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Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways.

Chi X, Sartor MA, Lee S, Anurag M, Patil S, Hall P, Wexler M, Wang XS.

Brief Bioinform. 2019 Oct 18. pii: bbz093. doi: 10.1093/bib/bbz093. [Epub ahead of print]


Secreted nuclear protein DEK regulates hematopoiesis through CXCR2 signaling.

Capitano ML, Mor-Vaknin N, Saha AK, Cooper S, Legendre M, Guo H, Contreras-Galindo R, Kappes F, Sartor MA, Lee CT, Huang X, Markovitz DM, Broxmeyer HE.

J Clin Invest. 2019 May 20;129(6):2555-2570. doi: 10.1172/JCI127460. eCollection 2019 May 20.


Somatic expression of piRNA and associated machinery in the mouse identifies short, tissue-specific piRNA.

Perera BPU, Tsai ZT, Colwell ML, Jones TR, Goodrich JM, Wang K, Sartor MA, Faulk C, Dolinoy DC.

Epigenetics. 2019 May;14(5):504-521. doi: 10.1080/15592294.2019.1600389. Epub 2019 Apr 8.


Soy Isoflavone Supplementation Increases Long Interspersed Nucleotide Element-1 (LINE-1) Methylation in Head and Neck Squamous Cell Carcinoma.

Rozek LS, Virani S, Bellile EL, Taylor JMG, Sartor MA, Zarins KR, Virani A, Cote C, Worden FP, Mark MEP, McLean SA, Duffy SA, Yoo GH, Saba NF, Shin DM, Kucuk O, Wolf GT.

Nutr Cancer. 2019;71(5):772-780. doi: 10.1080/01635581.2019.1577981. Epub 2019 Mar 12.


IDH1-R132H acts as a tumor suppressor in glioma via epigenetic up-regulation of the DNA damage response.

Núñez FJ, Mendez FM, Kadiyala P, Alghamri MS, Savelieff MG, Garcia-Fabiani MB, Haase S, Koschmann C, Calinescu AA, Kamran N, Saxena M, Patel R, Carney S, Guo MZ, Edwards M, Ljungman M, Qin T, Sartor MA, Tagett R, Venneti S, Brosnan-Cashman J, Meeker A, Gorbunova V, Zhao L, Kremer DM, Zhang L, Lyssiotis CA, Jones L, Herting CJ, Ross JL, Hambardzumyan D, Hervey-Jumper S, Figueroa ME, Lowenstein PR, Castro MG.

Sci Transl Med. 2019 Feb 13;11(479). pii: eaaq1427. doi: 10.1126/scitranslmed.aaq1427.


Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood.

Kochmanski J, Marchlewicz EH, Cavalcante RG, Sartor MA, Dolinoy DC.

Epigenetics. 2018;13(7):779-792. doi: 10.1080/15592294.2018.1507198. Epub 2018 Aug 23.


Expressed HNSCC variants by HPV-status in a well-characterized Michigan cohort.

Qin T, Zhang Y, Zarins KR, Jones TR, Virani S, Peterson LA, McHugh JB, Chepeha D, Wolf GT, Rozek LS, Sartor MA.

Sci Rep. 2018 Jul 30;8(1):11458. doi: 10.1038/s41598-018-29599-w.


Longitudinal Effects of Developmental Bisphenol A Exposure on Epigenome-Wide DNA Hydroxymethylation at Imprinted Loci in Mouse Blood.

Kochmanski JJ, Marchlewicz EH, Cavalcante RG, Perera BPU, Sartor MA, Dolinoy DC.

Environ Health Perspect. 2018 Jul 23;126(7):077006. doi: 10.1289/EHP3441. eCollection 2018 Jul.


Cadmium Exposure Inhibits Branching Morphogenesis and Causes Alterations Consistent With HIF-1α Inhibition in Human Primary Breast Organoids.

Rocco SA, Koneva L, Middleton LYM, Thong T, Solanki S, Karram S, Nambunmee K, Harris C, Rozek LS, Sartor MA, Shah YM, Colacino JA.

Toxicol Sci. 2018 Aug 1;164(2):592-602. doi: 10.1093/toxsci/kfy112.


Heterogeneity of Human Breast Stem and Progenitor Cells as Revealed by Transcriptional Profiling.

Colacino JA, Azizi E, Brooks MD, Harouaka R, Fouladdel S, McDermott SP, Lee M, Hill D, Madden J, Boerner J, Cote ML, Sartor MA, Rozek LS, Wicha MS.

Stem Cell Reports. 2018 May 8;10(5):1596-1609. doi: 10.1016/j.stemcr.2018.03.001. Epub 2018 Mar 29.


The NIEHS TaRGET II Consortium and environmental epigenomics.

Wang T, Pehrsson EC, Purushotham D, Li D, Zhuo X, Zhang B, Lawson HA, Province MA, Krapp C, Lan Y, Coarfa C, Katz TA, Tang WY, Wang Z, Biswal S, Rajagopalan S, Colacino JA, Tsai ZT, Sartor MA, Neier K, Dolinoy DC, Pinto J, Hamanaka RB, Mutlu GM, Patisaul HB, Aylor DL, Crawford GE, Wiltshire T, Chadwick LH, Duncan CG, Garton AE, McAllister KA; TaRGET II Consortium, Bartolomei MS, Walker CL, Tyson FL.

Nat Biotechnol. 2018 Mar 6;36(3):225-227. doi: 10.1038/nbt.4099. No abstract available.


Integrating DNA Methylation and Hydroxymethylation Data with the Mint Pipeline.

Cavalcante RG, Patil S, Park Y, Rozek LS, Sartor MA.

Cancer Res. 2017 Nov 1;77(21):e27-e30. doi: 10.1158/0008-5472.CAN-17-0330.


HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers.

Koneva LA, Zhang Y, Virani S, Hall PB, McHugh JB, Chepeha DB, Wolf GT, Carey TE, Rozek LS, Sartor MA.

Mol Cancer Res. 2018 Jan;16(1):90-102. doi: 10.1158/1541-7786.MCR-17-0153. Epub 2017 Sep 19.


annotatr: genomic regions in context.

Cavalcante RG, Sartor MA.

Bioinformatics. 2017 Aug 1;33(15):2381-2383. doi: 10.1093/bioinformatics/btx183.


Developmental programming: Interaction between prenatal BPA and postnatal overfeeding on cardiac tissue gene expression in female sheep.

Koneva LA, Vyas AK, McEachin RC, Puttabyatappa M, Wang HS, Sartor MA, Padmanabhan V.

Environ Mol Mutagen. 2017 Jan;58(1):4-18. doi: 10.1002/em.22071. Epub 2017 Jan 12.


Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer.

Zhang Y, Yu J, Grachtchouk V, Qin T, Lumeng CN, Sartor MA, Koenig RJ.

Oncotarget. 2017 Jan 24;8(4):5761-5773. doi: 10.18632/oncotarget.14050.


Novel Epigenetic Biomarkers Mediating Bisphenol A Exposure and Metabolic Phenotypes in Female Mice.

Anderson OS, Kim JH, Peterson KE, Sanchez BN, Sant KE, Sartor MA, Weinhouse C, Dolinoy DC.

Endocrinology. 2017 Jan 1;158(1):31-40. doi: 10.1210/en.2016-1441.


Adipogenic Differentiation of Thyroid Cancer Cells Through the Pax8-PPARγ Fusion Protein Is Regulated by Thyroid Transcription Factor 1 (TTF-1).

Xu B, O'Donnell M, O'Donnell J, Yu J, Zhang Y, Sartor MA, Koenig RJ.

J Biol Chem. 2016 Sep 9;291(37):19274-86. doi: 10.1074/jbc.M116.740324. Epub 2016 Jul 19.


Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver.

Faulk C, Kim JH, Jones TR, McEachin RC, Nahar MS, Dolinoy DC, Sartor MA.

Environ Epigenet. 2015 Dec;1(1). pii: dvv006. Epub 2015 Jan 1.


Epigenome-wide DNA methylation analysis implicates neuronal and inflammatory signaling pathways in adult murine hepatic tumorigenesis following perinatal exposure to bisphenol A.

Weinhouse C, Sartor MA, Faulk C, Anderson OS, Sant KE, Harris C, Dolinoy DC.

Environ Mol Mutagen. 2016 Jul;57(6):435-46. doi: 10.1002/em.22024. Epub 2016 Jun 23.


Transcriptomic profiling of curcumin-treated human breast stem cells identifies a role for stearoyl-coa desaturase in breast cancer prevention.

Colacino JA, McDermott SP, Sartor MA, Wicha MS, Rozek LS.

Breast Cancer Res Treat. 2016 Jul;158(1):29-41. doi: 10.1007/s10549-016-3854-4. Epub 2016 Jun 15.


Detection of differential DNA methylation in repetitive DNA of mice and humans perinatally exposed to bisphenol A.

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

Epigenetics. 2016 Jul 2;11(7):489-500. doi: 10.1080/15592294.2016.1183856. Epub 2016 Jun 6.


Mono-2-ethylhexyl phthalate disrupts neurulation and modifies the embryonic redox environment and gene expression.

Sant KE, Dolinoy DC, Jilek JL, Sartor MA, Harris C.

Reprod Toxicol. 2016 Aug;63:32-48. doi: 10.1016/j.reprotox.2016.03.042. Epub 2016 May 7.


Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signatures.

Zhang Y, Koneva LA, Virani S, Arthur AE, Virani A, Hall PB, Warden CD, Carey TE, Chepeha DB, Prince ME, McHugh JB, Wolf GT, Rozek LS, Sartor MA.

Clin Cancer Res. 2016 Sep 15;22(18):4735-45. doi: 10.1158/1078-0432.CCR-16-0323. Epub 2016 Apr 18.


A Mouse Model of X-linked Intellectual Disability Associated with Impaired Removal of Histone Methylation.

Iwase S, Brookes E, Agarwal S, Badeaux AI, Ito H, Vallianatos CN, Tomassy GS, Kasza T, Lin G, Thompson A, Gu L, Kwan KY, Chen C, Sartor MA, Egan B, Xu J, Shi Y.

Cell Rep. 2016 Feb 9;14(5):1000-1009. doi: 10.1016/j.celrep.2015.12.091. Epub 2016 Jan 21.


ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts.

Cavalcante RG, Patil S, Weymouth TE, Bendinskas KG, Karnovsky A, Sartor MA.

Bioinformatics. 2016 May 15;32(10):1536-43. doi: 10.1093/bioinformatics/btw016. Epub 2016 Jan 21.


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

Lee C, Patil S, Sartor MA.

Bioinformatics. 2016 Apr 1;32(7):1100-2. doi: 10.1093/bioinformatics/btv694. Epub 2015 Nov 25.


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 Dec 1;6(38):40418-32. doi: 10.18632/oncotarget.6340.


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; Investigators of the University of Michigan Head and Neck Specialized Programs of Research Excellence (SPORE) Program.

Head Neck. 2016 Apr;38 Suppl 1:E1325-31. doi: 10.1002/hed.24223. Epub 2015 Nov 13.


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;15:825. 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.


Hypoxia and hypoxia mimetics decrease aquaporin 5 (AQP5) expression through both hypoxia inducible factor-1α and proteasome-mediated pathways.

Kawedia JD, Yang F, Sartor MA, Gozal D, Czyzyk-Krzeska M, Menon AG.

PLoS One. 2013;8(3):e57541. doi: 10.1371/journal.pone.0057541. Epub 2013 Mar 1.


Microarray analysis reveals novel features of the muscle aging process in men and women.

Liu D, Sartor MA, Nader GA, Pistilli EE, Tanton L, Lilly C, Gutmann L, IglayReger HB, Visich PS, Hoffman EP, Gordon PM.

J Gerontol A Biol Sci Med Sci. 2013 Sep;68(9):1035-44. doi: 10.1093/gerona/glt015. Epub 2013 Feb 15.


Comprehensive analysis of DNA methylation in head and neck squamous cell carcinoma indicates differences by survival and clinicopathologic characteristics.

Colacino JA, Dolinoy DC, Duffy SA, Sartor MA, Chepeha DB, Bradford CR, McHugh JB, Patel DA, Virani S, Walline HM, Bellile E, Terrell JE, Stoerker JA, Taylor JM, Carey TE, Wolf GT, Rozek LS.

PLoS One. 2013;8(1):e54742. doi: 10.1371/journal.pone.0054742. Epub 2013 Jan 24.


A genome-wide siRNA screen reveals positive and negative regulators of the NOD2 and NF-κB signaling pathways.

Warner N, Burberry A, Franchi L, Kim YG, McDonald C, Sartor MA, Núñez G.

Sci Signal. 2013 Jan 15;6(258):rs3. doi: 10.1126/scisignal.2003305.

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