Publications
Papers published by Expression Analysis with links to abstracts
Hardin, J., Finnell, R., Wang, D., Hogan, M., Horovitz, J., Shu, J., Shaw, G. Whole Genome Microarray Analysis From Neonatal Blood Cards BMC Genetics
Shabalin, A., Weigman, V.J., Perou, C.M., Nobel, A.B. (2009) Finding Large Average Submatrices in High Dimensional Data. To appear in JASA.
Hester, S., Reid, L., Viale, A., Nowak, N., Jones, W. D., Parker, J. S., Knudtson, K., Ward, W., Tiesman, J., Massimi, A., & Denslow, N., (2009) Comparison of comparative genomic hybridization technologies across microarray platforms J Biomol Tech, 20(2): 135–151.
Kular RK, Cvetanovic M, Siferd S, Kini AR, Opal P. (2009) Neuronal differentiation is regulated by LANP, a member of the INHAT complex. J Biol Chem. 2009 Jan 9. [Epub ahead of print] PMID: 19136565
Parker, JS, et al. (2009) Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes to appear in Journal of Clinical Oncology.
Royland J, Parker JS, Gilbert M. (2008) A genomic analysis of subclinical hypothyroidism in hippocampus and neocortex of the developming brain. Journal of Neuroendocrinology, in press.
Pine, P. S., Boedigheimer, M., Rosenzweig, B. A., Turpaz, Y., He, Y. D., Delenstarr, G., Ganter, B., Jarnagin, K., Jones, W. D., Reid, L., and Thompson, K. L., (2008) Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed tissue RNA reference samples Pharmacogenomics, 9(11), 1753-1763.
Wang SE, Xiang B, Guix M, Olivares MG, Parker J, Chung CH, Pandiella A, Arteaga CL.(2008) Transforming Growth Factor {beta} Engages TACE and ErbB3 to Activate PI3K/Akt in ErbB2-overexpressing Breast Cancer and Desensitizes Cells to Trastuzumab. Mol Cell Biol. Jul 14.
Charles et al. (2008) Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males. BMC Medical Genomics, 1:38
Shi, L., Jones, W. D., Jensen, R. V., et al. (2008) The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies BMC Bioinformatics, 9(Suppl 9):S10.
Jones, W. D. (2008) Comment on “Quality assessment for short oligonucleotide microarray data” Technometrics, 50(3), 265-267.
Connor EE, Siferd S, Elsasser TH, Evock-Clover CM, Van Tassell CP, Sonstegard TS, Fernandes VM, Capuco AV. (2008) Effects of increased milking frequency on gene expression in the bovine mammary gland. BMC Genomics.9:362. PMID: 18671851 [PubMed - indexed for MEDLINE]
Wakamatsu N, Collins JB, Parker JS, Tessema M, Clayton NP, Ton TV, Hong HH, Belinsky S, Devereux TR, Sills RC, Lahousse SA. (2008) Gene expression studies demonstrate that the K-ras/Erk MAP kinase signal transduction pathway and other novel pathways contribute to the pathogenesis of cumene-induced lung tumors. Toxicol Pathol.;36(5):743-52.
Gohlke JM, Armant O, Parham FM, Smith MV, Zimmer C, Castro DS, Nguyen L, Parker JS, Gradwohl G, Portier CJ, Guillemot F. (2008) Characterization of the proneural gene regulatory network during mouse telencephalon development. BMC Biology. 6:15
Silva JM, Marran K, Parker JS, Silva J, Golding M, Schlabach MR, Elledge SJ, Hannon GJ, Chang K. (2008) Profiling Essential Genes in Human Mammary Cells by Multiplex RNAi Screening. Science 319 (5863), 617.
Risher, J.D., Rivenbark, A.G., Jones, W. D., and Coleman, W.B. (2008) Overexpression of DNA methyltransferase 3b contributes to a hypermethylator phenotype in human breast cancer cell lines Molecular Cancer 7:15.
Muse et al (2007) RNA polymerase is poised for activation across the genome. Nature Genetics, 39, 1507 - 1511.
Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G, Hannon GJ. (2007) A biochemical approach to identifying microRNA targets. PNAS, 104: 19291-19296.
Christine H. Chung, Joel Parker, Shawn Levy, Robbert J. Slebos, Adam P. Dicker and Ulrich Rodeck. (2007 “Gene expression profiles as markers of aggressive disease - EGFR as a factor” Int J Radiat Oncol Biol Phys. 2007, in press.
Thomson JM, Parker JS, Hammond SM. (2007) Microarray analysis of miRNA gene expression. Methods in Enzymology, 427:107-122.
Hoadley, KA, Weigman, VJ, Fan, C., Sawyer, LR., He, X., Troester, MA.,Sartor, CI., Rieger-House, T., Bernard, PS., Carey, LA., Perou, CM. EGFR associated expression profiles vary with breast tumor subtype. BMC Genomics 8:258, July 2007.
Roberts A, McMillan L, Wang W, Parker J, Rusyn I, Threadgill D. (2007) Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Bioinformatics, 23(13):i401-i407.
Herschkowitz, JI*, Simin, K*, Weigman, VJ, et al. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biology, 8:R76, May 2007
Shi, L., Jones, W. D., Jensen, R., Wolfinger, R., Kawasaki, E., Herman, D., Guo, L., Goodsaid, F., and Tong, W. (2007) Reply to MAQC papers over the cracks Nature Biotechnology, 25(1), 28-29.
Shi, L., Jones, W. D., Jensen, R., Wolfinger, R., Kawasaki, E., Herman, D., Guo, L., Goodsaid, F., and Tong, W. (2007) Reply to Statistical methods and microarray data Nature Biotechnology, 25(1), 26-27.
Rivenbark, A, Jones, W. D., and Risher, J., Coleman, W. B. (2006 DNA Methylation-Dependent Epigenetic Regulation of Gene Expression in MCF-7 Breast Cancer Cells. Epigenetics, 1(1), 32-44.
Shi, L, Reid, LH, Jones, WD, et al. 2006. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol., 24(9):1151-1161.
Shippy, R, Fulmer-Smentak, S, Jensen, RV, Jones, WD, et al. 2006. Using RNA sample titrations to assess microarray platform performace and normalization techniques. Nat. Biotechnol., 24(9):1123-1131.
Reid, LH and Warrington, JA. 2006. A note on nomenclature. Nat. Biotechnol., 24(9):1103.
Goralski, T and Pusztai, L. 2006. Expression Profile Predicts Best Preoperative Chemotherapy Regimen for Individual Breast Cancer Patients Affymetrix Microarray Bulletin, 2(2):4-8
McPhail, S and Goralski, T. 2005. Overcoming Challenges of Using Blood Samples with Gene Expression Microarrays to Advance Patient Stratification in Clinical Trials. Drug Discovery Today, 10(22):1485-1487
External RNA Controls Consortium (L Reid corresponding author). 2005 Proposed methods for testing and selecting ERCC External RNA Controls BMC Genomics, 6:150.
Parker, J. 2005. Getting More Out of Public Microarray Data. Pharmaceutical Discovery, 5(2).
McPhail, S. 2005 Harnessing the Potential of Genomic Data. Pharmaceutical Discovery, 5(1).
Papers published using data generated at Expression Analysis
Ginsburg, G and Angrist, M. 2006. The future may be closer than you think: a response from the Personalized Medicine Coalition to the Royal Society's report on personalized medicine. Personalized Medicine, 3(2):119-123.
Seo, D, Wang, T, Dressman, H, Herderick, EE, Iversen, ES, Dong, C, Vata, K, Milano, CA, Rigat, F, Pittman, J, Nevins, JR, West, M, and Goldschmidt-Clermont, PJ. 2004 Gene expression phenotypes of atherosclerosis. Arteriosclerosis, Thrombosis, and Vascular Biology, 24(10):1922-1927.
Tadashi, O and Hogan, BL. 2004 Hyperactive Wnt signaling changes the developmental potential of embryonic lung endoderm Journal of Biology, 3:11.
Berchuck, A, Iversen, ES, Lancaster, JM, Dressman, HK, West, M, Nevins, JR and Marks, JR. 2004. Prediction of optimal versus suboptimal cytoreduction of advanced stage serous ovarian cancer using American Journal of Obstetrics and Gynecology, 190:910-923.
Maddala, R, Deng, PF, Costello, JM, Wawrousek, EF, Zigler, JS, Rao, VP. 2004. Impaired cytoskeletal organization and membrane integrity in lens fibers of a Rho GTPase functional knockout transgenic mouse. Lab Investigation, 84(6):679-692.
Pittman, J, Huang, E, Dressman, H, Horng, CF, Cheng, SH, Tsou, MH, Chin, CM, Bild, A, Iversen, ES, Huang, A, Nevins, JR and West, M. 2004. Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes. PNAS, 101(22):8431-8436.
Yao, WD, Gainetdinov, RR, Arbuckle, MI, Sotnikova, TD, Cyr, M, Beaulieu, JM, Torres, GE, Grant, SG, Caron, MG. 2004. Identification of PSD-95 as a regulator of dopamine-mediated synaptic and behavioral plasticity. Neuron, 41(4):625-638.
Hashimoto, T, Lawton, MT, Yang, G-Y, Wen, G, Chaly, T Jr., Stewart, CL, Dressman, HK, Barbaro, NM, Marchuck, DA, Young, WL. 2004. Gene Microarray Analysis of Human Brain Arteriovenous Malformations. Neurosurgery, 54:410-423.
Huang, ES, Black, EP, Dressman, H, West, M and Nevins, JR. 2003. Gene expression phenotypes of oncogenic signaling pathways. Cell Cycle 2(5):415-417.
Ellis, MJ, Rosen, E, Dressman, H and Marks, J. 2003. Neoadjuvant comparisons of aromatase inhibitors and tamoxifen: pretreatment determinants of response J Steroid Biochem Mol Biol., 86:301-307.
Nevins, JR., Huang, ES, Huang, AT, Dressman, H, Pittman, J, and West, M. 2003. Towards integrated clinico-genomic models for personalized medicine: combining gene expression signatures and clinical factors in breast cancer outcomes prediction. Human Moecluar Genetics, 12 Suppl 2:R153-7.
Black, E P, Huang, E, Dressman, H, Ishida, S, West, M, and Nevins, JR. 2003. Distinct gene expression phenotypes of cells lacking Rb and Rb family members. Cancer Research, 63:3716-3723.
Huang, E, Cheng, SH, Dressman, H, Pittman, J, Tsou, M-H, Horng, C-F, Bild, A, Iversen, ES, Liao, M, Chen, C-M, West, M, Nevins, JR and Huang, AT. 2003. Gene expression predictors of breast cancer outcomes. Lancet, 361(55):1590-1596.
Huang, E, Ishida, S, Pittman, J, Dressman, H, Bild, A, Kloos, M, D'Amico, M, Pestell, RG, West, M and Nevins, JR. 2003. Gene expression phenotypic models that predict the activity of oncogenic pathways. Nature Genet., 34:226-230.
Oliver, TG, Grasfeder, LL, Carrol, AL, Kaiser, C, Gillingham, CL, Lin, SM, Wickramasinghe, R, Scott, MP, Wechsler-Reya, RJ. 2003. Transcriptional profiling of the Sonic hedgehog response: a critical role for N-myc in proliferation PNAS, 100(12):7331-7336.