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publications by UHN staff
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Staff members at UHNMAC have had their material published in books and articles. Peruse our listings!
(Names of contributing staff members are highlighted in red)

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Books/Chapters
Books/Chapters
Genomics and Pharmacogenomics in Anticancer Drug development and Clinical Response. Edited by Federico Innocenti; Published by SpringerLink, 2009; ISBN: 1588296467
Includes: Chapter 1 Toward the Realization of the Promise of Microarrays in Oncology. (Natalie Stickle, Neil Winegarden)
Genomics: Essential Methods. Edited by Mike Starkey and Ramnath Elaswarapu; Published by Wiley and Blackwell, 2011; ISBN: 978-0-470-71157-6
Includes: Chapter 5 RNA Amplification Strategies: Toward Single-Cell Sensitivity. (Natalie Stickle, Norman N. Iscove, Carl Virtanen, Mary Barbara, Carolyn Modi, Toni Di Berardino, Ellen Greenblatt, Ted Brown and Neil Winegarden)
Clinical Bioinformatics Edited by Ronald J.A. Trent; Series: Methods in Molecular Medicine, Volume 141; Published by Springer Protocols, 2007; ISBN: 978-1-58829-791-4
Includes: Clinical Uses of Microarrays in Cancer Research (Carl Virtanen, James Woodgett)
DNA Microarrays: Methods Express Edited by Mark Schena; Published by Scion Publishing Ltd, 2007; ISBN: 9781904842156
Includes: Chapter 12 Enhanced microarray hybridization using surface acoustic wave mixing (Natalie Stickle, Kelly Jackson, Andreas Toegl, Frank Feist, Neil Winegarden)
Promoter and CpG Island Microarrays Edited by Neil Winegarden and Mark Takahashi; Published by DNA Press, 2005; ISBN: 0974876569

Journal Publications
2012 (1 publication)
Dhillon SS, Gingerich S, Virtanen C, Belsham DD. Gene array analysis of embryonic - versus adult-derived hypothalamic NPY-expressing cell lines. Mol Cell Endocrinol. 2012 358(1):116-26

2011 (7 publications)
Badea I, Virtanen C, Verrall RE, Rosenberg A, Foldvari M. Effect of topical interferon-γ gene therapy using gemini nanoparticles on pathophysiological markers of cutaneious scleroderma in Tsk/+ mice. Gene Therapy. 2011 online Nov, 2011
Gandhi R, Takahashi M, Virtanen C, Syed K, Davey JR, Mahomed NN. Microarray analysis of the infrapatellar fat pad in knee osteoarthritis: relationship with joint inflammation. J. Rheumatol. 2011 38(9):1966-1972
George SH, Greenaway J, Milea A, Clary V, Shaw S, Sharma M, Virtanen C, Shaw PA. Identification of abrogated pathways in fallopian tube epithelium from BRCA1 mutation carriers. J Pathol. 2011 225(1):106-17
Siu A, Virtanen C, Jongstra J. PIM kinase isoform specific regulation of MIG6 expression and EGFR signaling in prostate cancer cells.. Oncotarget. 2011 online Dec, 2011
Karisch R, Fernandez M, Taylor P, Virtanen C, St-Germain JR, Jin LL, Harris IS, Mori J, Mak TW, Senis YA, Ostman A, Moran MF, Neel BG. Global proteomic assessment of the classical protein-tyrosine phosphatome and "redoxome". Cell 2011 146(5):826-40
Shimizu M, Cohen B, Goldvasser P, Berman H, Virtanen C, Reedijk M. Plasminogen activator uPA is a direct transcriptional target of the JAG1-notch receptor signaling pathway in breast cancer. Cancer Res. 2011 71(1) 277-86
Tone AA, Virtanen C, Shaw PA, Brown TJ. Decreased progesterone receptor isoform expression in luteal phase fallopian tube epithelium and high-grade serous carcinoma. Endocr Relat Cancer. 2011 18(2):221-34

2010 (5 publications)
Singh RR, Ho D, Nilchi A, Gulak G, Yau, P, Genov R. A CMOS/Thin-Film fluorescence contact imaging microsystem for DNA analysis IEEE Circuits and Systems I: Regular Papers 2010 57(5):1029
Jackson K, Paris J, Takahashi M. ChIPing away at global transcriptional regulation Methods Mol Biol. 2010 632:173
May T, Virtanen C, Sharma M, Milea A, Begley H, Rosen B, Murphy KJ, Brown TJ, Shaw PA. Low malignant potential tumors with micropapillary features are molecularly similar to low-grade serous carcinoma of the ovary. Gynecologic Oncology 2010, 117(1):9-17
Tsao J, Yau P, Winegarden N. Profiling microRNA expression with the Illumina BeadChip platform Methods Mol Biol. 2010 632:73
Yoo J-K, Galligan CL, Virtanen C, Fish EN. Identification of a novel antigen-presenting cell population modulating antiinfluenza type 2 immunity. JEM 2010, 207(7):1435-1451

2009 (2 publications)
Virtanen C, Paris J, Takahashi M. Identification and characterization of a novel gene, DAPR, involved in skeletal muscle differentiation and PKB signaling. J Biol Chem 2009, 284(3):1636-1643
Kaminsky ZA, Tang T, Wang S-C, Ptak C, Oh GHT, Wong AHC, Feldcamp LA, Virtanen C, Halfvarson J, Tysk C, McRae AF, Visscher PM, Montgomery GW, Gottesman II, Martin NG, Petronis A. DNA methylation profiles in monozygotic and dizygotic twins. Nature Genetics 2009, 41:240-245

2008 (3 publications)
Tone AA, Begley H, Sharma M, Murphy J, Rosen B, Brown TJ, Shaw PA. Gene expression profiles of luteal phase fallopian tubes epithelium from BRCA mutation carriers resemble high-grade serous carcinoma. Clin Cancer Res 2008 14(13):4067-78
Virtanen C, Takahashi M. Muscling in on Microarrays. Appl Physiol Nutr Metab. 2008 33(1):124-9 Review
Virtanen C, Woodgett J. Clincial uses of microarrays in cancer research. Methods Mol. Med. 2008 141:87-113 Review

2007



2006 (3 publications)
Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarray R, Salit M, Sherlock G, Spellman P, Winegarden N. Top-down standards will not serve systems biology. Nature 2006, 440:24
Flanagan JM, Popendikyte V, Pozdniakovaite N, Sobolev M, Assadzadeh A, Schumacher A, Zangeneh M, Lau L,Virtanen C, Wang SC, Petronis A. Intra- and Interindividual Epigenetic Variation in Human Germ Cells. Am J Hum Genet, 2006, 79(1):67-84
Schumacher A, Kapranov P, Kaminsky Z, Flanagan J, Assadzadeh A, Yau P, Virtanen C, Winegarden N, Cheng J, Gingeras T, Petronis A. Microarray-based DNA methylation profiling: technology and applications. Nuc. Acids Res. 2006, 34(2):528-542

2005 (5 publications)
Wong N, Chan KYY, Macgregor PF, Lai PBS, Squire JA, Beheshti B,Albert M, Leung TWT. Transcriptional Profiling Identifies Gene Expression Changes Associated with IFN-α Tolerance in Hepatitis C-Related Hepatocellular Carcinoma Cells. Clinical Cancer Res, 2005, 11:1319-1326
Chan KYY, Wong N, Lai PBS, Squire JA, Macgregor PF, Beheshti B, Albert M, To KF, Johnson PJ. Transcriptional profiling on chromosome 19p indicated frequent downregulation of ACP5 expression in hepatocellular carcinoma. Int J Cancer, 2005, 114(6):902-8
Coles JG, Boscarino C, Takahashi M, Grant D, Chang A, Ritter J, Dai X, Du C, Musso G, Yamabi, H, Goncalves J, Kumar AS, Woodgett J, Lu H, Hannigan G. Cardioprotective stress response in the human fetal heart. J. Thorac. Cardiovasc. Surg. 2005, 129(5):1128-36
Heisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, Takahashi M, Yau P, Huang THM, Farnham PJ, Jurisica I, Woodgett JR, Bremner R, Penn LZ, Der SD. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. NAR, 2005, 33(9):2952-2961
Lee C-H, Macgregor PF. Drug Resistance and Microarrays: how far are we from personalized cancer treatment? Modern Drug Discovery, 7(7):45-49. Review.

2004 (4 publications)
Lightfoot J, Hitzler JK, Zipursky A., Albert M, Macgregor PF. Distinct gene signatures of transient leukemia and acute megakaryoblastic leukemia in Down syndrome. Leukemia, 2004, 18(10);1617-1623
Lee C-H, Macgregor PF. Using Microarrays to Overcome Resistance to Chemotherapy in Cancer Patients. Pharmacogenomics, 2004, 5(6): 611-625. Review.
Konstantinov IE, Coles JG, Boscarino C, Takahashi M, Goncalves J, Ritter J, Van Arsdell GS. Gene Expression profiles in children undergoing cardiac surgery for right heart obstructive lesions. Journal of Thoracic and Cardiovascular Surgery, 2004, 127(3):746-754
Paris J, Virtanen C, Lu Z, Takahashi M. Identification of MEF2-regulated genes during muscle differentiation. Physiol. Genomics 2004, 20:143-151

2003 (4 publications)
Chen L, Goryachev A, Sun J, Kim P, Zhang H, Phillips J, Squire J, Macgregor PF, Lebel S, Edwards AM, Cao Q, Furuya N. Altered expression of genes involved in hepatic morphogenesis and fibrogenesis are identified by cDNA microarray analysis in billiary atresia. Hepatology 2003, 38(3), 567-576
Oberley, MJ, Tsao J, Yau P, Farnham PJ. High-Throughput Screening of Chromatin Immunoprecipitates Using CpG-Island Microarrays. Methods in Enzymology, 2003, 376:315-334
Macgregor PF. Gene expression in cancer: the application of microarrays. Expert Rev Mol Diagn. 2003 3(2):185-200. Review.
Winegarden, N. Microarrays in cancer: moving from hype to clinical reality. Lancet. 2003 362(9394):1428 Commentary

2002 (5 publications)
Bayani J, Brenton JD, Macgregor PF, Beheshti B, Albert M, Nallainathan D, Karaskova J, Rosen B, Murphy J, Laframboise J, Zanke B, and Squire JA. Parallel Analysis of Sporadic Primary Ovarian Carcinomas by Spectral Karyotyping, Comparative Genomic Hybridization, and Expression Microarrays. Cancer Research, 2002, 62(12):3466-3476
Claudio JO, Masih-Khan E, Tang H, Goncalves J, Voralia M, Li ZH, Nadeem V, Cukerman E, Francisco-Pabalan O, Liew CC, Woodgett JR, Stewart AK. A molecular compendium of genes expressed in multiple myeloma. Blood. 2002, 100(6):2175-2186
Macgregor PF, Squire JA. Application of microarrays to the analysis of gene expression in cancer. Clin Chem. 2002, 48(8):1170-7 Review
Haq R, Brenton JD, Takahashi M, inan D, Rottapel R, Zanke B. Constitutive p38HOG Mitogen-activated Protein Kinase Activation Induces Permanent Cell Cycle Arrest and Senescence. Cancer Res. 2002, 62(17):5076-5082
Iscove NN, Barbara M, Gu M, Gibson M, Modi C, Winegarden N. Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nature Biotechnology. 2002, 20(9):940-943

2001 (1 publication)
Yarwood SJ, Woodgett JR. Extracellular matrix composition determines the transcriptional response to epidermal growth factor receptor activation. Proc. Natl. Acad. Sci. USA, 2001 98(8):4472-4477