information storage and retrieval

Summary

Summary: A branch of computer or library science relating to the storage, locating, searching, and selecting, upon demand, relevant data on a given subject.

Top Publications

  1. pmc The Protein Data Bank
    H M Berman
    Research Collaboratory for Structural Bioinformatics RCSB, Rutgers University, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 28:235-42. 2000
  2. pmc KEGG: kyoto encyclopedia of genes and genomes
    M Kanehisa
    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 28:27-30. 2000
  3. ncbi TM4: a free, open-source system for microarray data management and analysis
    A I Saeed
    Institute for Genomic Research, Rockville, MD, USA
    Biotechniques 34:374-8. 2003
  4. pmc GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    Elizabeth I Boyle
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3710-5. 2004
  5. 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
  6. ncbi The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M Hucka
    Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 19:524-31. 2003
  7. pmc The Gene Ontology (GO) database and informatics resource
    M A Harris
    GO EBI, Hinxton, UK
    Nucleic Acids Res 32:D258-61. 2004
  8. pmc Gene expression atlas at the European bioinformatics institute
    Misha Kapushesky
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 38:D690-8. 2010
  9. pmc An overview of MetaMap: historical perspective and recent advances
    Alan R Aronson
    Lister Hill National Center for Biomedical Communications, US National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Am Med Inform Assoc 17:229-36. 2010
  10. pmc Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)
    Shawn N Murphy
    Laboratory of Computer Science, Massachusetts General Hospital, Boston, Massachusetts 02129, USA
    J Am Med Inform Assoc 17:124-30. 2010

Detail Information

Publications352 found, 100 shown here

  1. pmc The Protein Data Bank
    H M Berman
    Research Collaboratory for Structural Bioinformatics RCSB, Rutgers University, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 28:235-42. 2000
    ..This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource...
  2. pmc KEGG: kyoto encyclopedia of genes and genomes
    M Kanehisa
    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 28:27-30. 2000
    ..The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/)...
  3. ncbi TM4: a free, open-source system for microarray data management and analysis
    A I Saeed
    Institute for Genomic Research, Rockville, MD, USA
    Biotechniques 34:374-8. 2003
  4. pmc GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    Elizabeth I Boyle
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3710-5. 2004
    ..GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script...
  5. 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...
  6. ncbi The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M Hucka
    Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 19:524-31. 2003
    ..Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively...
  7. 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...
  8. pmc Gene expression atlas at the European bioinformatics institute
    Misha Kapushesky
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 38:D690-8. 2010
    ..Currently, the database contains information about more than 200,000 genes from nine species and almost 4500 biological conditions studied in over 30,000 assays from over 1000 independent studies...
  9. pmc An overview of MetaMap: historical perspective and recent advances
    Alan R Aronson
    Lister Hill National Center for Biomedical Communications, US National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Am Med Inform Assoc 17:229-36. 2010
    ..Near-term plans for MetaMap development include the incorporation of chemical name recognition and enhanced WSD...
  10. pmc Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)
    Shawn N Murphy
    Laboratory of Computer Science, Massachusetts General Hospital, Boston, Massachusetts 02129, USA
    J Am Med Inform Assoc 17:124-30. 2010
    ..The current version of this software has been released into the public domain and is available at the URL: http://www.i2b2.org/software...
  11. ncbi Exploring the functional landscape of gene expression: directed search of large microarray compendia
    Matthew A Hibbs
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
    Bioinformatics 23:2692-9. 2007
    ..This vast repository is still underutilized due to the lack of methods for fast, accurate exploration of the entire compendium...
  12. ncbi How important are comprehensive literature searches and the assessment of trial quality in systematic reviews? Empirical study
    M Egger
    Department of Social and Preventive Medicine, University of Berne, Switzerland
    Health Technol Assess 7:1-76. 2003
  13. 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...
  14. pmc PDBe: Protein Data Bank in Europe
    S Velankar
    Protein Databank in Europe, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D308-17. 2010
    ..PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis...
  15. pmc Big data: The future of biocuration
    Doug Howe
    The Zebrafish Information Network, 5291 University of Oregon, Eugene, Oregon 97403 5291, USA
    Nature 455:47-50. 2008
  16. 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...
  17. 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...
  18. 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...
  19. ncbi Java Treeview--extensible visualization of microarray data
    Alok J Saldanha
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3246-8. 2004
    ..An applet version is also available that can be used on any website with no special server-side setup...
  20. pmc DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
    Ioannis Xenarios
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, PO Box 951570, UCLA, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 30:303-5. 2002
    ..Tools have been developed that allow users to analyze, visualize and integrate their own experimental data with the information about protein-protein interactions available in the DIP database...
  21. pmc The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    Barry Smith
    Department of Philosophy and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York 14203, USA
    Nat Biotechnol 25:1251-5. 2007
    ..We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved...
  22. ncbi Open source system for analyzing, validating, and storing protein identification data
    Robertson Craig
    Beavis Informatics Ltd, and Manitoba Center for Proteomics, Winnipeg, Manitoba, Canada
    J Proteome Res 3:1234-42. 2004
    ..The components of the system have been made available as open source development projects. A publicly available system has been established, comprised of a group of data analysis servers and one main database server...
  23. pmc APD: the Antimicrobial Peptide Database
    Zhe Wang
    Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198 6805, USA
    Nucleic Acids Res 32:D590-2. 2004
    ..APD is a useful tool for studying the structure-function relationship of antimicrobial peptides. The database can be accessed via a web-based browser at the URL: http://aps.unmc.edu/AP/main.html...
  24. ncbi The MIPS mammalian protein-protein interaction database
    Philipp Pagel
    Institute for Bioinformatics MIPS, GSF National Research Center for Environment and Health, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Bioinformatics 21:832-4. 2005
    ..The content is based on published experimental evidence that has been processed by human expert curators. We provide the full dataset for download and a flexible and powerful web interface for users with various requirements...
  25. pmc Linking genes to literature: text mining, information extraction, and retrieval applications for biology
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish Nacional Cancer Research Centre CNIO, Madrid, Spain
    Genome Biol 9:S8. 2008
    ..Additional descriptions of some of the systems discussed here are available on the internet http://zope.bioinfo.cnio.es/bionlp_tools/...
  26. pmc How do consumers search for and appraise health information on the world wide web? Qualitative study using focus groups, usability tests, and in-depth interviews
    Gunther Eysenbach
    Unit for Cybermedicine and eHealth, Department of Clinical Social Medicine, University of Heidelberg, Bergheimer Str 58, 69115 Heidelberg, Germany
    BMJ 324:573-7. 2002
    ..To describe techniques for retrieval and appraisal used by consumers when they search for health information on the internet...
  27. ncbi Consumer health information seeking on the Internet: the state of the art
    R J Cline
    Department of Health Science Education, University of Florida, Gainesville 32611, USA
    Health Educ Res 16:671-92. 2001
    ..Both interpersonal and mass communication concepts open avenues for investigation and understanding the influence of the Internet on health beliefs and behaviors, health care, medical outcomes, and the health care system...
  28. ncbi PISCES: a protein sequence culling server
    Guoli Wang
    Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
    Bioinformatics 19:1589-91. 2003
    ..PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output...
  29. 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...
  30. ncbi The UCSC Known Genes
    Fan Hsu
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz Santa Cruz, CA 95064, USA
    Bioinformatics 22:1036-46. 2006
    ..Although UCSC Known Genes offers the highest genomic and CDS coverage among major human and mouse gene sets, more detailed analysis suggests all of them could be further improved...
  31. pmc BioCaster: detecting public health rumors with a Web-based text mining system
    Nigel Collier
    National Institute of Informatics, ROIS, PRESTO, Japan
    Bioinformatics 24:2940-1. 2008
    ..Evaluation of the system for topic recognition and entity identification is conducted on a gold standard corpus of annotated news articles...
  32. 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/...
  33. pmc Extracting medication information from clinical text
    Ozlem Uzuner
    Department of Information Studies, University at Albany, State University of New York, Albany, NY, USA
    J Am Med Inform Assoc 17:514-8. 2010
    ..However, they are limited in recognizing duration and reason fields and would benefit from future research...
  34. pmc The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories
    Griffin M Weber
    Information Technology, Harvard Medical School, 107 Avenue Louis Pasteur, Boston, MA 02115, USA
    J Am Med Inform Assoc 16:624-30. 2009
    ..This will guide us in creating a future technical architecture that is scalable to a national level, compliant with ethical guidelines, and protective of the interests of the participating hospitals...
  35. pmc Chemical Entities of Biological Interest: an update
    Paula de Matos
    Chemoinformatics and Metabolism Team, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D249-54. 2010
    ....
  36. pmc Automated generation of heuristics for biological sequence comparison
    Guy St C Slater
    The Ensembl Group, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 6:31. 2005
    ....
  37. pmc Infrastructure for the life sciences: design and implementation of the UniProt website
    Eric Jain
    Swiss Prot group, Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
    BMC Bioinformatics 10:136. 2009
    ..Following several years of intense development and a year of public beta testing, the http://www.uniprot.org domain was switched to the newly developed site described in this paper in July 2008...
  38. ncbi UniRef: comprehensive and non-redundant UniProt reference clusters
    Baris E Suzek
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Bioinformatics 23:1282-8. 2007
    ..Clustering of protein sequence space based on sequence similarity helps organize all sequences into manageable datasets and reduces sampling bias and overrepresentation of sequences...
  39. ncbi Data deposition and annotation at the worldwide protein data bank
    Shuchismita Dutta
    Research Collaboratory for Structural Bioinformatics Protein Data Bank RCSB PDB, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 8087, USA
    Mol Biotechnol 42:1-13. 2009
    ..This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included...
  40. pmc Update of TTD: Therapeutic Target Database
    Feng Zhu
    Department of Pharmacy and Computation and Systems Biology, Center for Computational Science and Engineering, Singapore MIT Alliance, National University of Singapore, Singapore
    Nucleic Acids Res 38:D787-91. 2010
    ..This database can be accessed at http://bidd.nus.edu.sg/group/cjttd/TTD.asp...
  41. ncbi Online predicted human interaction database
    Kevin R Brown
    Division of Cancer Informatics, Ontario Cancer Institute, University of Toronto, Canada
    Bioinformatics 21:2076-82. 2005
    ....
  42. ncbi The CellML Model Repository
    Catherine M Lloyd
    Auckland Bioengineering Institute, The University of Auckland, Auckland 1010, New Zealand
    Bioinformatics 24:2122-3. 2008
    ..As the CellML community grows, and more people add their models to the repository, model annotation will become increasingly important to facilitate data searches and information retrieval...
  43. pmc Agreement, the f-measure, and reliability in information retrieval
    George Hripcsak
    Department of Medical Informatics, Columbia University, 622 West 168th Street, VC5, New York, NY 10032, USA
    J Am Med Inform Assoc 12:296-8. 2005
    ..Positive specific agreement-or the equivalent F-measure-may be an appropriate way to quantify interrater reliability and therefore to assess the reliability of a gold standard in these studies...
  44. pmc Development of a methodological PubMed search filter for finding studies on measurement properties of measurement instruments
    Caroline B Terwee
    Department of Epidemiology and Biostatistics and the EMGO Institute for Health and Care Research, VU University Medical Center, Van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands
    Qual Life Res 18:1115-23. 2009
    ....
  45. ncbi Next-generation digital information storage in DNA
    George M Church
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 337:1628. 2012
    ..We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing...
  46. ncbi Inter-species normalization of gene mentions with GNAT
    Jörg Hakenberg
    Department of Computer Science and Engineering, Arizona State University, Tempe, AZ 85287, USA
    Bioinformatics 24:i126-132. 2008
    ....
  47. pmc Framework for a protein ontology
    Darren A Natale
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven St, NW, Washington, DC 20007, USA
    BMC Bioinformatics 8:S1. 2007
    ..Here we describe the initial development of PRO, illustrated using human and mouse proteins involved in the transforming growth factor-beta and bone morphogenetic protein signaling pathways...
  48. pmc Relations as patterns: bridging the gap between OBO and OWL
    Robert Hoehndorf
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Bioinformatics 11:441. 2010
    ..Since the Web Ontology Language (OWL) is an expressive language with a formal semantics, it is suitable to de ne the meaning of relations accurately...
  49. ncbi TANDEM: matching proteins with tandem mass spectra
    Robertson Craig
    Manitoba Centre for Proteomics, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
    Bioinformatics 20:1466-7. 2004
    ..AVAILABILITY: The source code and binaries for this software are available at http://www.proteome.ca/opensource.html, for Windows, Linux and Macintosh OSX. The source code is made available under the Artistic License, from the authors...
  50. ncbi Knowledge discovery by automated identification and ranking of implicit relationships
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 620 Parrington Oval Rm 106, Norman, OK 73019, USA
    Bioinformatics 20:389-98. 2004
    ....
  51. pmc The Database of Interacting Proteins: 2004 update
    Lukasz Salwinski
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, 90095 1570, USA
    Nucleic Acids Res 32:D449-51. 2004
    ....
  52. ncbi The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text
    Thomas C Rindflesch
    Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
    J Biomed Inform 36:462-77. 2003
    ..The approach has the potential to support a range of applications, including information retrieval and ontology engineering...
  53. pmc CAMP: a useful resource for research on antimicrobial peptides
    Shaini Thomas
    Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai, India
    Nucleic Acids Res 38:D774-80. 2010
    ..CAMP will be a useful database for study of sequence-activity and -specificity relationships in AMPs. CAMP is freely available at http://www.bicnirrh.res.in/antimicrobial...
  54. ncbi Optimal search filters for renal information in EMBASE
    Arthur V Iansavichus
    Division of Nephrology, University of Western Ontario, London, Canada
    Am J Kidney Dis 56:14-22. 2010
    ..EMBASE is a popular database used to retrieve biomedical information. Our objective was to develop and test search filters to help clinicians and researchers efficiently retrieve articles with renal information in EMBASE...
  55. ncbi The metabolomics standards initiative
    Susanna Assunta Sansone
    Nat Biotechnol 25:846-8. 2007
  56. ncbi The Protein Data Bank
    Helen M Berman
    RCSB, Department of Chemistry, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ, USA
    Acta Crystallogr D Biol Crystallogr 58:899-907. 2002
    ..The reader should come away with an understanding of the scope of the PDB and what is provided by the resource...
  57. pmc Introducing meta-services for biomedical information extraction
    Florian Leitner
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Genome Biol 9:S6. 2008
    ..This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations...
  58. pmc A globally optimal k-anonymity method for the de-identification of health data
    Khaled El Emam
    CHEO Research Institute, 401 Smyth Road, Ott, ON K1H8L1, Canada
    J Am Med Inform Assoc 16:670-82. 2009
    ..Often legislative requirements to obtain consent are waived if the information collected or disclosed is de-identified...
  59. pmc Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
    Chi Hua Tung
    Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan
    Genome Biol 8:R31. 2007
    ..3D-BLAST searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequence similarity...
  60. ncbi NetMatch: a Cytoscape plugin for searching biological networks
    A Ferro
    Dipartimento di Matematica e Informatica, Universita di Catania, Viale A Doria 6, I 95125 Catania, Italy
    Bioinformatics 23:910-2. 2007
    ..To make the query creation process easy, a drawing tool is provided. Cytoscape is a bioinformatics software platform for the visualization and analysis of biological networks...
  61. ncbi CFinder: locating cliques and overlapping modules in biological networks
    Balázs Adamcsek
    Department of Biological Physics, Eotvos University, Pázmány P stny 1A, H 1117 Budapest, Hungary
    Bioinformatics 22:1021-3. 2006
    ..Availability: CFinder (for Windows, Linux and Macintosh) and its manual can be downloaded from http://angel.elte.hu/clustering. Supplementary information: Supplementary data are available on Bioinformatics online...
  62. ncbi Literature mining and database annotation of protein phosphorylation using a rule-based system
    Z Z Hu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
    Bioinformatics 21:2759-65. 2005
    ..While of great value, such information is limited in databases owing to the laborious process of literature-based curation. Computational literature mining holds promise to facilitate database curation...
  63. ncbi BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
    Steffen Durinck
    Department of Electronical Engineering, ESAT SCD, K U Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Bioinformatics 21:3439-40. 2005
    ..g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining...
  64. pmc Active computerized pharmacovigilance using natural language processing, statistics, and electronic health records: a feasibility study
    Xiaoyan Wang
    Department of Biomedical Informatics, Columbia University, 622 West 168 Street, VC5, New York, NY 10032, USA
    J Am Med Inform Assoc 16:328-37. 2009
    ..Our results demonstrate that the framework is feasible although there are some challenging issues. To the best of our knowledge, this is the first study using comprehensive unstructured data from the EHR for pharmacovigilance...
  65. ncbi Understanding and using the medical subject headings (MeSH) vocabulary to perform literature searches
    H J Lowe
    Laboratory of Computer Science, Massachussetts General Hospital, Harvard Medical School, Boston
    JAMA 271:1103-8. 1994
    ..The increasing importance of the MEDLINE database as an information resource and the trend toward individuals performing their own bibliographic searches makes it crucial that health care professionals become familiar with MeSH...
  66. ncbi A reference ontology for biomedical informatics: the Foundational Model of Anatomy
    Cornelius Rosse
    Departments of Biological Structure, and Medical Education and Biomedical Informatics, Structural Informatics Group, University of Washington, Seattle, WA 98195, USA
    J Biomed Inform 36:478-500. 2003
    ....
  67. ncbi Pathway studio--the analysis and navigation of molecular networks
    Alexander Nikitin
    Ariadne Genomics, Inc, 9700 Great Seneca Hgwy, Rockville, MD 20850, USA
    Bioinformatics 19:2155-7. 2003
    ..It comes with the built-in natural language processing module MedScan and the comprehensive database describing more than 100 000 events of regulation, interaction and modification between proteins, cell processes and small molecules...
  68. pmc MeSH Up: effective MeSH text classification for improved document retrieval
    Dolf Trieschnigg
    European Bioinformatics Institute, Hinxton, UK
    Bioinformatics 25:1412-8. 2009
    ..Different methods of automating the assignment of MeSH concepts have been proposed to replace manual annotation, but they are either limited to a small subset of MeSH or have only been compared with a limited number of other systems...
  69. pmc Comparison of top-performing search strategies for detecting clinically sound treatment studies and systematic reviews in MEDLINE and EMBASE
    Sharon S L Wong
    School of Nutrition, Faculty of Community Services, Ryerson University, 350 Victoria Street, Toronto, Ontario, M5B 2K3 Canada
    J Med Libr Assoc 94:451-5. 2006
  70. pmc COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer
    Simon A Forbes
    Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 38:D652-7. 2010
    ..Graphical views provide easily interpretable summaries of large quantities of data, and export functions can provide precise details of user-selected data...
  71. ncbi MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications
    W Hayes McDonald
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
    Rapid Commun Mass Spectrom 18:2162-8. 2004
    ....
  72. pmc The KEGG databases at GenomeNet
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 30:42-6. 2002
    ..The KEGG databases are updated daily and made freely available (http://www.genome.ad.jp/kegg/)...
  73. pmc PharmGKB: the Pharmacogenetics Knowledge Base
    Micheal Hewett
    Stanford Medical Informatics, 251 Campus Drive, MSOB X 215, Stanford, CA 94305 5479, USA
    Nucleic Acids Res 30:163-5. 2002
    ..The PharmGKB project was initiated in April 2000 and the first version of the knowledge base went online in February 2001...
  74. ncbi Cloud computing: a new business paradigm for biomedical information sharing
    Arnon Rosenthal
    The MITRE Corporation, Bedford, MA, USA
    J Biomed Inform 43:342-53. 2010
    ..We often find a rough parity (in principle), but one needs to examine individual acquisitions--is a loosely managed lab moving to a well managed cloud, or a tightly managed hospital data center moving to a poorly safeguarded cloud?..
  75. ncbi State of the nation in data integration for bioinformatics
    Carole Goble
    School of Computer Science, University of Manchester, Oxford Road, Manchester M139PL, UK
    J Biomed Inform 41:687-93. 2008
    ..The paper expands on that talk. We attempt to place some perspective on past efforts, highlight the reasons for success and failure, and indicate some pointers to the future...
  76. pmc Protecting privacy using k-anonymity
    Khaled El Emam
    Children s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1J 8L1, Canada
    J Am Med Inform Assoc 15:627-37. 2008
    ..To alleviate such concerns, it is possible to anonymize the data before disclosure. One popular anonymization approach is k-anonymity. There have been no evaluations of the actual re-identification probability of k-anonymized data sets...
  77. ncbi OBO-Edit--an ontology editor for biologists
    John Day-Richter
    Berkeley Bioinformatics and Ontology Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Bioinformatics 23:2198-200. 2007
    ..OBO-Edit is particularly valuable for viewing and editing biomedical ontologies. Availability: https://sourceforge.net/project/showfiles.php?group_id=36855...
  78. pmc A journey to Semantic Web query federation in the life sciences
    Kei Hoi Cheung
    Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06511, USA
    BMC Bioinformatics 10:S10. 2009
    ....
  79. pmc GeneDB: a resource for prokaryotic and eukaryotic organisms
    Christiane Hertz-Fowler
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 32:D339-43. 2004
    ..The current release stores 11 datasets of which six are curated and maintained by biologists, who review and incorporate information from the scientific literature, public databases and the respective research communities...
  80. ncbi Biological knowledge management: the emerging role of the Semantic Web technologies
    Erick Antezana
    Department of Biology at the Norwegian University of Science and Technology
    Brief Bioinform 10:392-407. 2009
    ..Ontologies and Semantic Web technologies revolutionize these efforts. Here, we review the benefits, trends, current possibilities, and the potential this holds for the biosciences...
  81. pmc EMMA--mouse mutant resources for the international scientific community
    Phil Wilkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D570-6. 2010
    ..g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server. EMMA database access is publicly available at http://www.emmanet.org...
  82. ncbi Dynamic exploration and editing of KEGG pathway diagrams
    Christian Klukas
    Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
    Bioinformatics 23:344-50. 2007
    ....
  83. ncbi Secure Dynamic access control scheme of PHR in cloud computing
    Tzer Shyong Chen
    Department of Information Management, Tunghai University, Taichung, Taiwan
    J Med Syst 36:4005-20. 2012
    ....
  84. pmc The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
    Brigitte Boeckmann
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 31:365-70. 2003
    ..Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org...
  85. pmc MedlineRanker: flexible ranking of biomedical literature
    Jean Fred Fontaine
    Computational Biology and Data Mining Group, Max Delbruck Center for Molecular Medicine, Robert Rossle Strasse 10, D 13125, Berlin, Germany
    Nucleic Acids Res 37:W141-6. 2009
    ..We show that our tool can be highly accurate and that it is able to process millions of abstracts in a practical amount of time. MedlineRanker is free for use and is available at http://cbdm.mdc-berlin.de/tools/medlineranker...
  86. pmc Description of a rule-based system for the i2b2 challenge in natural language processing for clinical data
    Lois C Childs
    Lockheed Martin, Inc, Valley Forge, Philadelphia, PA, USA
    J Am Med Inform Assoc 16:571-5. 2009
    ..The Challenge results suggest that rule-based systems guided by human medical expertise are capable of solving complex problems in machine processing of medical text...
  87. ncbi Automated extraction of information on protein-protein interactions from the biological literature
    T Ono
    Otsuka GEN Research Institute, Otsuka Pharmaceutical Co Ltd, 463 10 Kagasuno, Kawauchi cho, Tokushima, 771 0192, Japan
    Bioinformatics 17:155-61. 2001
    ..Our aim is to develop an efficient method for extracting information on protein-protein interaction from scientific literature...
  88. ncbi Analyzing gene expression data in terms of gene sets: methodological issues
    Jelle J Goeman
    Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
    Bioinformatics 23:980-7. 2007
    ..This article aims to clarify the assumptions behind different approaches and to indicate a preferential methodology of gene set testing...
  89. ncbi Improved BLAST searches using longer words for protein seeding
    Sergey A Shiryev
    Department of Health and Human Services, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
    Bioinformatics 23:2949-51. 2007
    ..2.16 of blastall. A Linux executable used to produce the results herein is available at: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/protein_longwords..
  90. pmc Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
    A A Schaffer
    National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 29:2994-3005. 2001
    ..The use of composition-based statistics is particularly beneficial for large-scale automated applications of PSI-BLAST...
  91. ncbi The minimum information about a proteomics experiment (MIAPE)
    Chris F Taylor
    The HUPO Proteomics Standards Initiative, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 25:887-93. 2007
    ....
  92. pmc Importance of multi-modal approaches to effectively identify cataract cases from electronic health records
    Peggy L Peissig
    Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, Wisconsin 54449, USA
    J Am Med Inform Assoc 19:225-34. 2012
    ..We describe the construction and validation of an EHR-based algorithm to identify subjects with age-related cataracts...
  93. ncbi Gene set analysis in the cloud
    Lu Zhang
    Laboratory of Cardiovascular Research, CRP Sante, Luxembourg L 1150, Luxembourg
    Bioinformatics 28:294-5. 2012
    ..The resulting tool, YunBe, is ready to use on Amazon Web Services. Moreover, here we compare its performance to those obtained with desktop and computing cluster solutions...
  94. pmc Reconciliation of the cloud computing model with US federal electronic health record regulations
    Eugene J Schweitzer
    Department of Surgery, Division of Transplantation, University of Maryland Medical School, Baltimore, Maryland, USA
    J Am Med Inform Assoc 19:161-5. 2012
    ..EHRs built with the cloud computing model can achieve acceptable privacy and security through business associate contracts with cloud providers that specify compliance requirements, performance metrics and liability sharing...
  95. ncbi Computational polypharmacology with text mining and ontologies
    Conrad Plake
    Biotechnology Center of Technische Universität Dresden, Germany
    Curr Pharm Biotechnol 12:449-57. 2011
    ..We conclude that mining the literature on drugs and proteins offers unique opportunities to support the laborious and expensive process of drug development...
  96. pmc Accuracy of geographically targeted internet advertisements on Google AdWords for recruitment in a randomized trial
    Ray B Jones
    Faculty of Health, Education, and Society, University of Plymouth, Plymouth, United Kingdom
    J Med Internet Res 14:e84. 2012
    ..They offer the potential to recruit from targeted control areas in cluster randomized controlled trials (RCTs), but little is known about the feasibility of accurately targeting ads by location and comparing with control areas...
  97. ncbi Poor reporting and inadequate searches were apparent in systematic reviews of adverse effects
    Su Golder
    Centre for Reviews and Dissemination, University of York, York, YO10 5DD, UK
    J Clin Epidemiol 61:440-8. 2008
    ..The aim of this study was to survey the methods used to identify relevant studies for systematic reviews of adverse effects...
  98. pmc Degree centrality for semantic abstraction summarization of therapeutic studies
    Han Zhang
    Department of Medical Informatics, China Medical University, Shenyang, China
    J Biomed Inform 44:830-8. 2011
    ..The results showed that recall for system results was 72%, precision was 73%, and F-score was 0.72. The system F-score was considerably higher than that for the baseline (0.47)...
  99. pmc AskHERMES: An online question answering system for complex clinical questions
    Yonggang Cao
    Department of Health Sciences, University of Wisconsin Milwaukee, 2400 E Hartford Avenue, Milwaukee, WI 53211, USA
    J Biomed Inform 44:277-88. 2011
    ..We have built a clinical question answering system named AskHERMES to perform robust semantic analysis on complex clinical questions and output question-focused extractive summaries as answers...
  100. pmc Database resources of the National Center for Biotechnology
    David L Wheeler
    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 31:28-33. 2003
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov...
  101. pmc Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction
    Aurélie Névéol
    National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
    J Biomed Inform 44:310-8. 2011
    ..Our experience suggests using an automatic tool to assist large-scale manual annotation projects. This helps speed-up the annotation time and improve annotation consistency while maintaining high quality of the final annotations...

Research Grants69

  1. High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributi
    Sonia Dua; Fiscal Year: 2013
    ..The contractor is responsible for providing staff with the credentials required by CLIA. ..
  2. Bioconductor: an open computing resource for genomics
    Martin Morgan; Fiscal Year: 2010
    ..While that type of "success measure" is hard to assess, more effort in this area in subsequent proposals would be helpful. ..
  3. Acquisition of a TIRF/Widefield fluorescence microscope for cell biology and neur
    Bryon D Grove; Fiscal Year: 2013
    ..This TIRF/wide field fluorescence microscope system will advance the basic science research of our faculty members in a wide range of fields and will lead to development of new research areas. ..
  4. WHOLE SLIDE IMAGING SYSTEM FOR TRANSLATIONAL NEUROSCIENCE
    Jin Moo Lee; Fiscal Year: 2010
    ..Data sharing provides great dividends by facilitating comparisons between disease models, and allowing new research findings on existing data without having to perform additional animal experiments. ..
  5. Intrinsic plasticity and information storage in cerebellar Purkinje cells
    CHRISTIAN ROBERT HANSEL; Fiscal Year: 2012
    ....
  6. Virtual reality system for cancer patients'shoulder pain and psychosocial impact
    Grigore C Burdea; Fiscal Year: 2012
    ..The ability of the product to also be used in the future in acute post-surgery rehabilitation further reduces health care costs by accelerating return to productive life. ..
  7. Epigenetic Mechanisms of Memory Storage
    EDWIN G ABEL; Fiscal Year: 2013
    ....
  8. Regulation and Neural Function of Atypical PKC
    Todd C Sacktor; Fiscal Year: 2011
    ..This application is to characterize the functional mechanisms by which PKM6 maintains long-term information at synapses and during behavioral memory storage. ..
  9. Assessing GABAergic Involvement in Schizophrenia-Like Cognitive Deficits in Rats
    Mark Renato Stefani; Fiscal Year: 2012
    ....
  10. CRCNS: PKMzeta-Dependent Protein Synthesis Maintains Synaptic Plasticity
    HAREL ZEEV SHOUVAL; Fiscal Year: 2013
    ..We are eager to extend this type of outreach to the domain of the interaction between theory and experiment in biological sciences. ..
  11. CELLULAR SUBSTRATES OF CEREBELLAR INFORMATION STORAGE
    David J Linden; Fiscal Year: 2010
    ..In addition, they have potential clinical relevance for both cerebellar motor disorders and disorders of learning and memory generally...
  12. Integrated Desktop Software for Management of Hepatitic C Data
    Johanna C Craig; Fiscal Year: 2010
    ..Moreover, our design will streamline the serious bottleneck of data management, significantly compressing the time between data collection and cure discovery. ..
  13. Arm Motor Rehabilitation, Entertainment and Cognition System for the Elderly
    Grigore C Burdea; Fiscal Year: 2013
    ..The approach can be extended to other patient populations with motor and cognitive co-morbidities acute, sub-acute and chronic, adult and paediatric. ..
  14. Conditional Inactivation of Synaptic proteins in transgenic mice
    Craig C Garner; Fiscal Year: 2010
    ....
  15. CELLULAR SUBSTRATES OF CEREBELLAR INFORMATION STORAGE
    David J Linden; Fiscal Year: 2013
    ..To extend analysis of meta-plastic effects, we shall assess the interaction of LTD(mGluR1) with short-term retrograde modulation of glutamate release that uses mGluR1-driven endocannabinoid signaling. ..
  16. BioHDF - Open Binary File Standards for Bioinformatics
    Todd M Smith; Fiscal Year: 2010
    ....
  17. CARRA: Accelerating Toward an Evidence Based Culture in Pediatric Rheumatology
    Carol A Wallace; Fiscal Year: 2010
    ..If successful, CARRA's exponential progress will serve as a model to be emulated by other emerging clinical research networks in rare diseases of adults and children. ..
  18. Genome Analyzer for the Institute of Diabetes, Obesity, and Metabolism
    Klaus H Kaestner; Fiscal Year: 2010
    ....
  19. Regulation and Neural Function of Atypical PKC
    Todd C Sacktor; Fiscal Year: 2013
    ..These 3 aims will provide fundamental new information on a potential molecular mechanism for maintaining synaptic and behavioral information storage, which may be relevant to both normal memory and its disorders. ..
  20. The First Comprehensive Neural Connectivity Map of Mouse
    PARTHA PRATIM MITRA; Fiscal Year: 2010
    ..If successful, the project has the potential to fundamentally transform our understanding of the architecture of the normal and disordered brain. ..
  21. Petascale Molecular Dynamics Data Processing System
    Klaus Schulten; Fiscal Year: 2010
    ..These views reveal the chemical detail needed to develop new pharmacological treatments. ..
  22. PROTEIN KINASE C ISOZYMES IN HIPPOCAMPAL PLASTICITY
    Todd C Sacktor; Fiscal Year: 2013
    ....
  23. Functions of Dopamine D4 Receptors in Prefrontal Cortex
    Zhen Yan; Fiscal Year: 2012
    ....
  24. CRCNS: Spatial &Temporal Aspects of cAMP/PKA Signaling Underlying Information
    KIM L BLACKWELL; Fiscal Year: 2012
    ..Successful completion of the research will form the basis for investigating how alterations in this pathway contributes to psychiatric disease such as schizophrenia and alcoholism. ..
  25. Single-molecule nanomagnetic assays for ultrasmall sample clinical diagnostics
    Dmitri Litvinov; Fiscal Year: 2010
    ..This research is expected to enable a new generation of highly reliable molecular diagnostic instrumentation with significantly enhanced sensitivity and high specificity. ..
  26. An Extensible Resource for Genomic Analysis and Petascale Storage
    Harel Weinstein; Fiscal Year: 2012
    ..The institution has committed significant resources, including cost sharing, to this instrument that wil function as an essential tool for basic and translational biomedical research and information sharing. ..
  27. High Performance Clustered Storage for Image Management
    PETER KARL SORGER; Fiscal Year: 2010
    ....
  28. Integrated software application for management of Hepatitis C Virus data
    Johanna C Craig; Fiscal Year: 2013
    ..These goals fall well within the scope of the NIH to promote basic research in the field of bioinformatics and information sciences, and could lead to enormous public benefit. ..
  29. Regulation of microRNA biogenesis by neurotrophins
    CLAUDIA ROXANA RUIZ; Fiscal Year: 2013
    ..The following specific aims will be addressed: 1) Investigate the mechanisms underlying upregulation of the microRNA processing factor, Lin28, by BDNF;2) Determine whether Lin28 levels can be locally controlled at synapses. ..
  30. NARP AND GLUTAMATE RECEPTOR CLUSTERING
    Paul F Worley; Fiscal Year: 2012
    ..Proposed studies will define the molecular basis of the action of Narp, and its role in synaptic plasticity and diseases of cognition. ..
  31. Interaction of Opposing Forms of Synaptic Plasticity in Hippocampal Circuits
    ADAM JAMES ILIFF; Fiscal Year: 2013
    ....
  32. BREAST CANCER SURVEILLANCE IN A DEFINED POPULATION
    DIANA SM BUIST; Fiscal Year: 2011
    ..abstract_text> ..
  33. Cancer Genomics Center
    Raju Kucherlapati; Fiscal Year: 2009
    ..Our proposed approach also has the ability to generate additional useful data for tumor and patient stratification. ..
  34. Role of Arc in synaptic/experience-dependent plasticity in mouse visual cortex
    JASON DENNIS SHEPHERD; Fiscal Year: 2012
    ..We will also test the hypothesis that normal Arc levels are critical for brain function and that abnormal regulation of Arc expression contributes to the synaptic dysfunction observed in neurological disorders. ..
  35. Structure-function determination of the Hepatitis C Virus negative RNA strand???s
    EDWARD ANHOA PHAM; Fiscal Year: 2013
    ....
  36. Specialized Programs of Translational Research in Acute Stroke at the Partners
    Steven M Greenberg; Fiscal Year: 2013
    ..If our study is successful, we can potentially expand use of lytics to a stroke patient population for whom little acute intervention is currently offered. ..
  37. Assessment of serum peptide profiling to detect cancer-specific patterns
    Paul Tempst; Fiscal Year: 2010
    ..Such a test could, for example, identify patients with newly diagnosed cancer who might safely avoid surgery or radiation. ..
  38. Role of Arc in synaptic/experience-dependent plasticity in mouse visual cortex
    JASON DENNIS SHEPHERD; Fiscal Year: 2013
    ..abstract_text> ..
  39. CRCNS: Analysis of synchronization in hybrid neural circuits
    CARMEN CASTRO CANAVIER; Fiscal Year: 2013
    ..cortical networks is hypothesized to mediate cognitive functions such as attention, perception, and information storage and retrieval. A better understanding of these mechanisms will provide tools to determine how synchronization goes ..
  40. LOCALIZATION OF MRNAS AT SYNAPTIC SITES ON DENDRITES
    Oswald Steward; Fiscal Year: 2011
    ..These studies will provide novel insights into the basic mechanisms underlying information storage in the brain and neurological disorders that disrupt this fundamental mechanism, including Fragile-X Mental Retardation Syndrome. ..
  41. The Missing Circuit: The First Brainwide Connectivity Map for Mouse
    PARTHA PRATIM MITRA; Fiscal Year: 2013
    ..In this way it borrows from, yet differs significantly from, the model offered by the Allen Institute, which has previously demonstrated the potential of industrial automation for neuroscience. ..
  42. A Data Center for the Discovery of the Genetic Basis of Human Disease
    Larry J Shapiro; Fiscal Year: 2010
    ..This application is to build a 15,238 building gross square feet (bgsf) data center expansion to support the data storage and processing requirements of The Genome Center at Washington University School of Medicine. ..
  43. Wireless Multi-Modal Brain Monitoring
    BRUCE LANNING; Fiscal Year: 2010
    ....
  44. Exploring New Methods for Protecting and Distributing Confidential Research Data
    FELICIA B LECLERE; Fiscal Year: 2010
    ..The computing architecture described here will also improve data security and, thus, encourage more widespread sharing of research data. ..
  45. Neurocognitive Effects of Stress
    Jeansok John Kim; Fiscal Year: 2012
    ..abstract_text> ..
  46. Investigation of Cloud Computing to Support Data-Parallel Health Research
    Geoffrey C Fox; Fiscal Year: 2010
    ..We will develop and demonstrate our infrastructure in collaboration with several existing biological and biomedical projects. ..
  47. Enterprise Research Data Storage for Data-Intensive Computation
    John J Hutton; Fiscal Year: 2010
    ..Investment of NCRR funds to improve research data anagement will strengthen the Medical Center's ability to conduct the research so ecessary to fulfill its mission. ..
  48. Shared Resource for Disease Model Surgical Critical Care and Data Mangement
    Hansell H Stedman; Fiscal Year: 2010
    ....
  49. Oscillatory Contributions to Working Memory and Attention
    Bradley R Postle; Fiscal Year: 2013
    ..In addition to the basic science questions outlined here, there is translational relevance for this work for the diagnosis and treatment of psychiatric disorders that are associated with abnormal neural oscillations. ..
  50. Field Deployable, Automatic, EEG Seizure Detector and Brain Dysfunction Monitor
    STEPHANE BIBIAN; Fiscal Year: 2010
    ....
  51. SOUTHWEST ONCOLOGY GROUP STATISTICAL CENTER
    MICHAEL LEO LEBLANC; Fiscal Year: 2013
    ..abstract_text> ..
  52. The Zebrafish Connectome
    Florian Engert; Fiscal Year: 2010
    ..We will combine functional imaging using calcium indicators with serial electron microscopy-assisted reconstruction of the zebrafish brain. ..
  53. Surgical Care and Outcomes Assessment Program Comparative Effectiveness Research
    David R Flum; Fiscal Year: 2010
    ..Surgical and interventional services span the continuum of healthcare conditions and SCOAP CERTN will have immediate capacity for investigators interested in almost any of AHRQ's priority conditions. ..
  54. Indo-US Collaborative Stroke Registry and Infrastructure Development
    Aneesh B Singhal; Fiscal Year: 2013
    ..The user-driven web-based platform will allow research teams to share and compare multi-ethnic data, and accelerate the pace of stroke clinical, genetic and imaging research around the world. ..
  55. NEUROBEHAVIORAL RELATIONS IN SENESCENT HIPPOCAMPUS
    Carol Barnes; Fiscal Year: 2009
    ..abstract_text> ..
  56. Heart Failure Clinical Research Network Coordinating Center
    Adrian Hernandez; Fiscal Year: 2013
    ..These trials will change professional guidelines, will provide the Phase II data necessary for appropriate large outcomes trials, and will ultimately improve clinical care of patients suffering with heart failure...
  57. NEUROBEHAVIORAL RELATIONS IN SENESCENT HIPPOCAMPUS
    Carol A Barnes; Fiscal Year: 2013
    ....
  58. BIOINFORMATICS CORE
    Carolyn J Hovde; Fiscal Year: 2011
    ..BSU will also significantly enhance its telecommunications connections by leveraging INBRE funds with NSF instrumentation awards, institutional support, and service fees in individual grants...
  59. Data Center Core Consolidation
    Mark Groudine; Fiscal Year: 2010
    ..The resulting increases in research capacity, throughput, and energy-efficiency provided by new Data Center will catalyze numerous Hutchinson Center research advances in cancer and other life-threatening diseases. ..
  60. NIH Director's Pioneer Award
    Younan Xia; Fiscal Year: 2010
    ..Such a toolset based on spatially and temporally addressable nanostructures is complementary to many other bioimaging techniques under development, and will find broad use in studying complex biological systems. ..
  61. Prediction of Protein Crystallization and Diffraction Quality
    Ethan A Merritt; Fiscal Year: 2010
    ..This work will increase the efficiency and overall success rate of these research programs by ameliorating a key bottleneck, the difficulty of obtaining high-quality crystals of the biological entity being studied. ..
  62. Dynamically scalable accessible analysis for next generation sequence data
    JAMES contact TAYLOR; Fiscal Year: 2010
    ....
  63. Non-Intrusive Automated Portable Data Collection System for Aging Surveys
    Cindy Crump; Fiscal Year: 2009
    ....
  64. Cellular Learning and information Outside of the Brain
    Michael Levin; Fiscal Year: 2005
    ..The device and protocols we propose will ultimately also enable powerful large-scale pharmaceutical screens of drug and proteomic libraries to identify novel psychoactive compounds of high biomedical relevance to human beings. ..
  65. BIOMEDICAL RESEARCH SUPPORT
    SAMUEL SHACKS; Fiscal Year: 1991
    ....
  66. SEQUENTIAL ANALYSIS OF HEMATOLOGIC MEASUREMENTS
    Christine McLaren; Fiscal Year: 1992
    ....
  67. NEURONAL INFORMATION STORAGE IN CEREBELLAR DEEP NUCLEI
    David Linden; Fiscal Year: 2004
    ..In addition, they have potential clinical relevance for both cerebellar motor disorders and disorders of learning and memory generally. ..
  68. ETHANOL INHIBITION OF NMDA RECETOR MEDIATED RESPONSES
    David Lovinger; Fiscal Year: 2000
    ..It is hoped that the outcome of these experiments will provide a basis for the development of treatments that can counteract some of the damaging neural effects of EtOH...
  69. ETHANOL INHIBITION OF NMDA RECEPTOR MEDIATED RESPONSES
    Danny Winder; Fiscal Year: 2004
    ..It is hoped that the outcome of these experiments will provide a basis for the development of treatments that can counteract some of the damaging neural effects of EtOH...