Publications
Papers published by Expression Analysis with links to abstracts
Moore, J. H. and J. S. Parker. (2000). Evolutionary Computation in Microarray Data Analysis Methods of Microarray Data Analysis, Kluwer Academic Press, Boston
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., 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
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
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
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
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;
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.
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
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.
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-β 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
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.
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.
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.
Korde Larissa A; Lusa Lara; McShane Lisa; Lebowitz Peter F; Lukes LuAnne; Camphausen Kevin; Parker Joel S; Swain Sandra M; Hunter Kent; Zujewski Jo Anne. 2010; 119(3):685-99 Gene Expression Pathway Analysis to Predict Response to Neoadjuvant Docetaxel and Capecitabine for Breast Cancer Breast Cancer Research and Treatment
Prat A, Parker JS, Karginova O, Fan C, Livasy C, Herschkowitz JI, He X, Perou CM. 2010 Sep 2;12(5):R68 Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer Breast Cancer Research
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
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
A Bild, J S Parker, A M Gustafson, C R Acharya, K A Hoadley, C Anders, P K Marcom, L A Carey, A Potti, J R Nevins and C M Perou (2009) An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer Breast Cancer Research 28;11(4):R55.
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.
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.
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
L A Korde, L Lusa, L McShane, P F Lebowitz, L Lukes, K Camphausen, J S Parker, S M Swain, K Hunter and J Zujewski (2010) Gene expression pathway analysis to predict response to neoadjuvant docetaxel and capecitabine for breast cancer Breast Cancer Research and Treatment 119(3):685-99.
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
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
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
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
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
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
Shabalin, A., Weigman, V.J., Perou, C.M., Nobel, A.B. (2009) Finding Large Average Submatrices in High Dimensional Data JASA
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.
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
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
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 studie 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
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
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
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.
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
Laakso, M; Karinen, S; Lehtonen, R; Hautaniemi, S. 2010. Computational Identification of Cancer Susceptibility Loci Methods in Microbiology, 653(1):87-103
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
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
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
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