nucleic acid databases

Summary

Summary: DATABASES containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.

Top Publications

  1. pmc miRBase: tools for microRNA genomics
    Sam Griffiths-Jones
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
    Nucleic Acids Res 36:D154-8. 2008
  2. pmc miRBase: microRNA sequences, targets and gene nomenclature
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 34:D140-4. 2006
  3. pmc The COG database: an updated version includes eukaryotes
    Roman L Tatusov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Bioinformatics 4:41. 2003
  4. ncbi Repbase Update, a database of eukaryotic repetitive elements
    J Jurka
    Genetic Information Research Institute, Mountain View, CA 94043, USA
    Cytogenet Genome Res 110:462-7. 2005
  5. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
  6. ncbi Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
  7. pmc ISfinder: the reference centre for bacterial insertion sequences
    P Siguier
    Laboratoire de Microbiologie et Genetique Moleculaires, C N R S 118, route de Narbonne, F 31062 Toulouse Cedex, France
    Nucleic Acids Res 34:D32-6. 2006
  8. pmc The microRNA Registry
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 9SA, UK
    Nucleic Acids Res 32:D109-11. 2004
  9. pmc Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers
    George Adrian Calin
    Department of Microbiology and Immunology, Division of Clinical Pharmacology, Biostatistics Section, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Proc Natl Acad Sci U S A 101:2999-3004. 2004
  10. ncbi A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
    Stephen A Goff
    Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA
    Science 296:92-100. 2002

Research Grants

  1. dbVision: A Toolbox for bioimage databases
    Kaushal Solanki; Fiscal Year: 2009
  2. DNA Fingerprinting and Civil Liberties
    Benjamin Moulton; Fiscal Year: 2005
  3. PATTERN RECOGNITION IN NUCLEIC ACID SEQUENCE DATABASES
    Christian Burks; Fiscal Year: 1991
  4. Cancer Relevent Proteins in the Human Prostate Proteome
    Sarka Beranova Giorgianni; Fiscal Year: 2003
  5. GENETIC MICROSYSTEMS GMS417 ARRAY SEQUENCER/418 ARRAYER
    Lorraine Flaherty; Fiscal Year: 2000
  6. FUNCTIONAL GENOMICS BY TAGGED SEQUENCE MUTAGENESIS
    H Ruley; Fiscal Year: 2002
  7. CONTROL OF VEGF STIMULATED ENDOTHELIAL PROLIFERATION
    MARK ALLIEGRO; Fiscal Year: 2000
  8. Developing tools for Bio-Molecular Image Informatics
    BANGALORE MANJUNATH; Fiscal Year: 2005
  9. COMPUTATIONAL ANALYSIS OF GENOME EXPRESSION DATA
    Michael Zhang; Fiscal Year: 2002
  10. Infrastructure equipment for gene expression analysis
    Sorin Draghici; Fiscal Year: 2003

Detail Information

Publications262 found, 100 shown here

  1. pmc miRBase: tools for microRNA genomics
    Sam Griffiths-Jones
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
    Nucleic Acids Res 36:D154-8. 2008
    ..miRBase is available at http://microrna.sanger.ac.uk/...
  2. pmc miRBase: microRNA sequences, targets and gene nomenclature
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 34:D140-4. 2006
    ..miRBase Sequences is the primary online repository for miRNA sequence data and annotation. miRBase Targets is a comprehensive new database of predicted miRNA target genes. miRBase is available at http://microrna.sanger.ac.uk/...
  3. pmc The COG database: an updated version includes eukaryotes
    Roman L Tatusov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Bioinformatics 4:41. 2003
    ..Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies...
  4. ncbi Repbase Update, a database of eukaryotic repetitive elements
    J Jurka
    Genetic Information Research Institute, Mountain View, CA 94043, USA
    Cytogenet Genome Res 110:462-7. 2005
    ..Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst.org/Repbase_Update.html...
  5. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
    ..The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'...
  6. ncbi Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
    ..All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST...
  7. pmc ISfinder: the reference centre for bacterial insertion sequences
    P Siguier
    Laboratoire de Microbiologie et Genetique Moleculaires, C N R S 118, route de Narbonne, F 31062 Toulouse Cedex, France
    Nucleic Acids Res 34:D32-6. 2006
    ..Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication...
  8. pmc The microRNA Registry
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 9SA, UK
    Nucleic Acids Res 32:D109-11. 2004
    ..sanger.ac.uk/Software/Rfam/mirna/), and all sequence and annotation data are freely available for download. Release 2.0 of the database contains 506 miRNA entries from six organisms...
  9. pmc Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers
    George Adrian Calin
    Department of Microbiology and Immunology, Division of Clinical Pharmacology, Biostatistics Section, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Proc Natl Acad Sci U S A 101:2999-3004. 2004
    ..These data provide a catalog of miR genes that may have roles in cancer and argue that the full complement of miRs in a genome may be extensively involved in cancers...
  10. ncbi A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
    Stephen A Goff
    Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA
    Science 296:92-100. 2002
    ..Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops...
  11. pmc At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies
    Kevin E Ashelford
    Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, P O Box 915, Cardiff CF10 3TL, United Kingdom
    Appl Environ Microbiol 71:7724-36. 2005
    ..The program is called Pintail, is released under the terms of the GNU General Public License open source license, and is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/...
  12. 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
    ....
  13. pmc Tools for the automatic identification and classification of RNA base pairs
    Huanwang Yang
    Department of Chemistry and Chemical Biology, Rutgers University, NJ 08854 8087, USA
    Nucleic Acids Res 31:3450-60. 2003
    ..rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/...
  14. pmc Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    T Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:5069-72. 2006
    ..Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria...
  15. pmc Rfam: an RNA family database
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 31:439-41. 2003
    ..wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database...
  16. ncbi TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
    ..The system can run on multi-CPU architectures including SMP and PVM...
  17. pmc The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
    Jamie J Cannone
    Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712 1095, USA
    BMC Bioinformatics 3:2. 2002
    ..This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields...
  18. ncbi Recombination drives the evolution of GC-content in the human genome
    Julien Meunier
    UMR 5558 CNRS, Université Lyon I, Villeurbanne, France
    Mol Biol Evol 21:984-90. 2004
    ..These results have important implications for understanding the spatial and temporal variations of substitution processes in a broad range of sexual organisms, and for detecting the hallmarks of natural selection in DNA sequences...
  19. pmc The vertebrate genome annotation (Vega) database
    L G Wilming
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nucleic Acids Res 36:D753-60. 2008
    ..In addition, we offer manual annotation of a number of haplotype regions in mouse and human and regions of comparative interest in pig and dog that are unique to Vega...
  20. pmc cisRED: a database system for genome-scale computational discovery of regulatory elements
    G Robertson
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
    Nucleic Acids Res 34:D68-73. 2006
    ..The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally...
  21. pmc PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
    Magali Lescot
    Vakgroep Moleculaire Genetica, Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, K L Ledeganckstraat 35, B 9000 Gent, Belgium
    Nucleic Acids Res 30:325-7. 2002
    ..New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/...
  22. pmc Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
    Manhong Dai
    Molecular and Behavioural Neuroscience Institute and Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 33:e175. 2005
    ..It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions...
  23. pmc TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies
    Fang Zhao
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 33:D103-7. 2005
    ..TRED can provide good training datasets for further genome-wide cis-regulatory element prediction and annotation, assist detailed functional studies and facilitate the decipher of gene regulatory networks (http://rulai.cshl.edu/TRED)...
  24. pmc Rfam: updates to the RNA families database
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Nucleic Acids Res 37:D136-40. 2009
    ..Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/...
  25. pmc PolyA_DB: a database for mammalian mRNA polyadenylation
    Haibo Zhang
    Center for Computational Biology and Bioengineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
    Nucleic Acids Res 33:D116-20. 2005
    ..The database is accessible via the website (http://polya.umdnj.edu/polyadb)...
  26. pmc VISTA Enhancer Browser--a database of tissue-specific human enhancers
    Axel Visel
    Genomics Division, MS 84 171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
    Nucleic Acids Res 35:D88-92. 2007
    ..These experimentally validated training sets are expected to provide a basis for a wide range of downstream computational and functional studies of enhancer function...
  27. pmc The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
    J R Cole
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 33:D294-6. 2005
    ..The RDP-II email address for questions or comments is rdpstaff@msu.edu...
  28. pmc NCBI reference sequences (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 35:D61-5. 2007
    ..The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence...
  29. pmc The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
    Shu Ouyang
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:D360-3. 2004
    ..Collectively, these databases provide a resource for the identification, classification and analysis of repetitive sequences in plants...
  30. ncbi A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
    Jun Yu
    Beijing Genomics Institute Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China
    Science 296:79-92. 2002
    ..4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences...
  31. pmc ORegAnno: an open-access community-driven resource for regulatory annotation
    Obi L Griffith
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
    Nucleic Acids Res 36:D107-13. 2008
    ..All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org...
  32. ncbi Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage
    Jean Vincent Chamary
    Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
    Mol Biol Evol 21:1014-23. 2004
    ..Therefore, by elimination, we propose this to be strong evidence for selectively driven codon usage in mammals...
  33. pmc Fast and effective prediction of microRNA/target duplexes
    Marc Rehmsmeier
    Universitat Bielefeld, International NRW Graduate School in Bioinformatics and Genome Research, Postfach 10 01 31, 33501 Bielefeld, Germany
    RNA 10:1507-17. 2004
    ..RNAhybrid, with its accompanying programs RNAcalibrate and RNAeffective, is available for download and as a Web tool on the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/)...
  34. ncbi Computational identification of novel microRNAs and targets in Brassica napus
    Fu Liang Xie
    Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
    FEBS Lett 581:1464-74. 2007
    ..The program is allowed to be run on Windows Operation System platform. miRNAassist is freely available if required...
  35. ncbi Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity
    Michael Hiller
    Institute of Computer Science, Friedrich Schiller University Jena, Chair for Bioinformatics, Ernst Abbe Platz 2, 07743 Jena, Germany
    Nat Genet 36:1255-7. 2004
    ..Because of their subtle effects on mRNA and protein structures, these splice acceptors are often overlooked or underestimated, but they may have a great impact on biology and disease...
  36. pmc GenBank
    Dennis A Benson
    Department of Health and Human Services, 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 33:D34-8. 2005
    ..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov...
  37. pmc Origin and evolution of human microRNAs from transposable elements
    Jittima Piriyapongsa
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
    Genetics 176:1323-37. 2007
    ..Our results indicate that TEs provide a natural mechanism for the origination miRNAs that can contribute to regulatory divergence between species as well as a rich source for the discovery of as yet unknown miRNA genes...
  38. pmc RTPrimerDB: the real-time PCR primer and probe database
    Filip Pattyn
    Centre for Medical Genetics, Gent University Hospital, 1K5, De Pintelaan 185, B 9000 Gent, Belgium
    Nucleic Acids Res 31:122-3. 2003
    ..Real-time PCR primer/probe records are available at http://www.realtimeprimerdatabase.ht.st...
  39. ncbi EGene: a configurable pipeline generation system for automated sequence analysis
    Alan M Durham
    Depto de Ciências da Computação, Instituto de Matemática e Estatística São Paulo, SP, 05508 900, Brazil
    Bioinformatics 21:2812-3. 2005
    ..EGene comes with CoEd, a visual tool to facilitate pipeline construction and documentation. A series of components to build pipelines for sequence processing is provided...
  40. pmc RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
    Eckart Bindewald
    Basic Research Program, SAIC Frederick and Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Nucleic Acids Res 36:D392-7. 2008
    ..This database is useful for analyzing RNA structures as well as for designing novel RNA structures on a nanoscale. The database can be accessed at: http://rnajunction.abcc.ncifcrf.gov/..
  41. pmc Genomewide comparative analysis of alternative splicing in plants
    Bing Bing Wang
    Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 3260, USA
    Proc Natl Acad Sci U S A 103:7175-80. 2006
    ..We created a comprehensive web-interfaced database to compile and visualize the evidence for alternative splicing in plants (Alternative Splicing in Plants, available at www.plantgdb.org/ASIP)...
  42. ncbi Identification of soybean microRNAs and their targets
    Baohong Zhang
    Department of Biology, East Carolina University, Greenville, NC 27858, USA
    Planta 229:161-82. 2008
    ....
  43. ncbi Toward the full set of human mitochondrial aminoacyl-tRNA synthetases: characterization of AspRS and TyrRS
    Luc Bonnefond
    Department Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse, UPR 9002, Institut de Biologie Moleculaire et Cellulaire du CNRS, 15 rue Rene Descartes, F 67084 Strasbourg CEDEX, France
    Biochemistry 44:4805-16. 2005
    ..Their sequence analysis confirms and further extends the view that, except for lysyl- and glycyl-tRNA synthetases, human mitochondrial and cytosolic enzymes are coded by two different sets of genes...
  44. pmc The Rice Annotation Project Database (RAP-DB): 2008 update
    Tsuyoshi Tanaka
    National Institute of Agrobiological Sciences, Ibaraki 305 8602, Japan
    Nucleic Acids Res 36:D1028-33. 2008
    ..We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/...
  45. pmc RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database
    Dag Harmsen
    Institut für Hygiene und Mikrobiologie, Universitat Wurzburg, D 97080 Wurzburg, Germany
    Nucleic Acids Res 30:416-7. 2002
    ..The RIDOM web site is directly accessible on the World Wide Web at http://www.ridom.de/. The email address for questions and comments is webmaster@ridom.de...
  46. pmc oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes
    Shannan J Ho Sui
    Centre for Molecular Medicine and Therapeutics, University of British Columbia Vancouver, BC, Canada
    Nucleic Acids Res 33:3154-64. 2005
    ..Simulation studies indicate that oPOSSUM produces few false positives using empirically defined thresholds and can tolerate up to 50% noise in a set of co-expressed genes...
  47. ncbi Global functional profiling of gene expression
    Sorin Draghici
    Department of Computer Science, Wayne State University, 5143 Cass Avenue, Detroit, MI 48202, USA
    Genomics 81:98-104. 2003
    ..OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms...
  48. pmc A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis
    Ik Young Choi
    Soybean Genomics and Improvement Laboratory, USDA, ARS, Beltsville, Maryland 20705, USA
    Genetics 176:685-96. 2007
    ....
  49. pmc ppdb: a plant promoter database
    Yoshiharu Y Yamamoto
    Center for Gene Research, Nagoya University, Nagoya 464 8602, Japan
    Nucleic Acids Res 36:D977-81. 2008
    ..Each regulatory sequence is hyperlinked to literary information, a PLACE entry served by a plant cis-element database, and a list of promoters containing the regulatory sequence...
  50. pmc Automated de novo prediction of native-like RNA tertiary structures
    Rhiju Das
    Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Box 357350, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 104:14664-9. 2007
    ....
  51. pmc TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase
    David H Ardell
    Department of Molecular Evolution, Evolutionary Biology Center Norbyvägen 18C Uppsala University SE 752 36 Uppsala Sweden
    Nucleic Acids Res 34:893-904. 2006
    ..Our results demonstrate that TFAM is an effective tool for the bioinformatics, comparative genomics and evolutionary study of tRNA identity...
  52. pmc Lateral transfer of mating system in Stemphylium
    Patrik Inderbitzin
    Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
    Proc Natl Acad Sci U S A 102:11390-5. 2005
    ..Another group of selfers in Stemphylium only had forward-oriented MAT1-1 at their MAT loci, constituting an additional and third origin of selfing in Stemphylium...
  53. pmc Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design
    Hin Hark Gan
    Department of Chemistry, New York University, 251 Mercer Street, New York, 10012 NY, USA
    Nucleic Acids Res 31:2926-43. 2003
    ..Thus, our graph theory approach to RNA structures has implications for RNA genomics, structure analysis and design...
  54. pmc 5S Ribosomal RNA Database
    Maciej Szymanski
    Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12, 61704 Poznan, Poland
    Nucleic Acids Res 30:176-8. 2002
    ..These include 536 eubacterial, 61 archaebacterial, 1611 eukaryotic and 72 organelle sequences. The database is available on line through the World Wide Web at http://biobases.ibch.poznan.pl/5SData/...
  55. pmc Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective
    R Henrik Nilsson
    Department of Plant and Environmental Sciences, Goteborg University, Sweden
    PLoS ONE 1:e59. 2006
    ..Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries...
  56. ncbi MFEprimer: multiple factor evaluation of the specificity of PCR primers
    Wubin Qu
    Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing, China
    Bioinformatics 25:276-8. 2009
    ..Furthermore, we maintained a Primer3Plus server with a modified Primer3Manager for one-stop primer design and specificity checking...
  57. pmc The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community
    Martha B Arnaud
    Department of Genetics, Stanford University Medical School, Stanford, CA 94305 5120, USA
    Nucleic Acids Res 38:D420-7. 2010
    ..All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at aspergillus-curator@genome.stanford.edu...
  58. pmc SoyBase, the USDA-ARS soybean genetics and genomics database
    David Grant
    USDA ARS CICGRU, Department of Agronomy, Iowa State University, Ames, IA 50011, USA
    Nucleic Acids Res 38:D843-6. 2010
    ..SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies. SoyBase can be accessed at http://soybase.org...
  59. pmc JASPAR: an open-access database for eukaryotic transcription factor binding profiles
    Albin Sandelin
    Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, S 17177 Stockholm, Sweden
    Nucleic Acids Res 32:D91-4. 2004
    ..JASPAR is available at http://jaspar. cgb.ki.se...
  60. pmc The Genographic Project public participation mitochondrial DNA database
    Doron M Behar
    PLoS Genet 3:e104. 2007
    ..We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool...
  61. pmc PlantProm: a database of plant promoter sequences
    Ilham A Shahmuradov
    Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
    Nucleic Acids Res 31:114-7. 2003
    ..and the application of a support ftp: vector machine approach for promoter identification is under development. PlantProm DB is available at http://mendel.cs.rhul.ac.uk/ and http://www.softberry.com/...
  62. ncbi Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing
    Michael Krawczak
    Institut für Medizinische Informatik und Statistik, Christian Albrechts Universitat, Kiel, Germany
    Hum Mutat 28:150-8. 2007
    ..6% of disease-causing missense substitutions in human genes are likely to affect the mRNA splicing phenotype. Taken together, our results are consistent with correct donor splice-site recognition being a key step in exon recognition...
  63. pmc The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
    J R Cole
    Center for Microbial Ecology, 2225A Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 31:442-3. 2003
    ..The RDP-II email address for questions or comments is rdpstaff@msu.edu...
  64. pmc Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs
    Jun Xie
    State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 220 Handan Road, 200433 Shanghai, China
    Nucleic Acids Res 35:D183-7. 2007
    ..Thus our sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research. The database is free available at http://gene.fudan.sh.cn/snoRNAbase.nsf...
  65. pmc The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
    J R Cole
    Center for Microbial Ecology, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 35:D169-72. 2007
    ..In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website (http://rdp.cme.msu.edu/)...
  66. pmc Distribution and effects of nonsense polymorphisms in human genes
    Yumi Yamaguchi-Kabata
    Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS ONE 3:e3393. 2008
    ..In particular, little is known about the distribution of nonsense polymorphisms in human genes despite their drastic effects on gene products...
  67. pmc SCOR: a Structural Classification of RNA database
    Peter S Klosterman
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    Nucleic Acids Res 30:392-4. 2002
    ..A classification of the well-characterized tertiary interactions found in the larger RNA structures is also included along with examples. The SCOR database is accessible at http://scor.lbl.gov...
  68. pmc Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers
    Zhenbao Yu
    Health Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada
    Nucleic Acids Res 35:4535-41. 2007
    ..Hence, SNPs located in miRNA-binding sites affect miRNA target expression and function, and are potentially associated with cancers...
  69. pmc 3D-footprint: a database for the structural analysis of protein-DNA complexes
    Bruno Contreras-Moreira
    Estacion Experimental de Aula Dei, Consejo Superior de Investigaciones Cientificas, Fundación ARAID, Paseo María Agustín 36, Zaragoza, Spain
    Nucleic Acids Res 38:D91-7. 2010
    ..3D-footprint is available at http://floresta.eead.csic.es/3dfootprint with demo buttons and a comprehensive tutorial that illustrates the main uses of this resource...
  70. ncbi Codon usage bias amongst plant viruses
    M J Adams
    Plant Pathogen Interactions Division, Rothamsted Research, Harpenden, Herts, UK
    Arch Virol 149:113-35. 2004
    ..Mutational bias, rather than translational selection appears to account for the majority of the variation detected. The software is available at http://www.dpvweb.net/analysis/codons.php...
  71. pmc Kalign--an accurate and fast multiple sequence alignment algorithm
    Timo Lassmann
    Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, S 17177 Stockholm, Sweden
    BMC Bioinformatics 6:298. 2005
    ..Current MSA methods suffer from being either too inaccurate or too computationally expensive to be applied effectively in large-scale comparative genomics...
  72. ncbi Identification and characterization of new plant microRNAs using EST analysis
    Bao Hong Zhang
    The Institute of Environmental and Human Health, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
    Cell Res 15:336-60. 2005
    ..Environmental stresses and developmental switching may be the signals for synthesis and regulation of miRNAs in plants. A model for miRNA induction and expression, and gene regulation by miRNA is hypothesized...
  73. pmc fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
    Taishin Kin
    Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology AIST Aomi 2 42, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 35:D145-8. 2007
    ..fRNAdb provides an efficient interface to help users filter out particular transcripts under their own criteria to sort out functional RNA candidates. fRNAdb is available at http://www.ncrna.org/..
  74. pmc HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites
    Vidhya Jagannathan
    Swiss Institute for Experimental Cancer Research and Swiss Institute of Bioinformatics, Ch des Boveresses 155, CH 1066 Epalinges, Switzerland
    Nucleic Acids Res 34:D90-4. 2006
    ..HTPSELEX is available from ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex/ and http://www.isrec.isb-sib.ch/htpselex...
  75. ncbi Nucleotide sequence database policies
    Soren Brunak
    Science 298:1333. 2002
  76. ncbi Predictive identification of exonic splicing enhancers in human genes
    William G Fairbrother
    Department of Biology, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 297:1007-13. 2002
    ..The motifs identified enable prediction of the splicing phenotypes of exonic mutations in human genes...
  77. pmc UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002
    Graziano Pesole
    Dipartimento di Fisiologia e Biochimica Generali, Universita di Milano, Via Celoria 26, 20133 Milano, Italy
    Nucleic Acids Res 30:335-40. 2002
    ..All Internet resources we implemented for retrieval and functional analysis of 5'- and 3'-UTRs of eukaryotic mRNAs are accessible at http://bighost.area.ba.cnr.it/BIG/UTRHome/...
  78. pmc InSatDb: a microsatellite database of fully sequenced insect genomes
    Sunil Archak
    Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500 076, India
    Nucleic Acids Res 35:D36-9. 2007
    ..A separate 'Analysis' section illustrates the comparative genomic analysis that can be carried out using the output. InSatDb is available at www.cdfd.org.in/insatdb...
  79. pmc Aptamer database
    Jennifer F Lee
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712, USA
    Nucleic Acids Res 32:D95-100. 2004
    ..The database is updated monthly and is publicly available at http://aptamer. icmb.utexas.edu/...
  80. pmc An enhanced MITOMAP with a global mtDNA mutational phylogeny
    Eduardo Ruiz-Pesini
    Center for Molecular and Mitochondrial Medicine and Genetics MAMMAG and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of California, Irvine, CA 92697 3900, USA
    Nucleic Acids Res 35:D823-8. 2007
    ..These additions position MITOMAP for the implementation of our automated mtDNA sequence analysis system, Mitomaster...
  81. pmc Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA
    Mayumi Nakano
    Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19714, USA
    Nucleic Acids Res 34:D731-5. 2006
    ..Interpretation of the small RNA MPSS data is facilitated by the inclusion of extensive repeat data in our genome viewer. All the data and the tools introduced in this article are available at http://mpss.udel.edu...
  82. ncbi A hitchhiker's guide to expressed sequence tag (EST) analysis
    Shivashankar H Nagaraj
    Department of Chemistry and Biomolecular Sciences and Biotechnology Research Institute, Macquarie University, Sydney, Australia
    Brief Bioinform 8:6-21. 2007
    ..An investigation of EST analysis platforms reveals that they all terminate prior to downstream functional annotation including gene ontologies, motif/pattern analysis and pathway mapping...
  83. pmc S/MARt DB: a database on scaffold/matrix attached regions
    Ines Liebich
    Research Group Bioinformatics, GBF, Mascheroder Weg 1, D 38124 Braunschweig, Germany
    Nucleic Acids Res 30:372-4. 2002
    ..S/MARt DB is closely linked to the TRANSFAC database on transcription factors and their binding sites. It is freely accessible through the World Wide Web (http://transfac.gbf.de/SMARtDB/) for non-profit research...
  84. pmc Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species
    C Y Turenne
    National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Population and Public Health Branch, Canada
    J Clin Microbiol 39:3637-48. 2001
    ....
  85. ncbi Recent segmental duplications in the human genome
    Jeffrey A Bailey
    Department of Genetics, Center for Computational Genomics, and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA
    Science 297:1003-7. 2002
    ..Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity...
  86. pmc The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences
    Wolfgang Helmberg
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 45, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:W173-5. 2004
    ..The results of the submission are returned as a table of potential allele hits, along with the respective base changes and an interactive sequence viewer for close examination of the alignment...
  87. ncbi EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
    Jongsik Chun
    Interdisciplinary Program in Bioinformatics, Seoul National University, 56 1 Shillim dong, Kwanak gu, Seoul 151 742, Republic of Korea
    Int J Syst Evol Microbiol 57:2259-61. 2007
    ..The EzTaxon server is freely accessible over the Internet at http://www.eztaxon.org/..
  88. ncbi Identification of Heterodera glycines (soybean cyst nematode [SCN]) cDNA sequences with high identity to those of Caenorhabditis elegans having lethal mutant or RNAi phenotypes
    Nadim W Alkharouf
    United States Department of Agriculture, ARS, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705 2350, USA
    Exp Parasitol 115:247-58. 2007
    ..Endogenous Hg-rps-23 exhibited typical RNA silencing as shown by RT-PCR. However, an unrelated gene Hg-unc-87 did not exhibit RNA silencing in the Hg-rps-23 dsRNA-treated worms, demonstrating the specificity of the silencing...
  89. pmc mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences
    Max Ingman
    Centre for Integrative Genomics, University of Lausanne, Switzerland
    Nucleic Acids Res 34:D749-51. 2006
    ..Recent expansions in the capabilities of mtDB include a haplotype search function and the ability to identify and download sequences carrying particular variants...
  90. pmc TRED: a transcriptional regulatory element database, new entries and other development
    C Jiang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring, Harbor NY 11724, USA
    Nucleic Acids Res 35:D137-40. 2007
    ..Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research...
  91. ncbi Zerg: a very fast BLAST parser library
    Apua C M Paquola
    Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo 05508 900, Sao Paulo, SP, Brazil
    Bioinformatics 19:1035-6. 2003
    ..It is optimized for speed, being especially useful for large-scale genomic analysis. Benchmark tests show that Zerg is over two orders of magnitude faster than some widely used BLAST parsers...
  92. ncbi On biased distribution of introns in various eukaryotes
    A Sakurai
    Institute for Advanced Biosciences, Keio University, 5322 Endo, Fujisawa City, Kanagawa, Japan
    Gene 300:89-95. 2002
    ....
  93. pmc Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns
    Colin N Dewey
    National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Genomics 7:311. 2006
    ..We explored the connections between the length of vertebrate introns, the strength of splice sites, exonic splicing signals, and evolution of flanking exons...
  94. pmc GenBank: update
    Dennis A Benson
    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 32:D23-6. 2004
    ..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov...
  95. pmc ACLAME: a CLAssification of Mobile genetic Elements
    Raphael Leplae
    Service de Conformation de Macromolécules Biologiques et de Bioinformatique, Universite Libre de Bruxelles, Belgium
    Nucleic Acids Res 32:D45-9. 2004
    ....
  96. pmc Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae
    Jonathan L Jacobs
    Department of Cell Biology and Molecular Genetics, University of Maryland, 2135 Microbiology Building, College Park, MD 20742, USA
    Nucleic Acids Res 35:165-74. 2007
    ....
  97. pmc Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding
    Pierre Taberlet
    Laboratoire d Ecologie Alpine, CNRS UMR 5553, Universite Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
    Nucleic Acids Res 35:e14. 2007
    ....
  98. ncbi Computational prediction of rice (Oryza sativa) miRNA targets
    Sunil Archak
    Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500076, India
    Genomics Proteomics Bioinformatics 5:196-206. 2007
    ..Such an extent of cross-species conservation and algorithmic consensus confers confidence in the list of rice miRNA targets predicted in this study...
  99. ncbi SNPper: retrieval and analysis of human SNPs
    A Riva
    Children s Hospital Informatics Program, Children s Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
    Bioinformatics 18:1681-5. 2002
    ..Although large collections of SNPs exist in public databases, researchers need tools to effectively retrieve and manipulate them...
  100. ncbi Understanding human disease mutations through the use of interspecific genetic variation
    M P Miller
    Department of Biology, Arizona State University, Tempe, AZ 85287 1501, USA
    Hum Mol Genet 10:2319-28. 2001
    ....
  101. pmc ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data
    Olivier Arnaiz
    Centre de Genetique Moleculaire, CNRS, 91198 Gif sur Yvette, France
    Nucleic Acids Res 35:D439-44. 2007
    ..Future ParameciumDB development plans include coordination of human curation of the near 40 000 gene models by members of the research community...

Research Grants73

  1. dbVision: A Toolbox for bioimage databases
    Kaushal Solanki; Fiscal Year: 2009
    ..This STTR Phase II proposal targets this critical need in continuing to develop a simple and flexible image database system that would help the scientists analyze and mine large data collections. ..
  2. DNA Fingerprinting and Civil Liberties
    Benjamin Moulton; Fiscal Year: 2005
    ..abstract_text> ..
  3. PATTERN RECOGNITION IN NUCLEIC ACID SEQUENCE DATABASES
    Christian Burks; Fiscal Year: 1991
    ..With the established measures and model, we will scan the GenBank database for anomalously curved regions, and determine whether or not they are correlated with the functional roles of coincident or neighboring sequences...
  4. Cancer Relevent Proteins in the Human Prostate Proteome
    Sarka Beranova Giorgianni; Fiscal Year: 2003
    ....
  5. GENETIC MICROSYSTEMS GMS417 ARRAY SEQUENCER/418 ARRAYER
    Lorraine Flaherty; Fiscal Year: 2000
    ..Furthermore, this array system will facilitate the development of improved bioinformatics methods for analysis of genomic expression data. ..
  6. FUNCTIONAL GENOMICS BY TAGGED SEQUENCE MUTAGENESIS
    H Ruley; Fiscal Year: 2002
    ..The flanking sequences, designated PSTs, will be compared with the nucleic acid databases to identify instances in which the provirus has disrupted known genes or previously characterized cDNAs...
  7. CONTROL OF VEGF STIMULATED ENDOTHELIAL PROLIFERATION
    MARK ALLIEGRO; Fiscal Year: 2000
    ..This library will be analyzed using standard sequencing techniques and nucleic acid databases. The applicant proposes a third aim to test the hypothesis that pigpen plays a role in RNA biogenesis ..
  8. Developing tools for Bio-Molecular Image Informatics
    BANGALORE MANJUNATH; Fiscal Year: 2005
    ..abstract_text> ..
  9. COMPUTATIONAL ANALYSIS OF GENOME EXPRESSION DATA
    Michael Zhang; Fiscal Year: 2002
    ..abstract_text> ..
  10. 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. ..
  11. Novel algorithms and organisms for Onto-Tools
    Sorin Draghici; Fiscal Year: 2007
    ..The enhanced Onto-Tools will continue to be freely available. Onto-Analyzer and the software evolution tools developed under this proposal will be made freely available to the research community, as well. ..
  12. Phage Display Tools for Automated Blood Typing
    Donald Siegel; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  13. MENTORED QUANTITATIVE RESEARCH CAREER DEVELOPMENT AWARD
    Elisabetta Manduchi; Fiscal Year: 2005
    ..5) To continue participation in the PCBI reading group, in the organization of the two-semester Computational Biology course, and in the coordination of the Computational Biology/Bioinformatics Seminar series at Upenn. ..
  14. Large-Scale Low-Cost Genotyping for the Haplotype Map
    Kelly Frazer; Fiscal Year: 2004
    ..e. 2.25 million SNPs in 270 samples, plus 15 duplicates and 3 blanks) within one year, at the cost and quality specified by the HapMap Project, is well within our capacity. ..
  15. GEISHA, a Chicken Embryo Gene Expression Resource
    PARKER ANTIN; Fiscal Year: 2009
    ..This centralized repository for in situ hybridization gene expression information will provide a valuable and comprehensive resource for the biomedical research community. ..
  16. Mechanisms and significance of cublin-mediated HDL uptake
    WILLIAM ARGRAVES; Fiscal Year: 2009
    ..Together, these studies will provide new insights into the function of cubilin in maternal-embryonic.lipoprotein transport, embryonic development and adult kidney function. ..
  17. Mitochondrial Diabetes & Manganic Porphyrin Treatment
    Douglas C Wallace; Fiscal Year: 2010
    ..These mice will also be treated with the metalloporphyrinmimetics to determine if these drugs will then delay the development of the symptoms and the accumulation of the somatic mtDNA mutations. ..
  18. REGULATION OF CYTOKINE GENES IN MUCOSAL VIRAL INFECTION
    Allan Brasier; Fiscal Year: 2006
    ..Expression of dominant-negative NF-KB and CBP/p300 coactivators will be used to determine their effect on coactivator recruitment. These studies will identify signaling mechanisms and protein interactions in viral-induced inflammation. ..
  19. Community Consultation as an Ethics Method
    Pilar Ossorio; Fiscal Year: 2006
    ..This project wilt yield several manuscripts aimed at professional, policy and public (non-expert) audiences. ..
  20. Cancer Center Microarray Bioinformatics Facility
    W Argraves; Fiscal Year: 2006
    ..Finally, the resource facility will create an internet-accessible database of gene expression profile information collected by HCC investigators to make this data available to the scientific community at large. ..
  21. Genome Sequence Analysis: Theory and Practice
    Carol Bult; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  22. 2006 Thiol-based Redox Regulation and Signaling Gordon Research Conference
    VADIM GLADYSHEV; Fiscal Year: 2006
    ..A diverse mix of established and emerging leaders in the field, and of junior and senior investigators will be included in the program. [unreadable] [unreadable] [unreadable]..
  23. Automated Storage and Retrieval of Biological Systems
    Dan Roden; Fiscal Year: 2008
    ..Accordingly, this proposal requests a high end instrument to accomplish these goals, and to thereby enable a new era of Personalized Medicine. [unreadable] [unreadable] [unreadable] [unreadable]..
  24. Application of Bioinformatics to Retinal Gene Regulation
    Jiang Qian; Fiscal Year: 2006
    ..abstract_text> ..
  25. Evolution of Sex Determination in Sticklebacks
    CATHERINE PEICHEL; Fiscal Year: 2008
    ..abstract_text> ..
  26. High Throughput Sequencer
    WILLIAM MCCOMBIE; Fiscal Year: 2007
    ..The availability of this technology on site is essential not only to support important ongoing research efforts but also to encourage new project development in a timely and cost-effective fashion. [unreadable] [unreadable] [unreadable]..
  27. Mucosal Immunity to Toxoplasma gondii
    L Sibley; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  28. Genetics of Dengue Vector Competence in Aedes aegypti
    William Black; Fiscal Year: 2005
    ..DS2 and DR2 will be used in the construction of recombinant inbred lines for use in a subtractive hybridization approach to clone cDNAs putatively encoded bydmib3and to assist in a collaborative effort to positionally clone dmib3. ..
  29. A Mouse Model of Gaucher Disease
    Ernest Beutler; Fiscal Year: 2005
    ..In particular, electron microscopy and light microscopy will be used to attempt to demonstrate the development of Gaucher cells in the chimeric mice. ..
  30. KNOWLEDGE EMPOWERMENT FOR YOUTH WITH SOLID TUMORS
    Judith Jones; Fiscal Year: 2004
    ..Once developed, the CD-ROM will be marketed so that it will be available to all adolescents with solid tumors. ..
  31. Microarray Analysis of Acute Ethanol Effects in Brain
    Michael Miles; Fiscal Year: 2003
    ..These findings might generate novel insights for the treatment of alcoholism. ..
  32. Large-scale sequencing and assembly of the rat genome
    Robert Holt; Fiscal Year: 2002
    ....
  33. MONOCLONAL ITP AUTOANTIBODIES--PARADIGM FOR AUTOIMMUNITY
    Donald Siegel; Fiscal Year: 2002
    ..Ultimately, the proposed approach may be applied to the understanding of other autoimmune disorders. ..
  34. METHODS FOR FUNCTIONAL/COMPARATIVE GENOMICS
    Xun Gu; Fiscal Year: 2003
    ..abstract_text> ..
  35. Intelligent Information Systems for Systems Biology
    Leroy Hood; Fiscal Year: 2003
    ..Finally, we propose some novel educational programs designed to put graduate students together into interdisciplinary teams for problem solving. ..
  36. Redox mechanism of cancer prevention by selenium
    VADIM GLADYSHEV; Fiscal Year: 2002
    ..These approaches should yield insight into the mechanism of the anticancer effect of selenium and may lead to the identification of human cancers most susceptible to selenium chemoprevention. ..
  37. MOLECULAR MECHANISMS OF OLFACTORY INTEGRATION
    TIMOTHY MCCLINTOCK; Fiscal Year: 2003
    ..The Principal Investigator will transfect mutant forms of these proteins into primary cultured olfactory neurons to assess whether they have predicted effects on olfactory transduction. ..
  38. Genetic Association in Austism Disorder
    Kelly Frazer; Fiscal Year: 2004
    ..The identification of autism-associated genetic markers will allow the development of diagnostic tools to identify individuals with high risk of developing autism, and could ultimately lead to therapeutic breakthroughs. ..
  39. FUNCTION AND CONSERVATION IN GLOBIN LOCUS CONTROL REGION
    Ross Hardison; Fiscal Year: 2001
    ..5 and isolate the binding proteins. ..
  40. RIBOSOMAL FRAMESHIFTING AS A PROBE OF 5S RRNA FUNCTION
    JONATHAN DINMAN; Fiscal Year: 2004
    ..The proposed research will serve to further our understanding of this ubiquitous yet little understood rRNA and will place us in the unique position to link functional aspects of 5S rRNA to its structure within the ribosome. ..
  41. FORMATION AND SURVIVAL OF RED BLOOD CELLS
    Ernest Beutler; Fiscal Year: 2001
    ..Should these point mutations fail to alter gene transcription, a search will be made for other potential mutations in linkage disequilibrium with the known -5,-8 and -24 polymorphisms, by sequencing upstream through the promotor. ..
  42. Protein targeting and secretion in Toxoplasma
    Boris Striepen; Fiscal Year: 2004
    ..Mutant analysis will also provide critical information towards the function of the individual secretory organelles involved. ..
  43. CD-HIT: A Fast Program to Cluster and Compare Large Sets of Biological Sequences
    Weizhong Li; Fiscal Year: 2010
    ..Continued development of CD-HIT will better serve researchers who are facing more challenges in sequence analysis by the explosive growth of public sequence databases. ..
  44. A Mitochondrial Etiology of Autism
    Douglas C Wallace; Fiscal Year: 2010
    ..If mitochondrial defects are found, selected patients will be tested using non-invasive biophysical and biochemical tools to determine if they manifest a functional mitochondrial defect. ..
  45. AMYLOIDOGENIC EFFECTS OF CHOLINERGIC DENERVATION
    Thomas Beach; Fiscal Year: 2002
    ..This could lead to impaired cerebral vasoregulation and increased susceptibility to ischemia, further compromising cortical function in AD. ..
  46. Molecular Pathology of Cardic Arrhythmias
    Dan Roden; Fiscal Year: 2003
    ..abstract_text> ..
  47. Calcium ATPases in Apicomplexan Parasites as Potential D
    L Sibley; Fiscal Year: 2006
    ..Knowledge gained through these studies may improve the ability to pharmacologically inhibit key calcium regulatory enzymes and hence block motility and invasion by this important group of parasites. ..
  48. CONSTRUCTION OF UNIGEN STYLE RAT MAP USING RAT RHS
    Howard Jacob; Fiscal Year: 2001
    ..The combined efforts (MCW and U. of Iowa) will result in more than 1/3 of all rat genes mapped and placed on the RH "backbone" map facilitating comparative genomics with sequence "hooks". ..
  49. Characterization of the SARSCoV frameshift signal
    Jonathan D Dinman; Fiscal Year: 2010
    ....
  50. Bioinformatics Software for Analyzing Microbial Genomes
    Steven Salzberg; Fiscal Year: 2006
    ..Both the software and the operon database will be freely available to the scientific community. ..
  51. First International Biocurator Meeting
    Seung Rhee; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  52. Genetic and Genomic Analysis of apoAV
    Len Pennacchio; Fiscal Year: 2006
    ..abstract_text> ..
  53. MITOCHONDRIAL GENETICS AND AGING
    Douglas Wallace; Fiscal Year: 2005
    ..Changes in mitochondrial gene expression will be assessed using our Emory Mitochondrial Gene Chip (Mitochip), and the effect of over expression of anti-oxidant genes on longevity will be evaluated by aging studies. ..
  54. ORTHOPOXVIRUS GENOMIC AND BIOINFORMATICS RESOURCE CENTER
    ELLIOT LEFKOWITZ; Fiscal Year: 2003
    ..abstract_text> ..
  55. CHARACTERIZATION & ORGANIZATION OF TRANSPOSABLE ELEMENTS
    Zhijian Tu; Fiscal Year: 2006
    ..Finally, this work will enhance our understanding of the basic genetics of An. gambiae by systematically investigating TEs, which are substantial and potentially potent components of the genome...
  56. Novel genetic markers for the yellow fever mosquito
    Zhijian Tu; Fiscal Year: 2003
    ..aegypti in natural populations. ..
  57. MOLECULAR AND GENETIC BASIS OF CELL PROLIFERATION
    MICHAEL TYERS; Fiscal Year: 2005
    ..The Gordon Conferences format provides a unique environment that encourages informal and open discussion among the participants and this in turn fosters initiation of collaborative efforts and stimulates future research directions. ..
  58. ANT Defects in Neurodegenerative Diseases
    Douglas Wallace; Fiscal Year: 2005
    ..These studies, upon completion, will provide critical new insights into the role of ANTs in mitochondrial function and neurodegenerative diseases. ..
  59. Computational and Functional Analysis of Gene Networks
    MARC HALFON; Fiscal Year: 2006
    ..abstract_text> ..
  60. HEPATIC DRUG TRANSPORTERS IN DRUG DISPOSITION
    Dan Roden; Fiscal Year: 2006
    ..Moreover, variability in the extent of rifampin-mediated induction of the drug metabolizing enzyme, CYP3A, among subjects with variant OATP-C alleles, will also be tested. [unreadable] [unreadable]..
  61. Development of a Urological CD Cell Typing System
    Peter Nelson; Fiscal Year: 2009
    ..These studies will involve the evaluation of in vitro growth characteristics, cellular gene expression, organ topography, inter-species conservation, and transgenic animal models. ..
  62. MOLECULAR ALTERATIONS IN PROSTATE CANCER PROGRESSION
    Peter Nelson; Fiscal Year: 2002
    ..3) Compile and evaluate a panel of cancer-phenotype associated products for prognostic relevance. ..
  63. TM4: Software for High-Dimensional Data Analysis
    John Quackenbush; Fiscal Year: 2009
    ....
  64. EXPRESSION PROFILING OF RODENT MODELS OF HUMAN DISEASE
    John Quackenbush; Fiscal Year: 2004
    ..abstract_text> ..
  65. Parallel high sensitivity gene expression monitoring
    Jean Marie Rouillard; Fiscal Year: 2007
    ..Further validation will be by conducting new experiments to detect weakly expressed genes involved in adipogenesis, and to monitor bacterial gene expression in infected host cells. [unreadable] [unreadable] [unreadable]..
  66. 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. ..
  67. 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). ..
  68. 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. ..
  69. Receptor Phosphatases and Process Outgrowth
    Eduardo Macagno; Fiscal Year: 2005
    ....
  70. In-depth Biology Foundations:Quantitative Scientists (RMI)
    WILMA OLSON; Fiscal Year: 2008
    ..unreadable] [unreadable]..
  71. P.syringe effectors' interference with plant defenses
    BORIS VINATZER; Fiscal Year: 2003
    ..The long-term goal is to dissect plant defense pathways further by identifying the molecular components of defense pathways including the molecular plant effector molecules. ..
  72. Discovery of Cis-regulatory Modules in Human Genome
    Xiaoman Li; Fiscal Year: 2009
    ....
  73. The Odd-Even Effect of Polymorphic CA repeats in the 5' Regulatory Region of the
    IVAN GORLOV; Fiscal Year: 2008
    ..The results obtained in this study will improve our understanding of how genetic polymorphisms in this key gene modulate breast cancer risk. [unreadable] [unreadable] [unreadable]..