2011 Publications

2011 Publications

Prospective multicenter phase II trial of systemic ADH-1 in combination with melphalan via isolated limb infusion in patients with advanced extremity melanoma.
Beasley GM, Riboh JC, Augustine CK, Zager JS, Hochwald SN, Grobmyer SR, Peterson B, Royal R, Ross MI, Tyler DS.
J Clin Oncol. 2011 Mar 20;29(9):1210-5. Epub 2011 Feb 22.

Acute endotoxin-induced thymic atrophy is characterized by intrathymic inflammatory and wound healing responses.
Billard MJ, Gruver AL, Sempowski GD.
PLoS One. 2011 Mar 18;6(3):e17940.

Smoothelin-like 1 Protein Is a Bifunctional Regulator of the Progesterone Receptor during Pregnancy.
Bodoor K, Lontay B, Safi R, Weitzel DH, Loiselle D, Wei Z, Lengyel S, McDonnell DP, Haystead TA.
J Biol Chem. 2011 Sep 9;286(36):31839-51. Epub 2011 Jul 19.

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS.
Genome Res. 2011 Mar;21(3):456-64. Epub 2010 Nov 24.

SIGNATURE: A workbench for gene expression signature analysis.
Chang JT, Gatza ML, Lucas JE, Barry WT, Vaughn P, Nevins JR.
BMC Bioinformatics. 2011 Nov 14;12:443.

Comparison of genomics and functional imaging from canine sarcomas treated with thermoradiotherapy predicts therapeutic response and identifies combination therapeutics.
Chi JT, Thrall DE, Jiang C, Snyder S, Fels D, Landon C, McCall L, Lan L, Hauck M, MacFall JR, Viglianti BL, Dewhirst MW.
Clin Cancer Res. 2011 Apr 15;17(8):2549-60. Epub 2011 Feb 3.

The copper regulon of the human fungal pathogen Cryptococcus neoformans H99.
Ding C, Yin J, Tovar EM, Fitzpatrick DA, Higgins DG, Thiele DJ.
Mol Microbiol. 2011 Aug 8. doi: 10.1111/j.1365-2958.2011.07794.x. [Epub ahead of print]

A methodology for utilization of predictive genomic signatures in FFPE samples.
Freedman JA, Augustine CK, Selim AM, Holshausen KC, Wei Z, Tsamis KA, Hsu DS, Dressman HK, Barry WT, Tyler DS, Nevins JR.
BMC Med Genomics. 2011 Jul 11;4:58.

Prediction and genetic demonstration of a role for activator E2Fs in Myc-induced tumors.
Fujiwara K, Yuwanita I, Hollern DP, Andrechek ER.
Cancer Res. 2011 Mar 1;71(5):1924-32. Epub 2011 Jan 18.

Analysis of tumor environmental response and oncogenic pathway activation identifies distinct basal and luminal features in HER2-related breast tumor subtypes.
Gatza ML, Kung HN, Blackwell KL, Dewhirst MW, Marks JR, Chi JT.
Breast Cancer Res. 2011 Jun 7;13(3):R62. [Epub ahead of print]

HER2 overexpression elicits a proinflammatory IL-6 autocrine signaling loop that is critical for tumorigenesis.
Hartman ZC, Yang XY, Glass O, Lei G, Osada T, Dave SS, Morse MA, Clay TM, Lyerly HK.
Cancer Res. 2011 Jul 1;71(13):4380-91. Epub 2011 Apr 25.

Cell identity regulators link development and stress responses in the Arabidopsis root.
Iyer-Pascuzzi AS, Jackson T, Cui H, Petricka JJ, Busch W, Tsukagoshi H, Benfey PN.
Dev Cell. 2011 Oct 18;21(4):770-82.

Regulator of G protein signaling 5 is highly expressed in parathyroid tumors and inhibits signaling by the calcium-sensing receptor.
Koh J, Dar M, Untch BR, Dixit D, Shi Y, Yang Z, Adam MA, Dressman H, Wang X, Gesty-Palmer D, Marks JR, Spurney R, Druey KM, Olson JA Jr.
Mol Endocrinol. 2011 May;25(5):867-76. Epub 2011 Mar 10.

Glutamine synthetase is a genetic determinant of cell type-specific glutamine independence in breast epithelia.
Kung HN, Marks JR, Chi JT.
PLoS Genet. 2011 Aug;7(8):e1002229. Epub 2011 Aug 11.

Peripheral blood signatures of lead exposure.
Labreche HG, Meadows SK, Nevins JR, Chute JP.
PLoS One. 2011;6(8):e23043. Epub 2011 Aug 1.

Integrating factor analysis and a transgenic mouse model to reveal a peripheral blood predictor of breast tumors.
LaBreche HG, Nevins JR, Huang E.
BMC Med Genomics. 2011 Jul 22;4:61.

Immunophenotypic and gene expression analysis of monoclonal B-cell lymphocytosis shows biologic characteristics associated with good prognosis CLL.
Lanasa MC, Allgood SD, Slager SL, Dave SS, Love C, Marti GE, Kay NE, Hanson CA, Rabe KG, Achenbach SJ, Goldin LR, Camp NJ, Goodman BK, Vachon CM, Spector LG, Rassenti LZ, Leis JF, Gockerman JP, Strom SS, Call TG, Glenn M, Cerhan JR, et al.
Leukemia. 2011 Sep;25(9):1459-66. doi: 10.1038/leu.2011.117. Epub 2011 May 27.

Heterogeneity in MYC-induced mammary tumors contributes to escape from oncogene dependence.
Leung JY, Andrechek ER, Cardiff RD, Nevins JR.
Oncogene. 2011 Sep 26. doi: 10.1038/onc.2011.433. [Epub ahead of print]

Whole blood gene expression analyses in patients with single versus recurrent venous thromboembolism.
Lewis DA, Stashenko GJ, Akay OM, Price LI, Owzar K, Ginsburg GS, Chi JT, Ortel TL.
Thromb Res. 2011 Jul 5. [Epub ahead of print]

Role of miR-204 in the regulation of apoptosis, endoplasmic reticulum stress response, and inflammation in human trabecular meshwork cells.
Li G, Luna C, Qiu J, Epstein DL, Gonzalez P.
Invest Ophthalmol Vis Sci. 2011 May 6;52(6):2999-3007. Print 2011 May.

MicroRNA-24 regulates the processing of latent TGF-beta1 during cyclic mechanical stress in human trabecular meshwork cells through direct targeting of FURIN.
Luna C, Li G, Qiu J, Epstein DL, Gonzalez P.
J Cell Physiol. 2011 May;226(5):1407-14. doi: 10.1002/jcp.22476.

Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer.
Matsumura N, Huang Z, Mori S, Baba T, Fujii S, Konishi I, Iversen ES, Berchuck A, Murphy SK.
Genome Res. 2011 Jan;21(1):74-82. Epub 2010 Dec 14.

Bayesian probit regression model for the diagnosis of pulmonary fibrosis: proof-of-principle.
Meltzer EB, Barry WT, D'Amico TA, Davis RD, Lin SS, Onaitis MW, Morrison LD, Sporn TA, Steele MP, Noble PW.
BMC Med Genomics. 2011 Oct 5;4:70.

Estrogen-related receptor-α is a metabolic regulator of effector T-cell activation and differentiation.
Michalek RD, Gerriets VA, Nichols AG, Inoue M, Kazmin D, Chang CY, Dwyer MA, Nelson ER, Pollizzi KN, Ilkayeva O, Giguere V, Zuercher WJ, Powell JD, Shinohara ML, McDonnell DP, Rathmell JC.
Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18348-53. Epub 2011 Oct 31.

Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.
Miller HB, Robinson TJ, Gordan R, Hartemink AJ, Garcia-Blanco MA.
RNA. 2011 Apr;17(4):665-74. Epub 2011 Jan 31.

Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae.
Muller LA, McCusker JH.
FEMS Yeast Res. 2011 Nov;11(7):587-94. doi: 10.1111/j.1567-1364.2011.00748.x. Epub 2011 Sep 8.

Phase II prospective open-label trial of recombinant interleukin-11 in women with mild von Willebrand disease and refractory menorrhagia.
Ragni MV, Jankowitz RC, Jaworski K, Merricks EP, Kloos MT, Nichols TC.
Thromb Haemost. 2011 Aug 11;106(4). [Epub ahead of print]

Genome-scale ribosome footprinting identifies a primary role for endoplasmic reticulum-bound ribosomes in the translation of the mRNA transcriptome.
Reid DW, Nicchitta CV.
J Biol Chem. 2011 Dec 23. [Epub ahead of print]

Deletion of Cryptococcus neoformans AIF ortholog promotes chromosome aneuploidy and fluconazole-resistance in a metacaspase-independent manner.
Semighini CP, Averette AF, Perfect JR, Heitman J.
PLoS Pathog. 2011 Nov;7(11):e1002364. Epub 2011 Nov 17.

Using a stem cell-based signature to guide therapeutic selection in cancer.
Shats I, Gatza ML, Chang JT, Mori S, Wang J, Rich J, Nevins JR.
Cancer Res. 2011 Mar 1;71(5):1772-80. Epub 2010 Dec 17.

Neuronal GPCR controls innate immunity by regulating noncanonical unfolded protein response genes.
Sun J, Singh V, Kajino-Sakamoto R, Aballay A.
Science. 2011 May 6;332(6030):729-32. Epub 2011 Apr 7.

Dasatinib (BMS-35482) has synergistic activity with paclitaxel and carboplatin in ovarian cancer cells.
Teoh D, Ayeni TA, Rubatt JM, Adams DJ, Grace L, Starr MD, Barry WT, Berchuck A, Murphy SK, Secord AA.
Gynecol Oncol. 2011 Apr;121(1):187-92. Epub 2011 Jan 3.

Network calisthenics: Control of E2F dynamics in cell cycle entry.
Wong JV, Dong P, Nevins JR, Mathey-Prevot B, You L.
Cell Cycle. 2011 Sep 15;10(18). [Epub ahead of print]

Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells.
Wong JV, Yao G, Nevins JR, You L.
Methods Enzymol. 2011;497:221-37.

Viral-mediated noisy gene expression reveals biphasic E2f1 response to MYC.
Wong JV, Yao G, Nevins JR, You L.
Mol Cell. 2011 Feb 4;41(3):275-85.