Genomes and Genes
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.
Publications236 found, 100 shown here
- Initial sequencing and analysis of the human genomeE 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...
- Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlationsMichael 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...
- A census of human cancer genesP 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
- The GOA database in 2009--an integrated Gene Ontology Annotation resourceDaniel 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...
- Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene listsDa 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....
- Origins, evolution, and phenotypic impact of new genesHenrik Kaessmann
Center for Integrative Genomics, University of Lausanne, CH 1015 Lausanne, Switzerland
Genome Res 20:1313-26. 2010Ever 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...
- The human genome browser at UCSCW 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...
- Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genesBeate Neumann
MitoCheck Project Group, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
Nature 464:721-7. 2010Despite 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...
- Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancerAndrew E Teschendorff
University College London, London WC1E 6BT, UK
Genome Res 20:440-6. 2010Polycomb group proteins (PCGs) are involved in repression of genes that are required for stem cell differentiation...
- The KEGG resource for deciphering the genomeMinoru 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...
- Associating genes and protein complexes with disease via network propagationOron Vanunu
School of Computer Science, Tel Aviv University, Tel Aviv, Israel
PLoS Comput Biol 6:e1000641. 2010A 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 ..
- WebGestalt: an integrated system for exploring gene sets in various biological contextsBing 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. 2005High-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'...
- FragGeneScan: predicting genes in short and error-prone readsMina 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 ..
- GENCODE: producing a reference annotation for ENCODEJennifer Harrow
Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK
Genome Biol 7:S4.1-9. 2006The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions...
- Current tools for the identification of miRNA genes and their targetsN 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 ..
- The evolutionary origin of orphan genesDiethard 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...
- Forkhead box M1 regulates the transcriptional network of genes essential for mitotic progression and genes encoding the SCF (Skp2-Cks1) ubiquitin ligaseI 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...
- GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological informationRuben 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...
- 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. 2009McKusick'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...
- De novo origin of human protein-coding genesDong 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...
- Initial sequencing and comparative analysis of the mouse genomeRobert 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 ..
- Collisions between replication and transcription complexes cause common fragile site instability at the longest human genesAnne 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. 2011We 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...
- Mammalian microRNAs: experimental evaluation of novel and previously annotated genesH 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...
- Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disordersAda Hamosh
Nucleic Acids Res 33:D514-7. 2005Online 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...
- Recent de novo origin of human protein-coding genesDavid G Knowles
Smurfit Institute of Genetics, University of Dublin, Trinity College, Ireland
Genome Res 19:1752-9. 2009The origin of new genes is extremely important to evolutionary innovation. Most new genes arise from existing genes through duplication or recombination...
- The sequence of the human genomeJ 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...
- Leber congenital amaurosis: genes, proteins and disease mechanismsAnneke 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 ..
- Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphomaMara 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 (..
- The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent agesYuri 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. 2009The 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...
- Molecular mechanisms of epistasis within and between genesBen 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...
- Gene finding in novel genomesIan 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...
- 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. 2009Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species...
- Endogenous retroviral LTRs as promoters for human genes: a critical assessmentCarla 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...
- Two genes encode distinct glutamate decarboxylasesM 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 ..
- Accurately assessing the risk of schizophrenia conferred by rare copy-number variation affecting genes with brain functionSoumya 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...
- A guide to web tools to prioritize candidate genesLeon Charles Tranchevent
Katholieke Universiteit Leuven, Belgium
Brief Bioinform 12:22-32. 2011Finding the most promising genes among large lists of candidate genes has been defined as the gene prioritization problem...
- Transposases are the most abundant, most ubiquitous genes in natureRamy K Aziz
Computation Institute, University of Chicago, Chicago, IL 60637, USA
Nucleic Acids Res 38:4207-17. 2010b>Genes, like organisms, struggle for existence, and the most successful genes persist and widely disseminate in nature...
- The power of protein interaction networks for associating genes with diseasesSaket 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. 2010Understanding the association between genetic diseases and their causal genes is an important problem concerning human health...
- Genes and social behaviorGene E Robinson
Department of Entomology, University of Illinois at Urbana Champaign, 505 South Goodwin Avenue, Urbana, IL 61801, USA
Science 322:896-900. 2008What 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 ..
- Distinctive chromatin in human sperm packages genes for embryo developmentSaher 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...
- Circadian genes, rhythms and the biology of mood disordersColleen 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...
- The semaphorin genes encode a family of transmembrane and secreted growth cone guidance moleculesA 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 ..
- Human DNA repair genesR 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...
- The Gene Ontology (GO) database and informatics resourceM 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...
- The male-specific region of the human Y chromosome is a mosaic of discrete sequence classesHelen 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...
- A family of potassium channel genes related to eag in Drosophila and mammalsJ W Warmke
Laboratory of Genetics, University of Wisconsin, Madison 53706
Proc Natl Acad Sci U S A 91:3438-42. 1994We have identified a conserved family of genes related to Drosophila eag, which encodes a distinct type of voltage-activated K+ channel...
- Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networksAllan 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 ..
- Network-based global inference of human disease genesXuebing 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 ..
- Overview of BioCreative II gene normalizationAlexander A Morgan
Biomedical Informatics, Stanford University, Stanford, CA, 94305, USA
Genome Biol 9:S3. 2008The 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...
- Overview of BioCreative II gene mention recognitionLarry 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...
- Normalization of oligonucleotide arrays based on the least-variant set of genesStefano 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 ..
- The effect of sequencing errors on metagenomic gene predictionKatharina 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...
- GeneTUKit: a software for document-level gene normalizationMinlie 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...
- Genomic footprints of a cryptic plastid endosymbiosis in diatomsAhmed 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...
- Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemiaChristopher 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)...
- Ultraconserved elements in the human genomeGill 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 ..
- The genetics of addictions: uncovering the genesDavid 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...
- Coexpression analysis of human genes across many microarray data setsHomin 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, ..
- Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotypeOlivier 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...
- Association of genetic risk variants with expression of proximal genes identifies novel susceptibility genes for cardiovascular diseaseLasse 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 ..
- Microsatellites within genes: structure, function, and evolutionYou 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...
- Obese and diabetes: two mutant genes causing diabetes-obesity syndromes in miceD L Coleman
Diabetologia 14:141-8. 1978
- Inter-species normalization of gene mentions with GNATJörg 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 ..
- Selection of reference genes for gene expression studies in rat oligodendrocytes using quantitative real time PCRKatherine 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 ..
- Genes affecting the regulation of SUC2 gene expression by glucose repression in Saccharomyces cerevisiaeL 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.
- Linking genes to literature: text mining, information extraction, and retrieval applications for biologyMartin 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/...
- PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloningYuko 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. 2009PosMed (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 ..
- Network properties of human disease genes with pleiotropic effectsSreenivas 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.
- Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genesArtem 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...
- Cholesterol-related genes in Alzheimer's diseaseM 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...
- 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 ..
- ENDEAVOUR update: a web resource for gene prioritization in multiple speciesLeon 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 (..
- Stress-related differential expression of multiple beta-carotene ketolase genes in the unicellular green alga Haematococcus pluvialisJun Chao Huang
Department of Botany, The University of Hong Kong, Pokfulam Road, Hong Kong, PR China
J Biotechnol 122:176-85. 2006..Here we report the identification and expression of three different beta-carotene ketolase genes (bkt) that are involved in the biosynthesis of astaxanthin in a single strain of the alga...
- Bioinformatic identification and characterization of human endothelial cell-restricted genesManoj Bhasin
Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
BMC Genomics 11:342. 2010In 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 ..
- Confirmed rare copy number variants implicate novel genes in schizophreniaGloria W C Tam
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Biochem Soc Trans 38:445-51. 2010..Identification of sets of genes underlying human mental disorders is a path towards this objective...
- A high-density association screen of 155 ion transport genes for involvement with common migraineDale 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 ..
- Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graphAdam 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...
- Time to give up on a single explanation for autismFrancesca 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...
- Annotating genes and genomes with DNA sequences extracted from biomedical articlesMaximilian 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...
- Expression of the zebrafish CD133/prominin1 genes in cellular proliferation zones in the embryonic central nervous system and sensory organsMaura 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...
- Natural products version 2.0: connecting genes to moleculesChristopher 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 ..
- Functional genomic identification of genes required for male gonadal differentiation in Caenorhabditis elegansAndrea 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 ..
- High-performance gene name normalization with GeNoJoachim Wermter
Jena University Language and Information Engineering Lab, Friedrich Schiller Universitat Jena, Fürstengraben 30, 07743 Jena, Germany
Bioinformatics 25:815-21. 2009..Their recognition and normalization remains a challenging task because of widespread gene name ambiguities within species, across species, with common English words and with medical sublanguage terms...
- Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesisBrett M Tyler
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
Science 313:1261-6. 2006..share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles...
- Preferential regulation of duplicated genes by microRNAs in mammalsJingjing Li
Department of Molecular Genetics, University of Toronto, 1 King s College Circle, Toronto, ON, M5S 1A8, Canada
Genome Biol 9:R132. 2008..Specifically, while mammalian paralogs are known to overcome their initial complete functional redundancy through variation in regulation and expression, the potential involvement of microRNAs in this process has not been investigated...
- CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1Y Kawaguchi
Department of Pharmacology, Kyoto University Faculty of Medicine, Japan
Nat Genet 8:221-8. 1994..Southern blot analyses and genomic cloning demonstrates the existence of related genes. These results raise the possibility that similar abnormalities in related genes may give rise to diseases similar ..
- WAF1, a potential mediator of p53 tumor suppressionW S El-Deiry
Oncology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
Cell 75:817-25. 1993The ability of p53 to activate transcription from specific sequences suggests that genes induced by p53 may mediate its biological role as a tumor suppressor...
- Functional analysis of peroxisome-proliferator-responsive element motifs in genes of fatty acid-binding proteinsChristian Schachtrup
Department of Biochemistry, University of Munster, Wilhelm Klemm Str 2, 48149 Munster, Germany
Biochem J 382:239-45. 2004..In the same way, C2C12 myoblasts transfected with promoter fragments of E-FABP and H-FABP genes containing putative PPREs are also not activated through stimulation of PPARs with bezafibrate applied to the ..
- Haploid genetic screens in human cells identify host factors used by pathogensJan E Carette
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
Science 326:1231-5. 2009..Using this approach, we identified host factors essential for infection with influenza and genes encoding important elements of the biosynthetic pathway of diphthamide, which are required for the cytotoxic ..
- WEGO: a web tool for plotting GO annotationsJia Ye
James D Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310008, China
Nucleic Acids Res 34:W293-7. 2006..genomics.org.cn. There are two available mirror sites at http://wego2.genomics.org.cn and http://wego.genomics.com.cn. Any suggestions are welcome at firstname.lastname@example.org...
- AUGUSTUS: ab initio prediction of alternative transcriptsMario Stanke
Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
Nucleic Acids Res 34:W435-9. 2006..where user-defined regular expressions can be searched against putative proteins encoded by the predicted genes. The AUGUSTUS web interface and the downloadable open-source stand-alone program are freely available from http://..
- Balancing selection is the main force shaping the evolution of innate immunity genesAnna Ferrer-Admetlla
Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Unitat de Biologia Evolutiva, Barcelona, Catalonia, Spain
J Immunol 181:1315-22. 2008..Potentially lethal pathogens are likely to have exerted important selective pressures on our genome, so immunity genes can be expected to show molecular signatures of the adaptation of human populations to these recent conditions...
- Differential expression of multiple fork head related genes during gastrulation and axial pattern formation in the mouse embryoH Sasaki
Department of Cell Biology, Vanderbilt University Medical School, Nashville, Tennessee 37232
Development 118:47-59. 1993Four genes encoding fork-head-domain-containing proteins (FD genes) have been isolated from a mouse 8.5 days post coitum (p.c.) embryo cDNA library. Two are mouse homologues of rat HNF-3 beta and HNF-3 alpha...
- GeneMark: web software for gene finding in prokaryotes, eukaryotes and virusesJohn Besemer
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
Nucleic Acids Res 33:W451-4. 2005..In addition, genes in prokaryotic sequences from novel genomes can be identified using models derived on the spot upon sequence ..
- Perspective on genes and mutations causing retinitis pigmentosaStephen P Daiger
Department of Ophthalmology and Visual Science, School of Medicine, The University of Texas Health Science Center, Houston, TX 77030, USA
Arch Ophthalmol 125:151-8. 2007Exceptional progress has been made during the past two decades in identifying genes causing inherited retinal diseases such as retinitis pigmentosa...
- Background selection in single genes may explain patterns of codon biasLaurence Loewe
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
Genetics 175:1381-93. 2007..Here we focus on the level of a single gene or small group of genes and investigate how the effects of background selection caused by nonsynonymous mutations are influenced by the ..
- The locus of evolution: evo devo and the genetics of adaptationHopi E Hoekstra
Department of Organismic and Evolutionary Biology and The Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA
Evolution 61:995-1016. 2007..affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes. This argument rests on two claims: (1) the modular nature of cis-regulatory elements largely frees them from ..
- Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysisSteffen Grossmann
Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
Bioinformatics 23:3024-31. 2007MOTIVATION: High-throughput experiments such as microarray hybridizations often yield long lists of genes found to share a certain characteristic such as differential expression...
- Natural selection on genes that underlie human disease susceptibilityRan Blekhman
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Curr Biol 18:883-9. 2008What evolutionary forces shape genes that contribute to the risk of human disease? Do similar selective pressures act on alleles that underlie simple versus complex disorders [1-3]? Answers to these questions will shed light onto the ..
- Impact of Antibiotics and Vaccines on the in vivo Evolution of S. pneumoniaeGarth Ehrlich; Fiscal Year: 2009..if coats (what the vaccine is directed against) or whether these escape strains are truly they possess most of the genes of the clonal lineages that have just hidden in new outer fundamentally alters their cell surface which could ..
- Fibrotic Sequelae of Childhood Renal DiseaseAgnes Fogo; Fiscal Year: 2007..Apart from the genes responsible for the manifestation of cyst formation per se, the loss of renal function in PKD is determined by ..
- Development of CNS-targeted AAV vectorsMiguel Esteves; Fiscal Year: 2009..AAV capsid library with a diversity of 5x109 clones generated by DNA shuffling of AAV1, 2, 5, 8, 9, and rh10 Cap genes, to identify new brain- and spinal cord-tropic AAV capsids after intravenous or ICV delivery in adult animals...
- Development of CNS-targeted AAV vectorsMIGUEL S ESTEVES; Fiscal Year: 2010..AAV capsid library with a diversity of 5x109 clones generated by DNA shuffling of AAV1, 2, 5, 8, 9, and rh10 Cap genes, to identify new brain- and spinal cord-tropic AAV capsids after intravenous or ICV delivery in adult animals...
- DNA methylation in aging, race and prostate cancerRajvir 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 ..
- BIOLOGY OF EARLY RENAL CYSTOGENESIS IN THE CPK MOUSELisa Guay Woodford; Fiscal Year: 2003..cystic disease in both humans and mouse models involves a multigenic pathway in which the disease-susceptibility genes act by cellular recessive mechanisms...
- Colitis Induced by immune responses to luminal bacteria-mouseRYAN BALFOUR SARTOR; Fiscal Year: 2010..4 genes associated with Crohn's disease (NOD 2, ATG 16L1, NCF4, IGRM) regulate bacterial killing, suggesting that ..
- CELL CYCLE REGULATION OF THE YEAST HO GENELINDA BREEDEN; Fiscal Year: 2001A large number of yeast genes, including several of the cyclins, are required for the transition between G1 and S. These genes are transcribed at two different times...
- RpoS-mediated virulence regulation in Borrelia burgdorferiJON SCOTT BLEVINS; Fiscal Year: 2010..The optimal experimental approach to identify genes that respond to a particular regulator would be to expose the bacteria to the specific condition(s) that activate ..
- Cohort Study of Genetic Susceptibility to Cutaneous Malignant MelanomaJiali 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...
- Cohort Study of Genetic Susceptibility to Cutaneous Malignant MelanomaJiali Han; Fiscal Year: 2009..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...
- Cohort Study of Genetic Susceptibility to Cutaneous Malignant MelanomaJiali Han; Fiscal Year: 2009..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...
- Genetic control of limb development by PbxLicia Selleri; Fiscal Year: 2010..While the fly has only one TALE-encoding gene, Exd, the mouse has four Pbx genes (Pbx1-4)...
- Novel genomic effects of Y-linked polymorphismsDaniel L Hartl; Fiscal Year: 2010..is polymorphic for sequences that differentially affect the expression of many hundreds of autosomal and X-linked genes. The quantitative effects of different Y chromosome on gene expression are termed YRV (Y-linked regulatory ..
- Molecular Pathphysiology of FSHD muscular dystrophy via genome-wide approachesYi Wen Chen; Fiscal Year: 2009..The shortening of the D4Z4 array is believed to have a de-repression effect on genes in or near the D4Z4 region...
- Role of Genes in Exceptional Longevity in HumansNir Barzilai; Fiscal Year: 2007..The long-term goal of this Program is to identify genes that contribute to exceptional longevity in humans, and to assess the associations among these genes with age-..
- Insulin Clearance: Candidate and Positional Genetic DeterminantsMARK GOODARZI; Fiscal Year: 2010..Insulin clearance is a highly heritable trait. Preliminary data show that haplotypes in the genes for adenosine monophosphate deaminase (AMPD1 and AMPD2) and the AMP-activated protein kinase (AMPK) 12 subunit are ..
- Insulin Clearance: Candidate and Positional Genetic DeterminantsMARK GOODARZI; Fiscal Year: 2009..Insulin clearance is a highly heritable trait. Preliminary data show that haplotypes in the genes for adenosine monophosphate deaminase (AMPD1 and AMPD2) and the AMP-activated protein kinase (AMPK) 12 subunit are ..
- MOLECULAR GENETICS OF NUCLEOLAR DOMINANCECRAIG STUART PIKAARD; Fiscal Year: 2010..phenomenon that occurs in plant and animal genetic hybrids and describes the transcription of ribosomal RNA (rRNA) genes inherited from only one parent due to the selective silencing of the other progenitor's rRNA genes...
- Disparities in cervical cancer precursors and deregulation of imprinted genesSusan Kay Murphy; Fiscal Year: 2010..We posit that deregulation of genomically imprinted genes, a group of approximately 50 known growth-regulatory genes where only one allele is normally active, may predict ..
- MAPPING AND CLONING TRANSLOCATION BREAKPOINTSJanet 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...
- Ion Channel Function in Auditory & Vestibular hair cellsJeffrey Holt; Fiscal Year: 2009..The overall goal is to identify the genes and proteins in sensory hair cells that are responsible for the generation and propagation of sensory information ..