Submit Specimens client login


Papers published by Expression Analysis with links to abstracts

Huixiao Hong, Lei Xu, Jie Liu, Wendell D Jones, Zhenqiang Su, Baitang Ning, Roger Perkins,Weigong Ge,Kelci Miclaus, Li Zhang, Kyunghee Park, Bridgett Green, Tao Han, Hong Fang, Christophe G. Lambert, Silvia C. Vega,1 Simon M. Lin, Nadereh Jafari, Wendy Czika, Russell D. Wolfinger, Federico Goodsaid, Weida Tong, and Leming Shi (2012) Technical Reproducibility of Genotyping SNP Arrays Used in Genome-Wide Association Studies PLOS One

Fan C, Prat A, Parker JS, Liu Y, Carey LA, Troester MA, Perou CM. 2011 Jan 9;4:3 Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures BMC Med Genomics

Ellis MJ, Suman VJ, Hoog J, Lin L, Snider J, Prat A, Parker JS, Luo J Deschryver K, Allred DC, Esserman LJ, Unzeitig GW, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Watson MA, Leitch M, Hunt K, Olson JA. 2011 Jun10;29(17):2342-9 Randomized Phase II Neoadjuvant Comparison Between Letrozole, Anastrozole, and Exemestane for Postmenopausal Women with Estrogen Receptor-Rich Stage 2 to 3 Breast Cancer: Clinical and Biomarker Outcomes and Predictive Value of the Baseline PAM50-Based Intrinsic Subtype--ACOSOG Z1031 Journal of Clinical Oncology

Elloumi F, Hu Z, Li Y, Parker JS, Gulley ML, Amos KD, Troester MA. 2011 Jun 30;4(1):54. Systematic Bias in Genomic Classification Due to Contaminating Non-noplastic Tissure in Breast Tumor Samples BMC Med Genomics

Harrell JC, Prat A, Parker JS, Fan C, He X, Carey L, Anders C, Ewend M, Perou CM. 2011 Genomic Analysis Identifies Unique Signatures Predictive of Brain, Lung, and Liver Relapse Breast Cancer Research Treatment

T G Bivona, H Hieronymus, J Parker, K Chang, M Taron, R Rosell, P Moonsamy, K Dahlman, V A Miller, C Costa, G Hannon and C L Sawyers (2011) FAS and NF-kB signalling modulate dependence of lung cancers on mutant EGFR Nature

Hollenbach, P W.; Nguyen, A N.; Brady, H; Williams, Michelle, Ning Y; Richard N; Krushel, L; Aukerman, S L.; Heise, C; MacBeth, K J. 2010. A Comparison of Azacitidine and Decitabine Activities in Acute Myeloid Leukemia Cell Lines Plos One, 5(2):1-10

Z Jiang, T Deng, R Jones, H Li, J I Herschkowitz, J C Liu, VJ Weigman, M S Tsao, T F Lane, C M Perou, and E Zacksenhaus (2010) RB Deletion in Mouse Mammery Progenitors Induces Luminal-B or Basal-Like/EMT Tumor Subtypes Depending on P53 Status The Journal of Clinical Investigation

P Van Loo, SH Nordgard, OC Lingjaerde, HG Russness, IH Rye, W Sun, VJ Weigman, P Marynen, A Zetterberg, B Naume, CM Perou, AL Borresen-Dale, and VN Kristensen (2010) Allele-specific copy number analysis of tumors National Academy of Sciences

A K Dunbier, H Anderson, Z Ghazoui, E J Folkerd, R A'Hern, R J Crowder, J Hoog, I E Smith, P Osin, A Nerurkar, J S Parker, C M Perou, M J Ellis and M Dowsett (2010) Relationship Between Plasma Estradiol Levels and Estrogen-Responsive Gene Expression in Estrogen Receptor-Positive Breast Cancer in Postmenopausal Women Journal of Clinical Oncology 28(7):1161-7.

Sandhu, R., Parker, J. S., Jones, W. D., Livasy, C. A., and Coleman, W. B (2010) Microarray-Based Profiling for Molecular Classification of Breast Cancer and Identification of New Targets for Therapy Lab Lab Medicine, 41:364-372.

Shi, L., Campbell, G., Jones, W. D., et al. (2010) MAQC-II Project: a comprehensive survey of common practices for the development and validation of microarray-based predictive models Nature Biotechnology doi: 10.1038/nbt. 1665

H Hong, L Shi, Z Su1, W Ge, W D Jones, W Czika, K Miclaus, C G Lambert, S C Vega, J Zhang, B Ning, J Liu, B Green, L Xu, H Fang, R Perkins, S M Lin, N Jafari, K Park, T Ahn, M Chierici, C Furlanello, L Zhang, R D Wolfinger, F Goodsaid and W Tong (2010) Assessing sources of inconsistencies in genotype and their effects on genome-wide association studies The Pharmacogenomics Journal

R M Parry, W Jones, T H Stokes, J H Phan, R A Moffitt, H Fang, L Shi, A Oberthuer, M Fischer, W Tong and M D Wang (2010) k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction The Pharmacogenomics Journal

K J Mavrakis, A L Wolfe, E Oricchio, T Palomero, K D Keersmaecker, K McJunkin, J Zuber, T James, A A Khan, C S Leslie, J S Parker, P J Paddison, W Tam, A Ferrando, and HG Guido (2010) Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia Nature Cell Biology 12(4):372-9.

E E Connor, S Kahl, T Elsasser, J S Parker, R W Li, C P Van Tassell, R L Baldwin, and S M Barao (2010) Enhanced mitochondrial complex gene function and reduced liver size may mediate improved feed efficiency of beef cattle during compensatory growth Functional and Integrative Genomics, 10(1) :39-51

C H Chung, P R Pohlmann, M L Rothenberg, B B Burkey, J S Parker, K Palka, J Aulino, I Puzanov, and B Murphy (2010) Insulin-like growth factor-1 receptor inhibitor, AMG-479, in cetuximab-refractory head and neck squamous cell carcinoma Head and Neck

M Tsuchiya, J S Parker, H Kono, M Matsuda, H Fujii, and I Rusyn (2010) Gene expression in nontumoral liver tissue and recurrence-free survival in hepatitis C virus-positive hepatocellular carcinoma Molecular Cancer

R Sandhu, J S Parker, W D Jones, C Livasy, and W B Coleman (2010) Microarray-Based Gene Expression Profiling for Molecular Classification of Breast Cancer and Identification of New Targets for Therapy Lab Medicine, June 41:6

MAQC Consortium (2010) The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation microarray-based predictive models Nature Biotechnology

T Nielsen, J S Parker, S Leung, K D Voduc, M Ebbert, T L Vickery, S R Davies, J E Snider, I J Stijleman, J Reed, M C U Cheang, E R Mardis, C M Perou, P S Bernard, and M J Ellis (2010) A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor positive breast cancer Clinical Cancer Research

A Prat, J S Parker, O Karginova, C Fan, C Livasy, J I Herschkowitz, X He, and C M Perou (2010) Phenotypic and Molecular Characterization of the Claudin-low Intrinsic Subtype of Breast Cancer Breast Cancer Research

C K Anders, C Fan, J S Parker, and L A Carey (2010) Breast Carcinomas Arising at a Young Age: Unique Biology or a Surrogate for Aggressive Intrinsic Subtypes? Journal of Clinical Oncology

Liu, X., Parker, J., Fan, C., Perou, C. M. and Marron, J. S. (2009), Chapter 14: Visualization of Cross-Platform Microarray Normalization, Batch Effects and Noise in Microarray Experiments: Sources and Solutions, Andreas Scherer (ed.), John Wiley & Sons, Inc.

Cheang Maggie C U; Chia Stephen K; Voduc David; Gao Dongxia; Leung Samuel; Snider Jacqueline; Watson Mark; Davies Sherri; Bernard Philip S; Parker Joel S; Perou Charles M; Ellis Matthew J; Nielsen Torsten O (2009) Ki67 Index, HER2 Status, and Prognosis of Patients With Luminal B Breast Cancer JNCI 101(10):736-50.

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

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.

Hardin, J., Finnell, R., Wang, D., Hogan, M., Horovitz, J., Shu, J., Shaw, G. (2009) Whole Genome Microarray Analysis From Neonatal Blood Cards BMC Genetics

W Y Kim, S Perera, B Zhou, J Carretero, J J Yeh, S A Heathcote, A L Jackson, P Nikolinakos, B Ospina, G Naumov, K A Brandstetter, V J Weigman, S Zaghlul, D N Hayes, R F Padera, J V Heymach, A L Kung, N E Sharpless, W G Kaelin Jr., and K K Wong (2009) HIF2a Cooperates with RAS to Promote Lung Tumorigenesis in Mice The Journal of Clinical Investigation

O Jarinova, A FR Stewart, R Roberts, G Wells, P Lau, T Naing, C Buerki, B W McLean, R C Cook, J S Parker and R McPherson (2009) Functional Analysis of the Chromosome 9p21.3 Coronary Artery Disease Risk Locus Arteriosclerosis Thrombosis Vascular Biology

Hennessy, B.T., Gonzales-Angulo, A. M., Stemke-Hale, K., Gilcrease, M. Z., Krishnamurthy, S., Lee, J. S., Fridlyand, J., Sahin, A., Agarwal, R., Joy, C., Liu, W., Stivers, D., Baggerly, K., Carey, M., Lluch, A., Monteagudo, C., He, X., Weigman, V., Fan, C., Palazzo, J., Hortobagyi, G. N., Nolden, L. K., Wang, N. J., Valero, V., Gray, J. W., Perou, C. M. and Mills, G. B. (2009) Characterization of a Naturally Occurring Breast Cancer Subsequent Enriched in Epithelial-to-Mesenchymal Transition and Stem Cell Characteristics AACR Journal

X Liu, J Parker, C Fan, C M Perou, and J S Marron (2009) Visualization of Cross-Platform Microarray Normalization, Batch Effects and Noise in Mircroarray Experiments: Sources and Solutions Sources and Solutions, Andreas Scherer (ed.), John Wiley & Sons, Inc. Chichester, UK, 167-181.

Duewer, D., Jones, W. D., Reid, L., and Salit, M. (2009) Learning from microarray interlaboratory studies: measures of precision for gene expression BMC Genomics, 10:153.

Schumacher, M., Staedtler, F., Jones, W. D., and Scherer, A. (2009) Chapter 5: Aspects of Technical Bias, Batch Effects and Noise in Microarray Experiments Sources and Solutions, A. Scherer (ed.), John Wiley & Sons.

April C., Klotzle B., Royce T., Wickham-Garcia E., Boyaniwsky T., Izzo J., Cox D., Jones W. D., Rubio R., Holton K., Matulonis U., Quackenbush, J., Fan, J. (2009) Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Tissue Samples PLoS ONE 4(12): e8162. doi:10.1371/journal.pone.0008162.

Thorner A R; Hoadley K A; Parker J S; Winkel S; Millikan R C; Perou C M (2009) In Vitro and In Vivo Analysis of B-Myb in Basal-Like Breast Cancer Oncogene 28(5):742-51.

Schisler JC, Charles PC, Parker JS, Hilliard EG, Mapara S, Meredith D, Lineberger RE, Wu SS, Alder BD, Stouffer GA, Patterson C. (2009) Stable Patterns of Gene Expression Regulating Carbohydrate Metabolism Determined by Geographic Ancestry PLoS One Dec 9;4(12):e8183.

Brian Bierie, Christine H. Chung, Joel S. Parker, Daniel G. Stover, Nikki Cheng, Anna Chytil, Mary Aakre, Yu Shyr, and Harold L. Moses (2009). Abrogation of TGF-? Signaling Enhances Chemokine Production and Correlates with Prognosis in Human Breast Cancer Journal of Clinical Investigation

Crowder RJ, Phommaly C, Tao Y, Hoog J, Luo J, Perou CM, Parker JS, Miller MA, Huntsman DG, Lin L, Snider J, Davies SR, Olson JA, Watson MA, Saporita A, Weber JD, Ellis MJ. (2009) PIK3CA and PIK3CB inhibition produce synthetic lethality when combined with estrogen deprivation in Estrogen Receptor-Positive Breast Cancer Cancer Research, 69(9):3955-62

C H Chung, J Aulino, N J Muldowney, H Hatakeyama, J Baumann, B Burkey, J Netterville, R Sinard, W G Yarbrough, A J Cmelak, R J Slebos, Y Shyr, J Parker, J Gilbert and B A Murphy (2009) Nuclear factor-kappa B pathway and response in a phase II trial of bortezomib and docetaxel in patients with recurrent and/or metastactic head and neck squamous cell carcinoma Annals of Oncology

R D Fannin, M Russo, T M O'Connell, K Gerrish, J H Winnike, J Macdonald, J Newton, S Malik, S O Sieber, J Parker, R Shah, T Zhou, P B Watkins, and R S Paules (2009) Acetaminophen Dosing of Humans Results in Blood Transcriptome and Metabolome Changes Consistent with Impaired Oxidative Phosphorylation Hepatology

A Shabalin, V J Weigman, C Perou, and A B Nobel (2009) Finding Large Average Submatrices in High Dimensional Data The Annals of Applied Statistics

J S Parker, M Mullins, M CU Cheung, S Leung, D Voduc, T Vickery, S Davies, C Fauron, X He, Z Hu, J F Quackenbush, I J Stijleman, J Palazzo, J S Marron, A B Nobel, E Mardis, T O Nielsen, M J Ellis, C M Perou and P S Bernard (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.

Uziel Tamar; Karginov Fedor V; Xie Suqing; Parker Joel S; Wang Yong-Dong; Gajjar Amar; He Lin; Ellison David; Gilbertson Richard J; Hannon Gregory; Roussel Martine F. (2009) The miR-17~92 cluster collaborates with the Sonic Hedgehog pathway in medulloblastoma PNAS, 106(8):2812-7.

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

Mori K, Blackshear PE, Lobenhofer EK, Parker JS, Orzech DP, Roycroft JH, Walker KL, Johnson KA, Marsh TA, Irwin RD, Boorman GA. (2007) Hepatic Transcript Levels for Genes Coding for Enzymes Associated with Xenobiotic Metabolism are Altered with Age Toxicol Pathol. 35(2):242-51

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.

Michael Mullins, Laurent Perreard, John F. Quackenbush, Nicholas Gauthier, Steven Bayer, Matthew Ellis, Joel Parker, Charles M. Perou, Aniko Szabo and Philip S. Bernard (2007). Agreement in Breast Cancer Classification between Microarray and Quantitative Reverse Transcription PCR from Fresh-Frozen and Formalin-Fixed, Paraffin-Embedded Tissues Clinical Chemistry, 53:1273-1279.

Perkins DO, Jeffries C, Jarskog LF, Thomson JM, Woods K, Newman MA, Parker JS, Jin J, Hammond SM. (2007) miRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder Genome Biology. Feb 27;8(2):R27.

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.

Dunnick, J., Blackshear, P., Kissling, G., Cunningham, M., Parker, J., Nyska, A. (2006) Critical Pathways in Heart Function: Bis(2-chloroethoxy)methane-induced Heart Gene Transcript Change in F344 Rats Pathology, 34(4):348-356

Perreard, L., Fan, C., Quackenbush, J.F., Mullins, M., Gauthier, N.P., Nelson, E., Mone, M., Hansen, H., Buys, S. S., Rasmussen, K., Orrico, A. R., Dreher, D., Walters, R., Parker, J., Hu, Z., He, X., Palazzo, J.P., Olopade, O., Szabo, A., Perou C.M., Bernard, P.S. (2006) Classification and Risk Stratification of Invasive Breast Carcinomas using a Real-Time Quantitative RT-PCR Assay Breast Cancer Research, 8:R23.

Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF, Livasy C, Carey LA, Reynolds E, Dressler L, Nobel A, Parker J, Ewend ME, Sawyer LR, Wu J, Liu Y, Nanda R, Tretiakova M, Ruiz Orrico A, Dreher D, Palazzo JP, Perreard L, Nelson E, Mone M, Hansen H, Mullins M, Quackenbush JF, Ellis MJ, Olopade OI, Bernard PS, Perou CM. (2006) The molecular portraits of breast tumors are conserved across microarray platforms BMC Genomics, 7(1):96.

Chung CH, Ely K, McGavran L, Varella-Garcia M, Parker J, Parker N, Jarrett C, Carter J, Murphy BA, Netterville J, Burkey BB, Sinard R, Cmelak A, Levy S, Yarbrough WG, Slebos RJ, Hirsch FR. (2006) Increased EGFR Gene copy number is associated with poor prognosis in head and neck squamous cell carcinomas Journal of Clinical Oncology 1;24(25):4170-6.

Thomson JM, Newman M, Parker JS, Morin-Kensicki EM, Wright T, Hammond SM (2006) Extensive Post-Transcriptional Regulation of microRNAs and its Implications for Cancer Genes in Development. Aug 15;20(16):2202-7.

Lai WS, Parker JS, Grissom SF, Stumpo DJ, Blackshear PJ. (2006) Novel mRNA Targets for Tristetraprolin (TTP) Identified by Global Analysis of Stabilized Transcripts in TTP-Deficient Fibroblasts Molecular and Cellular Biology. Oct 9;

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.

Boorman, G. A., R. D. Irwin, V. Vallant, D. K. Gerken, E. K. Lobenhofer, M. Hejtmancik, H. Toyoshiba, P. Hurban, A. Brys G. Travlos, J. Parker, C. Portier. (2005). Variation in the hepatic gene expression in the male Fischer rat. Toxicologic Pathology, 33(1):111-7.

Irwin, R. D., J. S. Parker, E. K. Lobenhofer, L. T. Burka, P. E. Blackshear, M. K. Vallant, E. K. Lebetkin, D. F. Gerken, G. A. Boorman. (2005). Transcriptional Profiling of the Left and Median Liver Lobes of Male F344/N Rats Following Exposure to Acetaminophen Toxicologic Pathology, 33(1):111–117

Powell, C.L., Oksana, K., Bradford, B.U., Parker, J.S., Lobenhofer, E.K., Denda, A., Uematsu, F., Nakae, D., Rusyn, I. (2005) Temporal Correlation of Pathology and DNA Damage With Gene Expression in a Choline-Deficient Model of Rat Liver Injury Hepatology, 42:1137-1147

Benito, M., J. Parker Q. Du, J. Wu, D. Xiang, C. M. Perou, J. S. Marron. (2004) Adjustment of Systematic Microarray Data Biases Bioinformatics, 20(1): 105–114

Chung C. H., J. S. Parker, G. Karaca, J. Wu, W. K. Funkhouser, D. Moore, D. Butterfoss, D. Xiang, X. Yin, W. W. Shockley, M. C. Weissler, L. G. Dressler, C. G. Shores, W. G. Yarbrough, C. M. Perou. (2004). Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression Cancer Cell, 5(5):489–500

Troester, M. A., K. A. Hoadley, J. S. Parker, C. M. Perou. (2004). Prediction of Toxicant-Specific Gene Expression Signatures following Chemotherapeutic Treatment of Breast Cell Lines. Environmental Health Perspectives, 112(16):1607–1613

Thomson, J. M., J. Parker, C. M. Perou, S. M. Hammond. (2004) A custom microarray platform for analysis of microRNA gene expression Nature Methods, 1(1):47–53

Ritchie, M.D., B. C. White, J. S. Parker, L.W. Hahn, and J. H. Moore. (2003). Optimization of neural network architecture using genetic programming improves detection and modeling of gene-gene interactions in studies of human diseases BMC Bioinformatics, 4:28

Sorlie, T., R. Tibshirani, J. Parker, T. Hastie, J. S. Marron, A. Nobel, S. Deng, H. Johnsen, R. Pesich, S. Geisler, J. Demeter, C. M. Perou, P. E. Lonning, P.O. Brown, A. L. Borresen-Dale, and D. Botstein. (2003) Repeated observation of breast tumor subtypes in independent gene expression data sets PNAS 100(14):8418–8423

Moore, J.H., J. S. Parker, N. J. Olsen, T. Aune. (2002). Symbolic discriminant analysis of microarray data in autoimmune disease Genetic Epidemiology, 23:57–69

Maas, K., S. Chan, J. Parker, A. Slater, J. H. Moore, N. Olsen, and T. Aune. (2002) Molecular portrait of Human Autoimmune Disease Journal of Immunology 169:5–9

Moore, J. H., J. S. Parker, and L. W. Hahn. (2001) Symbolic Discriminant Analysis for Mining Gene Expression Patterns Lecture Notes in Artificial Intelligence 2167:372–381

Moore, J. H. and J. S. Parker. (2000). Evolutionary Computation in Microarray Data Analysis Methods of Microarray Data Analysis, Kluwer Academic Press, Boston

Grill, C, Gheyas, jF, Dayananth P, Jin W, Ding, W, Qiu, P, Wang, Luquan, Doll, R J., English J M. 2004. Analysis of the ERK1,2 transcriptome in mammary epithelial cells The Biochemical society, 381(3): 635-644

Papers published using data generated at Expression Analysis

Fedik Rahimov, Oliver D. King, Doris G. Leung, Genila M. Bibat, Charles P. Emerson, Jr, Louis M. Kunkel, and Kathryn R. Wagner (2012) Transcriptional Profiling in Facioscapulohumeral Muscular Dystrophy to Identify Candidate Biomarkers PNAS

Roberts JL, Buckley RH, Luo B, Pei J, Lapidus A, Peri S, Wei Q, Shin J, Parrott RE, Dunbrack RL Jr, Testa JR, Zhong XP, Wiest DL (2012) CD45-deficient severe combined immunodeficiency caused by uniparental disomy Proc Natl Acad Sci Jun 11.

Khodakovskaya, M V.; Silva, Kanishka D.; Nedosek, D A.; Dervishi, E; Biris, A S.; Shashkov, E V.; Galanzha, E I.; Zharov, V P.2011. Complex genetic, photothermal, and photoacoustic analysis of nanoparticle-plant interactions PNAS, 108(3):1028-1033

Huang, Y T.; Karoly, E D.; Dailey, L A.; Schmitt, M T; Silbajoris, R; Graff, D W.; Devlin, R B. 2011. Comparison of Gene Expression Profiles Induced By Coarse, Fine, and Ultrafine Particulate Matter Journal of Toxicology, 74(5):296-312

Laakso, M; Karinen, S; Lehtonen, R; Hautaniemi, S. 2010. Computational Identification of Cancer Susceptibility Loci Methods in Microbiology, 653(1):87-103

Athanasiu, L; Mattingsdal, M; Kähler, A K.; Brown, A; Gustafsson, O; Agartz, I; Giegling, I; Muglia, P; Cichon,S; Rietschel, M; Pietiläinen, O P. H.; Pelotnem, L; Bramon, E, Collier, D; Clair, D St.; Engilbert, S; Petursson, H; Rujescu, D; Melle, I; Steen, V M.; Djurovic, S; Andreassen, O A. 2010. Gene variants associated with schizophrenia in a Norwegian genome-wide study are replicated in a large European cohort Journal of Psychiatric Research , 44(12): 748-753

Richards, M P; Proszkowiec- Weglarz, M; Rosebrough, R W.; McMurty, J P.; Angel, R. 2010. Effects of early neonatal development and delayed feeding immediately post-hatch on the hepatic lipogenic program in broiler chicks Comparative Biochemistry and Pphysiology,157(4):374-388

Kohler, M. E; Hallett, W H.D.; Chen, Q; Khan, J; Johnson, B D.; Orentas, R J.2010. Early expression of stem cell-associated genes within the CD8 compartment after treatment with a tumor vaccine Cellular Immunology, 265(1):65-73

Shi, M; Xie, D Engineering of red cells of Arabidopsis thaliana and comparative genome-wide gene expression analysis of red cells versus wild-type cells Planta, 233(4):787-805

Vistica, D T.; Hollingshead, M; Borgel, S D.; Kenney, S; Stockwin, L H.; Raffeld, M; Schrump, D S.; Burkett, S; Stone, G; Butcher, D O.; Shoemaker, R H. 2010 Therapeutic Vulnerability of an In Vivo Model of Alveolar Soft Part Sarcoma (ASPS) to Anti -Angiogenic Therapy Journal of Surgical Research, 162(2): 299-307

Huo, R; Ma, Q; Wu, J J.; Chin-Nuke, K; Jing, Y; Chen, J; Miyar, M E.; Davis, S C.; Li, J. 2010. Noninvasive Electromagnetic Fields on Keratinocyte Growth and Migration Journal of Surgical Research, 162(2):299-307

Sun, J; Li, R. 2010. Human Negative Elongation Factor Activates Transcription and Regulates Alternative Transcription Initiation The Journal of Biological Chemistry, 285: 6443-6452

Khodakovskaya, M; Sword, C; Wu, Q; Perera, I Y.; Boss, W F.; Brown, C S.; Sederoff, H W. 2010. Increasing inositol (1,4,5)-trisphosphate metabolism affects drought tolerance, carbohydrate metabolism and phosphate-sensitive biomass increases in tomato Plant Biotechnology Journal, 8(2): 170-183

Huang, Y-C T.; Li, Z; Hyseni, X; Schmitt, M; Devlin, R B.; Karoly, E D.; Soukup, J M. Identification of gene biomarkers for respiratory syncytial virus infection in a bronchial epithelial cell line Genomic Medicine, 2(3-4): 113-125

Chen, Y; Nadi N. S; Chavko, M; Auker, C R.; McCarron, R M. Microarray Analysis of Gene Expression in Rat Cortical Neurons Exposed to Hyperbaric Air and Oxygen Neurochemical research, 34(6): 1047-1056

Morales, A A.; Gutman, D; Cejas, P J.; Lee, K P.; Boise, L H. Reactive Oxygen Species Are Not Required for an Arsenic Trioxide-induced Antioxidant Response or Apoptosis Journal of Biological Chemistry

Newell, K A.; Asare, A; Kirk, A D.; Gisler, T D.; Bourcier, K; Suthanthiran, M; Burlingham, W J.; Marks, W H.; Sanz, I, Lechler, R I.; Hernandez-Fuentes, MP.; Turka, L A.; Seyfert-Margolis, V L. 2010. Identification of a B cell signature associated with renal transplant tolerance in humans Journal of Clinical Investigation, 120 (6): 1836-1847

Bailey, K; Xia, Y; Ward, W O.; Knapp, G; Mo, J; Mumford, J J.; Owen, R D.; Thai, S. 2009. Global Gene Expression Profiling of Hyperkeratotic Skin Lesions from Inner Mongolians Chronically Exposed to Arsenic Toxicologic Pathology, 37(7):849-859

Song, H; Chung, S-K; Xu, Y. 2009. Modeling Disease in Human ESCs Using an Efficient BAC-Based Homologous Recombination System Cell Stem Cell, 234:918-930

Smith, J J.; Kenney, R D.; Gagne, D J.; Frushour, B P.; Ladd, W; Galonek , H L.; Israelian, K; Song, J; Razvadauskaite, G; Lynch, A V.; Carney, D P.; Johnson, R J.; Lavu, S; Iffland, A; Elliot, P J.; Lambert, D P.; Elliston, K O.; Jirousek, M R.; Milne, J C.; Boss, O. 2009 Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo BMC Systems Biology, 3: 31

Bacolod, M D.; Lin, S. M; Johnson, S P.; Bullock, N S.; Colvin, M.; Bigner, D D.; Friedman, H S. 2009. The Gene Expression Profiles of Medulloblastoma Cell Lines Resistant to Preactivated Cyclophosphamide Current Cancer Drug Targets, doi: 10.1074/jbc.M806546200

Goetz, A K.; Dix, D J. 2009 Mode of Action for Reproductive and Hepatic Toxicity Inferred from a Genomic Study of Triazole Antifungals Toxicological Sciences, 110(2): 449-462

Hollenbach, P W., Nguyen, A, Brady, H, Williams, M, Ning, Y, Richards, N, Krushel L, Aukerman, S L., Heise, C, MacBeth K J. 2009. A Comparison of Azacitidine and Decitabine Activities in Acute Myeloid Leukemia Cell Lines Plos one, doi:10.1371/journal.pone.0009001

Gottipolu, R R., Wallenborn, J. G, Karoly E D., Schladweiler M C., ledbetter, A D., Krantz, T, Linak, W P., Nyska, A, Johnson, J, Thomas, R, Richards, J E., Jaskot, R H., Kodavanti U P. 2009. One-Month Diesel Exhaust Inhalation Produces Hypertensive Gene Expression Pattern in Healthy Rats Environmental Health Perspectives, 117(1): 38-46

Stockwin, L H.; Visitca, D T.; Kenney, S.; Schrump, D S.; Butcher, D O.; Raffeld, M; Shoemaker R H. 2009. Gene expression profiling of alveolar soft-part sarcoma (ASPS) BMC Cancer, 9:22 doi:10.1186/1471-2407-9-22

Daly, A K., Donaldson, P T., Bhatnager, P, Shen, Y, Pe’er, I, Floratos, A, Daly, M, Goldstein, D B., John, s, Nelson, M R., Graham, J, Park, B. K, Dillion J F., Bernal, W, Cordell, H J., Pirmohamed, M, Aithal, G P., Day C P. 2009. HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin Nature Genetics, 41, 816-819

Jones, S M.; Pons, L; Roberts, J L.; Scurlock, A M.; Perry, T T.; Kulis, M; Shreffler W G.; Steele, P; Henry, K A.; Adair, M; Francis, J M.; Durham, S; Vickery, B P.; Zhong, X; Burks, A. W. 2009. Clinical Efficacy and Immune Regulation with Peanut Ooral Immunotherapy The Journal of Allergy and Clinical Immunology, 124(2): 292-300

Harrill, J A.; Li, Z; Wright, F A.; Radio, N M.; Mundy, W R.; Tornero- Velez, R; Crofton, K M. 2008. Transcriptional response of rat frontal cortex following acute In Vivo exposure to the pyrethroid insecticides permethrin and deltamethrin BMC Genomics, 9:546

Kodvanti, U P., Schladweiler M C., Gilmour, P S., Wellenborn J G., Mandavilli, B S., Ledbetter, A D., Christiani, D C., Runge, M S., Karoly, E D., Costa D. L., Peddada, S, Jaskot, R, Richards, J H., Thomas, R, Madamanchi, N R., Nyska, A. 2008. The Role of Particulate Matter-Associated Zinc in Cardiac Injury in Rats Environmental Health Perspectives, 116(1):13-20

Charles, C A., Canic, M T, Vincek Vladmir, Nassiri, M, Stojadinovic, Kirsner R S. 2008. A gene signature of nonhealing venous ulcers: Potential diagnostic markers Journal of the American Academy of Dermatology, 59(5): 758-771

Sun, X; Rogoff, H A.; Li, C J. 2008. Asymmetric RNA duplexes mediate RNA interference in mammalian cells Nature Biotechnology, 26: 1379-1382

Hewitt, S M., Lewis, F A., Cao, Y, Conrad, R C., Cronin, M, Danenberg, K D., Goralski, T J., Langmore, J P., Raja, R G., Williams, P. M, Palma, J F., Warrington, J A. 2008. Tissue Handling and Specimen Preparation in Surgical Pathology: Issues Concerning the Recovery of Nucleic Acids From Formalin-Fixed, Paraffin-Embedded Tissue Archives of Pathology of Laboratory &Medicine, 132(12)

Laakso, M; Tuupanen, S; Karhu, A; Lehtonen, R; Aaltonen, L A.; Hautaniemi, S. 2007. Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays Bioinformatics, 23(15):1952-1961

McCord, Ron; Pierce, Michael; Xie, J; Sandeep, W; Mickel, C; Vershon, A K. 2007. Rfm1, a Novel Tethering Factor Required To Recruit the Hst1 Histone Deacetylase for Repression of Middle Sporulation Genes American Society for Microbiology, 19(1): 23-28

Graff, D W.; Schmitt, M T.; Dailey, L A.; Duvall, R M.; Karoly, E D.; Devlin, R B.2007. Assessing the Role of Particulate Matter Size and Composition on Gene Expression in Pulmonary Cells Informa Healthcare, 19(1):23-28

Gil, M, McKinney, C, Kyeon M L., Ells, J B., Phyillaier, M A., Nikodem V M. 2007. Regulation of GTP cyclohydrolase I expression by orphan receptor Nurr1 in cell culture and in vivo Journal of Neurochemistry, 101(1):142-150

Ocorr, K A., Crawley T, Gibson, G, Bodmer, R. 2007. Genetic Variation for Cardiac Dysfunction in Drosophila Plos One, doi:10.1371/journal.pone.0000601

Goyarts, E; Muizzuddin, N; Maes, D; Giacomoni, P U. 2007. Morphological Changes Associated with Aging Annals of the New York Academy of Sciences, 1119: 32-39

Karoly, E D., Li, Z, Dailey, L A., Hyseni, X, Huang, YC T. 2007. Up-regulation of Tissue Factor in Human Pulmonary Artery Endothelial Cells after Ultrafine Particle Exposure Environmental Health Prersectives, 115(4): 535-540

Greshock, J, Feng, B, Nogueir, C, Ivanova, E, Perna l, Nathanson, K, Protopopov, A, Weber, B L. and Chin L. 2007. A Comparison of DNA Copy Number Profiling Platforms Cancer Research, 67: 10173

McLean, A B., D’Amour, K A., Jones, K L., Krishnamoorthy, M, Kulik, M J., Reynolds, D M., Sheppard, A M., Liu, H, Xu, Y, Baetge, E E., Dalton, S, 2007. Activin A Efficiently Specifies Definitive Endoderm from Human Embryonic Stem Cells Only When Phosphatidylinositol 3-Kinase Signaling Is Suppressed Alpha med Press, 25(1): 29-38

Timmapuri, S J.; Otterburn, D M.; Arafat, H; Schwartz, M Z. 2006. Hepatocyte growth factor increases glucagon immunoreactivity in jejunal cells during intestinal adaptation Journal of pediatric Surgery, 41(1): 150-154

Kodavanti, U P.; Schladweiler, M C.; Ledbetter, A D.; Ortuno, R V.; Suffia, M; Evansky, P; Richards, J H.; Jaskot, R H.; Thomas, R; Karoly, E; Huang, Y T.; Costa, D L.; Gilmour, P S.; Pinkerton, K E. 2006. The Spontaneously Hypertensive Rat: An Experimental Model of Sulfur Dioxide–Induced Airways Disease Toxicological Sciences, 94(1):193-205

Gilmour, P S., Schladweiler, M C., Nyska, A, McGee, J K., Thomas, R, Jaskot, R H.,Schmid J, Kodavanti, U P. 2006. Systemic Imbalance of Essential Metals and Cardiac Gene Expression in Rats Following Acute Pulmonary Zinc Exposure Journal of Toxicology and environmental health, 69(22):2011-2032

Haddad, R, Tromp, G, Kuivaniemi, H, Chaiworapongsa, T, Kim, Y M., Mazor, M, Romero, R. 2006. Human spontaneous labor without histologic chorioamnionitis is characterized by an acute inflammation gene expression signature American journal of Obstetrics & gynecology, 195(2): 394-405

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.

Otterburn, D M.; Arthur, L. G; Timmapuri, S J.; McCahan, S M.; Schwartz, M Z. 2005. Proteasome gene upregulation: a possible mechanism for intestinal adaptation Journal of Pediatric Surgery, 40(2):377-380

Li, Z; Stonehuerner, J; Devlin, R B.; and Huang, Y T. 2005. Discrimination of Vanadium from Zinc Using Gene Profiling in Human Bronchial Epithelial Cells Environmental Health Perspectives, 113(12): 1747-1754

James, E R., Fresco, V M., Robertson, L L. 2005. Glucocorticoid-Induced Changes in the Global Gene Expression of Lens Epithelial Cells Journal of Ocular Pharmacology and Therapeutics, 21(1): 11-27

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.

Grill, C; Gheyas, F; Dayananth, P; Jin, W; Ding, W; Wang, L; Doll, R L.; English, J M. 2004. Analysis of the ERK1,2 transcriptome in mammary epithelial cells Biochemical Journal, 381:635-644

Tadashi, O and Hogan, BL. 2004 Hyperactive Wnt signaling changes the developmental potential of embryonic lung endoderm Journal of Biology, 3:11.

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.

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.

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.

Catherino, W H., Purpas, C, Tsibris J C M., Leppert, P C., Payson, M, Nieman , L K. Seqars, J H. 2003. Strategy for elucidating differentially expressed genes in leiomyomata identified by microarray technology Fertility and Sterility, 80(2): 282-290

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.