生物信息学相关重要资料

生物信息学：生物信息学时应用信息科学的知识和方法，搜集、整理、贮存、分析生命科学的一门新兴学科，是现代医学生物学研究和分析的必备工具。

CMBI曾就当今网上的各种专业网站及专业数据库作过报道，具体请参阅生物信息网站评述。

这次CMBI再从《Bioinformatics》这一国际上最为著名的专业杂志中摘编了两年来发表的最重要的一百多篇论文，供读者参考。

总论The Economic Value of BioinformationComputer applications in biomolecular sciencesbiotech-Bioinformatics in the pre- and post-genomic erasThe Babel of BioinformaticsPromoter prediction in the human genomeThe need for a human gene indexbiotech-Mining for medicines in silicoBIOMOLECULAR SIMULATIONSOn the Importance of Standardisation in Life SciencesDNA binding sites- representation and discovery EditorialAn insight into domain combinationsIE-Kb- intron exon knowledge basebioinf-Integration of information systemsHealth Information Systems and Health CommunicationsHigh content screening ?§C from cells to data to knowledgeWhole-cell biocomputingA classification of tasks in bioinformaticsBioinformatics?athe necessity of the quest for -first principles in lifeBioinformatics enters a new millenniumBioinformatics - Challenges in 2001Mouse as the measure of man蛋白Proteome Analysis Database- online application of InterPro and CluSTr for the functional classification of proteins in whole genomesThe utility of different representations of protein sequence for predicting functional class TargetDB- a database of peptides targeting proteins to subcellular locationsARED= human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteinsThe RESID Database of protein structure modifications and the NRL-3D Sequence¨CStructure DatabaseProtein Information Resource- a community resource for expert annotation of protein dataA Java applet for visualizing protein?§Cprotein interactionSTRAP- editor for STRuctural Alignments of ProteinsA collection of well characterised integral membrane proteinsPredicting protein?§Cprotein interactions from primary structureA genetic algorithm for designing gene- the G protein-coupled receptor protein superfamilyThe MetaFam Server- a comprehensive protein family resourceA simple probabilistic scoring method for protein domain identificationa software tool for low complexity proteins and protein domainstrEST, trGEN and Hits- access to databases of predicted protein sequencesThe COG database- new developments in phylogenetic classification of proteins from complete genomesA fully automatic evolutionary classification of protein foldsAccommodating Protein Flexibility in Computational Drug DesignThe mouse SWISS-2D PAGE database- a tool for proteomics study of diabetes and obesity BioMolQuest- integrated database-based retrieval of protein structural and functional informationVARSPLIC- alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL TRITON- in silico construction of protein mutants and prediction of their activitiesThe protein kinase resource and other bioinformation resourcesProDDO- a database of disordered proteins from the Protein Data Banka database of protein structural domainsThe SBASE protein domain libraryPDB-REPRDB- a database of representative protein chains from the Protein Data Bank TIGRFAMs- a protein family resource for the functional identification of proteinsNIFAS- visual analysis of domain evolution in proteinsPALI- a database of alignments and phylogeny of homologous protein structuresBioanalytical characterization of proteinsThe InterPro database, an integrated documentation resource for protein families, domains and functional sitesMulti-class protein fold recognition using support vector machines and neural networks ToothPrint, a proteomic database for dental tissuesMining literature for protein?§Cprotein interactionsEstimating the significance of sequence order in protein secondary structure and prediction Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequencesIdentification of novel multi-transmembrane proteins from genomic databasesPrediction of the coupling specificity of G protein coupled receptors to their G proteins iProClass- an integrated, comprehensive and annotated protein classification database Improved prediction of the number of residue contacts in proteins by recurrent neural networks InterPro?aan integrated documentation resource for protein families, domains and functional sites -databaseCluSTr- a database of clusters of SWISS-PROT+TrEMBL proteinsDIP- The Database of Interacting Proteins-2001 updateIterative sequence-secondary structure search for protein homologsProtein-protein interaction map inference using interacting domain profile pairsDaliLite workbench for protein structure comparisonMASIA- recognition of common patterns and properties in multiple aligned protein sequences Clustering of highly homologous sequences to reduce the size of large protein databasesOn the trail of protein sequencesAnalysis of conservation and substitutions of secondary structure elements within protein superfamiliesFORESST- fold recognition from secondary structure predictions of proteinsMetaFam- a unified classification of protein families-1Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database GlycoSuiteDB- a new curated relational database of glycoprotein glycan structures and their biological sourcesPALI?aa database of Phylogeny and ALIgnment of homologous protein structuresProtEST- protein multiple sequence alignments from expressed sequence tagsMetaFam- a unified classification of protein families. IIMaxSub- an automated measure for the assessment of protein structure prediction quality ASEdb- a database of alanine mutations and their effects on the free energy of binding in protein Automated extraction of information on protein?§Cprotein interactions from the biological literaturePANAL- an integrated resource for Protein sequence ANALysisAn Expressed Sequence Tag EST- Discovery of New G-Protein Coupled Receptors核酸ODNBase?aa web database for antisense oligonucleotide effectiveness studiesNTDB- Thermodynamic Database for Nucleic AcidsThe EMBL nucleotide sequence database数据库Kabat Database and its applications- future directionsPromEC- An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sitesPLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes PlasmoDB- An integrative database of the Plasmodium falciparum genomePlantsP- a functional genomics database for plant phosphorylationOrCGDB- a database of genes involved in oral cancerBBID- the biological biochemical image databaseThe life sciences Global Image Database (GID)Mendel-GFDb and Mendel-ESTS- databases of plant gene families and ESTs annotated with gene family numbers and gene family namesB-SPID- An object-relational database architecture to store, retrieve, and manipulate neuroimaging dataDatabase of Structural Motifs in ProteinsMendel, a database of nomenclature for sequenced plant genesDevelopment of the receptor database (RDB)- application to the endocrine disruptor problem LIGAND- chemical database for enzyme reactionsDisperse- a simple and efficient approach to parallel database searchingA National Cardiac Surgery DatabaseIMGT-HLA Database?aa sequence database for the human major histocompatibility complex DRAGON- Database Referencing of Array Genes OnlineIMGT, the international ImMunoGeneTics databaseICB database- the gyrB database for identification and classification of bacteriaHyPaLib- a database of RNAs and RNA structural elements defined by hybrid patternsHUNT- launch of a full-length cDNA database from the Helix Research InstituteGABAagent- a system for integrating data on GABA receptors-1HC Forum- a web site based on an international human cytogenetic databaseGOBASE- the organelle genome databaseGenomes OnLine Database (GOLD)- a monitor of genome projects world-wideGenMapDB- a database of mapped human BAC clonesFULL-malaria- a database for a full-length enriched cDNA library from human malaria parasite ISYS- a decentralized, component-based approach to the integration of heterogeneous bioinformatics resourcesLGICdb- the ligand-gated ion channel databaseSTRBase- a short tandem repeat DNA database for the human identity testing communityThe Molecular Biology Database Collection- an updated compilation of biological database resourcesThe Mouse Gene Expression DatabaseThe Mouse Genome Database (MGD)- integration nexus for the laboratory mouseThe RDP-II (Ribosomal Database Project)The Stanford Microarray DatabaseThe KMDB-MutationView- a mutation database for human disease genesThe University of Minnesota Biocatalysis-Biodegradation Database- emphasizing enzymes tmRDB (tmRNA database)VIDA-a virus database system for the organization of animal virus genome open reading frames The imprinted gene and parent-of-origin effect databaseThe Homeodomain Resource- sequences, structures, DNA binding sites and genomic information The EMOTIF databaseOrganelle genome resources at NCBIRECODE- a database of frameshifting, bypassing and codon redefinition utilized for gene expressionrSNP_Guide, a database system for analysis of transcription factor binding to target sequences- application to SNPs and site-directed mutationsBLAST Search Updater- a notification system for new database matchesSemi-automated update and cleanup of structural RNA alignment databasesViral Genome DataBaseRefSeq and LocusLink- NCBI gene-centered resourcesRHdb- the Radiation Hybrid databaseThe ARKdb- genome databases for farmed and other animalsrrndb- the Ribosomal RNA Operon Copy Number DatabaseThe Arabidopsis Information Resource (TAIR)Saccharomyces Genome Database provides tools to survey gene expression and functional analysis dataDatabase verification studies of SWISS-PROT and GenBankSearching Expressed Sequence Tag DatabasesSpliceDB- database of canonical and non-canonical mammalian splice sitesSRPDB (Signal Recognition Particle Database)TreeGeneBrowser- phylogenetic data mining of gene sequences from public databasesRISSC- a novel database for ribosomal 16S¨C23S RNA genes spacer regionsACTIVITY- a database on DNA-RNA sites activity adapted to apply sequence-activity relationships from one system to anotherDBTBS- a database of Bacillus subtilis promoters and transcription factorsViral Genome DataBaseUpdated database of patterns used to detect local similaritiesPathway analysis in metabolic databases via differential metabolic displayDatabase resources of the National Center for Biotechnology InformationA rapid classification protocol for the CATH Domain Database to support structural genomics PIR- a new resource for bioinformaticsdbSNP- the NCBI database of genetic variationALFRED- an allele frequency database for diverse populations and DNA polymorphismsThe Human Transcript Database- a catalogue of full length cDNA insertsAminoacyl-tRNA synthetases databaseCKAAPs DB- a conserved key amino acid positions databaseMethDB?aa public database for DNA methylation dataBIND?aThe Biomolecular Interaction Network DatabaseComprehensive Microbial ResourceThe mouse SWISS-2D PAGE databaseA comprehensive BAC resourceEuropean Large Subunit Ribosomal RNA DatabaseMView- a web-compatible database search算法biotech-Plant biotechnology web alertA new approach to sequence comparisonThe non-coding RNAs as riboregulatorsCompositional symmetries in complete genomesComparison of genomic DNA sequences- solved and unsolved problemsMathematical simulation and analysis of cellular metabolism and regulationAutomated image analysis for array hybridization experimentsA Bayesian framework for the analysis of microarray expression dataMathematica packages for simulation of experimental geneticsGenview and Gencode - a pair of programs to test theories of genetic code evolution Identifying splits with clear separation- a new class discovery method for gene expression data From complexity to simplicity- nature and symbolsGENIES- a natural-language processing system for the extraction of molecular pathways from journal articlesXML, bioinformatics and data integrationFinding pathogenicity islands and gene transfer events in genome dataFrequency-domain analysis of biomolecular sequencesAnalysis of temporal gene expression profilesPhyloBLAST- facilitating phylogenetic analysis of BLAST resultsOptimizing reduced-space sequence analysisValidating clustering for gene expression dataEfficient large-scale sequence comparison by locality-sensitive hashingCircles- automating the comparative analysis of RNA secondary structureBiochemical systems analysis of genome-wide expression dataMIPSIM- similarity analysis of molecular interaction potentialsStrategies for the development of a peptide computerBAliBASE (Benchmark Alignment dataBASE)- enhancements for repeats, transmembrane sequences and circular permutationsDesigning fast converging phylogenetic methodsA comparison of signal sequence prediction methods using a test set of signal peptidesAMADA- analysis of microarray dataPOWER_SAGE- comparing statistical tests for SAGE experimentsJ-Express- exploring gene expression data using JavaAn algorithm for finding signals of unknown length in DNA sequencesA new approach to sequence comparison- normalized sequence alignmentAlignment of 3D structures of macromolecular assembliesCAST- an iterative algorithm for the complexity analysis of sequence tractsASAP- analysis of peptide compositionMissing value estimation methods for DNA microarraysMocca- semi-automatic method for domain huntinga new method for the normalization of gene expression dataMutaProt- a web interface for structural analysis of point mutationsDNA Sequence Analysis and Comparative SequencingTRES- comparative promoter sequence analysis模型A knowledge model for analysis and simulation of regulatory networksVariations on probabilistic suffix trees- statistical modeling and prediction of protein families Rich probabilistic models for gene expressionA numerical model of acid-base transport in rat distal tubuleWeb-based access to mouse models of human cancersa phase-orientated computational model of oncogenesisYPDTM, PombePDTM and WormPDTM- model organism volumes of the BioKnowledgeTM Library, an integrated resource for protein informationSCORE- predicting the core of protein modelsA computer model to simulate family history of breast-ovarian cancerConceptual modelling of genomic information神经网络Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites METATOOL- for studying metabolic networksQuality control in mutation analysis- the European Molecular Genetics Quality Network (EMQN) Inferring qualitative relations in genetic networks and metabolic pathwaysPrediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural networkNeural network schemes for detecting rare events in human genomic DNADynamic simulation of the human red blood cell metabolic networkT-REX- reconstructing and visualizing phylogenetic trees and reticulation networksUsing a Neural Network to Screen a Population for Asthmahierarchical unsupervised growing neural network for clustering gene expression patterns Computational expansion of genetic networksWormBase- network access to the genome and biology of Caenorhabditis elegansUsing a Neural Network to Screen a Population for AsthmaDeveloping networks play a similar melodyGenetic network inference- from co-expression clustering to reverse engineering应用bioinfor-Metabolic flux balance analysis and the in silico analysisAtlas of Genetics and Cytogenetics in Oncology and HaematologyPDBsum- summaries and analyses of PDB structuresRegulonDB (version 3BodyMap incorporated PCR-based expression profiling data and a gene ranking system REBASE?arestriction enzymes and methylasesPseudoBase- structural information on RNA pseudoknotsCollecting and harvesting biological data- the GPCRDB and NucleaRDB information systems Efficient primer design algorithmsGlycoMod - A software tool for determining glycosylation compositionsGenetic Simulation LibraryGeneRAGE- a robust algorithm for sequence clustering and domain detectionGene recognition based on DAG shortest pathsFunctional and structural genomics using PEDANTAutomatic discovery of regulatory in promoter regions based on whole cell expression data and functionalFeature selection for DNA methylation based cancer classificationPASS- prediction of activity spectra for biologically active substancesE-CELL- software environment for whole-cell simulationDNAssist- the integrated editing and analysis of molecular biology sequences in WindowsDNA structure for sequences and repeats of all lengthsUniform integration of genome mapping data using intersection graphsDigital reviews in molecular biology- approaches to structured digital publicationThe TIGR Gene Indices- analysis of gene transcript sequences in highly sampled eukaryotic speciesFlexibility of the genetic code with respect to DNA structureRDP- detection of recombination amongst aligned sequencesA relational schema for both array-based and SAGE gene expression experimentsA graph layout algorithm for drawing metabolic pathwaysVisualizing associations between genome sequences and gene expression data using genome-mean expression profilesVirtual PCRThe massively parallel genetic algorithm for RNA foldingTAMBIS- Transparent Access to Multiple Bioinformatics Information SourcesIntegrating genomic homology into gene structure predictionSaturated BLAST- an automated multiple intermediate sequence search used to detect distanthomologyMolecular classification of multiple tumor typesPSEUDOEXONS AND REGULATORY ELEMENTS IN THE GENOMIC SEQUENCE OF THE -CHEMOKINE Processing and quality control of DNA array hybridization dataPredicting the oxidation state of cysteines by multiple sequence alignmentPhysical mapping with automatic capture of hybridization dataPHAT- a transmembrane-specific substitution matrixDetection of a surface-exposed PEST like sequence in the metabotropic glutamate receptor mGluR1Support vector machine classification and validation of cancer tissue samplesVisualization of expression clusters using Sammon??￥s non-linear mappingConstruction of DNA restriction maps based on a simplified experimentEvaluation of methods for the prediction of membrane spanning regionsExScript- AN EX-CENTRIC APPROACH TO THE DESCRIPTION OF TRANSCRIPT DIVERSITYbiotech-Immobilized RNA switches for the analysis of complex chemical and biological mixtures Identifying target sites for cooperatively binding factorsbiotech-The Internet in clinical trialsIdentifying the 3-terminal exon in human DNAMEDUSA-large scale automatic selection and visual assessment of PCR primer pairsAn integrated system for high throughput TaqManTM based SNP genotypingPrediction of quaternary structure from primary structureGABAagent- a system for integrating data on GABA receptorsA systematic approach to dynamic programming in bioinformaticsThe TRANSFAC system on gene expression regulationBIOINFORMATICS TOOLS FOR WHOLE GENOMESVisual Cloning 2000A Web interface generator for molecular biology programs in UnixA plant calmodulin-binding motor is part kinesin and part myosinA computer-driven approach to PCR-based differential screening, alternative to differential displayA Bayesian framework for the analysis of microarray expression dataIdentification and analysis of eukaryotic promoters其它Ontology for immunogenetics- the IMGT-ONTOLOGYSTACK- Sequence Tag Alignment and Consensus KnowledgebaseLegal ethical and risk issues in telemedicineUniversity bioinformatics programs on the riseLDB2000- sequence-based integrated maps of the human genomebiotech-web-Chemical biotechnology Pharmaceutical biotechnologyA browser for expression databiotech-Monitor- molecules and profilesClinical websites are currently dangerous to healthThe PDB data uniformity projectThe retrieval effectiveness of medical information on the web。