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Publications by PMGC staff
Home About Us Publications Publications by PMGC staff

Staff members at PMGC have had their material published in books and articles.
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(Names of contributing staff members are highlighted in red)

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Books/Chapters
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Genomics: Essential Methods. Edited by Starkey M and Elaswarapu R; Published by John Wiley & Sons, 2010; ISBN: 9780470711576

Includes: Chapter 5: RNA Amplification Strategies: Toward Single Cell Sensitivity (Natalie Stickle, Norman N. Iscove, Carl Virtanen, Mary Barbara, Carolyn Modi, Ari Baratz, Toni Di Berardino, Ellen Greenblatt, Ted Brown and Neil Winegarden)

Genomics and Pharmacogenomics in Anticancer Drug development and Clinical Response. Edited by Federico Innocenti; Published by Springer, 2008; ISBN: 1588296466

Includes: Chapter 1 Toward the Realization of the Promise of Microarrays in Oncology (Natalie Stickle 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 and 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 and Neil Winegarden)

Promoter and CpG Island Microarrays Edited by Neil Winegarden and Mark Takahashi; Published by DNA Press, 2006; ISBN: 0974876569

Includes: CPG Array Analysis: Putting the Pieces Together (Carl Virtanen and Zhibin Lu)

Promoter and CpG Island Microarrays Edited by Neil Winegarden and Mark Takahashi; Published by DNA Press, 2006; ISBN: 0974876569


Journal Publications
2014
Feigenberg T, Clarke B, Virtanen C, Plotkin A, Letarte M, Rosen B, Bernardini MQ, Kollara A, Brown TJ and Murphy KJ. Molecular profiling and clinical outcome of high-grade serous ovarian cancer presenting with low- versus high-volume ascites. Biomed Res Int. 2014 2014:367103.

Lau A, Kollara A, St John E, Tone AA, Virtanen C, Greenblatt EM, King WA and Brown TJ. Altered expression of inflammation-associated genes in oviductal cells following follicular fluid exposure: implications for ovarian carcinogenesis. Experimental Biology and Medicine (Maywood, N.J.). 2014 Jan;239(1):24-32.

Pollock RA, Abji F, Liang K, Chandran V, Pellett F, Virtanen C and Gladman DD. Gene Expression Differences between Psoriasis Patients with and without Inflammatory Arthritis. Journal of Investigative Dermatology. 2014 Sep 22;.

2013
Chan C, Virtanen C, Winegarden NA, Colgan TJ, Brown TJ and Greenblatt EM. Discovery of biomarkers of endometrial receptivity through a minimally invasive approach: a validation study with implications for assisted reproduction. Fertility and Sterility. 2013 Sep;100(3):810-7.

Kaanta AS, Virtanen C, Selfors LM, Brugge JS and Neel BG. Evidence for a multipotent mammary progenitor with pregnancy-specific activity. Breast Cancer Research. 2013 15(4):R65.

Ogawa S, Surapisitchat J, Virtanen C, Ogawa M, Niapour M, Sugamori KS, Wang S, Tamblyn L, Guillemette C, Hoffmann E, Zhao B, Strom S, Laposa RR, Tyndale RF, Grant DM and Keller G. Three-dimensional culture and cAMP signaling promote the maturation of human pluripotent stem cell-derived hepatocytes. Development. 2013 Aug;140(15):3285-96.

2012
Badea I, Virtanen C, Verrall RE, Rosenberg A and Foldvari M. Effect of topical interferon-gamma gene therapy using gemini nanoparticles on pathophysiological markers of cutaneous scleroderma in Tsk/+ mice. Gene Therapy. 2012 Oct;19(10):978-87.

Brustle A, Brenner D, Knobbe CB, Lang PA, Virtanen C, Hershenfield BM, Reardon C, Lacher SM, Ruland J, Ohashi PS and Mak TW. The NF-kappaB regulator MALT1 determines the encephalitogenic potential of Th17 cells. Journal of Clinical Investigation. 2012 Dec 3;122(12):4698-709.

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 Jul 6; 358(1):116-26

Ko MA, Zehong G, Virtanen C, Guindi M, Waddell TK, Keshavjee S, Darling GE. MicroRNA Expression Profiling of Esophageal Cancer Before and After Induction Chemoradiotherapy. Ann Thorac Surg. Epub 2012 Aug 29.

Maeda A, Leung MK, Conroy L, Chen Y, Bu J, Lindsay PE, Mintzberg S, Virtanen C, Tsao J, Winegarden NA, Wang Y, Morikawa L, Vitkin IA, Jaffray DA, Hill RP, Dacosta RS. In vivo optical imaging of tumor and microvascular response to ionizing radiation. PLoS One. 2012;7(8):e42133. Epub 2012 Aug 22.

Sasaki M, Knobbe CB, Munger JC, Lind EF, Brenner D, Brüstle A, Harris IS, Holmes R, Wakeham A, Haight J, You-Ten A, Li WY, Schalm S, Su SM, Virtanen C, Reifenberger G, Ohashi PS, Barber DL, Figueroa ME, Melnick A, Zúñiga-Pflücker JC, Mak TW. IDH1(R132H) mutation increases murine haematopoietic progenitors and alters epigenetics. Nature. 2012 Aug 30;488(7413):656-9.

Tone AA, Virtanen C, Shaw P, Brown TJ. Prolonged Postovulatory Proinflammatory Signaling in the Fallopian Tube Epithelium May Be Mediated through a BRCA1/DAB2 Axis. Clin Cancer Res. 2012 Aug 15;18(16):4334-44.

2011
Siu A, Virtanen C, Jongstra J. PIM kinase isoform specific regulation of MIG6 expression and EGFR signaling in prostate cancer cells. Oncotarget. 2011 Dec;2(12):1134-44.

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 Nov 10. doi: 10.1038/gt.2011.159

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

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
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
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
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

2007
2006
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
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
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
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
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
Yarwood SJ, Woodgett JR: Extracellular matrix composition determines the transcriptional response to epidermal growth factor receptor activation. (2001) Proc. Natl. Acad. Sci. USA, 98(8):4472-4477