2. Ahlbory-Dieker, D., et al., DNA binding by estrogen receptor-{alpha} is essential for the transcriptional response to estrogen in the liver and the uterus. Molecular Endocrinology, 2009.
3. Bergamaschi, A., et al., CAMK1D amplification implicated in epithelial–mesenchymal transition in basal-like breast cancer. Molecular Oncology, 2008. 2(4): p. 327-339.
4. Bernardino, A., D. Kaushal, and M. Philipp, The Antibiotics Doxycycline and Minocycline Inhibit the Inflammatory Responses to the Lyme Disease Spirochete Borrelia burgdorferi. The Journal of Infectious Diseases, 2009. 199(9).
5. Bles, N., et al., Gene Expression Profiling Defines ATP as a Key Regulator of Human Dendritic Cell Functions. J Immunol, 2007. 179(6): p. 3550-3558.
6. Bordignon, J., et al., Expression profile of interferon stimulated genes in central nervous system of mice infected with dengue virus Type-1. Virology, 2008. 377(2): p. 319-329.
7. Bruce, S., et al., Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture. BMC Genomics, 2007. 8(1): p. 365.
8. Castellot, J., et al., Use of CCN5 for treatment of smooth muscle proliferation disorders. 2008.
9. Cekaite, L., et al., Mapping of oxidative stress responses of human tumor cells following photodynamic therapy using hexaminolevulinate. BMC Genomics, 2007. 8: p. 273.
10. Cekanova, M., et al., Gene alterations by peroxisome proliferator-activated receptor agonists in human colorectal cancer cells. International journal of oncology, 2008. 32(4): p. 809.
11. Chausiaux, O.E., et al., Hypogonadal mouse, a model to study the effects of the endogenous lack of gonadotropins on apoptosis. Biol Reprod, 2008. 78(1): p. 77-90.
12. Cheang, M.C.U., M. van de Rijn, and T.O. Nielsen, Gene Expression Profiling of Breast Cancer. Annual Review of Pathology: Mechanisms of Disease, 2008. 3(1): p. 67-97.
13. Chen, H., et al., A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. Bioinformatics, 2008. 24(16): p. 1749.
14. Chung, L., et al., Molecular framework for response to imatinib mesylate in systemic sclerosis ClinicalTrials. gov identifier: NCT00506831. Arthritis & Rheumatism, 2009. 60(2).
15. Clarke, B., et al., Intraepithelial T cells and prognosis in ovarian carcinoma: novel associations with stage, tumor type, and BRCA1 loss. Modern Pathology, 2008. 22(3): p. 393-402.
16. Coulouarn, C., V. Factor, and S. Thorgeirsson, Transforming growth factor- gene expression signature in mouse hepatocytes predicts clinical outcome in human cancer Potential conflict of interest: Nothing to report. Data deposition is in Gene Expression Omnibus accession codes: GPL1528, GSE1898, and GSE4024. Hepatology, 2008. 47(6).
17. Coulouarn, C., et al., Oncogene-specific gene expression signatures at preneoplastic stage in mice define distinct mechanisms of hepatocarcinogenesis Potential conflict of interest: Nothing to report. Hepatology, 2006. 44(4).
18. Coussens, M., et al., Sirt1 Deficiency Attenuates Spermatogenesis and Germ Cell Function. PLoS ONE, 2008. 3(2): p. e1571.
19. Demeter, J., et al., The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res, 2007. 35(Database issue): p. D766-70.
20. Dessars, B., et al., Genotypic and Gene Expression Studies in Congenital Melanocytic Nevi: Insight into Initial Steps of Melanotumorigenesis. Journal of Investigative Dermatology, 2008. 129(1): p. 139-147.
21. Dragin, N., et al., Phenotype of the Cyp1a1/1a2/1b1 (-/-) Triple-Knockout Mouse. Molecular Pharmacology, 2008. 73(6): p. 1844.
22. Dunning, M., et al., Statistical issues in the analysis of Illumina data. BMC bioinformatics, 2008. 9(1): p. 85.
23. Espinosa, I., et al., Coordinate Expression of Colony-Stimulating Factor-1 and Colony-Stimulating Factor-1-Related Proteins Is Associated with Poor Prognosis in Gynecological and Nongynecological Leiomyosarcoma. American Journal of Pathology, 2009. 174(6): p. 2347.
24. Eun, J., et al., Transcriptomic configuration of mouse brain induced by adolescent exposure to 3, 4-methylenedioxymethamphetamine. Toxicology and Applied Pharmacology, 2009.
25. Eun, J., et al., Discriminating the molecular basis of hepatotoxicity using the large-scale characteristic molecular signatures of toxicants by expression profiling analysis. Toxicology, 2008. 249(2-3): p. 176-183.
26. Garcia, M., et al., LGR5 deficiency deregulates Wnt signaling and leads to precocious Paneth cell differentiation in the fetal intestine. Developmental Biology, 2009. 331(1): p. 58-67.
27. Han, S.H., et al., Gene expression patterns in glucose-stimulated podocytes. Biochem Biophys Res Commun, 2008. 370(3): p. 514-8.
28. Hasemann, M.S., et al., Mutation of C/EBP{alpha} predisposes to the development of myeloid leukemia in a retroviral insertional mutagenesis screen. Blood, 2008. 111(8): p. 4309-4321.
29. Hebrant, A., et al., Thyroid gene expression in familial non-autoimmune hyperthyroidism shows common characteristics with hyperfunctioning autonomous adenomas. Journal of Clinical Endocrinology & Metabolism, 2009.
30. Hendrickson, D.G., et al., Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance. PLoS ONE, 2008. 3(5): p. e2126.
31. Henry, T., et al., Type I interferon signaling is required for activation of the inflammasome during Francisella infection. J Exp Med, 2007. 204(5): p. 987-94.
32. Hermes, G., et al., Neurological and behavioral abnormalities, ventricular dilatation, altered cellular functions, inflammation, and neuronal injury in brains of mice due to common, persistent, parasitic infection. Journal of Neuroinflammation, 2008. 5(1): p. 48.
33. Herskovits, A.A., V. Auerbuch, and D.A. Portnoy, Bacterial ligands generated in a phagosome are targets of the cytosolic innate immune system. PLoS Pathog, 2007. 3(3): p. e51.
34. Hinrichs, C., et al., IL-2 and IL-21 confer opposing differentiation programs to CD8+ T cells for adoptive immunotherapy. Blood, 2008. 111(11): p. 5326.
35. Hollien, J., et al., Regulated Ire1-dependent decay of messenger RNAs in mammalian cells. Journal of Cell Biology, 2009. 186(3): p. 323.
36. Hu, P., M. Zhang, and J.L. Napoli, Ontogeny of rdh9 (Crad3) expression: ablation causes changes in retinoid and steroid metabolizing enzymes, but RXR and androgen signaling seem normal. Biochim Biophys Acta, 2007. 1770(4): p. 694-705.
37. Huffaker, S., et al., A primate-specific, brain isoform of KCNH2 affects cortical physiology, cognition, neuronal repolarization and risk of schizophrenia. Nature Medicine, 2009. 15(5): p. 509-518.
38. Ijssel, P. and B. Ylstra, Oligonucleotide Array Comparative Genomic Hybridization, in Comparative Genomics. 2008. p. 207-221.
39. Ito, S., et al., Dietary phytochemicals regulate whole-body CYP1A1 expression through an arylhydrocarbon receptor nuclear translocator-dependent system in gut. J Clin Invest, 2007. 117(7): p. 1940-50.
40. Kao, J., et al., Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery. PloS One, 2009. 4(7): p. e6146.
41. Kawahara, T., et al., SIRT6 Links Histone H3 Lysine 9 Deacetylation to NF- B-Dependent Gene Expression and Organismal Life Span. Cell, 2009. 136(1): p. 62-74.
42. Kawakami, Y., et al., Impaired neurogenesis in embryonic spinal cord of Phgdh knockout mice, a serine deficiency disorder model. Neuroscience Research, 2009. 63(3): p. 184-193.
43. Khaled, W.T., et al., The IL-4/IL-13/Stat6 signalling pathway promotes luminal mammary epithelial cell development. Development, 2007. 134(15): p. 2739-50.
44. Kim, C., et al., Experimental Malaria Infection Triggers Early Expansion of Natural Killer Cells. Infection and Immunity, 2008. 76(12): p. 5873.
45. Kim, Y. and J. Pollack, Comparative genomic hybridization on spotted oligonucleotide microarrays. Methods in molecular biology (Clifton, NJ), 2009. 556: p. 21.
46. Klapholz-Brown, Z., et al., Transcriptional Program Induced by Wnt Protein in Human Fibroblasts Suggests Mechanisms for Cell Cooperativity in Defining Tissue Microenvironments. PLoS ONE, 2007. 2(9): p. e945.
47. Köbel, M., et al., IGF2BP3 (IMP3) expression is a marker of unfavorable prognosis in ovarian carcinoma of clear cell subtype. Modern Pathology, 2009. 22(3): p. 469-475.
48. Koontz, T., et al., Altered development of the brain after focal herpesvirus infection of the central nervous system. J. Exp. Med., 2008. 205(2): p. 423-435.
49. Kouros-Mehr, H., et al., GATA-3 links tumor differentiation and dissemination in a luminal breast cancer model. Cancer Cell, 2008. 13(2): p. 141-52.
50. Kurrasch, D.M., et al., The Neonatal Ventromedial Hypothalamus Transcriptome Reveals Novel Markers with Spatially Distinct Patterning. J. Neurosci., 2007. 27(50): p. 13624-13634.
51. Leber, J.H., et al., Distinct TLR- and NLR-Mediated Transcriptional Responses to an Intracellular Pathogen. PLoS Pathogens, 2008. 4(1): p. e6.
52. Lee, C.-H., et al., Prognostic Significance of Macrophage Infiltration in Leiomyosarcomas. Clin Cancer Res, 2008. 14(5): p. 1423-1430.
53. Leung, J., S. Cases, and T. Vu, P311 functions in an alternative pathway of lipid accumulation that is induced by retinoic acid. Journal of Cell Science, 2008. 121(16): p. 2751.
54. Li, Q., et al., Interferon- initiates type 1 diabetes in nonobese diabetic mice. Proceedings of the National Academy of Sciences, 2008. 105(34): p. 12439.
55. Lin, P., et al., The Probiotic Lactobacillus GG may Augment Intestinal Host Defense by Regulating Apoptosis and Promoting Cytoprotective Responses in the Developing Murine Gut. Pediatric Research, 2008. 64(5): p. 511.
56. Liu, M., et al., Early days: genomics and human responses to infection. Curr Opin Microbiol, 2006. 9(3): p. 312-9.
57. Liu, Y., et al., Targeted Overexpression of Vav3 Oncogene in Prostatic Epithelium Induces Nonbacterial Prostatitis and Prostate Cancer. Cancer Research, 2008. 68(15): p. 6396.
58. Looney, M., et al., Microarray analysis of a mouse model of transfusion-related acute lung injury (TRALI) reveals prominent increased expression of neutrophil-derived chemokines. The FASEB Journal, 2007. 21(6): p. A1202.
59. Mace, K., et al., HOXA3 Modulates Injury-Induced Mobilization and Recruitment of Bone Marrow-Derived Cells. Stem Cells, 2009. 27(7): p. 1654.
60. Martiniova, L., et al., Characterization of an animal model of aggressive metastatic pheochromocytoma linked to a specific gene signature. Clinical and Experimental Metastasis, 2009. 26(3): p. 239-250.
61. Maynard-Smith, L.A., et al., A directed approach for engineering conditional protein stability using biologically silent small molecules. J Biol Chem, 2007. 282(34): p. 24866-72.
62. McWhirter, S., et al., A host type I interferon response is induced by cytosolic sensing of the bacterial second messenger cyclic-di-GMP. Journal of Experimental Medicine, 2009.
63. Ménesi, D., et al., Gene and protein expression profiling of the fat-1 mouse brain. Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA), 2009. 80(1): p. 33-42.
64. Mohan, S., Molecular Mechanisms of Soft Tissue Regeneration and Bone Formation in Mice: Implication in Fracture Repair and Wound Healing in Humans. 2008, Storming Media.
65. Mohan, S., et al., Chemical mutagenesis induced two high bone density mouse mutants map to a concordant distal chromosome 4 locus. Bone, 2007. 41(5): p. 860-8.
66. Muranski, P., et al., Tumor-specific Th17-polarized cells eradicate large established melanoma. Blood, 2008. 112(2): p. 362.
67. Myers, T., et al., Closing the phenotypic gap between transformed neuronal cell lines in culture and untransformed neurons. Journal of Neuroscience Methods, 2008. 174(1): p. 31-41.
68. Nebioglu, A., N-heterocyclic carbene silver (I) complexes from xanthines and their antimicrobial applications. 2007, University of Akron.
69. Palermo, A., et al., Nuclear reprogramming in heterokaryons is rapid, extensive, and bidirectional. The FASEB Journal, 2009. 23(5): p. 1431.
70. Pantoja, C., J. Huff, and K. Yamamoto, Glucocorticoid signaling defines a novel commitment state during adipogenesis in vitro. Molecular Biology of the Cell, 2008. 19(10): p. 4032.
71. Park, J., et al., Chemical Induction of Alkaline Phosphatase and Surface-Specific Embryonic Antigen-1 Positive Colonies from Mouse Embryonic Fibroblasts. Biology of Reproduction, 2009. 81(1 Supplement): p. 659.
72. Prokesch, A., et al., Novel Insights into Adipogenesis from Omics Data. Current Medicinal Chemistry, 2009. 16(23): p. 2952-2964.
73. Rabbani, E. and J. Donegan, Dual polarity analysis of nucleic acids. 2006, Google Patents.
74. Rappa, G., O. Fodstad, and A. Lorico, The stem cell-associated antigen CD133 (Prominin-1) is a molecular therapeutic target for metastatic melanoma. Stem Cells, 2008. 26(12): p. 3008.
75. Rodriguez, V., et al., Chromosome 8 BAC array comparative genomic hybridization and expression analysis identify amplification and overexpression of TRMT12 in breast cancer. Genes Chromosomes Cancer, 2007. 46(7): p. 694-707.
76. Rubin, B., T. Nielsen, and M. van de Rijin, Genomic and Expression Profiling of Benign and Malignant Nerve Sheath Profiling of Benign and Malignant Nerve Sheath. 2007, Storming Media.
77. Sansom, S., et al., The Level of the Transcription Factor Pax6 Is Essential for Controlling the Balance between Neural Stem Cell Self-Renewal and Neurogenesis. PLoS Genetics, 2009. 5(6).
78. Sarkozi, R., et al., Bortezomib-induced survival signals and genes in human proximal tubular cells. Journal of Pharmacology and Experimental Therapeutics, 2008. 327(3): p. 645.
79. Schwegmann, A., et al., Protein kinase C delta is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes. Proc Natl Acad Sci U S A, 2007. 104(41): p. 16251-6.
80. Seigel, G.M., et al., Human embryonic and neuronal stem cell markers in retinoblastoma. Mol Vis, 2007. 13: p. 823-32.
81. Sengupta, A., et al., Loss of housekeeping selenoprotein expression in mouse liver modulates lipoprotein metabolism. Biochem Biophys Res Commun, 2008. 365(3): p. 446-52.
82. Settivari, R., et al., Effects of short-term heat stress on endophytic ergot alkaloid-induced alterations in rat hepatic gene expression. Journal of Animal Science, 2009.
83. Shachaf, C., et al., Genomic and proteomic analysis reveals a threshold level of MYC required for tumor maintenance. Cancer Research, 2008. 68(13): p. 5132.
84. Shiloh, M., P. Manzanillo, and J. Cox, Mycobacterium tuberculosis senses host-derived carbon monoxide during macrophage infection. Cell Host & Microbe, 2008. 3(5): p. 323-330.
85. Sinha, S., et al., Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res., 2008. 18(3): p. 477-488.
86. So, A.Y.-L., et al., Conservation analysis predicts in vivo occupancy of glucocorticoid receptor-binding sequences at glucocorticoid-induced genes. Proceedings of the National Academy of Sciences, 2008. 105(15): p. 5745-5749.
87. Srivastava, A.K., et al., Tumor necrosis factor-alpha augments matrix metalloproteinase-9 production in skeletal muscle cells through the activation of transforming growth factor-beta-activated kinase 1 (TAK1)-dependent signaling pathway. J Biol Chem, 2007. 282(48): p. 35113-24.
88. Stanley, S.A., et al., The Type I IFN response to infection with Mycobacterium tuberculosis requires ESX-1-mediated secretion and contributes to pathogenesis. J Immunol, 2007. 178(5): p. 3143-52.
89. Su, S., et al., Transcriptomic analysis of EGb 761-regulated neuroactive receptor pathway in vivo. Journal of Ethnopharmacology, 2009. 123(1): p. 68-73.
90. Suzawa, M. and H. Ingraham, The herbicide atrazine activates endocrine gene networks via non-steroidal NR5A nuclear receptors in fish and mammalian cells. PloS One, 2008. 3(5).
91. Takami, T., et al., Loss of hepatocyte growth factor/c-Met signaling pathway accelerates early stages of N-nitrosodiethylamine induced hepatocarcinogenesis. Cancer Res, 2007. 67(20): p. 9844-51.
92. Taylor, E.L. and T.W. Gant, Emerging fundamental roles for non-coding RNA species in toxicology. Toxicology, 2008. 246(1): p. 34-9.
93. Teichert, F., et al., Metabolic Profilingof Transgenic Adenocarcinomaof MouseProstate (TRAMP) Tissueby H-NMRAnalysis: Evidence for Unusual Phospholipid Metabolism. The Prostate, 2008. 68: p. 1035-1047.
94. Urashima, T., et al., Molecular and physiological characterization of RV remodeling in a murine model of pulmonary stenosis. American Journal of Physiology- Heart and Circulatory Physiology, 2008. 295(3): p. H1351.
95. van den IJssel, P. and B. Ylstra, Oligonucleotide array comparative genomic hybridization. METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-, 2007. 396: p. 207.
96. Verdugo, R. and J. Medrano, Comparison of gene coverage of mouse oligonucleotide microarray platforms. BMC Genomics, 2006. 7(1): p. 58.
97. Verona, E.V., et al., Transforming Growth Factor-{beta} Signaling in Prostate Stromal Cells Supports Prostate Carcinoma Growth by Up-regulating Stromal Genes Related to Tissue Remodeling. Cancer Res, 2007. 67(12): p. 5737-5746.
98. Vijay-Kumar, M., et al., Deletion of TLR5 results in spontaneous colitis in mice. J Clin Invest, 2007. 117(12): p. 3909-21.
99. Wagner, B.K., et al., Large-scale chemical dissection of mitochondrial function. Nat Biotech, 2008. 26(3): p. 343-351.
100. Watabe, H., et al., Involvement of dynein and spectrin with early melanosome transport and melanosomal protein trafficking. J Invest Dermatol, 2008. 128(1): p. 162-74.
101. Wong, D.J., et al., Revealing Targeted Therapy for Human Cancer by Gene Module Maps. Cancer Res, 2008. 68(2): p. 369-378.
102. Woo, Y., et al., The nonhomologous end joining factor Artemis suppresses multi-tissue tumor formation and prevents loss of heterozygosity. Oncogene, 2007. 26(41): p. 6010-20.
103. Xiao, Y., et al., CD27 instructs CD4+ T cells to provide help for the memory CD8+ T cell response after protein immunization. The Journal of Immunology, 2008. 181(2): p. 1071.
104. Yang, J.Y., Microarrays--planning your experiment. Methods Mol Med, 2008. 141: p. 71-85.
105. Yang, X., et al., Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nature Genetics, 2009.
106. Yazlovitskaya, E., et al., Identification of Protein Markers of Lithium Radio-and Neuroprotective Effect. International Journal of Radiation Oncology, Biology, Physics, 2007. 69(3S): p. 126-126.
107. Yazlovitskaya, E.M., et al., Lithium treatment prevents neurocognitive deficit resulting from cranial irradiation. Cancer Res, 2006. 66(23): p. 11179-86.