genetic databases

Summary

Summary: DATABASES devoted to knowledge about specific genes and gene products.

Top Publications

  1. pmc Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    Ron Edgar
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Lister Hill Center, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:207-10. 2002
  2. 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
  3. pmc TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
    V Matys
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 34:D108-10. 2006
  4. ncbi Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    Adrian Alexa
    Max Planck Institute for Informatics Stuhlsatzenhausweg 85, D 66123 Saarbrucken, Germany
    Bioinformatics 22:1600-7. 2006
  5. 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
  6. ncbi Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 23:127-8. 2007
  7. 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
  8. 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
  9. ncbi The genetic association database
    Kevin G Becker
    Nat Genet 36:431-2. 2004
  10. ncbi MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
    Oliver Thimm
    Max Planck Institute for Molecular Plant Physiology, Golm, Germany
    Plant J 37:914-39. 2004

Detail Information

Publications255 found, 100 shown here

  1. pmc Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    Ron Edgar
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Lister Hill Center, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:207-10. 2002
    ..A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo...
  2. 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...
  3. pmc TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
    V Matys
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 34:D108-10. 2006
    ..The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html...
  4. ncbi Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    Adrian Alexa
    Max Planck Institute for Informatics Stuhlsatzenhausweg 85, D 66123 Saarbrucken, Germany
    Bioinformatics 22:1600-7. 2006
    ..g. based on Gene Ontology (GO). We develop methods that increase the explanatory power of this approach by integrating knowledge about relationships between the GO terms into the calculation of the statistical significance...
  5. 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
    ..Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php...
  6. ncbi Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 23:127-8. 2007
    ..Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported. AVAILABILITY: iTOL is available at http://itol.embl.de..
  7. 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
    ..Approximately 70 new entries are added and 700 entries are updated per month. OMIM is expanding content and organization in response to shifting biological paradigms and advancing biotechnology...
  8. 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
    ....
  9. ncbi The genetic association database
    Kevin G Becker
    Nat Genet 36:431-2. 2004
  10. ncbi MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
    Oliver Thimm
    Max Planck Institute for Molecular Plant Physiology, Golm, Germany
    Plant J 37:914-39. 2004
    ....
  11. pmc NCBI Reference Sequences: current status, policy and new initiatives
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 4As 47B, 45 Center Drive, Bethesda, MD, USA
    Nucleic Acids Res 37:D32-6. 2009
    ..In addition, we introduce RefSeqGene, a new initiative to support reporting variation data on a stable genomic coordinate system...
  12. pmc ONCOMINE: a cancer microarray database and integrated data-mining platform
    Daniel R Rhodes
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Neoplasia 6:1-6. 2004
    ..Furthermore, gene sets can be limited to clinically important annotations including secreted, kinase, membrane, and known gene-drug target pairs to facilitate the discovery of novel biomarkers and therapeutic targets...
  13. pmc The TIGR Rice Genome Annotation Resource: improvements and new features
    Shu Ouyang
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D883-7. 2007
    ..Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads...
  14. 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
    ..New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database...
  15. pmc Human non-synonymous SNPs: server and survey
    Vasily Ramensky
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 30:3894-900. 2002
    ..The strongest selective pressure was detected for proteins involved in transcription regulation...
  16. pmc The UCSC Table Browser data retrieval tool
    Donna Karolchik
    Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, School of Engineering, 1156 High Street, Santa Cruz, CA 95064 1077, USA
    Nucleic Acids Res 32:D493-6. 2004
    ..The Table Browser User's Guide located on the UCSC website provides instructions and detailed examples for constructing queries and configuring output...
  17. ncbi affy--analysis of Affymetrix GeneChip data at the probe level
    Laurent Gautier
    Center for Biological Sequence Analysis CBS, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    Bioinformatics 20:307-15. 2004
    ..The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used...
  18. ncbi The genomic landscapes of human breast and colorectal cancers
    Laura D Wood
    Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
    Science 318:1108-13. 2007
    ..These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy...
  19. pmc NCBI BLAST: a better web interface
    Mark Johnson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:W5-9. 2008
    ..Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement...
  20. 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...
  21. pmc EcoCyc: a comprehensive view of Escherichia coli biology
    Ingrid M Keseler
    SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    Nucleic Acids Res 37:D464-70. 2009
    ..A new advanced query page guides users in interactively constructing complex database queries against EcoCyc. A Macintosh version of EcoCyc is now available. A series of Webinars is available to instruct users in the use of EcoCyc...
  22. pmc BioMart Central Portal--unified access to biological data
    Syed Haider
    EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK
    Nucleic Acids Res 37:W23-7. 2009
    ..The website is free and open to all users and there is no login requirement...
  23. pmc The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    F Meyer
    Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, Argonne, IL 60439, USA
    BMC Bioinformatics 9:386. 2008
    ..High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers...
  24. pmc The microRNA.org resource: targets and expression
    Doron Betel
    Computational and Systems Biology Center, Memorial Sloan Kettering Cancer Center, NY, USA
    Nucleic Acids Res 36:D149-53. 2008
    ..The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation...
  25. pmc The Arabidopsis Information Resource (TAIR): gene structure and function annotation
    David Swarbreck
    Carnegie Institution, Department of Plant Biology, 260 Panama St, Stanford, CA 94305, USA
    Nucleic Acids Res 36:D1009-14. 2008
    ..A total of 681 new genes and 1002 new splice variants were added. Overall, 10,098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release...
  26. pmc The NCBI dbGaP database of genotypes and phenotypes
    Matthew D Mailman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892 6510, USA
    Nat Genet 39:1181-6. 2007
    ....
  27. pmc NCBI GEO: archive for high-throughput functional genomic data
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
    Nucleic Acids Res 37:D885-90. 2009
    ..This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/...
  28. ncbi The protein kinase complement of the human genome
    G Manning
    SUGEN Inc, 230 East Grand Avenue, South San Francisco, CA 94080, USA
    Science 298:1912-34. 2002
    ..We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons...
  29. pmc The Gene Ontology (GO) database and informatics resource
    M A Harris
    GO EBI, Hinxton, UK
    Nucleic Acids Res 32:D258-61. 2004
    ..The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses...
  30. ncbi A text-mining analysis of the human phenome
    Marc A van Driel
    Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Toernooiveld 1, 6525ED Nijmegen, The Netherlands
    Eur J Hum Genet 14:535-42. 2006
    ..Such predictions will further improve if a unified system of phenotype descriptors is developed. The phenotype similarity data are accessible through a web interface at http://www.cmbi.ru.nl/MimMiner/...
  31. pmc Walking the interactome for prioritization of candidate disease genes
    Sebastian Kohler
    Institute for Medical Genetics, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
    Am J Hum Genet 82:949-58. 2008
    ....
  32. 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...
  33. pmc The BioGRID Interaction Database: 2008 update
    Bobby Joe Breitkreutz
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Nucleic Acids Res 36:D637-40. 2008
    ..Source code for the BioGRID and the linked Osprey network visualization system is now freely available without restriction...
  34. pmc ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    Helen Parkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D868-72. 2009
    ..In this update, we describe the ArrayExpress developments over the last two years...
  35. ncbi IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments
    Chiara Romualdi
    Department of Biology, University of Padua, 35131 Padua, Italy
    Physiol Genomics 12:159-62. 2003
    ..Software is freely available at the site: http://telethon.bio.unipd.it/bioinfo/IDEG6_form/, together with additional information on statistical methodologies...
  36. ncbi TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
    Heiko A Schmidt
    Max Planck Institut fur Molekulare Genetik, Ihnestr 73, D 14195 Berlin, Germany
    Bioinformatics 18:502-4. 2002
    ..To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers...
  37. pmc ATTED-II provides coexpressed gene networks for Arabidopsis
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D987-91. 2009
    ..With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis...
  38. ncbi The Collaborative Cross, a community resource for the genetic analysis of complex traits
    Gary A Churchill
    The Jackson Laboratory, 600 Main Street Bar Harbor, Maine 04609, USA
    Nat Genet 36:1133-7. 2004
    ..The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease...
  39. pmc A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    Adam M Feist
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
    Mol Syst Biol 3:121. 2007
    ..The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism...
  40. pmc Dendroscope: An interactive viewer for large phylogenetic trees
    Daniel H Huson
    Center for Bioinformatics Tübingen ZBIT, Eberhard Karls Universitat Tubingen, Sand 14, 72076 Tubingen, Germany
    BMC Bioinformatics 8:460. 2007
    ..Moreover, many programs are difficult to install or are not available for all common operating systems...
  41. pmc Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    Ada Hamosh
    Nucleic Acids Res 33:D514-7. 2005
    ..has a full-text summary of a genetically determined phenotype and/or gene and has numerous links to other genetic databases such as DNA and protein sequence, PubMed references, general and locus-specific mutation databases, HUGO ..
  42. ncbi Systematic genetic analysis with ordered arrays of yeast deletion mutants
    A H Tong
    Banting and Best Department of Medical Research, University of Toronto, Toronto ON, Canada M5G 1L6
    Science 294:2364-8. 2001
    ..Systematic application of this approach should produce a global map of gene function...
  43. pmc ARB: a software environment for sequence data
    Wolfgang Ludwig
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 853530 Freising, Germany
    Nucleic Acids Res 32:1363-71. 2004
    ..Currently, the package is used by numerous working groups worldwide...
  44. pmc PlasmoDB: a functional genomic database for malaria parasites
    Cristina Aurrecoechea
    Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 37:D539-43. 2009
    ..Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis...
  45. pmc AgBase: a functional genomics resource for agriculture
    Fiona M McCarthy
    Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
    BMC Genomics 7:229. 2006
    ....
  46. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
    ..We conclude with a discussion of how the open-source nature of the project has contributed to the development effort...
  47. ncbi Using FlyAtlas to identify better Drosophila melanogaster models of human disease
    Venkateswara R Chintapalli
    Division of Molecular Genetics, University of Glasgow, Glasgow G11 6NU, UK
    Nat Genet 39:715-20. 2007
    ....
  48. ncbi A gene expression atlas of the model legume Medicago truncatula
    Vagner A Benedito
    Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
    Plant J 55:504-13. 2008
    ..The data presented here represent an unparalleled resource for legume functional genomics, which will accelerate discoveries in legume biology...
  49. pmc CancerGenes: a gene selection resource for cancer genome projects
    Maureen E Higgins
    Computational Biology Center Memorial Sloan Kettering Cancer Center, 1275 York Avenue, No 460 New York, NY 10021, USA
    Nucleic Acids Res 35:D721-6. 2007
    ..Users may view tabulated results through a web browser or may dynamically download them as a spreadsheet table. CancerGenes is available at http://cbio.mskcc.org/cancergenes...
  50. pmc Enzyme-specific profiles for genome annotation: PRIAM
    Clotilde Claudel-Renard
    Laboratoire de Genetique Cellulaire, INRA, INRA CNRS, BP27, 31326 Castanet Tolosan Cedex, France
    Nucleic Acids Res 31:6633-9. 2003
    ..The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes...
  51. pmc The influenza virus resource at the National Center for Biotechnology Information
    Yiming Bao
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Virol 82:596-601. 2008
  52. ncbi Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome
    J Zhang
    The Centre for Applied Genomics and the Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
    Cytogenet Genome Res 115:205-14. 2006
    ....
  53. pmc A systems biology approach for pathway level analysis
    Sorin Draghici
    Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48202, USA
    Genome Res 17:1537-45. 2007
    ..This analysis method has been implemented as a Web-based tool, Pathway-Express, freely available as part of the Onto-Tools (http://vortex.cs.wayne.edu)...
  54. pmc Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles
    Daniel R Rhodes
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 0940, USA
    Neoplasia 9:166-80. 2007
    ..Here, we provide an update on the initiative, describe the database and analysis modules, and highlight several notable observations. Results from this comprehensive analysis are available at http://www.oncomine.org...
  55. ncbi Approaches for extracting practical information from gene co-expression networks in plant biology
    Koh Aoki
    Kazusa DNA Research Institute, Kazusa Kamatari 2 6 7, Kisarazu, 292 0818, Japan
    Plant Cell Physiol 48:381-90. 2007
    ..Co-expression network analysis is a powerful approach for data-driven hypothesis construction and gene prioritization, and provides novel insights into the system-level understanding of plant cellular processes...
  56. ncbi Multiple sequence alignment using partial order graphs
    Christopher Lee
    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Bioinformatics 18:452-64. 2002
    ..Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment step. However, this leads to loss of information needed for accurate alignment, and gap scoring artifacts...
  57. pmc RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
    Socorro Gama-Castro
    Program of Computational Genomics, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, A P 565 A, Cuernavaca, Morelos 62100, Mexico
    Nucleic Acids Res 36:D120-4. 2008
    ..The data can be accessed through overviews of correlations about gene regulation. RegulonDB associated original literature, together with more than 4000 curation notes, can now be searched with the Textpresso text mining engine...
  58. pmc The Ensembl genome database project
    T Hubbard
    The Wellcome Trust Sanger Institute and European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 30:38-41. 2002
    ..The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops...
  59. ncbi A gene-coexpression network for global discovery of conserved genetic modules
    Joshua M Stuart
    Stanford Medical Informatics, 251 Campus Drive, Medical School Office Building X 215, Stanford, CA 94305 5329, USA
    Science 302:249-55. 2003
    ..By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules...
  60. 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
    ..EASE is a powerful tool for rapidly converting the results of functional genomics studies from 'genes' to 'themes'...
  61. ncbi The quest for orthologs: finding the corresponding gene across genomes
    Arnold Kuzniar
    Laboratory of Bioinformatics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
    Trends Genet 24:539-51. 2008
    ..Here, we evaluate the available bioinformatics tools and provide a set of guidelines to aid researchers in choosing the most appropriate tool for any situation...
  62. pmc BioMart--biological queries made easy
    Damian Smedley
    Ontario Institute for Cancer Research, MaRS Centre, 101 College Street, Toronto, Ontario, Canada
    BMC Genomics 10:22. 2009
    ..This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution...
  63. pmc TRANSFAC: transcriptional regulation, from patterns to profiles
    V Matys
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 31:374-8. 2003
    ..gbf.de. For CYTOMER free download versions are available at http://www.biobase.de:8080/index.html...
  64. pmc The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze 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
    Genome Biol 8:R183. 2007
    ..It is a powerful method to group functionally related genes and terms into a manageable number of biological modules for efficient interpretation of gene lists in a network context...
  65. pmc GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis
    Cristina Aurrecoechea
    Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 37:D526-30. 2009
    ..Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data...
  66. pmc The generic genome browser: a building block for a model organism system database
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11790, USA
    Genome Res 12:1599-610. 2002
    ..GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org...
  67. ncbi The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access
    Hideki Goda
    RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa 230 0045, Japan
    Plant J 55:526-42. 2008
    ..The data set presented here will be a versatile resource for future hormone studies, and constitutes a reference for genome-wide gene expression in Arabidopsis...
  68. pmc NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 6An 12J, 45 Center Drive, Bethesda, MD 20892 6510, USA
    Nucleic Acids Res 33:D501-4. 2005
    ....
  69. pmc Eigengene networks for studying the relationships between co-expression modules
    Peter Langfelder
    Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
    BMC Syst Biol 1:54. 2007
    ..Ample literature exists on how to detect biologically meaningful modules in networks but there is a need for methods that allow one to study the relationships between modules...
  70. ncbi Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database
    Lars Bertram
    Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease MIND, Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
    Nat Genet 39:17-23. 2007
    ..67 for protective alleles). Our database provides a powerful tool for deciphering the genetics of Alzheimer disease, and it serves as a potential model for tracking the most viable gene candidates in other genetically complex diseases...
  71. pmc The Unified Medical Language System (UMLS): integrating biomedical terminology
    Olivier Bodenreider
    Lister Hill Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:D267-70. 2004
    ..All vocabularies are available at no fee for research purposes within an institution, but UMLS users are required to sign a license agreement. The UMLS knowledge sources are distributed on CD-ROM and by FTP...
  72. pmc IMGT, the international ImMunoGeneTics information system
    Marie Paule Lefranc
    IMGT, the international ImMunoGeneTics information system, Universite Montpellier 2, Laboratoire d ImmunoGenetique Moleculaire LIGM, UPR CNRS 1142, Institut de Genetique Humaine IGH, 34396 Montpellier Cedex 5, France
    Nucleic Acids Res 37:D1006-12. 2009
    ..IMGT is freely available at http://www.imgt.org...
  73. pmc Ensembl Genomes: extending Ensembl across the taxonomic space
    P J Kersey
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D563-9. 2010
    ..Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site...
  74. ncbi A Chado case study: an ontology-based modular schema for representing genome-associated biological information
    Christopher J Mungall
    Lawrence Berkeley National Laboratory, Lawrence Berkeley National Lab, Mail Stop 64R0121, Berkeley, CA 94720, USA
    Bioinformatics 23:i337-46. 2007
    ..Our question was whether we could create a relational database schema that would be successfully reused...
  75. ncbi A new method to measure the semantic similarity of GO terms
    James Z Wang
    School of Computing, Clemson University, Clemson, SC 29634, USA
    Bioinformatics 23:1274-81. 2007
    ....
  76. ncbi GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
    Sean Davis
    Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    Bioinformatics 23:1846-7. 2007
    ..Facilitating analyses and meta-analyses of microarray data will increase the efficiency with which biologically important conclusions can be drawn from published genomic data...
  77. pmc PlantGDB: a resource for comparative plant genomics
    Jon Duvick
    Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
    Nucleic Acids Res 36:D959-65. 2008
    ..PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training...
  78. ncbi Graph-based analysis and visualization of experimental results with ONDEX
    Jacob Köhler
    Division of Biomathematics and Bioinformatics, Rothamsted Research, AL5 2JQ Harpenden, UK
    Bioinformatics 22:1383-90. 2006
    ..Software tools are needed to automate this task which at present is labor-intensive and requires considerable informatics and biological expertise...
  79. pmc VFDB: a reference database for bacterial virulence factors
    Lihong Chen
    State Key Laboratory for Molecular Virology and Genetic Engineering, Beijing 100052, China
    Nucleic Acids Res 33:D325-8. 2005
    ..Furthermore, a BLAST search tool against all known VF-related genes is also available. VFDB provides a unified gateway to store, search, retrieve and update information about VFs from various bacterial pathogens...
  80. pmc TB database: an integrated platform for tuberculosis research
    T B K Reddy
    Department of Biochemistry, Stanford University, CA 94305, USA
    Nucleic Acids Res 37:D499-508. 2009
    ..By bringing together M. tuberculosis genome annotation and gene-expression data with a suite of analysis tools, TBDB (http://www.tbdb.org/) provides a unique discovery platform for TB research...
  81. ncbi beadarray: R classes and methods for Illumina bead-based data
    Mark J Dunning
    Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
    Bioinformatics 23:2183-4. 2007
    ..Summarized data processed by Illumina's; BeadStudio software can also be read and analysed in the same manner...
  82. pmc The Sequence Ontology: a tool for the unification of genome annotations
    Karen Eilbeck
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
    Genome Biol 6:R44. 2005
    ....
  83. pmc Why highly expressed proteins evolve slowly
    D Allan Drummond
    Program in Computation and Neural Systems and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 4100, USA
    Proc Natl Acad Sci U S A 102:14338-43. 2005
    ..Our results suggest that proteins evolve at rates largely unrelated to their functions and can explain why highly expressed proteins evolve slowly across the tree of life...
  84. pmc From genomics to chemical genomics: new developments in KEGG
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 34:D354-7. 2006
    ..Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps...
  85. ncbi Systematic meta-analyses and field synopsis of genetic association studies in schizophrenia: the SzGene database
    Nicole C Allen
    Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
    Nat Genet 40:827-34. 2008
    ..As such, it could serve as a model for field synopses of genetic associations in other common and genetically complex disorders...
  86. pmc The diploid genome sequence of an Asian individual
    Jun Wang
    Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
    Nature 456:60-5. 2008
    ..These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics...
  87. pmc TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics
    Keiichi Mochida
    Plant Science Center, RIKEN, Yokohama 230 0045, Japan
    Plant Physiol 150:1135-46. 2009
    ..This informative content provides an informatics gateway for Triticeae genomics and grass comparative genomics. TriFLDB is publicly available at http://TriFLDB.psc.riken.jp/...
  88. pmc Large-scale assignment of orthology: back to phylogenetics?
    Toni Gabaldón
    Bioinformatics and Genomics Program, Center for Genomic Regulation, Doctor Aiguader 88, Barcelona, Spain
    Genome Biol 9:235. 2008
    ..Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies...
  89. ncbi FlyBase : a database for the Drosophila research community
    Rachel Drysdale
    Department of Genetics, University of Cambridge, Cambridge, UK
    Methods Mol Biol 420:45-59. 2008
    ..This review will introduce the FlyBase web server and query tools...
  90. pmc DOOR: a database for prokaryotic operons
    Fenglou Mao
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 37:D459-63. 2009
    ..We believe that DOOR provides a useful resource to many biologists working on bacteria and archaea, which can be accessed at http://csbl1.bmb.uga.edu/OperonDB...
  91. pmc MEME SUITE: tools for motif discovery and searching
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:W202-8. 2009
    ..All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net...
  92. pmc VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics
    Jian Yang
    State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100176, China
    Nucleic Acids Res 36:D539-42. 2008
    ..VFDB 2008 release offers more user-friendly tools for comparative pathogenomics and it is publicly accessible at http://www.mgc.ac.cn/VFs/...
  93. pmc Xenbase: a Xenopus biology and genomics resource
    Jeff B Bowes
    Department of Computer Science, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada
    Nucleic Acids Res 36:D761-7. 2008
    ....
  94. pmc Gene expression omnibus: microarray data storage, submission, retrieval, and analysis
    Tanya Barrett
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
    Methods Enzymol 411:352-69. 2006
    ..This chapter describes how data are stored, submission procedures, and mechanisms for data retrieval and query. GEO is publicly accessible at http://www.ncbi.nlm.nih.gov/projects/geo/...
  95. pmc PHI-base: a new database for pathogen host interactions
    Rainer Winnenburg
    Biomathematics and Bioinformatics Division, Rothamsted Research, Harpenden, AL5 2JQ, UK
    Nucleic Acids Res 34:D459-64. 2006
    ..g. NCBI taxonomy and EMBL). We welcome new data for inclusion in PHI-base, which is freely accessed at www4.rothamsted.bbsrc.ac.uk/phibase/...
  96. pmc The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species
    Kevin P Byrne
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Genome Res 15:1456-61. 2005
    ..cerevisiae (551, including 22 previously unidentified), Saccharomyces castellii (599), and Candida glabrata (404)...
  97. pmc An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants
    Nicole T Liberati
    Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
    Proc Natl Acad Sci U S A 103:2833-8. 2006
    ..Comparison of the genes disrupted in the PA14 transposon insertion library with an independently constructed insertion library in P. aeruginosa strain PAO1 provides an estimate of the number of P. aeruginosa essential genes...
  98. ncbi Bayesian identification of admixture events using multilocus molecular markers
    Jukka Corander
    Department of Mathematics and Statistics, PO Box 68, FIN 00014 University of Helsinki, Finland
    Mol Ecol 15:2833-43. 2006
    ..Our approach is illustrated by analyses of several challenging real and simulated data sets. The software (baps), implementing the methods introduced here, is freely available at http://www.rni.helsinki.fi/~jic/bapspage.html...
  99. pmc FlyMine: an integrated database for Drosophila and Anopheles genomics
    Rachel Lyne
    Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
    Genome Biol 8:R129. 2007
    ..It provides web access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists...
  100. pmc Prioritizing GWAS results: A review of statistical methods and recommendations for their application
    Rita M Cantor
    Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    Am J Hum Genet 86:6-22. 2010
    ..Reviews of published methods with recommendations for their application are provided within the framework for each approach...
  101. pmc PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification
    Athanasia Spandidos
    Department of Genetics, Harvard Medical School, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114 2790, USA
    Nucleic Acids Res 38:D792-9. 2010
    ..In all, 26,855 primer pairs covering most known mouse genes have been experimentally validated by QPCR, agarose gel analysis, sequencing and BLAST, and all validation data can be freely accessed from the PrimerBank web site...

Research Grants69

  1. THE ETHICS OF POST-CONFLICT AND POST-DISASTER DNA IDENTIFICATION
    Sarah Wagner; Fiscal Year: 2013
    ..anonymity, trust, data ownership, informed consent, and illicit use associated with the creation of large genetic databases in countries emerging from conflict or disaster...
  2. Therapeutic approaches for ABCA4-associated disorders
    RANDO L ALLIKMETS; Fiscal Year: 2013
    ..In the first Module, we propose to improve and expand our existing clinical and genetic databases of patients and well-characterized families where the disease is caused by mutations in the ABCA4 gene...
  3. Completing genetic analysis of the ABCA4 locus
    RANDO L ALLIKMETS; Fiscal Year: 2013
    ..To investigate these hypotheses, we will use our large clinical and genetic databases of sporadic and familial patients with ABCA4-associated diseases to determine all disease-associated ..
  4. ADHD biotypes using genetic and imaging approaches
    Joel T Nigg; Fiscal Year: 2013
    ..In Aim 1, existing genetic databases will be extended with Baysian methods, and gene pathways will be prioritized by informatics methods using ..
  5. BIOMEDICAL TRAINING IN ALCOHOLISM RESEARCH
    Andrew C Heath; Fiscal Year: 2013
    ..Trainees will learn to study this process through genetic including gene discovery-, longitudinal, and cognitive neuroscience approaches. ..
  6. Linking Data Sources from the Autism Genetic Resource Exchange (AGRE) with NDAR
    Clara M Lajonchere; Fiscal Year: 2010
    ..The availability of comprehensive clinical and genetic databases for autism spectrum disorders (ASD) such as Autism Speaks'Autism Genetic Resource Exchange (AGRE) has ..
  7. POLYMORPHISMS IN PG/COX PATHWAY AND COLORECTAL POLYPS
    Cornelia Ulrich; Fiscal Year: 2003
    ..Methods include screening of enzymes in the COX/PG pathway for new polymorphisms both by searching genetic databases and by using other techniques (dHPLC, enzyme mismatch cleavage, DNA sequencing)...
  8. Quantitative Optical Phase, Amplitude, and Polarization Microscopy
    Remy Tumbar; Fiscal Year: 2010
    ..more accurate (quantitative) automated histology of transparent, unstained, tissue samples, and complex genetic databases containing comprehensive, fully digital, quantitative multi-modal optical microscopy data on specific ..
  9. MENTORED QUANTITATIVE RESEARCH CAREER DEVELOPMENT AWARD
    Gregory Grant; Fiscal Year: 2005
    ..on ongoing research project on the statistics of gene expression analysis, disease gene locating, developing genetic databases, and other projects in computational biology, particularly those involving statistical analysis...
  10. 14th International HLA & Immunogenetics Workship (HIWS)
    John Hansen; Fiscal Year: 2005
    ..Genetic control of immune responses to infectious disease, cancer and autoimmune disorders, 3. Creation of genetic databases of immune response genes including HLA alleles and haplotypes, 4...
  11. TRINUCLEOTIDE REPEATS AND NEUROLOGIC DISEASE
    Russell Margolis; Fiscal Year: 2004
    ..Overall, the proposed experiments will enable a systematic test for CAG/CTG expansion mutations in a variety of devastating neurodegenerative diseases. ..
  12. Junction Adhesion Molecule CAR and the Immune System
    Steven Carson; Fiscal Year: 2007
    ..will be purified from Raji cells and identified by comparison of amino-terminal sequence with protein and genetic databases, cDNA encoding the protein will be obtained from a repository (if the protein is known and the cDNA ..
  13. GENETIC DATABASES--APPLICATIONS FOR MACHINE LEARNING
    Alan Lapedes; Fiscal Year: 1990
    ..Other machine learning algorithms, such as "classifier systems," will also be applied, as well as new approaches to information theoretic constructions of default hierarchies...
  14. PROTEINS INTERACTING WITH DISHEVELLED IN VERTEBRATES
    BENJAMIN CHEYETTE; Fiscal Year: 2003
    ..Mammalian homologs of confirmed Dishevelled-interactors will be identified by computerized search of the genetic databases, and obtained either from other investigators or by PCR from genetic libraries...
  15. Preventing the Incidentalome
    Isaac S Kohane; Fiscal Year: 2010
    ..This despite their annotation in authoritative genetic databases and texts as "highly penetrant" in causing disease congenitally or in childhood...
  16. Genome Evolution, Innovation and Adaptation in the Apicomplexa
    Jessica C Kissinger; Fiscal Year: 2010
    ..The results of these studies will be shared with the larger research community via publication and deposition in community databases and Bioinformatics Resource Centers. ..
  17. Annual Conference on Computational Genomics
    Carol Bult; Fiscal Year: 2008
    ..In subsequent years, The Conference will altemate between the Northeast (Boston/Cambridge) and the Mid-Atlantic Region (Virginia/Maryland). ..
  18. Genome Sequence Analysis: Theory and Practice
    Carol Bult; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  19. MouseCyc: A Biochemical Pathway Database for the Mouse
    Carol Bult; Fiscal Year: 2008
    ..The visualization and query interfaces for MouseCyc will further enhance the value of the mouse as a model system for understanding human biology and disease processes. ..
  20. The Place of Race in Gene Patenting and Drug Development
    Jonathan Kahn; Fiscal Year: 2008
    ..The guidelines will be employed when reviewing applications that use race and/or ethnicity in a manner that is premised upon an underlying assumption that such categories are somehow genetic. [unreadable] [unreadable] [unreadable]..
  21. GENETICS OF EARLY ONSET DEPRESSION
    James Potash; Fiscal Year: 2008
    ..abstract_text> ..
  22. Genetic Linkage and Association in Bipolar Disorder
    James Potash; Fiscal Year: 2009
    ..These new variants would then be tested for association in our sample. The important findings that have already emerged from our very carefully assessed sample argue for the benefits of extending this valuable resource. ..
  23. STRUCTURAL STUDIES ON FIBRINOGEN AND FIBRIN
    Russell Doolittle; Fiscal Year: 2003
    ..Combined with the full structures of the native molecules at high resolution, these results should dispel much of the mystery of fibrin formation. ..
  24. Abdominal Aortic Aneurysm
    M Tilson; Fiscal Year: 2005
    ..Recent approaches such as the search for candidate genes and the methodology of genome wide scanning among AAA families or sibling pairs will be discussed. ..
  25. TM4: Software for High-Dimensional Data Analysis
    John Quackenbush; Fiscal Year: 2009
    ....
  26. Epigenetic Variation and its Determinants in Depression
    James Potash; Fiscal Year: 2008
    ..Results from the novel studies proposed in this application should shed light on the epigenetic mechanisms and gene-environment interactions that result in vulnerability to depression. ..
  27. EXPRESSION PROFILING OF RODENT MODELS OF HUMAN DISEASE
    John Quackenbush; Fiscal Year: 2004
    ..abstract_text> ..
  28. COMPUTATIONAL ANALYSIS OF GENOME EXPRESSION DATA
    Michael Zhang; Fiscal Year: 2002
    ..abstract_text> ..
  29. Tool to Integrate Genomic and Proteomic Data of Aging
    ZOE LACROIX; Fiscal Year: 2002
    ..Aim 2: Enhance the access to information related to age-related diseases, disorders and disabilities through the exploration of multiple data sources. ..
  30. Integrated approaches to deriving predictive networks from public data sources
    John Quackenbush; Fiscal Year: 2010
    ..The end goals will not only be to create the framework for creating such predictive models, but to develop software and tools to allow others in the community to create models for their own systems of interest. ..
  31. Characterization of the flexible portions of fibrinogen
    Russell Doolittle; Fiscal Year: 2007
    ..These studies are aimed at determining the degree of specificity involved in the assembly of fibrin units and protofibrils as well as the relative locations of the regions involved. ..
  32. A Computational Genotyping System for Improved Influenza Surveillance
    Guoqing Lu; Fiscal Year: 2010
    ..With the genotyping database system, newly emerging influenza A viral genotypes can be identified in a timely and cost-effective manner. ..
  33. Fragment assembly and metabolic/species diversity analysis for Human microbiome p
    Yuzhen Ye; Fiscal Year: 2010
    ....
  34. STUDIES OF GENOMIC IMPRINTING IN BIPOLAR DISORDER
    James Potash; Fiscal Year: 2005
    ....
  35. MGED 9&10 Student Travel Awards
    Catherine Ball; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  36. Colliding Categories: Haplotypes, Race & Ethnicity
    Jonathan Kahn; Fiscal Year: 2003
    ..The project will disseminate its findings through a consensus article, web-based materials, a national conference to be held during its second year, and a published symposium growing out of that conference. ..
  37. ATHEROSCLEROSIS PREVENTION IN MICE BY MUTANT APO A-1
    GODFREY GETZ; Fiscal Year: 2001
    ....
  38. Identification of Novel Biomarkers in HD
    Tatiana Foroud; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  39. The ethics of consent for the public release of potentially identifiable DNA data
    Amy McGuire; Fiscal Year: 2009
    ..Moreover, it will increase our understanding of participants'judgments and attitudes toward data sharing, which will improve the overall conduct of biomedical research, build public trust, and foster research participation. ..
  40. Public HIV Drug Resistance Database
    ROBERT WILLIAM SHAFER; Fiscal Year: 2010
    ..UCL is on the forefront of research into the problem of transmitted drug resistance and Oxford University is on the forefront of research on virus evolution and population genetics. ..
  41. ROLE OF FRIZZLED RECEPTORS AND EMBRYOGENESIS
    Stephen Ekker; Fiscal Year: 2001
    ..Using these tools, we will identify the signaling cascades mediated by this family of receptor- like molecules in an attempt to understand in a broader context the role this new gene family plays in development. ..
  42. 'Training in Endocrinology and Neurobiology of Aging'
    Caleb Finch; Fiscal Year: 2007
    ..Opportunities for human studies on aging, including ethnic differences in aging processes, are provided through the Alzheimer Disease Research Center and the Diabetes Research Center. ..
  43. GENE EXPRESSION IN BRUCELLA-INFECTED MACROPHAGES
    Yongqun He; Fiscal Year: 2005
    ..abstract_text> ..
  44. Implications of Genomics Research on Racial Definition
    Seymour Garte; Fiscal Year: 2003
    ..A new paradigm of gene-specific variation will be developed for a biomedically useful method of division of the human population into groups based on criteria different from current definitions of race. ..
  45. HIGH THROUGHPUT ANNOTATION OF GENOMIC DNA SEQUENCE
    Christian Stoeckert; Fiscal Year: 2003
    ..To respond to the public community, queries to the web interface will be incorporated and bulk files provided in response to users of the allgenes.org site. Planned is the inclusion of on-demand annotation of new contigs. ..
  46. Plasmodium Genome Database
    Christian Stoeckert; Fiscal Year: 2008
    ..The overall goal of this project is to develop and maintain a database that expedites biological discovery, including the identification of drug targets and vaccine antigens useful in the fight against malaria. ..
  47. Evolutionary Approaches for synthetic Library Design
    ERIC GAUCHER; Fiscal Year: 2006
    ..This proposal builds the Foundation's expertise in molecular evolution and on Blue Heron's technology for gene synthesis and library generation. [unreadable] [unreadable] [unreadable]..
  48. Validation of C. elegans "fat genes" in the mouse
    Karen Reue; Fiscal Year: 2005
    ..This pilot study will reveal whether "fat genes" identified in the invertebrate C. elegans have a similar role in mammals, and may identify novel genes involved in fat storage and metabolism. ..
  49. GENE EXPRESSION BASED CLASSIFICATION OF GLIAL TUMORS
    Stanley Nelson; Fiscal Year: 2004
    ..3)To develop a set of genes with prognostic importance in low grade astrocytomas. 4)To validate the importance of the genes from specific aims 2 and 3 in the prognosis of low grade astrocytomas. ..
  50. PD GWAS Consortium
    Tatiana M Foroud; Fiscal Year: 2010
    ....
  51. T CELL AND EVOLUTION OF GENETIC ATHEROGENESIS
    GODFREY GETZ; Fiscal Year: 2001
    ....
  52. MOUSE GENETIC MAPPING RESOURCE
    Janan Eppig; Fiscal Year: 2001
    ..abstract_text> ..
  53. Directory and Information System components for genomes
    Donald Gilbert; Fiscal Year: 2003
    ..Such a module for automated, common-standard use of organism genome data is an important step toward a grid of data useable for the large-scale analyses desired bioscientists. ..
  54. DEVELOPMENT OF THE METACYC METABOLIC PATHWAY DATABASE
    Peter Karp; Fiscal Year: 2003
    ....
  55. Infrastructure equipment for gene expression analysis
    Sorin Draghici; Fiscal Year: 2003
    ..Furthermore, the system may be expanded in the future, to accommodate new investigators at a cost that is very feasible. ..
  56. Acquistion of an inFlux GMP cell sorter.
    Timothy Graubert; Fiscal Year: 2005
    ..This instrument will provide added value for many funded projects at Washington University that collectively accounted for over $328M in total awards from the NIH in 2002, placing it third among medical centers in the United States. ..
  57. Type 1 Diabetes Genetics Consortium
    Stephen Rich; Fiscal Year: 2007
    ..The Consortium will gain a better understandingof disease mechanisms, with a purpose of altering these mechanisms and pathways in individualsat risk of type 1 diabetes. ..
  58. Hemolytic Anemia: Models
    LUANNE PETERS; Fiscal Year: 2006
    ..5 isoform in the structure and assembly of the sarcoplasmic reticulum by an in vivo developmental study. ..
  59. ORGANELLE MEMBRANES IN PLATELET STORAGE POOL DISEASE
    LUANNE PETERS; Fiscal Year: 2009
    ..Lung fibrosis typically leads to death in the 4th to 5th decades. This study is designed to identify the underlying genetic causes of HPS, which will provide avenues of research for potential therapies. ..
  60. Functional Arterial Changes in Atherogenesis
    Iftikhar Kullo; Fiscal Year: 2007
    ..abstract_text> ..
  61. PCR Screening for CMV in Umbilical Cord Blood Stem Cells
    Christopher Hillyer; Fiscal Year: 2003
    ....
  62. Receptor Phosphatases and Process Outgrowth
    Eduardo Macagno; Fiscal Year: 2005
    ....
  63. Organized Self-Management Support for Chronic Depression
    Evette Ludman; Fiscal Year: 2005
    ....
  64. Visual Data Extraction and Conversion Programming Tool
    Hui Hsien Chou; Fiscal Year: 2005
    ..Therefore, this tool will provide great enabling power to biomedical scientists to help them make rapid advances in biomedical research and medicine. ..
  65. Functional discovery of Porphyromonas gingivalis genes
    Tsute Chen; Fiscal Year: 2006
    ..abstract_text> ..
  66. Statistical Methods for Gene Mapping-a New Paradigm
    Shili Lin; Fiscal Year: 2006
    ..4. To implement the methodology developed in user friendly, well-documented programs, and to make the package of the programs available to other interested researchers. ..
  67. Parallel Computer
    Jason Moore; Fiscal Year: 2004
    ..This resource will make it possible to carry out computationally intensive biomedical investigations otherwise not feasible thus significantly increasing the rate of scientific discovery in a variety of biomedical disciplines. ..
  68. GENETIC ARCHITECTURE OF PLASMA T-PA AND PAI-1
    Jason Moore; Fiscal Year: 2004
    ..This collaborative proposal provides a robust mechanism for highly focused translational research in the molecular genetics and biology of the role of the fibrinolytic system in arterial and cerebral thrombosis. ..