jan 10;493(7431):231-5. doi: 10.1038/nature11661. Epub 2012 Dec 2.

42.

Identification of proteins binding coding and non-coding human RNAs using protein microarrays.

Siprashvili Z, Webster DE, Kretz M, Johnston D, Rinn JL, Chang HY, Khavari PA.

BMC Genomics. 2012 Nov 16;13:633. doi: 10.1186/1471-2164-13-633.

43.

Genetic pathways in disorders of epidermal differentiation.

Lopez-Pajares V, Yan K, Zarnegar BJ, Jameson KL, Khavari PA.

Trends Genet. 2013 Jan;29(1):31-40. doi: 10.1016/j.tig.2012.10.005. Epub 2012 Nov 8. Review.

44.

Mosaic activating RAS mutations in nevus sebaceus and nevus sebaceus syndrome.

Sun BK, Saggini A, Sarin KY, Kim J, Benjamin L, LeBoit PE, Khavari PA.

J Invest Dermatol. 2013 Mar;133(3):824-827. doi: 10.1038/jid.2012.377. Epub 2012 Oct 25. No abstract available.

45.

Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts.

Lee CS, Ungewickell A, Bhaduri A, Qu K, Webster DE, Armstrong R, Weng WK, Aros CJ, Mah A, Chen RO, Lin M, Sundram U, Chang HY, Kretz M, Kim YH, Khavari PA.

Blood. 2012 Oct 18;120(16):3288-97. doi: 10.1182/blood-2012-04-423061. Epub 2012 Aug 30.

46.

Genomic profiling of a human organotypic model of AEC syndrome reveals ZNF750 as an essential downstream target of mutant TP63.

Zarnegar BJ, Webster DE, Lopez-Pajares V, Vander Stoep Hunt B, Qu K, Yan KJ, Berk DR, Sen GL, Khavari PA.

Am J Hum Genet. 2012 Sep 7;91(3):435-43. doi: 10.1016/j.ajhg.2012.07.007. Epub 2012 Aug 23.

47.

BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration.

Flockhart RJ, Webster DE, Qu K, Mascarenhas N, Kovalski J, Kretz M, Khavari PA.

Genome Res. 2012 Jun;22(6):1006-14. doi: 10.1101/gr.140061.112. Epub 2012 May 11. Erratum in: Genome Res. 2012 Jul;22(7):1382.

48.

Rapid identification of non-human sequences in high-throughput sequencing datasets.

Bhaduri A, Qu K, Lee CS, Ungewickell A, Khavari PA.

Bioinformatics. 2012 Apr 15;28(8):1174-5. doi: 10.1093/bioinformatics/bts100. Epub 2012 Feb 28.

49.

ZNF750 is a p63 target gene that induces KLF4 to drive terminal epidermal differentiation.

Sen GL, Boxer LD, Webster DE, Bussat RT, Qu K, Zarnegar BJ, Johnston D, Siprashvili Z, Khavari PA.

Dev Cell. 2012 Mar 13;22(3):669-77. doi: 10.1016/j.devcel.2011.12.001. Epub 2012 Feb 23.

50.

Suppression of progenitor differentiation requires the long noncoding RNA ANCR.

Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GX, Chow J, Kim GE, Rinn JL, Chang HY, Siprashvili Z, Khavari PA.

Genes Dev. 2012 Feb 15;26(4):338-43. doi: 10.1101/gad.182121.111. Epub 2012 Feb 2.

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