2009 Publications

2009 Publications

Genetic heterogeneity of Myc-induced mammary tumors reflecting diverse phenotypes including metastatic potential
Andrechek ER, Cardiff RD, Chang JT, Gatza ML,
Acharya CR, Potti A, Nevins JR.
Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16387-92.
PMID: 19805309

Gene expression profiles of tumor biology provide a novel approach to prognosis and may guide the selection of therapeutic targets in multiple myeloma
Anguiano A, Tuchman SA, Acharya C, Salter K, Gasparetto C, Zhan F, Dhodapkar M, Nevins J, Barlogie B, Shaughnessy JD Jr, Potti A
J Clin Oncol. 2009 Sep 1;27(25):4197-203
PMID: 19636021

Genomic and molecular profiling predicts response to temozolomide in melanoma
Augustine CK, Yoo JS, Potti A, Yoshimoto Y, Zipfel PA, Friedman HS, Nevins JR, Ali-Osman F, Tyler DS
Clin Cancer Res. 2009 Jan 15;15(2):502-10
PMID: 19147755

MYC activity mitigates response to rapamycin in prostate cancer through eukaryotic initiation factor 4E-binding protein 1-mediated inhibition of autophagy.
Balakumaran BS, Porrello A, Hsu DS, Glover W,
Foye A, Leung JY, Sullivan BA, Hahn WC, Loda M, Febbo PG.
Cancer Res..2009 Oct 1;69(19):7803-10.
PMID: 19773438

Microarray analysis of early stage serous ovarian cancers shows profiles predictive of favorable outcome
Berchuck A, Iversen ES, Luo J, Clarke JP, Horne H, Levine DA, Boyd J, Alonso MA, Secord AA, Bernardini MQ, Barnett JC, Boren T, Murphy SK, Dressman HK, Marks JR, Lancaster JM
Clin Cancer Res. 2009 Apr 1;15(7):2448-55
PMID: 19318476

Microarray analysis of gene expression in gynecologic cancers--still only the beginning.
Berchuck A.
Gynecol Oncol..2009 Jul;114(1):1-2
PMID: 19497432

An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer.
Bild AH, Parker JS, Gustafson AM, Acharya CR, Hoadley KA, Anders C, Marcom PK, Carey LA, Potti A, Nevins JR, Perou CM.
Breast Cancer Res..2009;11(4):R55.
PMID: 19638211

MicroRNAs and their target messenger RNAs associated with ovarian cancer response to chemotherapy.
Boren TP, Xiong Y, Hakam A, Wenham R, Apte S, Chan G, Kamath SG, Chen DT, Dressman HK, and Lancaster JM.
Gynecologic Oncology .2009 May;113(2):249-55
PMID: 19237188

A genomic strategy to elucidate modules of oncogenic pathway signaling networks.
Chang JT, Carvalho C, Mori S, Bild AH, Gatza ML, Wang Q, Lucas JE, Potti A, Febbo PG, West M, Nevins JR.
Mol Cell.. 2009 Apr 10;34(1):104-14.
PMID: 19362539

A combinatorial mechanism for determining the specificity of E2F activation and repression
Freedman JA, Chang JT, Jakoi L, Nevins JR
Oncogene.2009 Aug 13;28(32):2873-81. Epub 2009 Jun 22
PMID: 19543322

A combinatorial mechanism for determining the
specificity of E2F activation and repression.

Freedman JA, Chang JT, Jakoi L, Nevins JR.
Oncogene..2009 Aug 13;28(32):2873-81.
PMID: 19543322

A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia
Friedman DR, Weinberg JB, Barry WT, Goodman BK, Volkheimer AD, Bond KM, Chen Y, Jiang N, Moore JO, Gockerman JP, Diehl LF, Decastro CM, Potti A, Nevins JR
Clin Cancer Res. 2009 Nov 15;15(22):6947-55
PMID: 19861443;

Nucleolar proteins suppress Caenorhabditis elegans innate immunity by inhibiting p53/CEP-1.
Fuhrman LE, Goel AK, Smith J, Shianna KV, Aballay A.
PLoS Genet..2009 Sep;5(9):e1000657.
PMID: 19763173

Characterizing the developmental pathways TTF-1, NKX2-8, and PAX9 in lung cancer.
Hsu DS, Acharya CR, Balakumaran BS, Riedel RF, Kim MK, Stevenson M, Tuchman S, Mukherjee S, Barry W, Dressman HK, Nevins JR, Powers S, Mu D, Potti A.
Proc Natl Acad Sci U S A.2009 Mar 31;106(13):5312-7.
PMID: 19279207

Sample size calculation for microarray experiments
with blocked one-way design.

Jung SH, Sohn I, George SL, Feng L, Leppert PC.
BMC Bioinformatics..2009 May 28;10:164.
PMID: 19476634

Polycythemia vera erythroid precursors exhibit increased proliferation and apoptosis resistance associated with abnormal RAS and PI3K pathway activation.
Laubach JP, Fu P, Jiang X, Salter KH, Potti A, Arcasoy MO.
Exp Hematol. .2009 Dec;37(12):1411-22.
PMID: 19815050

Alterations in microRNA expression in stress-induced cellular senescence
Li G, Luna C, Qiu J, Epstein DL, Gonzalez P
Mech Ageing Dev. 2009 Nov-Dec;130(11-12):731-41
PMID: 19782699

A novel splice variant of GLI1 that promotes glioblastoma cell migration and invasion
Lo HW, Zhu H, Cao X, Aldrich A, Ali-Osman F
Cancer Res. 2009 Sep 1;69(17):6790-8
PMID: 19706761

Glioblastoma proto-oncogene SEC61gamma is required for tumor cell survival and response to endoplasmic reticulum stress.
Lu Z, Zhou L, Killela P, Rasheed AB, Di C, Poe WE, McLendon RE, Bigner DD, Nicchitta C, Yan H.
Cancer Res..2009 Dec 1;69(23):9105-11
PMID: 19920201

Cross-study projections of genomic biomarkers: an evaluation in cancer genomics.
Lucas JE, Carvalho CM, Chen JL, Chi JT, West M.
PLoS One..2009;4(2):e4523
PMID: 19225561

Role of miR-29b on the regulation of the extracellular matrix in human trabecular meshwork cells under chronic oxidative stress.
Luna C, Li G, Qiu J, Epstein DL, Gonzalez P.
Mol Vis. .2009 Nov 28;15:2488-97.
PMID: 19956414

Yin yang 1 modulates taxane response in epithelial ovarian cancer
Matsumura N, Huang Z, Baba T, Lee PS, Barnett JC, Mori S, Chang JT, Kuo WL, Gusberg AH, Whitaker RS, Gray JW, Fujii S, Berchuck A, Murphy SK
Mol Cancer Res. 2009 Feb;7(2):210-20
PMID: 19208743

Genomic strategy for targeting therapy in castration-resistant prostate cancer.
Mendiratta P, Mostaghel E, Guinney J, Tewari AK, Porrello A, Barry WT, Nelson PS, Febbo PG.
J Clin Oncol..2009 Apr 20;27(12):2022-9.
PMID: 19289629

Identification of osteopontin-dependent signaling pathways in a mouse model of human breast cancer
Mi Z, Guo H, Kuo PC
BMC Res Notes. 2009 Jul 1;2:119
PMID: 19570203;

Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma
Mito JK, Riedel RF, Dodd L, Lahat G, Lazar AJ, Dodd RD, Stangenberg L, Eward WC, Hornicek FJ, Yoon SS, Brigman BE, Jacks T, Lev D, Mukherjee S, Kirsch DG
PLoS One. 2009 Nov 30;4(11):e8075
PPMID: 19956606

Anchorage-independent cell growth signature identifies tumors with metastatic potential
Mori S, Chang JT, Andrechek ER, Matsumura N, Baba T, Yao G, Kim JW, Gatza M, Murphy S, Nevins JR
Oncogene. 2009 Aug 6;28(31):2796-805
PMID: 19483725

Utilization of genomic signatures to identify phenotype-specific drugs.
Mori S, Chang JT, Andrechek ER, Potti A, Nevins JR.
PLoS One..2009 Aug 28;4(8):e6772.
PMID: 19714244

Coordinated posttranscriptional mRNA population
dynamics during T-cell activation.

Mukherjee N, Lager PJ, Friedersdorf MB,
Thompson MA, Keene JD.
Mol Syst Biol..Mol Syst Biol.
PMID: 19638969

Repair-related activation of hedgehog signaling promotes cholangiocyte chemokine production
Omenetti A, Syn WK, Jung Y, Francis H, Porrello A, Witek RP, Choi SS, Yang L, Mayo MJ, Gershwin ME, Alpini G, Diehl AM
Hepatology. 2009 Aug;50(2):518-27
PMID: 19575365;

Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment.
Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN.
Methods Mol Biol.. 2009;553:57-77.
PMID: 19588101

p38gamma mitogen-activated protein kinase is a key regulator in skeletal muscle metabolic adaptation in mice
Pogozelski AR, Geng T, Li P, Yin X, Lira VA, Zhang M, Chi JT, Yan Z
PLoS One. 2009 Nov 20;4(11):e7934
PMID: 19936205

Age-specific differences in oncogenic pathway dysregulation and anthracycline sensitivity in patients with acute myeloid leukemia
Rao AV, Valk PJ, Metzeler KH, Acharya CR, Tuchman SA, Stevenson MM, Rizzieri DA, Delwel R, Buske C, Bohlander SK, Potti A, L?wenberg B
J Clin Oncol. 2009 Nov 20;27(33):5580-6
PMID: 19858393

Identification of CD15 as a marker for tumor-propagating cells in a mouse model of medulloblastoma
Read TA, Fogarty MP, Markant SL, McLendon RE, Wei Z, Ellison DW, Febbo PG, Wechsler-Reya RJ
Cancer Cell. 2009 Feb 3;15(2):135-47
PMID: 19185848

A role for E2F activities in determining the fate of Myc-induced lymphomagenesis.
Rempel RE, Mori S, Gasparetto M, Glozak MA, Andrechek ER, Adler SB, Laakso NM, Lagoo AS, Storms R, Smith C, Nevins JR.
PLoS Genet. .2009 Sep;5(9):e1000640.
PMID: 19749980

Basal cells as stem cells of the mouse trachea and human airway epithelium.
Rock JR, Onaitis MW, Rawlins EL, Lu Y, Clark CP,
Xue Y, Randell SH, Hogan BL.
Proc Natl Acad Sci U S A..2009 Aug 4;106(31):12771-5.
PMID: 19625615

Rho GTPase activity modulates Wnt3a/beta-catenin signaling.
Rossol-Allison J, Stemmle LN, Swenson-Fields KI, Kelly P, Fields PE, McCall SJ, Casey PJ, Fields TA.
Cell Signal. .2009 Nov;21(11):1559-68.
PMID: 19482078

Gene expression patterns in peripheral blood correlate with the extent of coronary artery disease.
Sinnaeve PR, Donahue MP, Grass P, Seo D, Vonderscher J, Chibout SD, Kraus WE, Sketch M Jr, Nelson C, Ginsburg GS, Goldschmidt-Clermont PJ, Granger CB
PLoS One..2009 Sep 14;4(9):e7037.
PMID: 19750006

A permutation-based multiple testing method for time-course microarray experiments
Sohn I, Owzar K, George SL, Kim S, Jung SH
BMC Bioinformatics. 2009 Oct 15;10:336
PMID: 19832992

Novel tumor sampling strategies to enable microarray gene expression signatures in breast cancer: a study to determine feasibility and reproducibility in the context of clinical care
Tebbit CL, Zhai J, Untch BR, Ellis MJ, Dressman HK, Bentley RC, Baker JA, Marcom PK, Nevins JR, Marks JR, Olson JA Jr
Breast Cancer Res Treat. 2009 Dec;118(3):635-43
PMID: 19224362

Gene and protein expression pilot profiling and biomarkers in an experimental mouse model of hypertensive glaucoma.
Walsh MM, Yi H, Friedman J, Cho KI, Tserentsoodol N,
McKinnon S, Searle K, Yeh A, Ferreira PA.
Exp Biol Med (Maywood).2009 Aug;234(8):918-30.
PMID: 19491369

Targeting interleukin 6 signaling suppresses glioma stem cell survival and tumor growth.
Wang H, Lathia JD, Wu Q, Wang J, Li Z, Heddleston JM, Eyler CE, Elderbroom J, Gallagher J, Schuschu J, MacSwords J, Cao Y, McLendon RE, Wang XF, Hjelmeland AB, Rich JN
Stem Cells.2009 Oct;27(10):2393-404
PMID: 19658188

Tnni3k modifies disease progression in murine models of cardiomyopathy.
Wheeler FC, Tang H, Marks OA, Hadnott TN, Chu PL, Mao L, Rockman HA, Marchuk DA.
PLoS Genet..2009 Sep;5(9):e1000647.
PMID: 19763165

Gene expression signatures diagnose influenza and other
symptomatic respiratory viral infections in humans.

Zaas AK, Chen M, Varkey J, Veldman T, Hero AO 3rd, Lucas J, Huang Y, Turner R, Gilbert A, Lambkin-Williams R, Oien NC, Nicholson B, Kingsmore S, Carin L, Woods CW, Ginsburg GS.
Cell Host Microbe. .2009 Sep 17;6(3):207-17.
PMID: 19664979