2014

Dombkowski AA, Sultana KZ, Craig DB. Protein disulfide engineering. FEBS Letters. 2014 Jan 21;588(2):206-12. Epub 2013 Nov 26. PubMed PMID: 24291258.

Caruso JA, Stemmer PM, Dombkowski A, Caruthers NJ, Gill R, Rosenspire AJ. A systems toxicology approach identifies Lyn as a key signaling phosphoprotein modulated by mercury in a B lymphocyte cell model. Toxicology and Applied Pharmacology. 2014 Jan 14. [Epub ahead of print]. PubMed PMID: 24440445.

2013

Caruthers NJ, Stemmer PM, Shin N, Dombkowski A, Caruso JA, Gill R, Rosenspire A. Mercury Alters B-Cell Protein Phosphorylation Profiles. Journal of Proteome Research. 2013 Dec 4. [Epub ahead of print]. PubMed PMID: 24224561.

Craig DB, Dombkowski AA. Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins. BMC Bioinformatics. 2013 Dec 1;14:346. PubMed PMID: 24289175; PubMed Central PMCID: PMC3898251.

Rowlands JC, Budinsky R, Gollapudi B, Black MB, Wolfinger RD, Cukovic D, Dombkowski A, Thompson CM, Urban JD, Thomas RS. A genomics-based analysis of relative potencies of dioxin-like compounds in primary rat hepatocytes. Toxicological Sciences. 2013 Dec;136(2):595-604. Epub 2013 Sep 17. PubMed PMID: 24046277.

Shukla U, Tumma N, Gratsch T, Dombkowski A, Novak RF. Insights into insulin-mediated regulation of CYP2E1: miR-132/-212 targeting of CYP2E1 and role of phosphatidylinositol 3-kinase, Akt (protein kinase B), mammalian target of rapamycin signaling in regulating miR-132/-212 and miR-122/-181a expression in primary cultured rat hepatocytes. Drug Metabolism and Disposition. 2013 Oct;41(10):1769-77. Epub 2013 Aug 6. PubMed PMID: 23920219; PubMed Central PMCID: PMC3781375.

Caldwell JT, Edwards H, Dombkowski AA, Buck SA, Matherly LH, Ge Y, Taub JW. Overexpression of GATA1 confers resistance to chemotherapy in acute megakaryocytic Leukemia. PLoS One. 2013 Jul 10;8(7):e68601. PubMed PMID: 23874683; PubMed Central PMCID: PMC3707876.

2012

Craig DB, Kannan S, Dombkowski AA. Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny. BMC Bioinformatics. 2012 May 8;13:84. PubMed PMID: 22568790; PubMed Central PMCID: PMC3424829.

Black MB, Budinsky RA, Dombkowski A, Cukovic D, LeCluyse EL, Ferguson SS, Thomas RS, Rowlands JC. Cross-species comparisons of transcriptomic alterations in human and rat primary hepatocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicological Sciences. 2012 May;127(1):199-215. Epub 2012 Feb 1. PubMed PMID: 22298810.

Simon KW, Ma H, Dombkowski AA, Cabelof DC. Aging alters folate homeostasis and DNA damage response in colon. Mechanisms of Ageing and Development. 2012 Feb-Mar;133(2-3):75-82. Epub 2012 Jan 25. PubMed PMID: 22306610.

Wu J, Liu S, Liu G, Dombkowski A, Abrams J, Martin-Trevino R, Wicha MS, Ethier SP, Yang ZQ. Identification and functional analysis of 9p24 amplified genes in human breast cancer. Oncogene. 2012 Jan 19;31(3):333-41. Epub 2011 Jun 13. PubMed PMID: 21666724; PubMed Central PMCID: PMC3886828.

Hou J, Wu J, Dombkowski A, Zhang K, Holowatyj A, Boerner JL, Yang ZQ. Genomic amplification and a role in drug-resistance for the KDM5A histone demethylase in breast cancer. American Journal of Translational Research. 2012;4(3):247-56. Epub 2012 Jul 22. PubMed PMID: 22937203; PubMed Central PMCID: PMC3426386.

Brush GS, Najor NA, Dombkowski AA, Cukovic D, Sawarynski KE. Yeast IME2 functions early in meiosis upstream of cell cycle-regulated SBF and MBF targets. PLoS One. 2012;7(2):e31575. Epub 2012 Feb 29. PubMed PMID: 22393365; PubMed Central PMCID: PMC3290606.

Craig DB, Kannan S, Dombkowski AA. Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny. BMC Bioinformatics. 2012 May 8;13(1):84. [Epub ahead of print]. PubMed PMID: 22568790.

Black MB, Budinsky RA, Dombkowski A, Cukovic D, LeCluyse EL, Ferguson SS, Thomas RS, Rowlands JC. Cross-species comparisons of transcriptomic alterations in human and rat primary hepatocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicol Sci. 2012 May;127(1):199-215. Epub 2012 Feb 1. PubMed PMID: 22298810.

Simon KW, Ma H, Dombkowski AA, Cabelof DC. Aging alters folate homeostasis and DNA damage response in colon. Mech Ageing Dev. 2012 Feb-Mar;133(2-3):75-82. Epub 2012 Jan 25. PubMed PMID: 22306610.

Brush GS, Najor NA, Dombkowski AA, Cukovic D, Sawarynski KE. Yeast IME2 functions early in meiosis upstream of cell cycle-regulated SBF and MBF targets. PLoS One. 2012;7(2):e31575. Epub 2012 Feb 29. PubMed PMID: 22393365.

2011

Bernardo MM, Meng Y, Lockett J, Dyson G, Dombkowski A, Kaplun A, Li X, Yin S, Dzinic S, Olive M, Dean I, Krass D, Moin K, Bonfil RD, Cher M, Sakr W, Sheng S. Maspin reprograms the gene expression profile of prostate carcinoma cells for differentiation. Genes Cancer. 2011 Nov;2(11):1009-22. PubMed PMID: 22737267.

Xavier AC, Edwards H, Dombkowski AA, Balci TB, Berman JN, Dellaire G, Xie C, Buck SA, Matherly LH, Ge Y, Taub JW. A Unique Role of GATA1s in Down Syndrome Acute Megakaryocytic Leukemia Biology and Therapy. PLoS One. 2011;6(11):e27486. Epub 2011 Nov 16. PubMed PMID: 22110660; PubMed Central PMCID: PMC3217966.

Zhang Y, Klein K, Sugathan A, Nassery N, Dombkowski A, Zanger UM, Waxman DJ. Transcriptional profiling of human liver identifies sex-biased genes associated with polygenic dyslipidemia and coronary artery disease. PLoS One. 2011;6(8):e23506. Epub 2011 Aug 12. PubMed PMID: 21858147; PubMed Central PMCID: PMC3155567.

Rowlands JC, Budinsky R, Gollapudi B, Novak R, Abdelmegeed M, Cukovic D, Dombkowski A. Transcriptional profiles induced by the Aryl Hydrocarbon Receptor agonists 2,3,7,8-tetrachlorodibenzo-p-dioxin, 2,3,7,8-tetrachlorodibenzofuran and 2,3,4,7,8-pentachlorodibenzofuran in primary rat hepatocytes. Chemosphere. 2011 Sep;85(2):232-8. Epub 2011 Jul 2. PubMed PMID: 21724226.

Wu J, Liu S, Liu G, Dombkowski A, Abrams J, Martin-Trevino R, Wicha MS, Ethier SP, Yang ZQ. Identification and functional analysis of 9p24 amplified genes in human breast cancer. Oncogene. 2011 Jun 13. doi: 10.1038/onc.2011.227. [Epub ahead of print] PubMed PMID: 21666724.

Wang LS, Dombkowski AA, Seguin C, Rocha C, Cukovic D, Mukundan A, Henry C, Stoner GD. Mechanistic basis for the chemopreventive effects of black raspberries at a late stage of rat esophageal carcinogenesis. Mol Carcinog. 2011 Apr;50(4):291-300. doi: 10.1002/mc.20634. PubMed PMID: 21465577.

Dombkowski AA, Sultana Z, Craig DB, Jamil H. In silico Analysis of Combinatorial microRNA Activity Reveals Target Genes and Pathways Associated with Breast Cancer Metastasis. Cancer Inform. 2011 Feb 17;10:13-29. PubMed PMID: 21552493; PubMed Central PMCID: PMC3085424.

Thirunavukkarasusx N, Ghosal KJ, Kukreja R, Zhou Y, Dombkowski A, Cai S, Singh BR. Microarray analysis of differentially regulated genes in human neuronal and epithelial cell lines upon exposure to type A botulinum neurotoxin. Biochem Biophys Res Commun. 2011 Feb 25;405(4):684-90. Epub 2011 Feb 1. PubMed PMID: 21291863.

2010

Ventrella-Lucente LF, Unnikrishnan A, Pilling AB, Patel HV, Kushwaha D, Dombkowski AA, Schmelz EM, Cabelof DC, Heydari AR. Folate deficiency provides protection against colon carcinogenesis in DNA polymerase beta haploinsufficient mice. J Biol Chem. 2010 Jun 18;285(25):19246-58. Epub 2010 Apr 19. PMID: 20404327.

Wauthier V, Sugathan A, Meyer RD, Dombkowski AA, Waxman DJ. Intrinsic sex differences in the early growth hormone responsiveness of sex-specific genes in mouse liver. Mol Endocrinol. 2010 Mar;24(3):667-78. Epub 2010 Feb 11.   PMID: 20150183.

Chopra DP, Dombkowski AA, Stemmer PM, Parker GC. Intestinal epithelial cells in vitro. Stem Cells Dev. 2010 Jan;19(1):131-42. Review. PMID: 19580443.

2009

Edwards H, Xie C, LaFiura KM, Dombkowski AA, Buck SA, Boerner JL, Taub JW, Matherly LH, Ge Y. RUNX1 regulates phosphoinositide 3-kinase/AKT pathway: role in chemotherapy sensitivity in acute megakaryocytic leukemia. Blood. 2009 Sep 24;114(13):2744-52. Epub 2009 Jul 28. PMID: 19638627.

Simon K, Mukundan A, Dewundara S, Van Remmen H, Dombkowski AA, Cabelof DC. Transcriptional profiling of the age-related response to genotoxic stress points to differential DNA damage response with age. Mech Ageing Dev. 2009 Sep;130(9):637-47. Epub 2009 Aug 11. PMID: 19679149.

2008

Moon A, Yong HY, Song JI, Cukovic D, Salagrama S, Kaplan D, Putt D, Kim H, Dombkowski A, Kim HR. Global gene expression profiling unveils S100A8/A9 as candidate markers in H-ras-mediated human breast epithelial cell invasion. Mol Cancer Res. 2008 Oct;6(10):1544-53. PMID: 18922970.

Stoner GD, Dombkowski AA, Reen RK, Cukovic D, Salagrama S, Wang LS, Lechner JF. Carcinogen-altered genes in rat esophagus positively modulated to normal levels of expression by both black raspberries and phenylethyl isothiocyanate. Cancer Res. 2008 Aug 1;68(15):6460-7. PMID: 18676871.

Holloway MG, Miles GD, Dombkowski AA, Waxman DJ. Liver-specific hepatocyte nuclear factor-4alpha deficiency: greater impact on gene expression in male than in female mouse liver. Mol Endocrinol. 2008 May;22(5):1274-86. Epub 2008 Feb 14. PMID: 18276827.

Ge Y, LaFiura KM, Dombkowski AA, Chen Q, Payton SG, Buck SA, Salagrama S, Diakiw AE, Matherly LH, Taub JW. The role of the proto-oncogene ETS2 in acute megakaryocytic leukemia biology and therapy. Leukemia. 2008 Mar;22(3):521-9. Epub 2007 Dec 20. PMID: 18094719.

Lechner JF, Reen RK, Dombkowski AA, Cukovic D, Salagrama S, Wang LS, Stoner GD. Effects of a black raspberry diet on gene expression in the rat esophagus. Nutr Cancer. 2008, 60 Suppl 1:61-9. PMID: 19003582.

2007

Reen RK, Dombkowski AA, Kresty LA, Cukovic D, Mele JM, Salagrama S, Nines R, Stoner GD. Effects of phenylethyl isothiocyanate on early molecular events in N-nitrosomethylbenzylamine-induced cytotoxicity in rat esophagus. Cancer Research, 2007, Jul 1;67(13):6484-92, PMID: 17616710.

2005

Yang VC, Naik SS, Song H, Dombkowski AA, Crippen G, Liang JF. Construction and characterization of a t-PA mutant for use in ATTEMPTS: A drug delivery system for achieving targeted thrombolysis. J Control Release. 2005 Dec 10;110(1):164-76. PMID: 16260060.

Ge Y, Dombkowski AA, Lafiura KM, Tatman D, Yedidi RS, Stout ML, Buck SA, Massey G, Becton DL, Weinstein HJ, Ravindranath Y, Matherly LH, Taub JW. Differential gene expression, GATA1 target genes and the chemotherapy sensitivity of down syndrome megakaryocytic leukemia. Blood. 2005 Oct 25; PMID: 16249385.

Dombkowski AA, Cukovic D, Novak RF. Secretome analysis of microarray data reveals extracellular events associated with proliferative potential in a cell line model of breast disease. Cancer Lett. 2005 Nov 16; PMID: 16298039.

2004

Dombkowski AA, Thibodeau BJ, Starcevic SL, and Novak RF. Gene-specific dye bias in microarray reference designs. FEBS Letters, 2004, Vol. 560, No. 3, 120-124. PMID: 14988009.

Lee I, Dombkowski AA, and Athey BD. Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray. Nucleic Acids Research, 2004, Vol. 32, No. 2, 681-690. PMID: 14757833

Wang G, Chuang L, Zhang X, Colton S, Dombkowski A, Reiners J, Diakiw A, and Xu S. The initiative role of XPC protein in cisplatin DNA damaging treatment-mediated cell cycle regulation. Nucleic Acids Research, 2004 Apr 23;32(7):2231-40.

2003

Dombkowski AA. Disulfide by Design: A computational method for the rational design of disulfide bonds in proteins. Bioinformatics, Sep 22;19(14):1852-3, 2003. PMID: 14512360.

Kane MD, Lin H-S, Dombkowski AA, Diakiw A, Nagel AC, Flexon A, Leifheit M, Sprague JE and Hollenberg PF. Accelerating Preclinical Drug Development Using A Microarray-Based Method for Detecting Oxidative Enzyme (P450) mRNA Induction and Other Metabolic Genes in the Rat. In: Microarray Methods and Applications: Nuts & Bolts. Hardiman, G., ed. DNA Press, 2003.