Publications

Qin T, Lee C, Cavalcante RC, Orchard P, Yao H, Zhang H, Wang S, Patil S, Boyle AP, Sartor MA. Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data. Genome Biol. 2022; in press.

Lee CT, Cavalcante RG, Lee C, Qin T, Patil S, Wang S, Tsai ZTY, Boyle AP, Sartor MA. Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions. NAR Genom Bioinform. 2020; 2(1):lqaa006.

Lee CT, Wang K, Qin T, Sartor MA. Testing proximity of genomic regions to transcription start sites and enhancers complements gene set enrichment testing. Frontiers in Genetics. 2020; 11:199.

Bagherian M, Kim RB, Jiang C, Sartor MA, Derksen H, Najarian K. Coupled matrix-matrix and coupled tensor-matrix completion methods for predicting drug-target interactions. Brief Bioinform. 2020; Mar 18.

Cavalcante RG, Patil S, Park Y, Rozek LS, Sartor MA. Integrating DNA methylation and hydroxymethylation data with the mint pipeline. Cancer Res. 2017; 77(21):e27-e30.

Cavalcante RG, Sartor MA. annotatr: genomic regions in context. Bioinformatics. 2017; 33(15):2381-2383.

Cavalcante RG, Patil S, Weymouth TE, Bendiskas KG, Karnovsky A, Sartor MA. ConceptMetab: a tool for exploring relationships among biologically-related compound sets. Bioinformatics. 2016; 32(10):1536-43.

Lee C, Patil S,Sartor MA. RNA-Enrich: A cut-off free functional enrichment testing method for RNA-seq with improved detection power. Bioinformatics. 2015; 32(7):1100-2.

Agarwal S, Macfarlan TS, Sartor MA, Iwase S. Sequencing of first-strand cDNA library reveals full-length transcriptomes. Nat Commun. 2015; 6:6002.

Bai Y, Hassler J, Ziyar A, Li P, Wright Z, Menon R, Omenn GS, Cavalcoli JD, Kaufman RJ, Sartor MA. Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data. PLoS One. 2014; 9(7):e100864.

Cavalcante R, Lee C, Patil S, Weymouth TE, Welch RP, Scott LJ, Sartor MA. Broad-Enrich: functional interpretation of large sets of broad genomic regions. Bioinformatics. (ECCB special issue) 2014; 30(17):i393-i400./li>

Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA. PePr: A peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. Bioinformatics. 2014; doi: 10.1093/bioinformatics/btu372.

Welch RP*, Lee C*, Imbriano PM, Patil S, Weymouth TE, Smith RA, Scott LJ, Sartor MA. ChIP-Enrich: Gene set enrichment testing for ChIP-seq data. NAR. 2014; doi:10.1093/nar/gku463 [Epub ahead of print].

Park Y, Figueroa ME, Rozek LS, Sartor MA. methylSig: a whole genome DNA methylation analysis pipeline. Bioinformatics. 2014; doi:10.1093/bioinformatics/btu339 [Epub ahead of print].

Kim JH, Karnovsky A, Mahavisno V, Weymouth T, Pande M, Dolinoy DC, Rozek LS, Sartor MA. LRpath analysis reveals common pathways dyregulated via DNA methylation across cancer types. BMC Genomics. 2012; 13:526.

Sartor MA, Ade A, Wright Z, States D, Omenn GS, Athey B, Karnovsky A. Metab2MeSH: Annotating Compounds with Medical Subject Headings (MeSH). Bioinformatics. 2012; 28(10):1408-10.

Farfan F, Ma J, Sartor MA, Michailidis G, Jagadish HV. THINK Back: KNowledge-based Interpretation of High Throughput data. BMC Bioinformatics, 2012; 13(Suppl 2):S4.

Karnovsky A, Weymouth T, Hull T, Tarcea VG, Scardoni G, Laudanna C, Sartor MA, Stringer KA, Jagadish HV, Burant C, Athey B, Omenn GS. MetScape 2 Bioinformatics Tool for the Analysis and Visualization of Metabolomics and Gene Expression Data. Bioinformatics, 2012; 28(3):373-80.

McEachin RC, Sannareddy KS, Cavalcoli JD, Karnovsky A, Vink JM, Sartor MA. Convergence of genetic influences in comorbidity. BMC Bioinformatics, 2012; 13(Suppl 2):S8.

Bai Y, Sartor M, Cavalcoli J. Current status and future perspectives for sequencing livestock genomes. J of Animal Science and Biotech. 2012; 3:8.

Ma J, Sartor MA*, Jagadish HV*. Appearance frequency modulated gene set enrichment testing. BMC Bioinformatics. 2011; 12(81). (*co-senior authors)

McEachin RC, Chen H, Sartor MA, Saccone SF, Keller BJ, Prossin AR, Cavalcoli JD, McInnis MG. A genetic network model of cellular responses to lithium treatment and cocaine abuse in bipolar disorder. BMC Syst Biol. 2010; 4(158).

Sartor MA, Mahavisno V, Keshamouni VG, Cavalcoli J, Wright Z, Karnovsky A, Kuick R, Jagadish HV, Mirel B, Weymouth T, Athey B, Omenn GS. ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics. 2010; 26: 456-463.

Wang XS, Prensner JR, Chen G, Cao Q, Han B, Dhanasekaran SM, Ponnala R, Cao X, Varambally S, Thomas DG, Giordano TJ, Beer DG, Palanisamy N, Sartor MA, Omenn GS, Chinnaiyan AM. An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nat Biotechnol. 2009; 27(11):1005-11. PMID: 19881495

Sartor MA, Leikauf GD, Medvedovic M. LRpath: A logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics. 2009; 25(2): 211-7.

Sartor MA, Tomlinson CR, Wesselkamper SC, Sivaganesan S, Leikauf GD, and Medvedovic M. Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. BMC Bioinformatics. 2006; 7: 538.

Sartor MA, Zorn AM, Schwanekamp J, Halbleib D, Karyala S, Howell ML, Dean GE, Medvedovic M, Tomlinson CR. A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Research. 2006; 34(1):185-200.

Sartor MA, Schwanekamp J, Halbleib D, Mohamed I, Karyala S, Medvedovic M and Tomlinson CR. Microarray results improve significantly as hybridization approaches equilibrium. Biotechniques. 2004; 36: 790-796.

Bakulski KM, Dou JF, Thompson RC, Lee C, Middleton LY, Perera BPU, Ferris SP, Jones TR, Neier K, Zhou X, Sartor MA, Hammoud SS, Dolinoy DC, Colacino JA. Single Cell Analysis of the Gene Expression Effects of Developmental Lead (Pb) Exposure on the Mouse Hippocampus. Toxicol Sci. 2020; 176(2):396-409.

Rozek LS, Dolinoy DC, Sartor MA, Omenn GS. Epigenetics: Relevance and Implications for Public Health. Annu. Rev. Public Health. 2014. 35:105-22.

Kim JH, Sartor MA, Rozek LS, Faulk C, Anderson OS, Jones TR, Nahar MS, Dolinoy DC. Perinatal bisphenol A exposure promotes dose-dependent alterations of the mouse methylome. BMC Genomics. 2014; 15(1):30.

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. Endoplasmic reticulum stress-induced transcriptional regulation increases protein synthesis leading to cell death. Nat Cell Biol. 2013; 15(5):481-90.

Warner N, Burberry A, Franchi L, Kim YG, McDonald C, Sartor MA, Núñez G. A Genome-Wide siRNA Screen Reveals Positive and Negative Regulators of the NOD2 and NF-κB Signaling Pathways. Sci Signal. 2013; 6(258):rs3.

Papagerakis S, Zheng L, Schnell S, Sartor MA, Somers E, Marder W, McAlpin B, Kim D, McHugh J, Papagerakis P. The circadian clock in oral health and diseases. J Dent Res. 2013; 93(1):27-35.

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. Comprehensive analysis of DNA methylation in head and neck squamous cell carcinoma indicates differences by survival and clinicopathologic characteristics. PLoS One. 2013; 8(1):e54742.

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. SEC24A deficiency lowers plasma cholesterol through reduced PCSK9 secretion. Elife. 2013; 2:e00444.

Xu QW, Zhao W, Wang Y, Sartor MA, Han DM, Deng J, Ponnala R, Yang JY, Zhang QY, Liao GQ, Qu YM, Li L, Liu FF, Zhao HM, Yin YH, Chen WF, Zhang Y, Wang XS. An Integrated Genome-Wide Approach to Discover Tumor-Specific Antigens as Potential Immunologic and Clinical Targets in Cancer. Cancer Res. 2012; 72(24):6351-61.

Kim DH, Sartor MA, Bain JR, Sandoval D, Stevens RD, Medvedovic M, Newgard CB, Woods SC, Seeley RJ. Rapid and Weight-independent improvement of glucose tolerance induced by a peptide designed to elicit apoptosis in adipose tissue endothelium. Diabetes. 2012.

Colacino JA, Arthur AE, Dolinoy DC, Sartor MA, Duffy SA, Chepeha DB, Bradford CR, Walline HM, McHugh JB, D'Silva N, Carey TE, Wolf GT, Taylor JM, Peterson KE, Rozek LS. Pre-treatment dietary intake is associated with tumor DNA methylation in head and neck squamous cell carcinomas. Epigenetics. 2012; 7(8).

Bakulski KM, Dolinoy DC, Sartor MA, Paulson HL, Konen JR, Lieberman AP, Albin RL, Hu H, Rozek LS. Genome-wide DNA methylation differences between late-onset alzheimer’s disease and cognitively normal controls in human frontal cortex. J Alzheimers Dis, 2012; 29(3):571-88.

Gordon PM, Liu D, Sartor MA, Iglayreger HB, Pistilli EE, Gutmann L, Nader GA, Hoffman EP. Resistance exercise training influences skeletal muscle immune activation: a microarray analysis. J Appl Physiol. 2012; 112(3):443-53.

Knauf JA, Sartor MA, Medvedovic M, Lundsmith E, Ryder M, Salzano M, Nikiforov YE, Giordano TJ, Ghossein RA, Fagin JA. Progression of BRAF-induced thyroid cancer is associated with epithelial-mesenchymal transition requiring concomitant MAP kinase and TGFbeta signaling. Oncogene. 2011; 30(28):3153-62.

Wilhide ME, Tranter M, Ren X, Chen J, Sartor MA, Medvedovic M, Jones WK. Identification of a NF-kB cardioprotective gene program: NF-kB regulation of Hsp70.1 contributes to cardioprotection after permanent coronary occlusion. J Mol Cell Cardiol. 2011; 51(1):82-9.

Senthamaraikannan P, Sartor MA, O'Connor KT, Neumann JC, Klyza JP Jr, Succop PA, Wagner BD, Karyala S, Medvedovic M, Menon AG. Identification of maternally regulated fetal gene networks in the placenta with a novel embryo transfer system in mice. Physiol Genomics. 2011; 43(7):317-24.

Liu D, Sartor MA, Nader GA, Gutmann L, Treutelaar MK, Pistilli EE, Iglayreger HB, Burant CF, Hoffman EP, Gordon PM. Skeletal muscle gene expression in response to resistance exercise: sex specific regulation. BMC Genomics. 2010; 11(659).

O'Geen H, Lin YH, Xu X, Echipare L, Komashko VM, He D, Frietze S, Tanabe O, Shi L, Sartor MA, Engel JD, Farnham PJ. Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes. BMC Genomics. 2010; 11(689).

Kivelä R, Silvennoinen M, Lehti M, Rinnankoski-Tuikka R, Purhonen T, Ketola T, Pullinen K, Vuento M, Mutanen N, Sartor MA, Reunanen H, Koch LG, Britton SL, Kainulainen H. Gene expression centroids that link with low intrinsic aerobic exercise capacity and complex disease risk. FASEB J. 2010; 24(11):4565-74.

Kadekaro AL, Leachman S, Kavanagh RJ, Swope V, Cassidy P, Supp D, Sartor M, Schwemberger S, Babcock G, Wakamatsu K, Ito S, Koshoffer A, Boissy RE, Manga P, Sturm RA, Abdel-Malek ZA. Melanocortin 1 receptor genotype: an important determinant of the damage response of melanocytes to ultraviolet radiation. FASEB J. 2010; 24(10):3850-60.

Tranter M, Ren X, Forde T, Wilhide ME, Chen J, Sartor MA, Medvedovic M, Jones WK. NF-kappaB driven cardioprotective gene programs; Hsp70.3 and cardioprotection after late ischemic preconditioning. J Mol Cell Cardiol. 2010; 49(4):664-72.

McEachin RC, Saccone NL, Saccone SF, Kleyman-Smith YD, Kar T, Kare RK, Ade AS, Sartor MA, Cavalcoli JD, McInnis MG. Modeling complex genetic and environmental influences on comorbid bipolar disorder with tobacco use disorder. BMC Med Genet. 2010; 11(1):14.

Stark JM, Barmada MM, Winterberg AV, Majumber N, Gibbons WJ Jr, Stark MA, Sartor MA, Medvedovic M, Kolls J, Bein K, Mailaparambil B, Krueger M, Heinzmann A, Leikauf GD, Prows DR. Genomewide association analysis of respiratory syncytial virus infection in mice. J Virol. 2010; 84(5):2257-69.

Peng Z, Geh E, Chen L, Meng Q, Fan Y, Sartor M, Shertzer HG, Liu Z, Puga A, Xia Y. Ikb kinase beta regulates redox homeostasis by controlling the constitutive levels of glutathione. Mol Pharmacol, 2010; 77(5):784-92.

Bein K, Wesselkamper SC, Liu X, Dietsch M, Majumder N, Concel VJ, Medvedovic M, Sartor MA, Henning LN, Venditto C, Borchers MT, Barchowsky A, Weaver TE, Tichelaar JW, Prows DR, Korfhagen TR, Hardie WD, Bachurski CJ, Leikauf GD. Surfactant-associated protein B is critical to survival in nickel-induced injury in mice. Am J Respir Cell Mol Biol. 2009; 41(2):226-36.

Ren XP, Wu J, Wang X, Sartor MA, Qian J, Jones K, Nicolaou P, Pritchard TJ, Fan GC. MicroRNA-320 is involved in the regulation of cardiac ischemia/reperfusion injury by targeting heat-shock protein 20. Circulation. 2009; 119(17):2357-66.

Trask H, Cowper-Sal·lari R, Sartor MA, Gui J, Heath CV, Renuka J, Higgins AJ, Andrews P, Korc M, Moore JH, and Tomlinson CR. Microarray analysis of cytoplasmic versus whole cell RNA reveals a considerable number of missed and false positive mRNAs. RNA. 2009; 15(10):1917-28.

Sartor MA, Schnekenburger M, Marlowe JL, Reichard JF, Wang Y, Fan Y, Ma C, Karyala S, Halbleib D, Liu X, Medvedovic M, Puga A. Genome-wide analysis of aryl hydrocarbon receptor binding targets reveals an extensive array of gene clusters that control morphogenetic and developmental programs. Env Health Persp. 2009; 117(7):1139-46.

Bradford EM, Sartor MA, Gawenis LR, Clarke LL, Shull GE. Reduced NHE3-Mediated Na+ absorption increases survival and decreases the incidence of intestinal obstructions in cystic fibrosis mice. Am J Physiol Gastrointest Liver Physiol. 2009; 296(4):G886-98.

Marshall AM, Pai VP, Sartor MA, Horseman ND. In vitro multipotent differentiation and barrier function of a human mammary epithelium. Cell Tissue Res. 2009; 335(2): 383-95.

Genter MB, Warner BM, Medvedovic M, Sartor MA. Comparison of rat olfactory mucosal responses to carcinogenic and non-carcinogenic chloracetanilides. Food Chem Toxicol. 2009; 47(6):1051-7.

Bakshi S, Zhang X, Godoy-Tundidor S, Cheng RY, Sartor MA, Medvedovic M, Ho SM. Transcriptome analyses in normal prostate epithelial cells exposed to low-dose cadmium: oncogenic and immunomodulations involving the action of tumor necrosis factor. Environ Health Perspect. 2008; 116(6): 769-76.

Borchers MT, Wesselkamper SC, Eppert BL, Motz GT, Sartor MA, Tomlinson CR, Medvedovic M, Tichelaar JW. Nonredundant functions of alphabeta and gammadelta T cells in acrolein-induced pulmonary pathology. Toxicol Sci. 2008; 105(1): 188-99.

Dragin N, Shi Z, Madan R, Karp CL, Sartor MA, Chen C, Gonzalez FJ, Nebert DW. Phenotype of the Cyp1a1/1a2/1b1-/- triple-knockout mouse. Mol Pharmacol. 2008; 73(6): 1844-56.

Reichard JF, Sartor MA, Puga A. BACH1 Is a Specific Repressor of HMOX1 That Is Inactivated by Arsenite. J Biol Chem. 2008; 283(33): 22363-70.

Tam NN, Szeto CY, Sartor MA, Medvedovic M, Ho SM. Gene expression profiling identifies lobe-specific and common disruptions of multiple gene networks in testosterone-supported, 17beta-estradiol- or diethylstilbestrol-induced prostate dysplasia in Noble rats. Neoplasia. 2008; 10(1): 20-40.

Ganguly K, Stoeger T, Wesselkamper SC Reinhard C, Sartor MA, Medvedovic M, Tomlinson CR, Bolle I, Mason JM, Leikauf GD, Schulz H. Candidate genes controlling pulmonary function: transcript profiling and predicted protein structure. Am J of Physiol. Genomics. 2007; 31(3): 410-21.

Hess-Wilson JK, Webb SL, Daly HK, Leung Y, Boldison J, Comstock CES, Sartor MA, Ho S, and Knudsen KE. Unique Bisphenol A Transcriptome in Prostate Cancer: Novel Effects on ERß Expression That Correspond to AR Mutation Status. Environmental Health Sciences. 2007; 115(11): 1646:53.

Hardie WD, Korfhagen TR, Sartor MA, Prestridge A, Medvedovic M, Le Cras TD, Ikegami M, Wesselkamper SC, Davidson C, Dietsch M, Nichols W, Whitsett JA, Leikauf GD. Genomic Profile of Matrix and Vasculature Remodeling in TGF {alpha}-induced Pulmonary Fibrosis. Am J Respir Cell Mol Biol. 2007; 37(3): 309-21.

Chang X, Fan Y, Karyala S, Schwemberger S, Tomlinson CR, Sartor MA, Puga A. Ligand-Independent Regulation of Transforming Growth Factor {beta}1 Expression and Cell Cycle Progression by the Aryl Hydrocarbon Receptor. Mol Cell Biol. 2007; 27(17):6127-39.

Kramer EL, Deutsch GH, Sartor MA, Hardie WD, Ikegami M, Korfhagen TR, Le Cras TD. Perinatal Increases in TGF-a Disrupt the Saccular Phase of Lung Morphogenesis & Cause Remodeling: Microarray Analysis. Am J Physiol Lung Cell Mol Physiol. 2007; 293(2): L314-27.

Mesa CJr., Mirza M, Mitsutake N, Sartor MA, Medvedovic M, Tomlinson CR, Knauf JA, Weber G, Fagin JA. Conditional activation of the RET/PTC3 and B-RAFV600E oncoproteins in thyroid cells is associated with unique patterns of gene expression that predict distinct functional properties and a preferential role of BRAF in extracellular matrix remodeling. Cancer Research. 2006; 66(13):6521-9.

Erwin CR, Jarboe MD, Sartor MA, Medvedovic M, Warner BW, Bates MD. Developmental Characteristics of Adapting Small Intestine Crypt Cells. Gastroent. 2006; 130(4):1324-32.

Wesselkamper SC, McDowell SA, Medvedovic M, Dalton TP, Deshmukh HS, Sartor MA, Case LM, Henning LN, Borchers MT, Tomlinson CR, Prows DR, Leikauf GD. The Role of Metallothionein in the Pathogenesis of Acute Lung Injury. Am J Respir Cell Mol Biol. 2006; 34(1):73-82.

Deng M, Chen WL, Takatori A, Peng Z, Zhang L, Mongan M, Parthasarathy R, Sartor M, Miller M, Yang J, Su B, Kao WW, Xia Y. A role for the mitogen-activated protein kinase kinase kinase 1 in epithelial wound healing. Mol Biol Cell. 2006; 17(8): 3446-55.