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Results: 1 to 20 of 64

1.

Genome-Wide Mapping of RNA Pol-II Promoter Usage in Mouse Tissues by ChIP-Seq.

Pal S, Gupta R, Davuluri RV.

Methods Mol Biol. 2014;1176:1-9. doi: 10.1007/978-1-4939-0992-6_1.

PMID:
25030914
[PubMed - in process]
2.

Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline.

Stong N, Deng Z, Gupta R, Hu S, Paul S, Weiner AK, Eichler EE, Graves T, Fronick CC, Courtney L, Wilson RK, Lieberman PM, Davuluri RV, Riethman H.

Genome Res. 2014 Jun;24(6):1039-50. doi: 10.1101/gr.166983.113. Epub 2014 Mar 27.

PMID:
24676094
[PubMed - in process]
3.

Isoform-level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes.

Pal S, Bi Y, Macyszyn L, Showe LC, O'Rourke DM, Davuluri RV.

Nucleic Acids Res. 2014 Apr;42(8):e64. doi: 10.1093/nar/gku121. Epub 2014 Feb 6.

PMID:
24503249
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

miR-218 opposes a critical RTK-HIF pathway in mesenchymal glioblastoma.

Mathew LK, Skuli N, Mucaj V, Lee SS, Zinn PO, Sathyan P, Imtiyaz HZ, Zhang Z, Davuluri RV, Rao S, Venneti S, Lal P, Lathia JD, Rich JN, Keith B, Minn AJ, Simon MC.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):291-6. doi: 10.1073/pnas.1314341111. Epub 2013 Dec 24.

PMID:
24368849
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts.

Ferdin J, Nishida N, Wu X, Nicoloso MS, Shah MY, Devlin C, Ling H, Shimizu M, Kumar K, Cortez MA, Ferracin M, Bi Y, Yang D, Czerniak B, Zhang W, Schmittgen TD, Voorhoeve MP, Reginato MJ, Negrini M, Davuluri RV, Kunej T, Ivan M, Calin GA.

Cell Death Differ. 2013 Dec;20(12):1675-87. doi: 10.1038/cdd.2013.119. Epub 2013 Sep 13.

PMID:
24037088
[PubMed - indexed for MEDLINE]
6.

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data.

Bi Y, Davuluri RV.

BMC Bioinformatics. 2013 Aug 27;14:262. doi: 10.1186/1471-2105-14-262.

PMID:
23981227
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer.

Ling H, Spizzo R, Atlasi Y, Nicoloso M, Shimizu M, Redis RS, Nishida N, GafĂ  R, Song J, Guo Z, Ivan C, Barbarotto E, De Vries I, Zhang X, Ferracin M, Churchman M, van Galen JF, Beverloo BH, Shariati M, Haderk F, Estecio MR, Garcia-Manero G, Patijn GA, Gotley DC, Bhardwaj V, Shureiqi I, Sen S, Multani AS, Welsh J, Yamamoto K, Taniguchi I, Song MA, Gallinger S, Casey G, Thibodeau SN, Le Marchand L, Tiirikainen M, Mani SA, Zhang W, Davuluri RV, Mimori K, Mori M, Sieuwerts AM, Martens JW, Tomlinson I, Negrini M, Berindan-Neagoe I, Foekens JA, Hamilton SR, Lanza G, Kopetz S, Fodde R, Calin GA.

Genome Res. 2013 Sep;23(9):1446-61. doi: 10.1101/gr.152942.112. Epub 2013 Jun 24.

PMID:
23796952
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing.

Ota H, Sakurai M, Gupta R, Valente L, Wulff BE, Ariyoshi K, Iizasa H, Davuluri RV, Nishikura K.

Cell. 2013 Apr 25;153(3):575-89. doi: 10.1016/j.cell.2013.03.024.

PMID:
23622242
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Isoform level expression profiles provide better cancer signatures than gene level expression profiles.

Zhang Z, Pal S, Bi Y, Tchou J, Davuluri RV.

Genome Med. 2013 Apr 17;5(4):33. doi: 10.1186/gm437. eCollection 2013.

PMID:
23594586
[PubMed]
Free PMC Article
10.

Estimation of Gene Expression at Isoform Level from mRNA-Seq Data by Bayesian Hierarchical Modeling.

Bhattacharjee M, Gupta R, Davuluri RV.

Front Genet. 2012 Nov 27;3:239. doi: 10.3389/fgene.2012.00239. eCollection 2012.

PMID:
23293650
[PubMed]
Free PMC Article
11.

A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection.

Deng Z, Wang Z, Stong N, Plasschaert R, Moczan A, Chen HS, Hu S, Wikramasinghe P, Davuluri RV, Bartolomei MS, Riethman H, Lieberman PM.

EMBO J. 2012 Nov 5;31(21):4165-78. doi: 10.1038/emboj.2012.266. Epub 2012 Sep 25.

PMID:
23010778
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Sequencing and analysis of a South Asian-Indian personal genome.

Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, Miller W, Santhosh S, Davuluri RV, Butte AJ, Schuster SC, Seshagiri S, Thomas G.

BMC Genomics. 2012 Aug 31;13:440. doi: 10.1186/1471-2164-13-440.

PMID:
22938532
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Alternative transcription and alternative splicing in cancer.

Pal S, Gupta R, Davuluri RV.

Pharmacol Ther. 2012 Dec;136(3):283-94. doi: 10.1016/j.pharmthera.2012.08.005. Epub 2012 Aug 14. Review.

PMID:
22909788
[PubMed - indexed for MEDLINE]
14.

The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type.

Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, Davuluri RV, Nagy R, de la Chapelle A.

Proc Natl Acad Sci U S A. 2012 May 29;109(22):8646-51. doi: 10.1073/pnas.1205654109. Epub 2012 May 14.

PMID:
22586128
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Identification of host-chromosome binding sites and candidate gene targets for Kaposi's sarcoma-associated herpesvirus LANA.

Lu F, Tsai K, Chen HS, Wikramasinghe P, Davuluri RV, Showe L, Domsic J, Marmorstein R, Lieberman PM.

J Virol. 2012 May;86(10):5752-62. doi: 10.1128/JVI.07216-11. Epub 2012 Mar 14.

PMID:
22419807
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

RP58/ZNF238 directly modulates proneurogenic gene levels and is required for neuronal differentiation and brain expansion.

Xiang C, Baubet V, Pal S, Holderbaum L, Tatard V, Jiang P, Davuluri RV, Dahmane N.

Cell Death Differ. 2012 Apr;19(4):692-702. doi: 10.1038/cdd.2011.144. Epub 2011 Nov 18.

PMID:
22095278
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Tree-based position weight matrix approach to model transcription factor binding site profiles.

Bi Y, Kim H, Gupta R, Davuluri RV.

PLoS One. 2011;6(9):e24210. doi: 10.1371/journal.pone.0024210. Epub 2011 Sep 2.

PMID:
21912677
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.

Kim H, Bi Y, Pal S, Gupta R, Davuluri RV.

BMC Bioinformatics. 2011 Jul 27;12:305. doi: 10.1186/1471-2105-12-305.

PMID:
21794104
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development.

Pal S, Gupta R, Kim H, Wickramasinghe P, Baubet V, Showe LC, Dahmane N, Davuluri RV.

Genome Res. 2011 Aug;21(8):1260-72. doi: 10.1101/gr.120535.111. Epub 2011 Jun 28.

PMID:
21712398
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Association of a microRNA/TP53 feedback circuitry with pathogenesis and outcome of B-cell chronic lymphocytic leukemia.

Fabbri M, Bottoni A, Shimizu M, Spizzo R, Nicoloso MS, Rossi S, Barbarotto E, Cimmino A, Adair B, Wojcik SE, Valeri N, Calore F, Sampath D, Fanini F, Vannini I, Musuraca G, Dell'Aquila M, Alder H, Davuluri RV, Rassenti LZ, Negrini M, Nakamura T, Amadori D, Kay NE, Rai KR, Keating MJ, Kipps TJ, Calin GA, Croce CM.

JAMA. 2011 Jan 5;305(1):59-67. doi: 10.1001/jama.2010.1919.

PMID:
21205967
[PubMed - indexed for MEDLINE]
Free PMC Article

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