Experts and Doctors on gene expression profiling in Nashville, Tennessee, United States


Locale: Nashville, Tennessee, United States
Topic: gene expression profiling

Top Publications

  1. Li B, Pozzi A, Young P. TNFalpha accelerates monocyte to endothelial transdifferentiation in tumors by the induction of integrin alpha5 expression and adhesion to fibronectin. Mol Cancer Res. 2011;9:702-11 pubmed publisher
  2. Zhang B, Jia W, Matsuda K, Kweon S, Matsuo K, Xiang Y, et al. Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk. Nat Genet. 2014;46:533-42 pubmed publisher
    ..11, 10q21.1 and 10q24.2. Furthermore, we replicated 22 previously reported CRC-associated loci. Our study provides insights into the genetic basis of CRC and suggests the involvement of new biological pathways. ..
  3. Mace L, Yermalitskaya L, Yi Y, Yang Z, Morgan A, Murray K. Transcriptional remodeling of rapidly stimulated HL-1 atrial myocytes exhibits concordance with human atrial fibrillation. J Mol Cell Cardiol. 2009;47:485-92 pubmed publisher
    ..Importantly, we identified novel pathways and molecules that were concordantly regulated in vivo. ..
  4. Smith C, WATSON J, Spencer W, O Brien T, Cha B, Albeg A, et al. Time-lapse imaging and cell-specific expression profiling reveal dynamic branching and molecular determinants of a multi-dendritic nociceptor in C. elegans. Dev Biol. 2010;345:18-33 pubmed publisher
  5. Loi S, Dushyanthen S, Beavis P, Salgado R, Denkert C, Savas P, et al. RAS/MAPK Activation Is Associated with Reduced Tumor-Infiltrating Lymphocytes in Triple-Negative Breast Cancer: Therapeutic Cooperation Between MEK and PD-1/PD-L1 Immune Checkpoint Inhibitors. Clin Cancer Res. 2016;22:1499-509 pubmed publisher
    ..Furthermore, Ras/MAPK activation and MHC expression may be predictive biomarkers of response to immune checkpoint inhibitors. ..
  6. Patterson M, Barske L, Van Handel B, Rau C, Gan P, Sharma A, et al. Frequency of mononuclear diploid cardiomyocytes underlies natural variation in heart regeneration. Nat Genet. 2017;49:1346-1353 pubmed publisher
    ..Our results corroborate the relevance of MNDCMs in heart regeneration. Moreover, they imply that intrinsic heart regeneration is not limited nor uniform in all individuals, but rather is a variable trait influenced by multiple genes. ..
  7. Smith J, Deane N, Wu F, Merchant N, Zhang B, Jiang A, et al. Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology. 2010;138:958-68 pubmed publisher
    ..A gene expression profile identified from an experimental model of colon cancer metastasis predicted cancer recurrence and death, independently of conventional measures, in patients with colon cancer. ..
  8. Thatcher E, Flynt A, Li N, Patton J, Patton J. MiRNA expression analysis during normal zebrafish development and following inhibition of the Hedgehog and Notch signaling pathways. Dev Dyn. 2007;236:2172-80 pubmed
  9. Pardo L, Schlüter A, Valor L, Barco A, Giralt M, Golbano A, et al. Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury. Glia. 2016;64:853-74 pubmed publisher
    ..Enhancing CREB activity in astrocytes thus emerges as a novel avenue in acute brain post-injury therapeutics. ..

More Information

Publications121 found, 100 shown here

  1. Liu Z, Aune T. Deregulated stress system in non-obese diabetic lymphocyte. Genes Immun. 2006;7:352-8 pubmed
  2. Nuotio Antar A, Hasty A, Kovacs W. Quantitation and cellular localization of 11beta-HSD1 expression in murine thymus. J Steroid Biochem Mol Biol. 2006;99:93-9 pubmed
  3. Kim J, Roh M, Abdulkadir S. Pim1 promotes human prostate cancer cell tumorigenicity and c-MYC transcriptional activity. BMC Cancer. 2010;10:248 pubmed publisher
    ..Pim1 promotes tumorigenicity at least in part by enhancing c-MYC transcriptional activity. We also made the novel discovery that treatment of cells with the c-MYC inhibitor 10058-F4 leads to a reduction in Pim1 protein levels. ..
  4. Gibbons J, Janson E, Hittinger C, Johnston M, Abbot P, Rokas A. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol. 2009;26:2731-44 pubmed publisher
  5. Stathopoulos G, Sherrill T, Karabela S, Goleniewska K, Kalomenidis I, Roussos C, et al. Host-derived interleukin-5 promotes adenocarcinoma-induced malignant pleural effusion. Am J Respir Crit Care Med. 2010;182:1273-81 pubmed publisher
    ..Because eosinophils can be found in malignant pleural effusions (MPE) from mice and humans, we asked whether IL-5 is involved in the pathogenesis of MPE...
  6. Petrenko V, Saini C, Giovannoni L, Gobet C, Sage D, Unser M, et al. Pancreatic ?- and ?-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression. Genes Dev. 2017;31:383-398 pubmed publisher
    ..Altogether, our data indicate that differential entrainment characteristics of circadian ?-cell and ?-cell clocks are an important feature in the temporal coordination of endocrine function and gene expression. ..
  7. Petit C, Mehta S, Roberts R, Gould K. Ace2p contributes to fission yeast septin ring assembly by regulating mid2+ expression. J Cell Sci. 2005;118:5731-42 pubmed
    ..Ace2p localizes symmetrically to dividing nuclei and functions independently of the septation initiation network. ..
  8. Wang X, Newkirk R, Carre W, Ghose P, Igobudia B, Townsel J, et al. Regulation of ANKRD9 expression by lipid metabolic perturbations. BMB Rep. 2009;42:568-73 pubmed
    ..These findings point to the possibility that ANKRD9 is involved in intracellular lipid accumulation. [BMB reports 2009; 42(9): 568-573]. ..
  9. Wang J, Duncan D, Shi Z, Zhang B. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res. 2013;41:W77-83 pubmed publisher
    ..WebGestalt can be freely accessed through or ..
  10. Russell A, Boone B, Jiang A, Sealy L. Genomic profiling of C/EBP?2 transformed mammary epithelial cells: a role for nuclear interleukin-1?. Cancer Biol Ther. 2010;10:509-19 pubmed publisher
    ..This study demonstrates the presence of nuclear proIL1? in transformed mammary epithelial cells providing the first evidence that IL1? may be a dual function cytokine. ..
  11. Kourteva Y, De Pasquale M, Allos T, McMunn C, D Aquila R. APOBEC3G expression and hypermutation are inversely associated with human immunodeficiency virus type 1 (HIV-1) burden in vivo. Virology. 2012;430:1-9 pubmed publisher
    ..These results indicate that A3G deaminase-dependent activity above a threshold level, and its deaminase-independent functions, contribute to decreasing Vif-positive virus replication in vivo...
  12. Sundberg J, Pratt C, Silva K, Kennedy V, Stearns T, Sundberg B, et al. Dermal lymphatic dilation in a mouse model of alopecia areata. Exp Mol Pathol. 2016;100:332-6 pubmed publisher
    ..These findings emphasize aspects of AA not commonly considered and provide potential targets for therapeutic intervention. ..
  13. Wang J, Mouradov D, Wang X, Jorissen R, Chambers M, Zimmerman L, et al. Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity. Gastroenterology. 2017;153:1082-1095 pubmed publisher
    ..Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine. ..
  14. Takahashi S, Onuma Y, Yokota C, Westmoreland J, Asashima M, Wright C. Nodal-related gene Xnr5 is amplified in the Xenopus genome. Genesis. 2006;44:309-21 pubmed
  15. TAMBOLI R, Hajri T, Jiang A, Marks Shulman P, Williams D, Clements R, et al. Reduction in inflammatory gene expression in skeletal muscle from Roux-en-Y gastric bypass patients randomized to omentectomy. PLoS ONE. 2011;6:e28577 pubmed publisher
    ..These data indicate that RYGB reduces skeletal muscle inflammation, and removal of omental fat further amplifies this response. NCT00212160. ..
  16. Mortensen B, Skaar E. Host-microbe interactions that shape the pathogenesis of Acinetobacter baumannii infection. Cell Microbiol. 2012;14:1336-44 pubmed publisher
    ..This review highlights some of the key attributes of A.?baumannii virulence with an emphasis on bacterial interactions with the innate immune system...
  17. Sobota R, Dara A, Manning J, Niangaly A, Bailey J, Kone A, et al. Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study. Malar J. 2016;15:150 pubmed publisher
    ..Low baseline expression of these genes may represent candidate markers for severe malaria. Despite the small sample size, results of this pilot study offer promising targets for follow-up analyses. ..
  18. Panaccione A, Chang M, Carbone B, Guo Y, Moskaluk C, Virk R, et al. NOTCH1 and SOX10 are Essential for Proliferation and Radiation Resistance of Cancer Stem-Like Cells in Adenoid Cystic Carcinoma. Clin Cancer Res. 2016;22:2083-95 pubmed publisher
    ..Sensitivity of these cells to Notch inhibition and their dependence on SKP2 offer new opportunities for targeted ACC therapies. ..
  19. Jackson R, Cho Y, Liang P. TIS11D is a candidate pro-apoptotic p53 target gene. Cell Cycle. 2006;5:2889-93 pubmed
    ..Inducible expression of TIS11D resulted in inhibition of cell proliferation and apoptosis. These data suggest TIS11D as a candidate p53 target gene that may be part of the network of genes responsible for p53-dependent apoptosis. ..
  20. Yi Y, Nowak N, Pacchia A, Morrison C. Chromosome 11 genomic changes in parathyroid adenoma and hyperplasia: array CGH, FISH, and tissue microarrays. Genes Chromosomes Cancer. 2008;47:639-48 pubmed publisher
    ..This genetic change was relatively independent of other chromosome 11 changes and present in slightly less than one-half of adenomas. 11q23 deletion along with relatively strong CCND1 expression was common in uremic hyperparathyroidism...
  21. Love H, Booton S, Boone B, Breyer J, Koyama T, Revelo M, et al. Androgen regulated genes in human prostate xenografts in mice: relation to BPH and prostate cancer. PLoS ONE. 2009;4:e8384 pubmed publisher
    ..Our results demonstrate the feasibility, and some of the problems, of using a mouse xenograft model to characterize the androgen regulated expression profiles of intact human prostate tissues. ..
  22. Wei C, Salichos L, Wittgrove C, Rokas A, Patton J. Transcriptome-wide analysis of small RNA expression in early zebrafish development. RNA. 2012;18:915-29 pubmed publisher
    ..Beside miRNAs, we also identified a large and unexpectedly diverse set of piRNAs expressed during early development. ..
  23. Johnson K, Phan T, Albertolle M, Guengerich F. Human mitochondrial cytochrome P450 27C1 is localized in skin and preferentially desaturates trans-retinol to 3,4-dehydroretinol. J Biol Chem. 2017;292:13672-13687 pubmed publisher
    ..Adrenodoxin reduction and hydrogen abstraction both contribute to rate limitation. ..
  24. Zhang Z, DuBois R. Detection of differentially expressed genes in human colon carcinoma cells treated with a selective COX-2 inhibitor. Oncogene. 2001;20:4450-6 pubmed
    ..Additional studies are underway to determine the biological function of the novel genes that were identified. ..
  25. Kobayashi H, Debusk L, Babichev Y, Dumont D, Lin P. Hepatocyte growth factor mediates angiopoietin-induced smooth muscle cell recruitment. Blood. 2006;108:1260-6 pubmed
    ..Collectively, our data reveal a novel mechanism of Ang/Tie2 signaling in regulating vascular maturation and suggest that a delicate balance between Ang1 and Ang2 is critical in this process. ..
  26. Wang S, Xiang B, Guix M, Olivares M, Parker J, Chung C, et al. Transforming growth factor beta engages TACE and ErbB3 to activate phosphatidylinositol-3 kinase/Akt in ErbB2-overexpressing breast cancer and desensitizes cells to trastuzumab. Mol Cell Biol. 2008;28:5605-20 pubmed publisher
  27. Russell S, Russell J, Trupin K, Gayden A, Opalenik S, Nanney L, et al. Epigenetically altered wound healing in keloid fibroblasts. J Invest Dermatol. 2010;130:2489-96 pubmed publisher
  28. Digby G, Noetzel M, Bubser M, Utley T, Walker A, BYUN N, et al. Novel allosteric agonists of M1 muscarinic acetylcholine receptors induce brain region-specific responses that correspond with behavioral effects in animal models. J Neurosci. 2012;32:8532-44 pubmed publisher
  29. Dees E, Miller P, Moynihan K, Pooley R, Hunt R, Galindo C, et al. Cardiac-specific deletion of the microtubule-binding protein CENP-F causes dilated cardiomyopathy. Dis Model Mech. 2012;5:468-80 pubmed publisher
    ..Finally, this study has broad implications for development and disease because CENP-F loss of function affects a diverse array of cell-type-specific activities in other organs. ..
  30. Loh J, Friedman D, Piazuelo M, Bravo L, Wilson K, Peek R, et al. Analysis of Helicobacter pylori cagA promoter elements required for salt-induced upregulation of CagA expression. Infect Immun. 2012;80:3094-106 pubmed publisher
    ..In summary, there is considerable heterogeneity among H. pylori strains in salt-regulated CagA expression, and these differences are attributable to variation in a specific DNA motif upstream of the cagA transcriptional start site. ..
  31. Wei J, Noto J, Zaika E, Romero Gallo J, Correa P, El Rifai W, et al. Pathogenic bacterium Helicobacter pylori alters the expression profile of p53 protein isoforms and p53 response to cellular stresses. Proc Natl Acad Sci U S A. 2012;109:E2543-50 pubmed
    ..Together, these results provide unique insights into the regulation of p53 protein and may contribute to the understanding of tumorigenesis associated with H. pylori. ..
  32. Reddy A, Zhang J, Davis N, Moffitt A, Love C, Waldrop A, et al. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017;171:481-494.e15 pubmed publisher
    ..These results comprehensively define the genetic drivers and their functional roles in DLBCL to identify new therapeutic opportunities in the disease. ..
  33. Winterbottom E, Fei D, Koestler D, Giambelli C, Wika E, Capobianco A, et al. GLI3 Links Environmental Arsenic Exposure and Human Fetal Growth. EBioMedicine. 2015;2:536-43 pubmed publisher
    ..Together, these studies identify GLI3 as a key signaling node that is affected by arsenic, mediating a subset of its effects on developmental signaling and fetal health. ..
  34. Chung C, Parker J, Karaca G, Wu J, Funkhouser W, Moore D, et al. Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression. Cancer Cell. 2004;5:489-500 pubmed
    ..This work represents an important step toward the identification of clinically significant biomarkers for HNSCC. ..
  35. Torres V, Attia A, Mason W, Hood M, Corbin B, Beasley F, et al. Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia. Infect Immun. 2010;78:1618-28 pubmed publisher
    ..These findings reveal that Fur is involved in initiating a regulatory program that organizes the expression of virulence factors during the pathogenesis of S. aureus pneumonia. ..
  36. Balko J, Cook R, Vaught D, Kuba M, Miller T, Bhola N, et al. Profiling of residual breast cancers after neoadjuvant chemotherapy identifies DUSP4 deficiency as a mechanism of drug resistance. Nat Med. 2012;18:1052-9 pubmed publisher
    ..Thus, DUSP4 downregulation activates the Ras-ERK pathway in BLBC, resulting in an attenuated response to anti-cancer chemotherapy. ..
  37. Money K, Olah Z, Korade Z, Garbett K, Shelton R, Mirnics K. An altered peripheral IL6 response in major depressive disorder. Neurobiol Dis. 2016;89:46-54 pubmed publisher
    ..Ultimately we hope that these studies will lead to validation of novel MDD drug targets focused on normalizing the altered IL6 response in patients. ..
  38. Nichols C, Sanders Bush E. Molecular genetic responses to lysergic acid diethylamide include transcriptional activation of MAP kinase phosphatase-1, C/EBP-beta and ILAD-1, a novel gene with homology to arrestins. J Neurochem. 2004;90:576-84 pubmed
    ..The genes thus far found to be responsive to LSD are beginning to give a more complete picture of the complex intracellular events initiated by hallucinogens. ..
  39. O Donnell S, Holm G, Pierce J, Tian B, Watson M, Chari R, et al. Identification of an NF-kappaB-dependent gene network in cells infected by mammalian reovirus. J Virol. 2006;80:1077-86 pubmed
    ..Together, these results suggest a genetic program for reovirus-induced apoptosis involving NF-kappaB-directed expression of cellular genes that activate death signaling pathways in infected cells...
  40. Geng Y, Hoke A, Delpire E. The Ste20 kinases Ste20-related proline-alanine-rich kinase and oxidative-stress response 1 regulate NKCC1 function in sensory neurons. J Biol Chem. 2009;284:14020-8 pubmed publisher
    ..In summary, our study demonstrates redundancy of kinases in the regulation of NKCC1 in dorsal root ganglion neurons. ..
  41. Razvi M, Peng D, Dar A, Powell S, Frierson H, Moskaluk C, et al. Transcriptional oncogenomic hot spots in Barrett's adenocarcinomas: serial analysis of gene expression. Genes Chromosomes Cancer. 2007;46:914-28 pubmed
    ..ANPEP is a secreted protein that may have diagnostic and/or prognostic significance for Barrett's progression. The use of genomic approaches in this study provided useful information about the molecular pathobiology of BAs. ..
  42. Thornburg N, Shepherd B, Crowe J. Transforming growth factor beta is a major regulator of human neonatal immune responses following respiratory syncytial virus infection. J Virol. 2010;84:12895-902 pubmed publisher
    ..These data suggest that TGF-? acts as a major regulator of RSV DC-T-cell responses, which could contribute to immunopathology during infancy. ..
  43. Greco F, Erlander M. Molecular classification of cancers of unknown primary site. Mol Diagn Ther. 2009;13:367-73 pubmed publisher
    ..Several clinical studies are in progress or planned to test this concept. ..
  44. Delahanty R, Xiang Y, Spurdle A, Beeghly Fadiel A, Long J, Thompson D, et al. Polymorphisms in inflammation pathway genes and endometrial cancer risk. Cancer Epidemiol Biomarkers Prev. 2013;22:216-23 pubmed publisher
    ..Impact statement: This study adds to the growing evidence that inflammation plays an important role in endometrial carcinogenesis. ..
  45. Saad R, Chen Z, Zhu S, Jia P, Zhao Z, Washington M, et al. Deciphering the unique microRNA signature in human esophageal adenocarcinoma. PLoS ONE. 2013;8:e64463 pubmed publisher
    ..This may provide some clues for the distinct molecular features of EAC to be considered in future studies of the role of miRNAs in EAC and their utility as disease biomarkers. ..
  46. Thomas E, Nakamura M, Wienke D, Isacke C, Pozzi A, Liang P. Endo180 binds to the C-terminal region of type I collagen. J Biol Chem. 2005;280:22596-605 pubmed
    ..The interaction between Endo180 and the C-terminal region of type I collagen appears to play an important role in cell-matrix adhesion. ..
  47. Mitchell A, Leak R, Garbett K, Zigmond M, Cameron J, Mirnics K. Physical activity-associated gene expression signature in nonhuman primate motor cortex. Obesity (Silver Spring). 2012;20:692-8 pubmed publisher
    ..We conclude that these genes are important in the physical activity-associated pathway in the motor cortex, and may be critical for physical activity-associated changes in body weight and neuroprotection. ..
  48. Chandler R, Chandler K, McFarland K, Mortlock D. Bmp2 transcription in osteoblast progenitors is regulated by a distant 3' enhancer located 156.3 kilobases from the promoter. Mol Cell Biol. 2007;27:2934-51 pubmed
  49. Rutzler M, Lu T, Zwiebel L. Galpha encoding gene family of the malaria vector mosquito Anopheles gambiae: expression analysis and immunolocalization of AGalphaq and AGalphao in female antennae. J Comp Neurol. 2006;499:533-45 pubmed
    ..In contrast, AGalphao is localized along the flagellar axon bundle but is absent from chemosensory sensilla, which suggests that this G-protein alpha subunit does not participate in olfactory signal transduction. ..
  50. Gregg J, Herring N, Naydenov A, Hanlin R, Konradi C. Downregulation of oligodendrocyte transcripts is associated with impaired prefrontal cortex function in rats. Schizophr Res. 2009;113:277-87 pubmed publisher
    ..Thus, CPZ exposure of rats can serve as a model to examine the contribution of oligodendrocyte perturbation to cognitive deficits observed in Sz. ..
  51. Lynch C, Hikosaka A, Acuff H, Martin M, Kawai N, Singh R, et al. MMP-7 promotes prostate cancer-induced osteolysis via the solubilization of RANKL. Cancer Cell. 2005;7:485-96 pubmed
    ..MMP-7-deficient mice demonstrated reduced prostate tumor-induced osteolysis and RANKL processing. This study suggests that inhibition of MMP-7 will have therapeutic benefit in the treatment of prostate cancer-induced osteolysis. ..
  52. Vaknin U, Hann S. The alpha1 subunit of GABAA receptor is repressed by c-myc and is pro-apoptotic. J Cell Biochem. 2006;97:1094-103 pubmed
    ..In addition, the regulation of GABAAR-alpha1 expression by c-myc provides a potential direct role for the Myc proteins in neurological processes and neurodegenerative disorders. ..
  53. Corbin B, Seeley E, Raab A, Feldmann J, Miller M, Torres V, et al. Metal chelation and inhibition of bacterial growth in tissue abscesses. Science. 2008;319:962-5 pubmed publisher
    ..These results demonstrate that calprotectin is a critical factor in the innate immune response to infection and define metal chelation as a strategy for inhibiting microbial growth inside abscessed tissue. ..
  54. Ghosh R, Narasanna A, Wang S, Liu S, Chakrabarty A, Balko J, et al. Trastuzumab has preferential activity against breast cancers driven by HER2 homodimers. Cancer Res. 2011;71:1871-82 pubmed publisher
    ..A clinical implication of our results is that high levels of HER2 homodimers may predict a positive response to trastuzumab. ..
  55. Greco F, Oien K, Erlander M, Osborne R, Varadhachary G, Bridgewater J, et al. Cancer of unknown primary: progress in the search for improved and rapid diagnosis leading toward superior patient outcomes. Ann Oncol. 2012;23:298-304 pubmed publisher
    ..The longer-term objective is to understand the biology of highly metastatic disease, leading to the development of future global therapeutic programs. Current clinical studies, such as CUP-ONE, will address some of these issues. ..
  56. Sun J, Gong X, Purow B, Zhao Z. Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PLoS Comput Biol. 2012;8:e1002488 pubmed publisher
  57. Przybysz A, Choe K, Roberts L, Strange K. Increased age reduces DAF-16 and SKN-1 signaling and the hormetic response of Caenorhabditis elegans to the xenobiotic juglone. Mech Ageing Dev. 2009;130:357-69 pubmed publisher
    ..Our studies provide a foundation for developing a molecular understanding of how age affects cytoprotective transcriptional pathways. ..
  58. HILLYER J. Transcription in mosquito hemocytes in response to pathogen exposure. J Biol. 2009;8:51 pubmed publisher
    ..A study published in BMC Genomics shows that hemocyte gene transcription in response to immune challenge is pathogen-specific and reaffirms the primary role of these cells in immunity. ..
  59. Spencer W, Zeller G, WATSON J, Henz S, Watkins K, McWhirter R, et al. A spatial and temporal map of C. elegans gene expression. Genome Res. 2011;21:325-41 pubmed publisher
  60. Soutto M, Belkhiri A, Piazuelo M, Schneider B, Peng D, Jiang A, et al. Loss of TFF1 is associated with activation of NF-?B-mediated inflammation and gastric neoplasia in mice and humans. J Clin Invest. 2011;121:1753-67 pubmed publisher
  61. Coggins S, Estévez Lao T, HILLYER J. Increased survivorship following bacterial infection by the mosquito Aedes aegypti as compared to Anopheles gambiae correlates with increased transcriptional induction of antimicrobial peptides. Dev Comp Immunol. 2012;37:390-401 pubmed publisher
    ..aegypti is better equipped to survive a bacterial infection than An. gambiae, and this correlates with Ae. aegypti's increased transcriptional induction of antimicrobial peptides and other humoral immune factors in response to infection...
  62. Rao M, Song W, Jiang A, Shyr Y, Lev S, Greenstein D, et al. VAMP-associated protein B (VAPB) promotes breast tumor growth by modulation of Akt activity. PLoS ONE. 2012;7:e46281 pubmed publisher
    ..Pharmacological inhibition of AKT significantly reduced three-dimensional spheroid growth induced by VAPB. Collectively, the genetic, functional and mechanistic analyses suggest a role of VAPB in tumor promotion in human breast cancer. ..
  63. McGirt L, Adams C, Baerenwald D, Zwerner J, Zic J, Eischen C. miR-223 regulates cell growth and targets proto-oncogenes in mycosis fungoides/cutaneous T-cell lymphoma. J Invest Dermatol. 2014;134:1101-1107 pubmed publisher
    ..Thus, miR-223 and its targets may be useful for the development of new therapeutics for MF/CTCL. ..
  64. Govindan J, Cheng H, Harris J, Greenstein D. Galphao/i and Galphas signaling function in parallel with the MSP/Eph receptor to control meiotic diapause in C. elegans. Curr Biol. 2006;16:1257-68 pubmed
    ..elegans, highlighting contrasts and parallels between MSP signaling in C. elegans and luteinizing hormone signaling in mammals. ..
  65. Jin R, Yi Y, Yull F, Blackwell T, Clark P, Koyama T, et al. NF-?B gene signature predicts prostate cancer progression. Cancer Res. 2014;74:2763-72 pubmed publisher
  66. Park Y, Franklin J, Settle S, Levy S, Chung E, Jeyakumar L, et al. Gene expression profile analysis of mouse colon embryonic development. Genesis. 2005;41:1-12 pubmed
  67. Ni T, Lemon W, Shyr Y, Zhong T. Use of normalization methods for analysis of microarrays containing a high degree of gene effects. BMC Bioinformatics. 2008;9:505 pubmed publisher
    ..The results indicate that our method may be used without prior knowledge of or assumptions about housekeeping genes to normalize microarrays that are quite different. ..
  68. Ivanov S, Goparaju C, Lopez P, Zavadil J, Toren Haritan G, Rosenwald S, et al. Pro-tumorigenic effects of miR-31 loss in mesothelioma. J Biol Chem. 2010;285:22809-17 pubmed publisher
    ..Taken together, our data suggest that tumor-suppressive propensity of miR-31 can be used for development of new therapies against mesothelioma and other cancers that show loss of the 9p21.3 chromosome. ..
  69. Guo Y, Sheng Q, Li J, Ye F, Samuels D, Shyr Y. Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS ONE. 2013;8:e71462 pubmed publisher
    ..Longer exons tended to have better concordance between the two normalization methods than shorter exons. ..
  70. Aung T, Ozaki M, Lee M, Schlötzer Schrehardt U, Thorleifsson G, Mizoguchi T, et al. Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci. Nat Genet. 2017;49:993-1004 pubmed publisher
    ..3 (TMEM136), 6p21 (AGPAT1), 3p24 (RBMS3) and 5q23 (near SEMA6A). These findings provide biological insights into the pathology of XFS and highlight a potential role for naturally occurring rare LOXL1 variants in disease biology. ..
  71. Cavalli F, Remke M, Rampášek L, Peacock J, Shih D, Luu B, et al. Intertumoral Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. 2017;31:737-754.e6 pubmed publisher
    ..Medulloblastoma subtypes identified through integrative clustering have important implications for stratification of future clinical trials. ..
  72. Williams A, Korolkova O, Sakwe A, Geiger T, James S, Muldoon R, et al. Human alpha defensin 5 is a candidate biomarker to delineate inflammatory bowel disease. PLoS ONE. 2017;12:e0179710 pubmed publisher
    ..These data give us both a potential diagnostic marker in Human α-Defensin-5 and insight to develop future mechanistic studies to better understand crypt biology in Crohn's colitis. ..
  73. Fang W, Brantley Sieders D, Parker M, Reith A, Chen J. A kinase-dependent role for EphA2 receptor in promoting tumor growth and metastasis. Oncogene. 2005;24:7859-68 pubmed
    ..Taken together, these results suggest that receptor phosphorylation and kinase activity of the EphA2 receptor, at least in part, contribute to tumor malignancy. ..
  74. Motsinger A, Lee S, Mellick G, Ritchie M. GPNN: power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease. BMC Bioinformatics. 2006;7:39 pubmed
    ..These results indicate that GPNN may be a useful pattern recognition approach for detecting gene-gene and gene-environment interactions. ..
  75. Garbett K, Ebert P, Mitchell A, Lintas C, Manzi B, Mirnics K, et al. Immune transcriptome alterations in the temporal cortex of subjects with autism. Neurobiol Dis. 2008;30:303-11 pubmed publisher
  76. Korade Z, Kenworthy A, Mirnics K. Molecular consequences of altered neuronal cholesterol biosynthesis. J Neurosci Res. 2009;87:866-75 pubmed publisher
  77. Lee H, Nam K, Park H, Kim M, Lafleur B, Aburatani H, et al. Gene expression profiling of metaplastic lineages identifies CDH17 as a prognostic marker in early stage gastric cancer. Gastroenterology. 2010;139:213-25.e3 pubmed publisher
    ..Expression of CDH17 and MUC13 was up-regulated in gastric cancer tissues. CDH17 is a promising prognostic marker for early stage gastric cancer. ..
  78. Miller T, Balko J, Ghazoui Z, Dunbier A, Anderson H, Dowsett M, et al. A gene expression signature from human breast cancer cells with acquired hormone independence identifies MYC as a mediator of antiestrogen resistance. Clin Cancer Res. 2011;17:2024-34 pubmed publisher
    ..Activation of the MYC pathway was associated with this resistance. ..
  79. Pitts R, Rinker D, Jones P, Rokas A, Zwiebel L. Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding. BMC Genomics. 2011;12:271 pubmed publisher
    ..Here we have demonstrated the use of RNA-seq to characterize the sensory specializations of an important disease vector and grounded future studies investigating chemosensory processes. ..
  80. Greco J, Pollins A, Boone B, Levy S, Nanney L. A microarray analysis of temporal gene expression profiles in thermally injured human skin. Burns. 2010;36:192-204 pubmed publisher
    ..Further analysis of genes that are either affected or remain not affected following injury to normal skin is expected to identify potential targets for therapeutic augmentation or silencing. ..
  81. Hood M, Jacobs A, Sayood K, Dunman P, Skaar E. Acinetobacter baumannii increases tolerance to antibiotics in response to monovalent cations. Antimicrob Agents Chemother. 2010;54:1029-41 pubmed publisher
    ..Taken together, these data demonstrate that A. baumannii sets in motion a global regulatory cascade in response to physiological NaCl concentrations, resulting in broad-spectrum tolerance to antibiotics...
  82. Liu Y, Hogan B. Differential gene expression in the distal tip endoderm of the embryonic mouse lung. Gene Expr Patterns. 2002;2:229-33 pubmed
    ..5 lung buds, versus more proximal regions. Twenty genes were identified, assigned to different categories based on sequence analysis, and their distal expression confirmed by whole-mount in situ hybridization. ..
  83. Fox R, Von Stetina S, Barlow S, Shaffer C, Olszewski K, Moore J, et al. A gene expression fingerprint of C. elegans embryonic motor neurons. BMC Genomics. 2005;6:42 pubmed
    ..These methods can now be applied to generate a gene expression map of the C. elegans nervous system. ..
  84. WATSON J, Wang S, Von Stetina S, Spencer W, Levy S, Dexheimer P, et al. Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system. BMC Genomics. 2008;9:84 pubmed publisher
    ..With its relative ease of implementation and greater sensitivity, WT-Pico is the preferred method of amplification for cases in which sample RNA is limiting. ..
  85. Bhaskara S, Chyla B, Amann J, Knutson S, Cortez D, Sun Z, et al. Deletion of histone deacetylase 3 reveals critical roles in S phase progression and DNA damage control. Mol Cell. 2008;30:61-72 pubmed publisher
    ..Moreover, we noted that Hdac3-/- MEFs were protected from DNA damage when quiescent, which may provide a mechanistic basis for the action of HDAC inhibitors on cycling tumor cells. ..
  86. Pyle A, Li B, Maupin A, Guzman R, Crimmins D, Olson S, et al. Biomechanical stress induces novel arterial intima-enriched genes: implications for vascular adaptation to stress. Cardiovasc Pathol. 2010;19:e13-20 pubmed publisher
    ..We report the novel finding of a group of genes, previously studied in stratified epithelium, that were regulated by prolonged cyclic stress in vascular smooth muscle cells. This may have important implications to vascular disease. ..
  87. Wang X, Slebos R, Wang D, Halvey P, Tabb D, Liebler D, et al. Protein identification using customized protein sequence databases derived from RNA-Seq data. J Proteome Res. 2012;11:1009-17 pubmed publisher
    ..Thus, sample-specific databases from RNA-Seq data can enable more sensitive and comprehensive protein discovery in shotgun proteomics studies. ..
  88. Zhou X, Slone J, Rokas A, Berger S, Liebig J, Ray A, et al. Phylogenetic and transcriptomic analysis of chemosensory receptors in a pair of divergent ant species reveals sex-specific signatures of odor coding. PLoS Genet. 2012;8:e1002930 pubmed publisher
    ..Our findings represent an important advance toward understanding the molecular basis of social interactions and the differential chemical ecologies among ant species. ..
  89. Stein S, Thomas E, Herzog B, Westfall M, Rocheleau J, Jackson R, et al. NDRG1 is necessary for p53-dependent apoptosis. J Biol Chem. 2004;279:48930-40 pubmed
    ..This report further supports the notion that p53 controls a network of genes that are required for its apoptotic function. ..
  90. Statnikov A, Wang L, Aliferis C. A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification. BMC Bioinformatics. 2008;9:319 pubmed publisher
  91. Ford G, Ford B, Steele E, Gates A, Hood D, Matthews M, et al. Analysis of transcriptional profiles and functional clustering of global cerebellar gene expression in PCD3J mice. Biochem Biophys Res Commun. 2008;377:556-561 pubmed publisher
  92. Jiang M, Fernandez S, Jerome W, He Y, Yu X, Cai H, et al. Disruption of PPARgamma signaling results in mouse prostatic intraepithelial neoplasia involving active autophagy. Cell Death Differ. 2010;17:469-81 pubmed publisher
    ..We conclude that disruption of PPARgamma signaling results in autophagy and oxidative stress during mPIN pathogenesis...