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Information Storage and Retrieval

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  • A Java API for working with PubChem datasets  Academic Article
  • A systematic approach to modeling, capturing, and disseminating proteomics experimental data  Academic Article
  • A test-bed for optimizing high-resolution single particle reconstructions  Academic Article
  • Accurate detection and genotyping of snps utilizing population sequencing data  Academic Article
  • An application of multivariate statistical analysis for Query-Driven Visualization  Academic Article
  • Bioeditor-simplifying macromolecular structure annotation  Academic Article
  • Biogps and gxd: Mouse gene expression data-the benefits and challenges of data integration  Academic Article
  • C-ME: A 3D community-based, real-time collaboration tool for scientific research and training  Academic Article
  • CEBS object model for systems biology data, SysBio-OM  Academic Article
  • Clock gene wikis available: join the "long tail"  Academic Article
  • DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs  Academic Article
  • Dizeez: an online game for human gene-disease annotation  Academic Article
  • Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation  Academic Article
  • Envelope: Interactive software for modeling and fitting complex isotope distributions  Academic Article
  • Exact reduced-complexity maximum likelihood reconstruction of multiple 3-d objects from unlabeled unoriented 2-d projections and electron microscopy of viruses  Academic Article
  • GeneDig: a web application for accessing genomic and bioinformatics knowledge  Academic Article
  • GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome  Academic Article
  • HD desktop: An integrated platform for the analysis and visualization of H/D exchange data  Academic Article
  • Human Proteinpedia enables sharing of human protein data  Academic Article
  • In silico gene function prediction using ontology-based pattern identification  Academic Article
  • Informatics and multiplexing of intact protein identification in bacteria and the archaea  Academic Article
  • Interoperability with Moby 1.0: it's better than sharing your toothbrush  Academic Article
  • Large-scate database searching using tandem mass spectra: looking up the answer in the back of the book  Academic Article
  • MDB: The metalloprotein database and browser at The Scripps Research Institute  Academic Article
  • MS1, MS2, and SQT: three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications  Academic Article
  • Metabolomic data streaming for biology-dependent data acquisition  Academic Article
  • Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database  Academic Article
  • Mining the Gene Wiki for functional genomic knowledge  Academic Article
  • Probability-based validation of protein identifications using a modified SEQUEST algorithm  Academic Article
  • Searching the Porphyromonas gingivalis genome with peptide fragmentation mass spectra  Academic Article
  • Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics  Academic Article
  • The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community  Academic Article
  • The Ribosomal Database Project  Academic Article
  • The gene wiki: Community intelligence applied to human gene annotation  Academic Article
  • The minimum information about a proteomics experiment (MIAPE)  Academic Article
  • The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models  Academic Article
  • Towards precise classification of cancers based on robust gene functional expression profiles  Academic Article
  • Validation of tandem mass spectrometry database search results using DTASelect  Academic Article
  • Xlandscape: The graphical display of word frequencies in sequences  Academic Article

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