2008 Publications

2008 Publications

Development of an inhaled endotoxin challenge protocol for characterizing evoked cell surface phenotype and genomic responses of airway cells in allergic individuals
Alexis NE, Brickety WJ, Lay JC, Wang Y, Roubey RA, Ting JP, Peden DB
Ann Allergy Asthma Immunol.100:206-15

Age-specific differences in oncogenic pathway deregulation seen in human breast tumors
Anders CK, Acharya CR, Hsu DS, Broadwater G, Garman K, Foekens JA, Zhang Y, Wang Y, Marcom K, Marks JR, Mukherjee S, Nevins JR, Blackwell KL, Potti A.
PLoS ONE.3(1):e1373

Young age at diagnosis correlates with worse prognosis and defines a subset of breast cancers with shared patterns of gene expression.
Anders CK, Hsu DS, Broadwater G, Acharya CR, Foekens JA, Zhang Y, Wang Y, Marcom PK, Marks JR, Febbo PG, Nevins JR, Potti A, Blackwell KL
J Clin Oncol.26(20):3324-30

The interplay of prolactin and the glucocorticoids in the regulation of beta cell gene expression, fatty acid oxidation, and glucose-stimulated insulin secretion: implications for carbohydrate metabolism in pregnancy.
Arumugam R, Horowitz E, Lu D, Collier JJ, Ronnebaum S, Fleenor D, Freemark M.
Endocrinology.July 3 Ahead of print

Epigenetic regulation of CD133 and tumorigenicity of CD133+ ovarian cancer cells
Baba T, Convery PA, Matsumura N, Whitaker RS, Kondoh E, Perry T, Huang Z, Bentley RC, Mori S, Fuji S, Marks JR, Berchuck A and Murphy SK
Oncogene.Epub 2008 Oct 6

MicroRNAs and their target messenger RNAs associated with endometrial carcinogenesis
Boren T, Xiong Y, Hakam A, Wenham R, Apte S, Wei Z, Kamath S, Chen DT, Dressman H, Lancaster JM.
Gynecol Oncol.110(2):206-15

The genomic analysis of erythrocyte microRNA expression in sickle cell diseases
Chen SY, Wang Y, Telen MJ, Chi JT
PLoS ONE.3(6):e2360

Cell identity mediates the response of Arabidopsis roots to abiotic stress
Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein J, Benfey PN.
Science.16;320(5878):942-5

Modeling cancer progression via pathway dependencies.
Edelman EJ, Guinney J, Chi JT, Febbo PG, Mukherjee S.
PLoS Comput Biol.4(2):e28

Genomic modeling of atherosclerosis in peripheral arterial disease and its variant phenotype in patients with diabetes
Evans DC, Sileshi B, Zakaria AM, Giangiacomo D, Manson RJ, Lawson JH.
Vascular.16 (4):225-35

Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling.
Ferrara CT, Wang P, Neto EC, Stevens RD, Bain JR, Wenner BR, Ilkayeva OR, Keller MP, Blasiole DA, Kendziorski C, Yandell BS, Newgard CB, Attie AD
PLoS Genet..4(3):e1000034

An E2F1-dependent gene expression program that determines the balance between proliferation and cell death
Hallstrom TC, Mori S, Nevins JR
Cancer Cell.13(1):11-22

Unfolded protein response genes regulated by CED-1 are required for Caenorhabditis elegans innate immunity
Haskins KA, Russell JF, Gaddis N, Dressman HK, Aballay A
Dev Cell.15(1):87-97

Post-mating gene expression profiles of female Drospholia melanogaster in response to time and to four male accessory gland proteins
McGraw LA, Clark AG, and Wolfner MF
Genetics.179:1395-408

Gene expression signatures of radiation response are specific, durable and accurate in mice and humans.
Meadows SK, Dressman HK, Muramoto GG, Himburg H, Salter A, Wei Z, Ginsburg G, Chao NJ, Nevins JR, Chute JP
PLoS ONE.3(4):e1912

Utilization of pathway signatures to reveal distinct types of B lymphoma in the Emicro-myc model and human diffuse large B-cell lymphoma.
Mori S, Rempel RE, Chang JT, Yao G, Lagoo AS, Potti A, Bild A, Nevins JR.
Cancer Research .68:8525-34

Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets.
Morris AR, Mukherjee N, Keene JD
Mol Cell Biol..28(12):4093-103

Dunning rat prostate adenocarcinomas and alternative splicing reporters: powerful tools to study epithelial plasticity in prostate tumors in vivo.
Oltean S, Febbo PG, Garcia-Blanco MA.
Clin Exp Metastasis.25(6):611-9

Identification of the cellular targets of the transcription factor TCERG1 reveals a prevalent role in mRNA processing
Pearson JL, Robinson TJ, Mu?oz MJ, Kornblihtt AR, Garcia-Blanco MA
J Biol Chem.283(12):7949-61

Lack of E2F2 leads to delayed cell cycle progression and inefficient erythropoiesis in EKLF-Deficient Mice
Pilon AM, Arcasoy MO, Dressman HK, Vayda SE, Maksimova YD, Beaupre J, Sangerman JI, Gallagher PG, and Bodine DM
MCB.in press

Utilization of genomic signatures to direct use of primary chemotherapy.
Potti A, Nevins JR
Curr Opin Genet Dev.18(1):62-7

Signal sequence- and translation-independent mRNA localization to the endoplasmic reticulum.
Pyhtila B, Zheng T, Lager PJ, Keene JD, Reedy MC, Nicchitta CV
RNA.14(3):445-53

A phase II prospective open-label escalating dose trial of recombinant interleukin-11 in mild von Willebrand disease.
Ragni MV, Jankowitz RC, Chapman HL, Merricks EP, Kloos MT, Dillow AM, Nichols TC.
Haemophilia.2008 Sep;14(5):968-77. Epub 2008 Aug 1.

High Oxygen prevents fetal lethality due to lack of catecholamines
Ream MA, Chandra R, Peavey M, Ray AM, Roffler-Tarlov S, Kim HG, Wetsel WC, Rockman HA, Chikaraishi DM
Am J Physiol Regul Integr Comp Physiol.295:R942-53

A Mep2-dependent Transcriptional Profile Links Permease Function to Gene Expression during Pseudohyphal Growth in Saccharomyces cerevisiae.
Rutherford JC, Chua G, Hughes T, Cardenas ME, Heitman J
Mol Biol Cell..19(7):3028-39.

Stimulation of human and rat islet beta-cell proliferation with retention of function by the homeodomain transcription factor Nkx6.1.
Schisler JC, Fueger PT, Babu DA, Hohmeier HE, Tessem JS, Lu D, Becker TC, Naziruddin B, Levy M, Mirmira RG, Newgard CB
Mol Cell Biol..28(10):3465-76

Innate immunity in Caenorhabditis elegans is regulated by neurons expressing NPR-1/GPCR
Styer KL, Singh V, Macosko E, Stelle SE, Burgmann CI, and Aballay A.
Science.Epub 2008 Sept 18

Patterns of cell signaling pathway activation that characterize mammary development
Xu M, Kao MC, Nunez-Iglesias J, Nevins JR, West M, Zhou XJ
Development.135(14):2403-13