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RNA-Enrich: A cut-off free functional enrichment testing method for RNA-seq with improved detection power.

Lee C, Patil S, Sartor MA.

Bioinformatics. 2015 Nov 25. pii: btv694. [Epub ahead of print]


Genomic binding and regulation of gene expression by the thyroid carcinoma-associated PAX8-PPARG fusion protein.

Zhang Y, Yu J, Lee C, Xu B, Sartor MA, Koenig RJ.

Oncotarget. 2015 Nov 16. doi: 10.18632/oncotarget.6340. [Epub ahead of print]


Stability of methylation markers in head and neck squamous cell carcinoma.

Virani S, Light E, Peterson LA, Sartor MA, Taylor JM, McHugh JB, Wolf GT, Rozek LS; and Investigators of the University of Michigan Head and Neck Specialized Programs of Research Excellence (SPORE) Program.

Head Neck. 2015 Nov 13. doi: 10.1002/hed.24223. [Epub ahead of print]


NDN and CD1A are novel prognostic methylation markers in patients with head and neck squamous carcinomas.

Virani S, Bellile E, Bradford CR, Carey TE, Chepeha DB, Colacino JA, Helman JI, McHugh JB, Peterson LA, Sartor MA, Taylor JM, Walline HM, Wolf GT, Rozek LS.

BMC Cancer. 2015 Oct 30;15(1):825. doi: 10.1186/s12885-015-1806-8.


Sequencing of first-strand cDNA library reveals full-length transcriptomes.

Agarwal S, Macfarlan TS, Sartor MA, Iwase S.

Nat Commun. 2015 Jan 21;6:6002. doi: 10.1038/ncomms7002.


Broad-Enrich: functional interpretation of large sets of broad genomic regions.

Cavalcante RG, Lee C, Welch RP, Patil S, Weymouth T, Scott LJ, Sartor MA.

Bioinformatics. 2014 Sep 1;30(17):i393-400. doi: 10.1093/bioinformatics/btu444.


Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data.

Bai Y, Hassler J, Ziyar A, Li P, Wright Z, Menon R, Omenn GS, Cavalcoli JD, Kaufman RJ, Sartor MA.

PLoS One. 2014 Jul 3;9(7):e100864. doi: 10.1371/journal.pone.0100864. eCollection 2014.


PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data.

Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA.

Bioinformatics. 2014 Sep 15;30(18):2568-75. doi: 10.1093/bioinformatics/btu372. Epub 2014 Jun 3.


ChIP-Enrich: gene set enrichment testing for ChIP-seq data.

Welch RP, Lee C, Imbriano PM, Patil S, Weymouth TE, Smith RA, Scott LJ, Sartor MA.

Nucleic Acids Res. 2014 Jul;42(13):e105. doi: 10.1093/nar/gku463. Epub 2014 May 30.


Regulation of the human endogenous retrovirus K (HML-2) transcriptome by the HIV-1 Tat protein.

Gonzalez-Hernandez MJ, Cavalcoli JD, Sartor MA, Contreras-Galindo R, Meng F, Dai M, Dube D, Saha AK, Gitlin SD, Omenn GS, Kaplan MH, Markovitz DM.

J Virol. 2014 Aug;88(16):8924-35. doi: 10.1128/JVI.00556-14. Epub 2014 May 28.


MethylSig: a whole genome DNA methylation analysis pipeline.

Park Y, Figueroa ME, Rozek LS, Sartor MA.

Bioinformatics. 2014 Sep 1;30(17):2414-22. doi: 10.1093/bioinformatics/btu339. Epub 2014 May 16.


Developmental transcriptome analysis of human erythropoiesis.

Shi L, Lin YH, Sierant MC, Zhu F, Cui S, Guan Y, Sartor MA, Tanabe O, Lim KC, Engel JD.

Hum Mol Genet. 2014 Sep 1;23(17):4528-42. doi: 10.1093/hmg/ddu167. Epub 2014 Apr 29.


Epigenetics: relevance and implications for public health.

Rozek LS, Dolinoy DC, Sartor MA, Omenn GS.

Annu Rev Public Health. 2014;35:105-22. doi: 10.1146/annurev-publhealth-032013-182513. Review.


Perinatal bisphenol A exposure promotes dose-dependent alterations of the mouse methylome.

Kim JH, Sartor MA, Rozek LS, Faulk C, Anderson OS, Jones TR, Nahar MS, Dolinoy DC.

BMC Genomics. 2014 Jan 17;15:30. doi: 10.1186/1471-2164-15-30.


Bisphenol A-associated alterations in the expression and epigenetic regulation of genes encoding xenobiotic metabolizing enzymes in human fetal liver.

Nahar MS, Kim JH, Sartor MA, Dolinoy DC.

Environ Mol Mutagen. 2014 Apr;55(3):184-95. doi: 10.1002/em.21823. Epub 2013 Nov 9.


The circadian clock in oral health and diseases.

Papagerakis S, Zheng L, Schnell S, Sartor MA, Somers E, Marder W, McAlpin B, Kim D, McHugh J, Papagerakis P.

J Dent Res. 2014 Jan;93(1):27-35. doi: 10.1177/0022034513505768. Epub 2013 Sep 24. Review.


Folliculin contributes to VHL tumor suppressing activity in renal cancer through regulation of autophagy.

Bastola P, Stratton Y, Kellner E, Mikhaylova O, Yi Y, Sartor MA, Medvedovic M, Biesiada J, Meller J, Czyzyk-Krzeska MF.

PLoS One. 2013 Jul 29;8(7):e70030. doi: 10.1371/journal.pone.0070030. Print 2013.


ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death.

Han J, Back SH, Hur J, Lin YH, Gildersleeve R, Shan J, Yuan CL, Krokowski D, Wang S, Hatzoglou M, Kilberg MS, Sartor MA, Kaufman RJ.

Nat Cell Biol. 2013 May;15(5):481-90. doi: 10.1038/ncb2738. Epub 2013 Apr 28.


Bisphenol A-associated epigenomic changes in prepubescent girls: a cross-sectional study in Gharbiah, Egypt.

Kim JH, Rozek LS, Soliman AS, Sartor MA, Hablas A, Seifeldin IA, Colacino JA, Weinhouse C, Nahar MS, Dolinoy DC.

Environ Health. 2013 Apr 16;12:33. doi: 10.1186/1476-069X-12-33.


SEC24A deficiency lowers plasma cholesterol through reduced PCSK9 secretion.

Chen XW, Wang H, Bajaj K, Zhang P, Meng ZX, Ma D, Bai Y, Liu HH, Adams E, Baines A, Yu G, Sartor MA, Zhang B, Yi Z, Lin J, Young SG, Schekman R, Ginsburg D.

Elife. 2013 Apr 9;2:e00444. doi: 10.7554/eLife.00444.

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