genes

Summary

Summary: Specific sequences of nucleotides along a molecule of DNA (or, in the case of some viruses, RNA) which represent functional units of HEREDITY. Most eukaryotic genes contain a set of coding regions (EXONS) that are spliced together in the transcript, after removal of intervening sequence (INTRONS) and are therefore labeled split genes.

Top Publications

  1. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
  2. ncbi Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations
    Michael W Pfaffl
    Physiology, FML Weihenstephan, Centre of Life and Food Science, Technical University of Munich, Germany
    Biotechnol Lett 26:509-15. 2004
  3. pmc A census of human cancer genes
    P Andrew Futreal
    Cancer Genome Project, Human Genome Analysis Group and Pfam Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Cambs, CB10 1SA, UK
    Nat Rev Cancer 4:177-83. 2004
  4. pmc Entrez Gene: gene-centered information at NCBI
    Donna Maglott
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20852, USA
    Nucleic Acids Res 39:D52-7. 2011
  5. ncbi Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
    Rainer Breitling
    Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
    FEBS Lett 573:83-92. 2004
  6. pmc McKusick's Online Mendelian Inheritance in Man (OMIM)
    Joanna Amberger
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Nucleic Acids Res 37:D793-6. 2009
  7. pmc Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Nucleic Acids Res 37:1-13. 2009
  8. pmc Mammalian microRNAs: experimental evaluation of novel and previously annotated genes
    H Rosaria Chiang
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 24:992-1009. 2010
  9. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
  10. pmc The KEGG resource for deciphering the genome
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 32:D277-80. 2004

Detail Information

Publications255 found, 100 shown here

  1. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  2. ncbi Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations
    Michael W Pfaffl
    Physiology, FML Weihenstephan, Centre of Life and Food Science, Technical University of Munich, Germany
    Biotechnol Lett 26:509-15. 2004
    ..prerequisite for internal standardisation of target gene expression data and many so called housekeeping genes with assumed stable expression can exhibit either up- or down-regulation under some experimental conditions...
  3. pmc A census of human cancer genes
    P Andrew Futreal
    Cancer Genome Project, Human Genome Analysis Group and Pfam Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Cambs, CB10 1SA, UK
    Nat Rev Cancer 4:177-83. 2004
  4. pmc Entrez Gene: gene-centered information at NCBI
    Donna Maglott
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20852, USA
    Nucleic Acids Res 39:D52-7. 2011
    ....
  5. ncbi Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
    Rainer Breitling
    Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
    FEBS Lett 573:83-92. 2004
    One of the main objectives in the analysis of microarray experiments is the identification of genes that are differentially expressed under two experimental conditions...
  6. pmc McKusick's Online Mendelian Inheritance in Man (OMIM)
    Joanna Amberger
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Nucleic Acids Res 37:D793-6. 2009
    McKusick's Online Mendelian Inheritance in Man (OMIM; http://www.ncbi.nlm.nih.gov/omim), a knowledgebase of human genes and phenotypes, was originally published as a book, Mendelian Inheritance in Man, in 1966...
  7. pmc Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Nucleic Acids Res 37:1-13. 2009
    ....
  8. pmc Mammalian microRNAs: experimental evaluation of novel and previously annotated genes
    H Rosaria Chiang
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 24:992-1009. 2010
    ..Analysis of these sequences confirmed 398 annotated miRNA genes and identified 108 novel miRNA genes...
  9. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ..less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the ..
  10. pmc The KEGG resource for deciphering the genome
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 32:D277-80. 2004
    ..been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes...
  11. pmc Origins, evolution, and phenotypic impact of new genes
    Henrik Kaessmann
    Center for Integrative Genomics, University of Lausanne, CH 1015 Lausanne, Switzerland
    Genome Res 20:1313-26. 2010
    Ever since the pre-molecular era, the birth of new genes with novel functions has been considered to be a major contributor to adaptive evolutionary innovation...
  12. pmc The human genome browser at UCSC
    W James Kent
    Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Genome Res 12:996-1006. 2002
    ..The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users...
  13. pmc The Gene Ontology (GO) database and informatics resource
    M A Harris
    GO EBI, Hinxton, UK
    Nucleic Acids Res 32:D258-61. 2004
    ..several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences...
  14. pmc BioGRID: a general repository for interaction datasets
    Chris Stark
    Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
    Nucleic Acids Res 34:D535-9. 2006
    ..User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID...
  15. pmc Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma
    Mara Compagno
    Institute for Cancer Genetics and the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA
    Nature 459:717-21. 2009
    ..Here we show that >50% of ABC-DLBCL and a smaller fraction of GCB-DLBCL carry somatic mutations in multiple genes, including negative (TNFAIP3, also called A20) and positive (CARD11, TRAF2, TRAF5, MAP3K7 (TAK1) and TNFRSF11A (..
  16. pmc WebGestalt: an integrated system for exploring gene sets in various biological contexts
    Bing Zhang
    Graduate School in Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Nucleic Acids Res 33:W741-8. 2005
    High-throughput technologies have led to the rapid generation of large-scale datasets about genes and gene products. These technologies have also shifted our research focus from 'single genes' to 'gene sets'...
  17. pmc Distinctive chromatin in human sperm packages genes for embryo development
    Saher Sue Hammoud
    Howard Hughes Medical Institute, Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
    Nature 460:473-8. 2009
    ..Furthermore, developmental promoters are generally DNA hypomethylated in sperm, but acquire methylation during differentiation. Taken together, epigenetic marking in sperm is extensive, and correlated with developmental regulators...
  18. pmc Associating genes and protein complexes with disease via network propagation
    Oron Vanunu
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 6:e1000641. 2010
    A fundamental challenge in human health is the identification of disease-causing genes. Recently, several studies have tackled this challenge via a network-based approach, motivated by the observation that genes causing the same or ..
  19. ncbi Microsatellites within genes: structure, function, and evolution
    You Chun Li
    Institute of Evolution, University of Haifa, Haifa, Israel
    Mol Biol Evol 21:991-1007. 2004
    ..more microsatellites, or simple sequence repeats (SSRs) have been found and characterized within protein-coding genes and their untranslated regions (UTRs). These data provide useful information to study possible SSR functions...
  20. ncbi The evolutionary origin of orphan genes
    Diethard Tautz
    Max Planck Institut für Evolutionsbiologie, August Thienemannstrasse 2, 24306 Plön, Germany
    Nat Rev Genet 12:692-702. 2011
    ..However, every evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood...
  21. pmc Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia
    Christopher T Johansen
    Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
    Nat Genet 42:684-7. 2010
    ..Here we show an accumulation of rare variants, or a mutation skew, in GWAS-identified genes in individuals with hypertriglyceridemia (HTG)...
  22. ncbi The sequence of the human genome
    J C Venter
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 291:1304-51. 2001
    ..for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence...
  23. pmc GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information
    Ruben Nogales-Cadenas
    Computer Architecture Department, Complutense University of Madrid, Madrid, Spain
    Nucleic Acids Res 37:W317-22. 2009
    ..In addition, GeneCodis can now be accessed through a public SOAP web services interface, enabling users to perform analysis from their own scripts and workflows. The application is freely available at http://genecodis.dacya.ucm.es...
  24. ncbi Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes
    Anne Helmrich
    Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Universite de Strasbourg, BP 10142 67404 Illkirch Cedex, France
    Mol Cell 44:966-77. 2011
    We show that the time required to transcribe human genes larger than 800 kb spans more than one complete cell cycle, while their transcription speed equals that of smaller genes...
  25. pmc The Comparative Toxicogenomics Database: update 2011
    Allan Peter Davis
    Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
    Nucleic Acids Res 39:D1067-72. 2011
    ..many features, statistical analyses and analytical tools, including GeneComps and ChemComps (to find comparable genes and chemicals that share toxicogenomic profiles), enriched Gene Ontology terms associated with chemicals, ..
  26. pmc GENCODE: producing a reference annotation for ENCODE
    Jennifer Harrow
    Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 7:S4.1-9. 2006
    The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions...
  27. ncbi More than just orphans: are taxonomically-restricted genes important in evolution?
    Konstantin Khalturin
    Zoological Institute, Christian Albrechts University Kiel, Olshausenstrasse 40, 24098 Kiel, Germany
    Trends Genet 25:404-13. 2009
    Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species...
  28. ncbi Human DNA repair genes
    R D Wood
    Imperial Cancer Research Fund, Clare Hall Laboratories, Blanche Lane, South Mimms, Herts EN6 3LD, UK
    Science 291:1284-9. 2001
    ..Toxic and mutagenic consequences are minimized by distinct pathways of repair, and 130 known human DNA repair genes are described here...
  29. pmc Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer
    Andrew E Teschendorff
    University College London, London WC1E 6BT, UK
    Genome Res 20:440-6. 2010
    Polycomb group proteins (PCGs) are involved in repression of genes that are required for stem cell differentiation...
  30. pmc Current tools for the identification of miRNA genes and their targets
    N D Mendes
    Equipe BAOBAB, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, CNRS, Univ Lyon 1, 43 Bd du 11 Nov 1918, 69622, Villeurbanne Cedex, France
    Nucleic Acids Res 37:2419-33. 2009
    ..The expansion of our catalogue of miRNA genes and the identification of the genes they regulate owe much to the development of sophisticated computational tools ..
  31. pmc Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    Ada Hamosh
    Nucleic Acids Res 33:D514-7. 2005
    Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support human genetics research and education and the practice of clinical genetics...
  32. pmc FragGeneScan: predicting genes in short and error-prone reads
    Mina Rho
    School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA
    Nucleic Acids Res 38:e191. 2010
    ..e. the metagenome). Identification of genes directly from short reads has become an important yet challenging problem in annotating metagenomes, since the ..
  33. pmc The power of protein interaction networks for associating genes with diseases
    Saket Navlakha
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies and Department of Computer Science, University of Maryland College Park, College Park, MD 20742, USA
    Bioinformatics 26:1057-63. 2010
    Understanding the association between genetic diseases and their causal genes is an important problem concerning human health...
  34. pmc Forkhead box M1 regulates the transcriptional network of genes essential for mitotic progression and genes encoding the SCF (Skp2-Cks1) ubiquitin ligase
    I Ching Wang
    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, College of Medicine, 60607 7170, USA
    Mol Cell Biol 25:10875-94. 2005
    ..and expression assays, we show that FoxM1 is essential for transcription of the mitotic regulatory genes Cdc25B, Aurora B kinase, survivin, centromere protein A (CENPA), and CENPB...
  35. pmc Recent de novo origin of human protein-coding genes
    David G Knowles
    Smurfit Institute of Genetics, University of Dublin, Trinity College, Ireland
    Genome Res 19:1752-9. 2009
    The origin of new genes is extremely important to evolutionary innovation. Most new genes arise from existing genes through duplication or recombination...
  36. ncbi Leber congenital amaurosis: genes, proteins and disease mechanisms
    Anneke I den Hollander
    Department of Human Genetics and Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P O Box 9101, 6500 HB Nijmegen, The Netherlands
    Prog Retin Eye Res 27:391-419. 2008
    ..Linkage analysis, homozygosity mapping and candidate gene analysis facilitated the identification of 14 genes mutated in patients with LCA and juvenile retinal degeneration, which together explain approximately 70% of the ..
  37. pmc AUGUSTUS: a web server for gene finding in eukaryotes
    Mario Stanke
    University of Gottingen, Institut fur Mikrobiologie und Genetik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 32:W309-12. 2004
    ..The advantage of our program becomes apparent especially for larger input sequences containing more than one gene. The server is available at http://augustus.gobics.de...
  38. pmc Identifying biological themes within lists of genes with EASE
    Douglas A Hosack
    Laboratory of Immunopathogenesis and Bioinformatics, PO Box B, SAIC Frederick, Inc, Frederick, MD 21702, USA
    Genome Biol 4:R70. 2003
    ..gene lists and are robust to varying methods of normalization, intensity calculation and statistical selection of genes. EASE is a powerful tool for rapidly converting the results of functional genomics studies from 'genes' to 'themes'...
  39. ncbi Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
    Olivier Jaillon
    UMR 8030 Genoscope, CNRS and Université d Evry, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    Nature 431:946-57. 2004
    ..Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish...
  40. pmc Gene finding in novel genomes
    Ian Korf
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    BMC Bioinformatics 5:59. 2004
    ..Computational gene prediction continues to be an important problem, especially for genomes with little experimental data...
  41. ncbi Inconsistency of phylogenetic estimates from concatenated data under coalescence
    Laura Salter Kubatko
    Department of Statistics and Evolution, The Ohio State University, Columbus, Ohio 43210, USA
    Syst Biol 56:17-24. 2007
    ..phylogenetic inference, the analysis of such data has largely relied on inference methods designed for single genes. One of the common approaches to analyzing data from multiple genes is concatenation of the individual gene data ..
  42. ncbi A guide to web tools to prioritize candidate genes
    Leon Charles Tranchevent
    Katholieke Universiteit Leuven, Belgium
    Brief Bioinform 12:22-32. 2011
    Finding the most promising genes among large lists of candidate genes has been defined as the gene prioritization problem...
  43. ncbi Functional classification of interferon-stimulated genes identified using microarrays
    M J de Veer
    Department of Cancer Biology, Lerner Research Institute, Cleveland, Ohio, USA
    J Leukoc Biol 69:912-20. 2001
    Interferons (IFNs) are a family of multifunctional cytokines that activate transcription of subsets of genes. The gene products induced by IFNs are responsible for IFN antiviral, antiproliferative, and immunomodulatory properties...
  44. pmc Genes and social behavior
    Gene E Robinson
    Department of Entomology, University of Illinois at Urbana Champaign, 505 South Goodwin Avenue, Urbana, IL 61801, USA
    Science 322:896-900. 2008
    What genes and regulatory sequences contribute to the organization and functioning of neural circuits and molecular pathways in the brain that support social behavior? How does social experience interact with information in the genome to ..
  45. ncbi Molecular mechanisms of epistasis within and between genes
    Ben Lehner
    European Molecular Biology Laboratory Centre for Genomic Regulation EMBL CRG Systems Biology, the Catalan Institute of Research and Advanced Studies ICREA, Centre for Genomic Regulation and the Pompeu Fabra University UPF, C Dr Aiguader 88, Barcelona 08003, Spain
    Trends Genet 27:323-31. 2011
    ..A more complete understanding of epistasis will be vital for making accurate predictions about the phenotypes of individuals...
  46. ncbi Two genes encode distinct glutamate decarboxylases
    M G Erlander
    Neuroscience Program, University of California Los Angeles 90024
    Neuron 7:91-100. 1991
    ..These forms, GAD65 and GAD67, derive from two genes. The distinctive properties of the two GADs provide a substrate for understanding not only the multiple roles of ..
  47. pmc Accurately assessing the risk of schizophrenia conferred by rare copy-number variation affecting genes with brain function
    Soumya Raychaudhuri
    Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
    PLoS Genet 6:e1001097. 2010
    ..One hypothesis is that CNV events cause disease by affecting genes with specific brain functions...
  48. pmc Detecting gene-gene interactions that underlie human diseases
    Heather J Cordell
    Institute of Human Genetics, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
    Nat Rev Genet 10:392-404. 2009
    ..I also discuss the difficulties in determining the biological relevance of statistical interactions...
  49. pmc A family of potassium channel genes related to eag in Drosophila and mammals
    J W Warmke
    Laboratory of Genetics, University of Wisconsin, Madison 53706
    Proc Natl Acad Sci U S A 91:3438-42. 1994
    We have identified a conserved family of genes related to Drosophila eag, which encodes a distinct type of voltage-activated K+ channel...
  50. pmc The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 106:7273-80. 2009
    The evolutionary rates of protein-coding genes in an organism span, approximately, 3 orders of magnitude and show a universal, approximately log-normal distribution in a broad variety of species from prokaryotes to mammals...
  51. pmc Transposases are the most abundant, most ubiquitous genes in nature
    Ramy K Aziz
    Computation Institute, University of Chicago, Chicago, IL 60637, USA
    Nucleic Acids Res 38:4207-17. 2010
    b>Genes, like organisms, struggle for existence, and the most successful genes persist and widely disseminate in nature...
  52. pmc Circadian genes, rhythms and the biology of mood disorders
    Colleen A McClung
    Department of Psychiatry and Center for Basic Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390 9070, USA
    Pharmacol Ther 114:222-32. 2007
    ..Recent genetic, molecular and behavioral studies implicate individual genes that make up the clock in mood regulation...
  53. pmc Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes
    Beate Neumann
    MitoCheck Project Group, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nature 464:721-7. 2010
    Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life...
  54. pmc Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels
    Milana Frenkel-Morgenstern
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 8:572. 2012
    ..When we compared the codon usage of cell cycle-regulated genes with that of other genes, we discovered that there is a significant preference for non-optimal codons...
  55. pmc A systems biology approach reveals that tissue tropism to West Nile virus is regulated by antiviral genes and innate immune cellular processes
    Mehul S Suthar
    Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
    PLoS Pathog 9:e1003168. 2013
    ..the loss of expression of several key components within the natural killer (NK) cell signaling pathway, including genes associated with NK cell activation, inflammatory cytokine production, and NK cell receptor signaling...
  56. ncbi The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes
    Helen Skaletsky
    Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 423:825-37. 2003
    ..These classes contain all 156 known transcription units, which include 78 protein-coding genes that collectively encode 27 distinct proteins. The X-transposed sequences exhibit 99% identity to the X chromosome...
  57. pmc De novo origin of human protein-coding genes
    Dong Dong Wu
    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
    PLoS Genet 7:e1002379. 2011
    ..Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee...
  58. pmc The GOA database in 2009--an integrated Gene Ontology Annotation resource
    Daniel Barrell
    Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D396-403. 2009
    ..ebi.ac.uk/QuickGO), which allows users to precisely tailor their annotation set...
  59. pmc Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks
    Allan Peter Davis
    Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
    Nucleic Acids Res 37:D786-92. 2009
    ..Over 116,000 interactions between 3900 chemicals and 13,300 genes have been curated from 270 species, and 5900 gene-disease and 2500 chemical-disease direct relationships have been ..
  60. pmc Network-based global inference of human disease genes
    Xuebing Wu
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST Department of Automation, Tsinghua University, Beijing, China
    Mol Syst Biol 4:189. 2008
    ..On the basis of the assumption that phenotypically similar diseases are caused by functionally related genes, we propose a computational framework that integrates human protein-protein interactions, disease phenotype ..
  61. pmc Overview of BioCreative II gene normalization
    Alexander A Morgan
    Biomedical Informatics, Stanford University, Stanford, CA, 94305, USA
    Genome Biol 9:S3. 2008
    The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature...
  62. pmc Automatic annotation of eukaryotic genes, pseudogenes and promoters
    Victor Solovyev
    Department of Computer Science, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
    Genome Biol 7:S10.1-12. 2006
    ..We have used Softberry gene finding software to predict genes, pseudogenes and promoters in 44 selected ENCODE sequences representing approximately 1% (30 Mb) of the human ..
  63. ncbi Additional gene ontology structure for improved biological reasoning
    Simen Myhre
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology NO 7489 Trondheim, Norway
    Bioinformatics 22:2020-7. 2006
    ..Our aim was to connect the three subontologies to enable GO to cover more biological knowledge, enable a more consistent use of GO and provide new opportunities for biological reasoning...
  64. ncbi Bayesian estimation of concordance among gene trees
    Cecile Ane
    Department of Statistics, University of Wisconsin, USA
    Mol Biol Evol 24:412-26. 2007
    ..Although various biological processes may cause different genes to have different genealogical histories (and hence different tree topologies), we also may expect that the number ..
  65. pmc Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes
    Xifeng Wu
    Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, 77030, USA
    Am J Hum Genet 78:464-79. 2006
    ..the data suggest that individuals with a higher number of genetic variations in DNA-repair and cell-cycle-control genes are at an increased risk for bladder cancer, confirming the importance of taking a multigenic pathway-based ..
  66. ncbi Endogenous retroviral LTRs as promoters for human genes: a critical assessment
    Carla J Cohen
    Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada V5Z1L3
    Gene 448:105-14. 2009
    ..TEs) in gene regulation and, indeed, laboratory investigations have confirmed many specific examples of mammalian genes regulated by promoters donated by endogenous retroviruses (ERVs) or other TEs...
  67. ncbi The semaphorin genes encode a family of transmembrane and secreted growth cone guidance molecules
    A L Kolodkin
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley 94720
    Cell 75:1389-99. 1993
    ..We report here on the cloning and characterization of two sema genes in Drosophila, one in human, and the identification of two related viral sequences, all of which encode proteins ..
  68. ncbi Obese and diabetes: two mutant genes causing diabetes-obesity syndromes in mice
    D L Coleman
    Diabetologia 14:141-8. 1978
  69. pmc Overview of BioCreative II gene mention recognition
    Larry Smith
    National Center for Biotechnology Information, Bethesda, Maryland, USA
    Genome Biol 9:S2. 2008
    ..We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions...
  70. pmc Performance of genotype imputation for rare variants identified in exons and flanking regions of genes
    Li Li
    Genetics, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
    PLoS ONE 6:e24945. 2011
    ..We utilized 8865 human samples with high depth resequencing data for the exons and flanking regions of 202 genes and Genome-Wide Association Study (GWAS) data to characterize the performance of genotype imputation for rare ..
  71. pmc Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species
    John J Wiens
    Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794 5245, USA
    Biol Lett 8:1043-6. 2012
    ..phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time...
  72. ncbi Validation of housekeeping genes for normalizing RNA expression in real-time PCR
    Keertan Dheda
    Royal Free Medical School, London, UK
    Biotechniques 37:112-4, 116, 118-9. 2004
    Analysis of RNA expression using techniques like real-time PCR has traditionally used reference or housekeeping genes to control for error between samples...
  73. pmc ENDEAVOUR update: a web resource for gene prioritization in multiple species
    Leon Charles Tranchevent
    Department of Electrical Engineering ESAT SCD, Katholieke Universiteit Leuven, Belgium
    Nucleic Acids Res 36:W377-84. 2008
    ..and open to all users and there is no login requirement) is a web resource for the prioritization of candidate genes. Using a training set of genes known to be involved in a biological process of interest, our approach consists of (..
  74. ncbi Ultraconserved elements in the human genome
    Gill Bejerano
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Science 304:1321-5. 2004
    ..These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and ..
  75. pmc Selection of stable reference genes for quantitative rt-PCR comparisons of mouse embryonic and extra-embryonic stem cells
    Kylee J Veazey
    College of Veterinary Medicine and Biomedical Sciences, Texas A and M University, College Station, Texas, United States of America
    PLoS ONE 6:e27592. 2011
    ..However, careful, empirical selection of appropriate reference genes is essential to accurately measuring transcriptional differences...
  76. pmc The effect of sequencing errors on metagenomic gene prediction
    Katharina J Hoff
    Department of Bioinformatics, Institute of Microbiology and Genetics, Georg August University Gottingen, Gottingen, Germany
    BMC Genomics 10:520. 2009
    ..Their gene prediction accuracy was mostly measured on error free DNA fragments...
  77. pmc Normalization of oligonucleotide arrays based on the least-variant set of genes
    Stefano Calza
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    BMC Bioinformatics 9:140. 2008
    ..spike-in experiment all existing normalization methods fail because of an imbalance between up- and down-regulated genes. This means it is still important to develop a normalization method that is robust against violation of the ..
  78. pmc GeneTUKit: a software for document-level gene normalization
    Minlie Huang
    Department of Computer Science and Technology, Tsinghua University, Beijing, China
    Bioinformatics 27:1032-3. 2011
    ..Manual annotation for this task is cost expensive, time consuming and labor intensive. Therefore, providing assistive tools to facilitate the task is of high value...
  79. ncbi Genomic footprints of a cryptic plastid endosymbiosis in diatoms
    Ahmed Moustafa
    Interdisciplinary Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
    Science 324:1724-6. 2009
    ..However, recent analyses have turned up a handful of nuclear genes in chromalveolates that are of green algal derivation...
  80. pmc Coexpression analysis of human genes across many microarray data sets
    Homin K Lee
    Columbia Genome Center, Columbia University, New York, New York 10032, USA
    Genome Res 14:1085-94. 2004
    ..We sought pairs of genes that were reliably coexpressed (based on the correlation of their expression profiles) in multiple data sets, ..
  81. ncbi Association of genetic risk variants with expression of proximal genes identifies novel susceptibility genes for cardiovascular disease
    Lasse Folkersen
    Atherosclerosis Research Unit, Experimental Cardiovascular Research Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
    Circ Cardiovasc Genet 3:365-73. 2010
    ..b>Genes in close proximity to these risk-SNPs are often thought to be pathogenetically important based on their location ..
  82. ncbi The genetics of addictions: uncovering the genes
    David Goldman
    Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, Rockville, Maryland 20852, USA
    Nat Rev Genet 6:521-32. 2005
    ..heritable, which is paradoxical because these disorders require use; a choice that is itself modulated by both genes and environment...
  83. ncbi Inter-species normalization of gene mentions with GNAT
    Jörg Hakenberg
    Department of Computer Science and Engineering, Arizona State University, Tempe, AZ 85287, USA
    Bioinformatics 24:i126-132. 2008
    ..Normalization helps to link objects of potential interest, such as genes, to detailed information not contained in a publication; it is also key for integrating different knowledge ..
  84. ncbi Selection of reference genes for gene expression studies in rat oligodendrocytes using quantitative real time PCR
    Katherine Nelissen
    Laboratory of Cell Physiology, Biomedical Research Institute, Hasselt University and Transnational University Limburg, Agoralaan Gebouw C, B 3590 Diepenbeek, Belgium
    J Neurosci Methods 187:78-83. 2010
    ..Normalization with multiple reference genes is becoming the standard, although the most suitable reference genes depend on the applied treatment as well as ..
  85. pmc Genes affecting the regulation of SUC2 gene expression by glucose repression in Saccharomyces cerevisiae
    L Neigeborn
    Genetics 108:845-58. 1984
    ..These findings suggest roles for the SNF1 through SNF6 and SSN6 genes in the regulation of SUC2 gene expression by glucose repression.
  86. ncbi Cholesterol-related genes in Alzheimer's disease
    M Axel Wollmer
    Psychiatric University Clinics, University of Basel, 4025 Basel, Switzerland
    Biochim Biophys Acta 1801:762-73. 2010
    ..Against this background several other genes with a role in cholesterol metabolism have been investigated for association with AD...
  87. pmc Network properties of human disease genes with pleiotropic effects
    Sreenivas Chavali
    The Unit for Clinical Systems Biology, University of Gothenburg, Medicinaregatan 5A, Gothenburg SE405 30, Sweden
    BMC Syst Biol 4:78. 2010
    ..Here, we hypothesized that the ability of human disease genes to cause pleiotropic effects would be associated with their network properties.
  88. pmc Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
    Nat Struct Mol Biol 17:629-34. 2010
    ..Despite detailed understanding of protein-coding gene expression, the transcription of noncoding RNA genes by RNA polymerase III (Pol III) is less well characterized...
  89. pmc Linking genes to literature: text mining, information extraction, and retrieval applications for biology
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish Nacional Cancer Research Centre CNIO, Madrid, Spain
    Genome Biol 9:S8. 2008
    ..Additional descriptions of some of the systems discussed here are available on the internet http://zope.bioinfo.cnio.es/bionlp_tools/...
  90. pmc PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning
    Yuko Yoshida
    Bioinformatics and Systems Engineering Division, RIKEN 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 37:W147-52. 2009
    PosMed (http://omicspace.riken.jp/) prioritizes candidate genes for positional cloning by employing our original database search engine GRASE, which uses an inferential process similar to an artificial neural network comprising ..
  91. pmc RNA dust: where are the genes?
    Piero Carninci
    Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    DNA Res 17:51-9. 2010
    ..However, in contrast with this paucity of protein coding 'genes', there is an enormous complexity in transcription and the protein coding mRNAs contribute to a very small ..
  92. pmc Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph
    Adam J Richards
    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
    Bioinformatics 26:i79-87. 2010
    ..Instead of testing for significance of individual terms, this study is concerned with the task of assessing the global functional coherence of gene sets, for which novel metrics and statistical methods have been devised...
  93. ncbi Time to give up on a single explanation for autism
    Francesca Happe
    Francesca Happé, Angelica Ronald and Robert Plomin are at the Institute of Psychiatry, Kings College London, De Crispigny Park, London SE5 8AF, UK
    Nat Neurosci 9:1218-20. 2006
    ..Twin data suggest largely nonoverlapping genes acting on each of these traits...
  94. pmc Bioinformatic identification and characterization of human endothelial cell-restricted genes
    Manoj Bhasin
    Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
    BMC Genomics 11:342. 2010
    In this study, we used a systematic bioinformatics analysis approach to elucidate genes that exhibit an endothelial cell (EC) restricted expression pattern, and began to define their regulation, tissue distribution, and potential ..
  95. ncbi Expression of the zebrafish CD133/prominin1 genes in cellular proliferation zones in the embryonic central nervous system and sensory organs
    Maura McGrail
    Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
    Dev Dyn 239:1849-57. 2010
    ..The expression patterns of the zebrafish prominin1a and b genes were analyzed during embryogenesis using whole mount in situ hybridization...
  96. pmc Natural products version 2.0: connecting genes to molecules
    Christopher T Walsh
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
    J Am Chem Soc 132:2469-93. 2010
    ..In this Perspective, we explore how connecting Nature's small molecules to the genes that encode them has sparked a renaissance in natural product research, focusing primarily on the biosynthesis of ..
  97. pmc A high-density association screen of 155 ion transport genes for involvement with common migraine
    Dale R Nyholt
    Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, PO Royal Brisbane Hospital, Brisbane4029, Queensland, Australia
    Hum Mol Genet 17:3318-31. 2008
    ..between monogenic Familial Hemiplegic Migraine (FHM) and common migraine subtypes, and the fact that all three FHM genes are involved in the transport of ions, suggest that ion transport genes may underlie susceptibility to common ..
  98. pmc Annotating genes and genomes with DNA sequences extracted from biomedical articles
    Maximilian Haeussler
    Faculty of Life Sciences, University of Manchester, Manchester, UK
    Bioinformatics 27:980-6. 2011
    ..Existing text-mining approaches focus on finding gene names or identifiers in English text. These are often not unique and do not identify the exact genomic location of a study...
  99. pmc Functional genomic identification of genes required for male gonadal differentiation in Caenorhabditis elegans
    Andrea K Kalis
    Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Genetics 185:523-35. 2010
    ..To identify genes involved in this process, we performed a genome-wide RNAi screen using sex-specifically expressed gonadal GFP ..

Research Grants73

  1. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2013
    ..There are no effective treatments for achromatopsia. - Four genes currently are known to cause achromatopsia...
  2. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2012
    ..There are no effective treatments for achromatopsia. - Four genes currently are known to cause achromatopsia...
  3. Discovery metabolite profiling of the prolyl peptidases
    Alan Saghatelian; Fiscal Year: 2009
    ..Researchers have recently developed a number of methods to identify the genes, proteins, and metabolites associated with disease...
  4. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..These tools will be made publicly available, including a friendly graphical user interface and visualization. ..
  5. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  6. Personalized Clinical Diagnostics and Beyond: Integrated Ring Resonator Arrays
    Ryan Bailey; Fiscal Year: 2009
    ..This technology promises to broadly impact the landscape of the biomedical sciences, both meeting the clinical diagnostic challenges of today and pioneering the paradigm-shifting discoveries of tomorrow. ..
  7. NIH Director's Pioneer Award
    Junying Yuan; Fiscal Year: 2009
    ..No Abstract provided ..
  8. NIH Director's Pioneer Award
    ERICH JARVIS; Fiscal Year: 2009
    ..Repairing the pathway in vocal learners, when damaged, would have profound impact for correcting neurological disorders of speech. ..
  9. High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributi
    Sonia Dua; Fiscal Year: 2013
    ..j. In special cases, assist Investigators in identifying SNPs in regions or in genes of interest in order to put together a custom SNP genotyping panel for use on their samples. k...
  10. Transcription factors regulating sensory gene expression and pain pathways
    Eric E Turner; Fiscal Year: 2011
    ..sensory axon growth, fail to develop proprioceptors, and have a profound defect in the expression of multiple genes related to pain pathways...
  11. Mice Humanized with Hepatocytes and iPS Cells from Patients with Metabolic Diseas
    Stephen C Strom; Fiscal Year: 2010
    ..Liver-based metabolic disease can result from mutations in genes in these critical pathways...
  12. Optimization of DNA Repair by Abh8
    Lauren Endres; Fiscal Year: 2013
    ..If these mutations disrupt the function of key regulatory genes involved in cell growth and homeostasis, premature aging or cancer can occur...
  13. Regulation of HSV-1 Gene Expression and Replication by Nuclear Hormone Receptors
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2013
    ..demonstrate that the liganded receptor (T3/TR, the hormone-receptor complex) controls the expression of HSV-1 key genes and replication...
  14. Role of the Y-Located TSPY Gene in Human Oncogenesis
    Yun Fai Chris Lau; Fiscal Year: 2013
    ..that TSPY interacts with androgen receptor (AR) and exacerbates its ligand-dependent transactivation of responsive genes while TSPX interacts but represses AR functions...
  15. The Primate Corpus Luteum: Functional Regression and Cardiovascular Impacts
    Randy L Bogan; Fiscal Year: 2012
    ..Direct binding of each LXR isoform to promoter regions of known LXR target genes will be determined during spontaneous luteolysis in vivo, and DNA microarray assays will be performed on luteal ..
  16. Identification of Genetic and Epigenetic Alterations in Spondyloarthritis
    Tibor T Glant; Fiscal Year: 2013
    ..However, the presence of HLA-B27 alone is not sufficient for disease development. A few non-MHC candidate genes have also been implicated in AS...
  17. Brain Activation responses in adolescents with genetic predisposition to obesity
    Susan Carnell; Fiscal Year: 2011
    ..on the K99 to investigate neural pathways associated with genetic obesity risk which could mediate the effect of genes on appetite and weight...
  18. H1R Signaling and Immune Deviation in EAE
    Cory Teuscher; Fiscal Year: 2013
    ..that Bphse and Shs reside within a functional linkage disequilibrium (LD)-domain linked to Hrh1 and may contain genes related to H1R folding, trafficking, or signaling...
  19. Pharmacogenetics of obesity and endocannabinergic modulation (POEM)
    Russell A Wilke; Fiscal Year: 2012
    ..from the International Human Haplotype Map (HapMap), we have begun genotyping three critical eCB/CB1 signaling genes, and testing for association between variation in these candidate genes and obesity and obesity-related metabolic ..
  20. Physiological role of PRDM16 in brown fat development and energy balance
    Patrick Seale; Fiscal Year: 2011
    ..Notably, BAT from c/EBPp-deficient fetal mice displayed dramatically reduced expression of thermogenic genes and elevated levels of muscle-specific transcripts analogous to what was observed in P/?OM) 6-deficient tissue...
  21. Ligand Directed Transdermal siRNA Delivery to Improve Wound Healing
    David M Evans; Fiscal Year: 2012
    ..a target gene expression, we have previously demonstrated that a multi-targeted siRNA cocktail targeting these genes can accelerate wound repair in acute wounds when administered in Histidine Lysine Polymer (HKP) - a branched ..
  22. Prevention of Acute Lung Injury by IL-6 activated STAT3
    Ana Moran; Fiscal Year: 2010
    ..Microarray analysis in rat lungs showed that T/HS increased the expression of genes in the ontologic category of cell death and altered 70% of known apoptosis-related genes...
  23. Principles of Therapy in Cerebellar Disease: Explorations in Ion Channel Mutants
    JOHN SAMUEL STAHL; Fiscal Year: 2013
    ..to genetic errors, other degenerative processes whose causes have yet to be discovered, and inherited mutations of genes that ultimately control neuronal activity patterns...
  24. Air Pollution on Adiposity and Vascular Dysfunction: White or Brown Matters?
    Qinghua Sun; Fiscal Year: 2013
    ..and assessed for indices for ER stress and apoptosis, mitochondria content, expression of key-mitochondrial genes and mitochondrial oxygen consumption (function)...
  25. A Hybrid PARP Inhibitor and Redox Catalyst for Lung Transplantation
    GARRY JOHN SOUTHAN; Fiscal Year: 2012
    ..PARP activation also induces a widespread expresion of pro-inflammatory genes that contribute to vascular permeability, lung edema, neutrophil infiltration, pulmonary shunt, and respiratory ..
  26. Role of SAMe on UBC9 and sumolyation in liver cancer and alcoholic liver injury
    Maria Lauda Tomasi; Fiscal Year: 2012
    ..In mammals two MAT genes, MAT1A and MAT2A, encode for two catalytic subunits of MAT, 11 and 12, respectively...
  27. Structure and function of urea transporters
    Ming Zhou; Fiscal Year: 2013
    ..Mice with one of the UT genes knocked out show reduced ability to absorb water, and genetic variations of human UT are directly linked to ..
  28. Discovery of Small Molecule MBT Domain Antagonists
    STEPHEN VERNON FRYE; Fiscal Year: 2010
    ..organisms have evolved elaborate mechanisms to enable differential and cell-type specific expression of genes. Epigenetics refers to these heritable changes in how the genome is accessed in different cell-types and during ..
  29. ROLE OF Rac AND REACTIVE OXYGEN SPECIES IN KAPOSI'S SARCOMA VIRAL ONCOGENESIS
    Enrique A Mesri; Fiscal Year: 2013
    ..Understanding the role of viral and cellular genes leading to KS carcinogenesis is paramount to developing rationally designed therapies for KS...
  30. A Redox-active PARP Inhibitor for Lung Transplantation
    ANDREW LURIE SALZMAN; Fiscal Year: 2012
    ..PARP-1 activation also induces a widespread expression of pro-inflammatory genes that contribute to vascular permeability, lung edema, neutrophil infiltration, pulmonary shunt, and respiratory ..
  31. Neurobehavioral Correlates of Familial/genetic obesity risk in adolescents
    Susan Carnell; Fiscal Year: 2013
    ..on the K99 to investigate neural pathways associated with genetic obesity risk which could mediate the effect of genes on appetite and weight...
  32. Regulation of ER stress-induced cell death
    Randal J Kaufman; Fiscal Year: 2013
    ..In addition, our preliminary unpublished findings show that CHOP does not significantly bind promoter elements of genes that encode apoptotic functions, but rather binds to promoters of genes that encode functions in protein synthesis...
  33. Inhibition of human neutrophil function by Francisella tularensis
    Lee Ann H Allen; Fiscal Year: 2012
    ..both targeted allelic replacement strategies and transposon mutant library screening to begin to define Ft genes required for virulence in this system...
  34. Genetics and Haloperidol Response
    Robert J Hitzemann; Fiscal Year: 2012
    ..to a high resolution (1-2 megabase pairs [Mbp]), to confirm the QTL haplotype structure and to determine which genes within the intervals have non-synonymous coding SNPs that match the predicted QTL haplotypes...
  35. Med1 in Liver Metabolism, Regeneration and Cancer
    Janardan K Reddy; Fiscal Year: 2013
    ..The Mediator complex is necessary for the expression of RNA polymerase II (PoI II)-transcribed genes. Studies with conditional Med1 null mutation have established that Med1 is required for fatty acid oxidation and ..
  36. MOLECULAR BASIS OF INSULIN RESISTANCE
    Maureen J Charron; Fiscal Year: 2010
    ..Several models with alterations in the intrauterine (IU) milieu display pathologic alterations in genes of hepatic glucose and lipid utilization (including PPAR? and G6Pase) often associated with T2DM...
  37. Functional Genomics of the Mitochondrial Proteome
    Dennis R Winge; Fiscal Year: 2011
    ..phenotypes in yeast, and use metabolomic profiling to identify enzymatic pathways that are regulated by these genes. Aim 3 will define the molecular mechanisms by which these OXPHOS assembly proteins regulate mitochondrial ..
  38. Translational Machinery in Stress Signaling and Tumor Suppression
    THOMAS J contact BEGLEY; Fiscal Year: 2010
    ..b>Genes for key translation, DNA damage and ER stress proteins have an over-representation of these codons...
  39. Targeting Inflammation for the Amelioration of Cisplatin-Hearing Loss
    Vickram Ramkumar; Fiscal Year: 2011
    ..Knockdown of STAT1 reduced the expression of inflammatory genes (such as TNF-a) and protected against cisplatin-induced hearing loss...
  40. IMMUNOGENETICS OF COLLAGEN INDUCED ARTHRITIS IN MICE
    Chella David; Fiscal Year: 2009
    ..The proposed experiments will test several new, original and innovative theories on the role of MHC genes in predisposition, onset, progression, severity and modulation in arthritis...
  41. Role of IKK in NSCLC: Modulation of SMRT and NF-kappaB
    Marty W Mayo; Fiscal Year: 2012
    ..NF-?B is a transcription factor that plays a key role in the activation of genes involved in cancer initiation and progression...
  42. Group A Streptococcus responses to oxidative stress
    Ioannis Gryllos; Fiscal Year: 2010
    ..To date, however, the GAS genes regulated in response to oxidative stress, including those regulated by PerR, have not been defined...
  43. GENETIC ANALYSIS OF POLARITY
    RUTH M STEWARD; Fiscal Year: 2010
    Abstract: The developmental mechanisms of human and Drosophila blood systems show remarkable parallels. Most genes essential for the formation and maturation of Drosophila hemocytes are conserved in humans, and the majority is associated ..
  44. Genistein, microRNAs and kidney cancer
    Rajvir Dahiya; Fiscal Year: 2013
    ..Second genistein induced tumor suppressor miRNAs can activate the transcription of tumor suppressor genes by binding to the 5'upstream region of the gene or activate translation by binding to the 5'untranslated ..
  45. Role and Regulation of INrf2
    ANIL KUMAR JAISWAL; Fiscal Year: 2013
    ..response to antioxidant and other stressors and translocates into the nucleus leading to activation of a myriad of genes that protect cells against stress and neoplasia...
  46. Remodeling Neuronal Chromatin in Mouse Models for Depression
    Schahram Akbarian; Fiscal Year: 2013
    ..in the genome were highly restricted overall, while enriched at several loci encoding glutamate receptor genes. This resulted in decreased levels of the NMDA receptor subunit Grin2b (NR2B) in prefrontal cortex and hippocampus...
  47. BIOCHEMISTRY OF PRE-MRNA SPLICING
    Adrian R Krainer; Fiscal Year: 2010
    ..Many genes express multiple mRNA and protein isoforms by alternative splicing of their primary transcripts...
  48. Tat and CDK9 on gene expression alterations coupled to HIV-1 Associated Dementia
    Xavier Grana; Fiscal Year: 2010
    ..forms Positive Transcription Elongation Factors (P-TEFb) thought to be required for the expression of cellular genes. We have investigated the effect of limiting CDK9 activity in a human astrocytoma cell line...
  49. Epigenetics of Sex Differences in Brain and Behavior
    BRIDGET NUGENT; Fiscal Year: 2012
    ..that newborn males and estradiol-treated females have lower levels of DNMT activity and decreased methylation of genes associated with masculinization of the POA compared to females...
  50. Genomics of Antiviral Responses of Anopheles gambiae Against O'nyong-nyong Virus
    Young S Hong; Fiscal Year: 2010
    ..is an exploratory project (R21) that will utilize a mosquito Anopheles gambiae as a model organism to discover genes and gene products involved in mosquito immune responses against arbovirus infections...
  51. Role of JAK2-PAK1 interaction in prolactin-dependent signaling
    Maria Diakonova; Fiscal Year: 2013
    ..In the current proposal we will study how JAK2 and PAK1 increase cell migration and cell survival, and which genes are regulated by these two proteins...
  52. Role of the Mammalian Siderophore in Cellular Iron Metabolism and Erythropoiesis
    Laxminarayana R Devireddy; Fiscal Year: 2012
    ..We have also identified several novel genes that are necessary for the biogenesis of the mammalian siderophore...
  53. Systematics of medically important Dermacentor tick vectors
    Dmitry A Apanaskevich; Fiscal Year: 2011
    ..To reconstruct a phylogeny for Dermacentor species using mitochondrial and nuclear genes. Impact...
  54. REGULATION OF GENE EXPRESSION BY DIETARY FAT
    Lisa M Salati; Fiscal Year: 2012
    ..transcriptional regulation, as a unique model we have generated a prototype for extending these findings to other genes. Because greater than 60% of genes undergo alternative splicing and many are also regulated by changes in splicing ..
  55. Hydrodynamic forces modulate renal tubular function
    Rajeev Rohatgi; Fiscal Year: 2012
    ..the mechanisms by which urine flow rate can activate prostaglandin synthesis in the kidney, we can identify mechanisms which regulate renal Na homeostasis as well as target genes and proteins to prevent the development of hypertension.
  56. Role of Diabetes in Development of Renal Cell Carcinoma
    SAMY LEWIZ HABIB; Fiscal Year: 2013
    ..One of the tumor suppressor genes involved in renal carcinogenesis is tuberous sclerosis gene (TSC2), which encodes tumor suppressor protein, ..
  57. MODULATION OF IFN ACTION VIA NOVEL REGULATORY FACTORS
    DHAN V KALVAKOLANU; Fiscal Year: 2013
    ..A gene expression micro- array analysis in our lab identified several IFN regulated genes, whose expression required C/EBP-2...
  58. Monitoring cellular redox signaling and oxidant stress in vivo
    Paul T Schumacker; Fiscal Year: 2010
    ..In Aim 2 we will activate expression of the RoGFP genes in primary cells cultured from these mice, using Cre recombinase to delete the stop codon...
  59. ICSBP Function During Myeloid Differentiation
    ELIZABETH ANN EKLUND; Fiscal Year: 2011
    ..However, initially identified target-genes did not suggest a mechanism by which ICSBP-deficiency predisposes to either of these events...
  60. Role of CD44 in experimental Multiple Sclerosis
    Mitzi Nagarkatti; Fiscal Year: 2013
    ..modulation dysregulation in microRNA expression that regulate the transcription of inflammatory cytokine genes leading to promotion of Th1/Th17 differentiation...
  61. Prolonged Inhibition of Pathologic Neovascularization by Catalytic Antioxidants
    JAMES FRANCIS MCGINNIS; Fiscal Year: 2013
    ..neovessels in the Very Low Density Lipoprotein Receptor null retina by modulating the expression of many retinal genes including Vascular Endothelial Growth Factor (VEGF)...
  62. Model of Timothy Syndrome to Screen Drugs with Induced Pluripotent Stem Cells
    Masayuki Yazawa; Fiscal Year: 2013
    ..Though many of the genes are reported to cause LQTS, the mechanisms underlying the disease in humans are incompletely understood...
  63. DNA methylation in aging, race and prostate cancer
    Rajvir Dahiya; Fiscal Year: 2006
    ..Specific hypotheses: 1) The DNA methylation status of most frequently deleted genes [ERs, E-cadherin, CD44 and GSTPI (glutathione S-transferase pi)] will be different in aging and race-related ..
  64. The Role of RNA Splicing Factors in Retinal Degeneration
    Michael Farkas; Fiscal Year: 2012
    ..While mutations in many genes have been implicated in the disease, we propose to investigate how mutations in genes required for RNA splicing ..
  65. Unbiased genome-wide screen to identify genes regulating mucous cell hyperplasia
    Jeffrey A Whitsett; Fiscal Year: 2010
    ..Synopsis: This Challenge Research project will undertake 1) a mouse genome-wide shRNA library screen to identify genes and associated gene networks inducing or inhibiting goblet cell differentiation and mucous hypersecretion, and 2) ..
  66. Cohort Study of Genetic Susceptibility to Cutaneous Malignant Melanoma
    Jiali Han; Fiscal Year: 2010
    ..a critical role in protecting against melanoma;however, epidemiologic data are limited due to a limited number of genes and polymorphisms examined in initial studies with small sample sizes...
  67. Genetic Control of Axial Patterning in Drosophila Eye
    Amit Singh; Fiscal Year: 2010
    ..DV patterning is the first axis formed in eye. Our goal is to identify key genes involved in early eye patterning...
  68. Serotonin, Autism, and investigating cell types for CNS disorders.
    Joseph D Dougherty; Fiscal Year: 2010
    ..Daniel Geschwind. His dissertation entailed gene expression profiling to identify neural stem and progenitor cell genes, followed by anatomical and functional studies of candidate genes...
  69. Mutational Cloning in Familial Dementia and Alzheimers Disease
    Wendy H Raskind; Fiscal Year: 2010
    ..The goal of this proposal is to identify novel genes that are responsible for mendelian, highly penetrant familial dementia (FD) of either Alzheimer's disease (AD)..
  70. Bacterial heme transport and hemoglobin expression
    Douglas Henderson; Fiscal Year: 2009
    ..coli with plasmids containing human hemoglobin genes and heme transport genes from a Gram-negative bacterium, and supplying heme in the media...
  71. Using Mass Spectroscopy to Characterize Transcription Proteins and F2-Isoprostane
    BETTYE HENNINTON; Fiscal Year: 2011
    ..gathered that indicates the Rap1p/Gcr1p complex participates in transcription directly by binding to their target genes. In vivo, the promoters of most genes encoding glycolytic and ribosomal proteins (RP) contain sites occupied by ..
  72. Genomic actions of progesterone receptors in human myometrial cells
    Sam Mesiano; Fiscal Year: 2010
    ..during most of human pregnancy via PR-B, which modulates the expression of a specific cohort of relaxatory genes, and b) the relaxatory effects of PR-B are blocked at parturition by PR-A...
  73. MAPPING AND CLONING TRANSLOCATION BREAKPOINTS
    Janet Rowley; Fiscal Year: 2004
    ..breakpoints in recurring chromosome rearrangements, and this has been the major tool leading to identification of genes critically involved in leukemia and lymphoma...