Experts and Doctors on gene expression profiling in Chapel Hill, North Carolina, United States


Locale: Chapel Hill, North Carolina, United States
Topic: gene expression profiling

Top Publications

  1. Niculescu M, da Costa K, Fischer L, Zeisel S. Lymphocyte gene expression in subjects fed a low-choline diet differs between those who develop organ dysfunction and those who do not. Am J Clin Nutr. 2007;86:230-9 pubmed
    ..These findings support our hypothesis that a person's susceptibility to organ dysfunction when fed a low-choline diet is modulated by specific SNPs in genes involved in folate and choline metabolism. ..
  2. Singleton D, Ramirez L, Aitken M. Characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading Acidovorax strain. Appl Environ Microbiol. 2009;75:2613-20 pubmed publisher
    ..Expression of each of the genes was induced most strongly by phenanthene and to a lesser extent by naphthalene, but other tested PAHs and PAH metabolites had negligible effects on gene transcript levels. ..
  3. Eulgem T, Weigman V, Chang H, McDowell J, Holub E, Glazebrook J, et al. Gene expression signatures from three genetically separable resistance gene signaling pathways for downy mildew resistance. Plant Physiol. 2004;135:1129-44 pubmed
    ..Previously defined and novel sequence motifs were found to be enriched in the promoters of genes coregulated by the local defense-signaling network. These putative promoter elements may operate downstream from signal convergence points...
  4. Hansen J, Holt L, Sartor R. Gene expression patterns in experimental colitis in IL-10-deficient mice. Inflamm Bowel Dis. 2009;15:890-9 pubmed publisher
    ..Although most upregulated genes in experimental colitis are immune-related, aquaporin-4 and mitochondrial ribosomal protein-L33, which have not been previously associated with inflammation, were most highly upregulated. ..
  5. McDonough H, Charles P, Hilliard E, Qian S, Min J, Portbury A, et al. Stress-dependent Daxx-CHIP interaction suppresses the p53 apoptotic program. J Biol Chem. 2009;284:20649-59 pubmed publisher
    ..By abrogating p53-dependent apoptotic pathways and by ubiquitination competitive with Daxx sumoylation, CHIP integrates the proteotoxic stress response of the cell with cell cycle pathways that influence cell survival. ..
  6. Bednarski B, Baldwin A, Kim H. Addressing reported pro-apoptotic functions of NF-kappaB: targeted inhibition of canonical NF-kappaB enhances the apoptotic effects of doxorubicin. PLoS ONE. 2009;4:e6992 pubmed publisher
    ..Therefore, combination therapies incorporating NF-kappaB inhibitors together with standard chemotherapies remains a viable method to improve the clinical outcomes in patients with advanced stage malignancies. ..
  7. Benton M, Rager J, Smeester L, Fry R. Comparative genomic analyses identify common molecular pathways modulated upon exposure to low doses of arsenic and cadmium. BMC Genomics. 2011;12:173 pubmed publisher
    ..These results highlight that even at low levels of exposure both metals can dramatically influence the expression of important cellular pathways. ..
  8. Wright F, Sullivan P, Brooks A, Zou F, Sun W, Xia K, et al. Heritability and genomics of gene expression in peripheral blood. Nat Genet. 2014;46:430-7 pubmed publisher
    ..Our results provide a new resource toward understanding the genetic control of transcription. ..
  9. Williams K, Taxman D, Linhoff M, Reed W, Ting J. Cutting edge: Monarch-1: a pyrin/nucleotide-binding domain/leucine-rich repeat protein that controls classical and nonclassical MHC class I genes. J Immunol. 2003;170:5354-8 pubmed
    ..These analyses show that Monarch-1 enhances nonclassical and classical MHC class I expression at the level of the promoter, RNA, and protein expression. ..

More Information

Publications118 found, 100 shown here

  1. Conway K, Edmiston S, Khondker Z, Groben P, Zhou X, Chu H, et al. DNA-methylation profiling distinguishes malignant melanomas from benign nevi. Pigment Cell Melanoma Res. 2011;24:352-60 pubmed publisher
    ..This first report of a DNA-methylation signature discriminating melanomas from nevi indicates that DNA methylation appears promising as an additional tool for enhancing melanoma diagnosis. ..
  2. Ullah H, Chen J, Temple B, Boyes D, Alonso J, Davis K, et al. The beta-subunit of the Arabidopsis G protein negatively regulates auxin-induced cell division and affects multiple developmental processes. Plant Cell. 2003;15:393-409 pubmed
    ..These results suggest that although auxin-regulated cell division is not coupled directly by a G protein, the Gbeta-subunit attenuates this auxin pathway upstream of the control of mRNA steady state levels. ..
  3. Xiong Q, Ancona N, Hauser E, Mukherjee S, Furey T. Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Res. 2012;22:386-97 pubmed publisher
    ..These demonstrate that GSAA can help uncover biological pathways underlying human diseases and complex traits. ..
  4. CHUGH P, Sin S, Ozgur S, Henry D, Menezes P, Griffith J, et al. Systemically circulating viral and tumor-derived microRNAs in KSHV-associated malignancies. PLoS Pathog. 2013;9:e1003484 pubmed publisher
    ..These could represent candidate biomarkers of disease and may contribute to the paracrine phenotypes that are a characteristic of KS. ..
  5. Rashotte A, Mason M, Hutchison C, Ferreira F, Schaller G, Kieber J. A subset of Arabidopsis AP2 transcription factors mediates cytokinin responses in concert with a two-component pathway. Proc Natl Acad Sci U S A. 2006;103:11081-5 pubmed
    ..Thus, the evolutionarily ancient two-component system that is used by cytokinin branches to incorporate a unique family of plant-specific transcription factors. ..
  6. Leduc I, Olsen B, Elkins C. Localization of the domains of the Haemophilus ducreyi trimeric autotransporter DsrA involved in serum resistance and binding to the extracellular matrix proteins fibronectin and vitronectin. Infect Immun. 2009;77:657-66 pubmed publisher
    ..We concluded that neither fibronectin binding nor vitronectin binding is required for high-level serum resistance in H. ducreyi...
  7. Kim W, Perera S, Zhou B, Carretero J, Yeh J, Heathcote S, et al. HIF2alpha cooperates with RAS to promote lung tumorigenesis in mice. J Clin Invest. 2009;119:2160-70 pubmed
    ..They further suggest a possible causal relationship between HIF2alpha and prognosis in patients with NSCLC. ..
  8. Lock E, Ziemiecke R, Marron J, Dittmer D. Efficiency clustering for low-density microarrays and its application to QPCR. BMC Bioinformatics. 2010;11:386 pubmed publisher
    ..Efficiency clustering as developed here serves as a compromise between the imprecision in assuming uniform efficiency, and the computational complexity and danger of over-fitting when using individually determined efficiencies. ..
  9. Zhong S, Zhang S, Bair E, Nares S, Khan A. Differential expression of microRNAs in normal and inflamed human pulps. J Endod. 2012;38:746-52 pubmed publisher
    ..These findings highlight the intricate and specific roles of miRNA in inflammation and immunity, both of which are key aspects of pulpal pathology. ..
  10. Prat A, Navarro A, Paré L, Reguart N, Galvan P, Pascual T, et al. Immune-Related Gene Expression Profiling After PD-1 Blockade in Non-Small Cell Lung Carcinoma, Head and Neck Squamous Cell Carcinoma, and Melanoma. Cancer Res. 2017;77:3540-3550 pubmed publisher
    ..i>Cancer Res; 77(13); 3540-50. ©2017 AACR. ..
  11. Lickwar C, Camp J, Weiser M, Cocchiaro J, Kingsley D, Furey T, et al. Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells. PLoS Biol. 2017;15:e2002054 pubmed publisher
  12. Joubert B, Franceschini N, Mwapasa V, North K, Meshnick S. Regulation of CCR5 expression in human placenta: insights from a study of mother-to-child transmission of HIV in Malawi. PLoS ONE. 2010;5:e9212 pubmed publisher
    ..Our findings also suggest that the measurement of placental expression of CCR5 alone is not an adequate indicator of the risk of mother-to-child transmission of HIV. ..
  13. Hair B, Troester M, Edmiston S, Parrish E, Robinson W, Wu M, et al. Body mass index is associated with gene methylation in estrogen receptor-positive breast tumors. Cancer Epidemiol Biomarkers Prev. 2015;24:580-6 pubmed publisher
    ..If our results are validated, obesity-associated methylation sites could serve as targets for prevention and treatment research. Cancer Epidemiol Biomarkers Prev; 24(3); 580-6. ©2015 AACR. ..
  14. Civelek M, Wu Y, Pan C, Raulerson C, Ko A, He A, et al. Genetic Regulation of Adipose Gene Expression and Cardio-Metabolic Traits. Am J Hum Genet. 2017;100:428-443 pubmed publisher
    ..These results provide candidate genes for further investigation of their potential roles in adipose biology and in regulating cardio-metabolic traits. ..
  15. Roll J, Rivenbark A, Jones W, Coleman W. DNMT3b overexpression contributes to a hypermethylator phenotype in human breast cancer cell lines. Mol Cancer. 2008;7:15 pubmed publisher
  16. Carson C, Omolo B, Chu H, Zhou Y, Sambade M, Peters E, et al. A prognostic signature of defective p53-dependent G1 checkpoint function in melanoma cell lines. Pigment Cell Melanoma Res. 2012;25:514-26 pubmed publisher
    ..Thus, p53 function, radio-sensitivity, and metastatic spread may be estimated in melanomas from a signature of gene expression. ..
  17. Sandhu R, Rivenbark A, Coleman W. Loss of post-transcriptional regulation of DNMT3b by microRNAs: a possible molecular mechanism for the hypermethylation defect observed in a subset of breast cancer cell lines. Int J Oncol. 2012;41:721-32 pubmed publisher
    ..In conlcusion, the molecular mechanism governing the DNMT3b-mediated hypermethylation defect in breast cancer cell lines involves the loss of post-transcriptional regulation of DNMT3b by regulatory miRs. ..
  18. Wilkerson M, Hayes D. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26:1572-3 pubmed publisher
    ..ConsensusClusterPlus is open source software, written in R, under GPL-2, and available through the Bioconductor project ( Supplementary data are available at Bioinformatics online. ..
  19. Barros S, Wirojchanasak S, Barrow D, Panagakos F, DeVizio W, Offenbacher S. Triclosan inhibition of acute and chronic inflammatory gene pathways. J Clin Periodontol. 2010;37:412-8 pubmed publisher
    ..Anti-inflammatory effects were found in this exploratory survey, including suppression of microbial-pathogen recognition pathway molecules and the suppression of acute and chronic mediators of inflammation. ..
  20. Rager J, Bailey K, Smeester L, Miller S, Parker J, Laine J, et al. Prenatal arsenic exposure and the epigenome: altered microRNAs associated with innate and adaptive immune signaling in newborn cord blood. Environ Mol Mutagen. 2014;55:196-208 pubmed publisher
    ..Results of this study highlight miRNAs as novel responders to prenatal arsenic exposure that may contribute to associated immune response perturbations. ..
  21. Bryson P, Shores C, Hart C, Thorne L, Patel M, Richey L, et al. Immunohistochemical distinction of follicular thyroid adenomas and follicular carcinomas. Arch Otolaryngol Head Neck Surg. 2008;134:581-6 pubmed publisher
    ..Our results show promise for multiple-protein IHC analysis algorithms and their diagnostic ability. Future studies should focus on clinical translation of these molecular differences for the diagnosis of follicular thyroid neoplasms. ..
  22. Pecaut M, Mao X, Bellinger D, Jonscher K, Stodieck L, Ferguson V, et al. Is spaceflight-induced immune dysfunction linked to systemic changes in metabolism?. PLoS ONE. 2017;12:e0174174 pubmed publisher
    ..Given the clear link between immune function and metabolism in many ground-based diseases, we propose a similar link may be involved in spaceflight-induced decrements in immune and metabolic function. ..
  23. Konopka J, Penalva L, Thompson J, White L, Beard C, Keene J, et al. A two-phase innate host response to alphavirus infection identified by mRNP-tagging in vivo. PLoS Pathog. 2007;3:e199 pubmed publisher
    ..Our findings suggest that the application of viral mRNP-tagging systems, as introduced here, will facilitate a much more detailed understanding of the highly coordinated host response to infectious agents. ..
  24. Stratford J, Bentrem D, Anderson J, Fan C, Volmar K, Marron J, et al. A six-gene signature predicts survival of patients with localized pancreatic ductal adenocarcinoma. PLoS Med. 2010;7:e1000307 pubmed publisher
    ..Genes in this signature, or the pathways that they fall into, may represent new therapeutic targets. Please see later in the article for the Editors' Summary. ..
  25. Makowski L, Zhou C, Zhong Y, Kuan P, Fan C, Sampey B, et al. Obesity increases tumor aggressiveness in a genetically engineered mouse model of serous ovarian cancer. Gynecol Oncol. 2014;133:90-7 pubmed publisher
    ..7cm(2) versus 1.2cm(2), p=0.0065). Gene expression and metabolomic profiling indicated statistically significant differences between the ovarian tumors from the obese versus non-obese mice, including metabolically relevant pathways. ..
  26. Bhati R, Patterson C, Livasy C, Fan C, Ketelsen D, Hu Z, et al. Molecular characterization of human breast tumor vascular cells. Am J Pathol. 2008;172:1381-90 pubmed publisher
    ..Therefore, these genetic markers may serve as potential targets for the development of angiogenesis inhibitors. ..
  27. Ribeiro C, Hurd H, Wu Y, Martino M, Jones L, Brighton B, et al. Azithromycin treatment alters gene expression in inflammatory, lipid metabolism, and cell cycle pathways in well-differentiated human airway epithelia. PLoS ONE. 2009;4:e5806 pubmed publisher
  28. Casbas Hernandez P, Fleming J, Troester M. Gene expression analysis of in vitro cocultures to study interactions between breast epithelium and stroma. J Biomed Biotechnol. 2011;2011:520987 pubmed publisher
    ..Coculture systems are manipulable systems that can yield important insights about cell-cell interactions and the cellular phenotypes that occur as tumor and stroma co-evolve. ..
  29. Stewart D, Yang Y, Makowski L, Troester M. Basal-like breast cancer cells induce phenotypic and genomic changes in macrophages. Mol Cancer Res. 2012;10:727-38 pubmed publisher
  30. Chen P, Smith T, Wu J, Siesser P, Bisnett B, Khan F, et al. Glycosylation of KEAP1 links nutrient sensing to redox stress signaling. EMBO J. 2017;36:2233-2250 pubmed publisher
  31. Gatti D, Zhao N, Chesler E, Bradford B, Shabalin A, Yordanova R, et al. Sex-specific gene expression in the BXD mouse liver. Physiol Genomics. 2010;42:456-68 pubmed publisher
    ..This study enhances our understanding of sex differences at the genome level and between species, as well as increasing our knowledge of the molecular underpinnings of sex differences in responses to xenobiotics. ..
  32. Woods C, Heuvel J, Rusyn I. Genomic profiling in nuclear receptor-mediated toxicity. Toxicol Pathol. 2007;35:474-94 pubmed
    ..This review will focus on genomics studies related to PPAR, CAR, PXR, RXR, LXR, FXR, and AHR. ..
  33. Comes N, Buie L, BORRAS T. Evidence for a role of angiopoietin-like 7 (ANGPTL7) in extracellular matrix formation of the human trabecular meshwork: implications for glaucoma. Genes Cells. 2011;16:243-59 pubmed publisher
    ..Together with previous findings, these properties strengthen ANGPTL7's candidacy for the regulation of IOP and glaucoma...
  34. Fontana J, Crews S. Transcriptome analysis of Drosophila CNS midline cells reveals diverse peptidergic properties and a role for castor in neuronal differentiation. Dev Biol. 2012;372:131-42 pubmed publisher
    ..This indicates a novel function for castor in regulating neuropeptide gene expression. ..
  35. Tateishi K, Okada Y, Kallin E, Zhang Y. Role of Jhdm2a in regulating metabolic gene expression and obesity resistance. Nature. 2009;458:757-61 pubmed publisher
    ..Our studies thus demonstrate an essential role for Jhdm2a in regulating metabolic gene expression and normal weight control in mice. ..
  36. WATSON V, Hardison N, Harris T, Motsinger Reif A, McLeod H. Genomic profiling in CEPH cell lines distinguishes between the camptothecins and indenoisoquinolines. Mol Cancer Ther. 2011;10:1839-45 pubmed publisher
    ..The remaining 3 QTLs (chromosomes 6 and 20) are considered specific to camptothecin-induced cytotoxicity. Finally, 8 QTLs were identified, which were unique to the indenoisoquinolines. ..
  37. Usary J, Zhao W, Darr D, Roberts P, Liu M, Balletta L, et al. Predicting drug responsiveness in human cancers using genetically engineered mice. Clin Cancer Res. 2013;19:4889-99 pubmed publisher
  38. Gralinski L, Bankhead A, Jeng S, Menachery V, Proll S, Belisle S, et al. Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury. MBio. 2013;4: pubmed publisher
    ..Similar transcriptional signatures were noted in 1918 and 2009 H1N1 influenza virus-infected mice, suggesting a common, potentially treatable mechanism in development of virus-induced ALI. ..
  39. Coleman W, Anders C. Discerning Clinical Responses in Breast Cancer Based On Molecular Signatures. Am J Pathol. 2017;187:2199-2207 pubmed publisher
    ..This review describes the molecular classification of breast cancer and the use of predictive/prognostic molecular signatures for guiding treatment decisions in breast cancer patients. ..
  40. Brown D, Davis A, Conlon F. Xtn3 is a developmentally expressed cardiac and skeletal muscle-specific novex-3 titin isoform. Gene Expr Patterns. 2006;6:913-8 pubmed
    ..Finally, we demonstrate that Xtn3 transcripts are detectable in adult heart and muscle tissues. ..
  41. Bhargava A, Clabaugh I, To J, Maxwell B, Chiang Y, Schaller G, et al. Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis. Plant Physiol. 2013;162:272-94 pubmed publisher
    ..The genes identified in this analysis represent a robust set of cytokinin-responsive genes that are useful in the analysis of cytokinin function in plants. ..
  42. Fiordalisi J, Johnson R, Weinbaum C, Sakabe K, Chen Z, Casey P, et al. High affinity for farnesyltransferase and alternative prenylation contribute individually to K-Ras4B resistance to farnesyltransferase inhibitors. J Biol Chem. 2003;278:41718-27 pubmed
    ..Our results imply that relevant FTI targets will lack both polybasic and potentially geranylgeranylated methionine-CAAX motifs. ..
  43. Jones C, Wilkinson K, Hung K, Weeks K, Spremulli L. Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs. RNA. 2008;14:862-71 pubmed publisher
    ..These data are consistent with a model in which the specialized mitochondrial ribosome preferentially allows passage of unstructured 5' sequences into the mRNA entrance site to participate in translation initiation. ..
  44. Kanther M, Sun X, Muhlbauer M, Mackey L, Flynn E, Bagnat M, et al. Microbial colonization induces dynamic temporal and spatial patterns of NF-?B activation in the zebrafish digestive tract. Gastroenterology. 2011;141:197-207 pubmed publisher
    ..The observed patterns of NF-?B-dependent responses to microbial colonization indicate that cells in the gastrointestinal tract respond robustly to the microbial environment. ..
  45. Abell A, Jordan N, Huang W, Prat A, Midland A, Johnson N, et al. MAP3K4/CBP-regulated H2B acetylation controls epithelial-mesenchymal transition in trophoblast stem cells. Cell Stem Cell. 2011;8:525-37 pubmed publisher
    ..Taken together, our data define an epigenetic switch that maintains the epithelial phenotype in TS cells and reveals previously unrecognized genes potentially contributing to breast cancer. ..
  46. Penland S, Keku T, Torrice C, He X, Krishnamurthy J, Hoadley K, et al. RNA expression analysis of formalin-fixed paraffin-embedded tumors. Lab Invest. 2007;87:383-91 pubmed
    ..Although only a minority of FFPE blocks could be analyzed, we show that informative RNA expression analysis can be derived from selected FFPE samples. ..
  47. Hu Z, Fan C, Livasy C, He X, Oh D, Ewend M, et al. A compact VEGF signature associated with distant metastases and poor outcomes. BMC Med. 2009;7:9 pubmed publisher
    ..This signature suggests that the response to hypoxia includes the ability to promote new blood and lymphatic vessel formation, and that the dual targeting of multiple cell types and pathways will be needed to prevent metastatic spread. ..
  48. Jurevics H, Largent C, Hostettler J, Sammond D, Matsushima G, Kleindienst A, et al. Alterations in metabolism and gene expression in brain regions during cuprizone-induced demyelination and remyelination. J Neurochem. 2002;82:126-36 pubmed
    ..The ability to correlate gene expression with known pathophysiological events should help in elucidating further function of such genes as related to demyelination/remyelination. ..
  49. Singh D, Orellana C, Hu Y, Jones C, Liu Y, Chiang D, et al. FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics. 2011;27:2633-40 pubmed publisher
    .. CONTACT: Supplementary data are available at Bioinformatics online. ..
  50. Li Z, Chen P, Su R, Hu C, Li Y, Elkahloun A, et al. PBX3 and MEIS1 Cooperate in Hematopoietic Cells to Drive Acute Myeloid Leukemias Characterized by a Core Transcriptome of the MLL-Rearranged Disease. Cancer Res. 2016;76:619-29 pubmed publisher
    ..Therefore, targeting the MEIS1/PBX3 interaction may represent a promising therapeutic strategy to treat these AML subtypes. ..
  51. Li J, Waters S, Drobna Z, Devesa V, Styblo M, Thomas D. Arsenic (+3 oxidation state) methyltransferase and the inorganic arsenic methylation phenotype. Toxicol Appl Pharmacol. 2005;204:164-9 pubmed
    ..This lineage-specific loss of function caused by the deletion event must have occurred in the Pan lineage after Homo-Pan divergence about 5 million years ago. ..
  52. Zhu X, Zeisel S. Gene expression profiling in phosphatidylethanolamine N-methyltransferase knockout mice. Brain Res Mol Brain Res. 2005;134:239-55 pubmed
    ..These findings are consistent with the biochemical changes that we previous reported in fetal brains from Pemt knockout mice. This is the first report of gene profiling in Pemt(-/-) mouse brain. ..
  53. Waage Baudet H, Dunty W, Dehart D, Hiller S, Sulik K. Immunohistochemical and microarray analyses of a mouse model for the smith-lemli-opitz syndrome. Dev Neurosci. 2005;27:378-96 pubmed
    ..The results of these studies aid in providing insight into the genesis of human cholesterol-related birth defects and neurodevelopmental disorders and highlight specific areas for future investigation. ..
  54. Mashek D, Li L, Coleman R. Rat long-chain acyl-CoA synthetase mRNA, protein, and activity vary in tissue distribution and in response to diet. J Lipid Res. 2006;47:2004-10 pubmed
    ..They further suggest that translational or posttranslational modifications are likely to contribute to the regulation of ACSL isoforms. ..
  55. Wu Y, Ferguson J, Wang H, Kelley R, Ren R, McDonough H, et al. PRDM6 is enriched in vascular precursors during development and inhibits endothelial cell proliferation, survival, and differentiation. J Mol Cell Cardiol. 2008;44:47-58 pubmed
  56. Dworkin I, Jones C. Genetic changes accompanying the evolution of host specialization in Drosophila sechellia. Genetics. 2009;181:721-36 pubmed publisher
    ..sechellia to its host. Our results suggest that a subset of genes reduce or lose function as a consequence of host specialization, which may explain why, in general, specialist insects tend to shift to chemically similar hosts. ..
  57. Yeh J. Prognostic signature for pancreatic cancer: are we close?. Future Oncol. 2009;5:313-21 pubmed publisher
    ..This review will therefore focus on the advantages of a prognostic gene signature for pancreatic cancer, the advances that have been made thus far, the approaches used and the challenges that remain...
  58. Dai X, Faber J. Endothelial nitric oxide synthase deficiency causes collateral vessel rarefaction and impairs activation of a cell cycle gene network during arteriogenesis. Circ Res. 2010;106:1870-81 pubmed publisher
    ..The collateral circulation is tissue- and life-saving in obstructive arterial disease. Disappointing outcomes in clinical trials aimed at augmenting collateral growth highlight the need for greater understanding of collateral biology...
  59. Cappell S, Baker R, Skowyra D, Dohlman H. Systematic analysis of essential genes reveals important regulators of G protein signaling. Mol Cell. 2010;38:746-57 pubmed publisher
    ..These insights to the G protein signaling network reveal the essential genome as an untapped resource for identifying new components and regulators of signal transduction pathways. ..
  60. Ikegami K, Egelhofer T, Strome S, Lieb J. Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2. Genome Biol. 2010;11:R120 pubmed publisher
    ..Although our data are derived from an amalgamation of cell types in mixed-stage embryos, the results suggest a model for the spatial arrangement of C. elegans chromosomes within the nucleus. ..
  61. Gray S, Foti S, Schwartz J, Bachaboina L, Taylor Blake B, Coleman J, et al. Optimizing promoters for recombinant adeno-associated virus-mediated gene expression in the peripheral and central nervous system using self-complementary vectors. Hum Gene Ther. 2011;22:1143-53 pubmed publisher
  62. Barrick C, Lenhart P, Dackor R, Nagle E, Caron K. Loss of receptor activity-modifying protein 3 exacerbates cardiac hypertrophy and transition to heart failure in a sex-dependent manner. J Mol Cell Cardiol. 2012;52:165-74 pubmed publisher
    ..These phenotypes were not present in female RenTgMK:RAMP3(-/-) mice. Collectively, these data demonstrate a sex-dependant, cardioprotective role of RAMP3 in the setting of chronic hypertension. ..
  63. Liu W, Monahan K, Pfefferle A, Shimamura T, Sorrentino J, Chan K, et al. LKB1/STK11 inactivation leads to expansion of a prometastatic tumor subpopulation in melanoma. Cancer Cell. 2012;21:751-64 pubmed publisher
    ..These results suggest that LKB1 inactivation in the context of RAS activation facilitates metastasis by inducing an SFK-dependent expansion of a prometastatic, CD24(+) tumor subpopulation. ..
  64. Sims R, van der Lee S, Naj A, Bellenguez C, Badarinarayan N, Jakobsdottir J, et al. Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease. Nat Genet. 2017;49:1373-1384 pubmed publisher
    ..These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to the development of Alzheimer's disease. ..
  65. Arnett H, Wang Y, Matsushima G, Suzuki K, Ting J. Functional genomic analysis of remyelination reveals importance of inflammation in oligodendrocyte regeneration. J Neurosci. 2003;23:9824-32 pubmed
    ..These data point to the induction of MHC-II by TNFalpha as an important regulatory event in remyelination and emphasize the active inflammatory response in regeneration after pathology in the brain. ..
  66. Bradford B, Lock E, Kosyk O, Kim S, Uehara T, Harbourt D, et al. Interstrain differences in the liver effects of trichloroethylene in a multistrain panel of inbred mice. Toxicol Sci. 2011;120:206-17 pubmed publisher
    ..These studies provide better understanding of the mechanisms of TCE-induced toxicity anchored on metabolism and genotype-phenotype correlations that may define susceptibility or resistance. ..
  67. Zhou Y, Xia K, Wright F. A powerful and flexible approach to the analysis of RNA sequence count data. Bioinformatics. 2011;27:2672-8 pubmed publisher
    ..An R package containing examples and sample datasets is available at; Supplementary data are available at Bioinformatics online. ..
  68. Yu D, Thelin W, Randell S, Boucher R. Expression profiles of aquaporins in rat conjunctiva, cornea, lacrimal gland and Meibomian gland. Exp Eye Res. 2012;103:22-32 pubmed publisher
    ..Our findings provide a comprehensive platform for further investigation into the physiological or pathophysiological relevance of AQPs in ocular surface...
  69. Richards K, Motsinger Reif A, Chen H, Fedoriw Y, Fan C, Nielsen D, et al. Gene profiling of canine B-cell lymphoma reveals germinal center and postgerminal center subtypes with different survival times, modeling human DLBCL. Cancer Res. 2013;73:5029-39 pubmed publisher
    ..Collectively, these studies identify molecular similarities to hDLBCL that introduce pet dogs as a representative model of hDLBCL for future studies, including therapeutic clinical trials...
  70. Heckscher E, Long F, Layden M, Chuang C, Manning L, Richart J, et al. Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience. Development. 2014;141:2524-32 pubmed publisher
  71. Silva G, Siegel M, Mose L, Parker J, Sun W, Perou C, et al. SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling. Genome Biol. 2017;18:66 pubmed publisher
    ..SynthEx robustly identifies CNAs using sequencing data without the additional costs associated with matched normal specimens. ..
  72. Westdorp K, Sand A, Moorman N, Terhune S. Cytomegalovirus Late Protein pUL31 Alters Pre-rRNA Expression and Nuclear Organization during Infection. J Virol. 2017;91: pubmed publisher
    ..Understanding these processes will help define approaches to stimulate cellular intrinsic stress responses that are capable of inhibiting CMV infection. ..
  73. Chandrasekharan S, Qiu T, Alkharouf N, Brantley K, Mitchell J, Liu E. Characterization of mice deficient in the Src family nonreceptor tyrosine kinase Frk/rak. Mol Cell Biol. 2002;22:5235-47 pubmed
    ..Significant decreases in the circulating levels of T3 but not T4 hormone are consistent with this observation and reminiscent of euthyroid sick syndrome, a stress-associated clinical condition...
  74. Zhang J, D Ercole A. Expression of Mcl-1 in cerebellar granule neurons is regulated by IGF-I in a developmentally specific fashion. Brain Res Dev Brain Res. 2004;152:255-63 pubmed
    ..These data suggest that anti-apoptotic Mcl-1 may mediate IGF-I pro-survival actions on granule neurons during the development of cerebellar cortex. They also point out pitfalls of cDNA array analyses. ..
  75. Gilmour P, Schladweiler M, Nyska A, McGee J, Thomas R, Jaskot R, et al. Systemic imbalance of essential metals and cardiac gene expression in rats following acute pulmonary zinc exposure. J Toxicol Environ Health A. 2006;69:2011-32 pubmed
    ..Imbalance of systemic metal homeostasis as a result of pulmonary zinc exposure may underlie the cause of extrapulmonary effects. ..
  76. Hoadley K, Weigman V, Fan C, Sawyer L, He X, Troester M, et al. EGFR associated expression profiles vary with breast tumor subtype. BMC Genomics. 2007;8:258 pubmed
    ..In vivo, the EGFR-signatures were of prognostic value, were associated with tumor subtype, and were uniquely associated with the high expression of distinct EGFR-RAS-MEK pathway genes. ..
  77. Guo J, Jin J, Cooper L. Dissection of sets of genes that control the character of wnt5a-deficient mouse calvarial cells. Bone. 2008;43:961-71 pubmed publisher
    ..Its function during mesenchymal stem cell differentiation as well as cell growth was suggested by comparing the gene expression profile of calvarial cells from the Wnt5a(-/-) and wild type mice. ..
  78. Montes M, Zhang X, Berthelot L, Laplaud D, Brouard S, Jin J, et al. Oligoclonal myelin-reactive T-cell infiltrates derived from multiple sclerosis lesions are enriched in Th17 cells. Clin Immunol. 2009;130:133-44 pubmed publisher
    ..The differentially expressed genes involved in regulation of Th17 cells represent promising targets for new therapies of relapsing-remitting MS. ..
  79. Gatti D, Harrill A, Wright F, Threadgill D, Rusyn I. Replication and narrowing of gene expression quantitative trait loci using inbred mice. Mamm Genome. 2009;20:437-46 pubmed publisher
  80. Offenbacher S, Barros S, Paquette D, Winston J, Biesbrock A, Thomason R, et al. Gingival transcriptome patterns during induction and resolution of experimental gingivitis in humans. J Periodontol. 2009;80:1963-82 pubmed publisher
  81. Carey L, Winer E, Viale G, Cameron D, Gianni L. Triple-negative breast cancer: disease entity or title of convenience?. Nat Rev Clin Oncol. 2010;7:683-92 pubmed publisher
    ..Increased understanding of the genetic abnormalities involved in the pathogenesis of TNBC, BLBC and BRCA1-associated tumors is opening up new therapeutic possibilities for these hard-to-treat breast cancers. ..
  82. Sun X, Casbas Hernandez P, Bigelow C, Makowski L, Joseph Jerry D, Smith Schneider S, et al. Normal breast tissue of obese women is enriched for macrophage markers and macrophage-associated gene expression. Breast Cancer Res Treat. 2012;131:1003-12 pubmed publisher
    ..Given the role of macrophages in carcinogenesis, these findings have important implications for breast cancer etiology and progression. ..
  83. Stoll G, Pietiläinen O, Linder B, Suvisaari J, Brosi C, Hennah W, et al. Deletion of TOP3β, a component of FMRP-containing mRNPs, contributes to neurodevelopmental disorders. Nat Neurosci. 2013;16:1228-1237 pubmed publisher
    ..Our results indicate a previously unknown role for TOP3β in mRNA metabolism and suggest that it is involved in neurodevelopmental disorders. ..
  84. Ellsworth S, Rabatic B, Chen J, Zhao J, Campbell J, Wang W, et al. Principal component analysis identifies patterns of cytokine expression in non-small cell lung cancer patients undergoing definitive radiation therapy. PLoS ONE. 2017;12:e0183239 pubmed publisher
  85. 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. ..
  86. Lightfoot H, Lark A, Livasy C, Moore D, Cowan D, Dressler L, et al. Upregulation of focal adhesion kinase (FAK) expression in ductal carcinoma in situ (DCIS) is an early event in breast tumorigenesis. Breast Cancer Res Treat. 2004;88:109-16 pubmed
    ..0001) and IDC (p = 0.02). We conclude that FAK overexpression in preinvasive, DCIS tumors precedes tumor cell invasion or metastasis, suggesting that FAK may function as a survival signal and be an early event in breast tumorigenesis. ..
  87. Karoly E, Schmid J, Hunter E. Ontogeny of transcription profiles during mouse early craniofacial development. Reprod Toxicol. 2005;19:339-52 pubmed
    ..We report here that, in the absence of morphological malformations following 24 h WEC, 329 genes were differentially expressed between in vivo and in vitro developing conceptuses. ..
  88. Chen Z, Hartmann H, Wu M, Friedman E, Chen J, Pulley M, et al. Expression analysis of the AtMLO gene family encoding plant-specific seven-transmembrane domain proteins. Plant Mol Biol. 2006;60:583-97 pubmed
  89. Thorner A, Hoadley K, Parker J, Winkel S, Millikan R, Perou C. In vitro and in vivo analysis of B-Myb in basal-like breast cancer. Oncogene. 2009;28:742-51 pubmed publisher
    ..These data provide insight into the influence of B-Myb in human breast cancer, which is of potential clinical importance for determining disease risk and for guiding treatment. ..
  90. Wright T, Brannon A, Gordan J, Mikels A, Mitchell C, Chen S, et al. Ror2, a developmentally regulated kinase, promotes tumor growth potential in renal cell carcinoma. Oncogene. 2009;28:2513-23 pubmed publisher
    ..These findings suggest a novel pathway of tumor-promoting activity by Ror2 within a subset of renal carcinomas, with significant implications for unraveling the tumorigenesis of RCC. ..
  91. Ramalingam S, Daughtridge G, Johnston M, Gracz A, Magness S. Distinct levels of Sox9 expression mark colon epithelial stem cells that form colonoids in culture. Am J Physiol Gastrointest Liver Physiol. 2012;302:G10-20 pubmed publisher
    ..These data suggest a dose-dependent role for Sox9 in normal CESCs and cells comprising colon tumors. Furthermore, distinct Sox9 levels represent a new biomarker to study CESC and progenitor biology in physiological and disease states. ..
  92. Leichty A, Pfennig D, Jones C, Pfennig K. Relaxed genetic constraint is ancestral to the evolution of phenotypic plasticity. Integr Comp Biol. 2012;52:16-30 pubmed publisher
    ..Thus, relaxed genetic constraint may be a cause--not a consequence--of the evolution of phenotypic plasticity, and thereby contribute to the evolution of novel traits. ..