生物信息学必读100篇文献

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 Bioinformation Computer applications in biomolecular sciences biotech-Bioinformatics in the pre- and post-genomic eras The Babel of Bioinformatics Promoter prediction in the human genome The need for a human gene index biotech-Mining for medicines in silico BIOMOLECULAR SIMULATIONS On the Importance of Standardisation in Life Sciences DNA binding sites- representation and discovery Editorial An insight into domain combinations IE-Kb- intron exon knowledge base bioinf-Integration of information systems Health Information Systems and Health Communications High content screening ?§C from cells to data to knowledge Whole-cell biocomputing A classification of tasks in bioinformatics Bioinformatics?athe necessity of the quest for -first principles in life Bioinformatics enters a new millennium Bioinformatics - Challenges in 2001 Mouse as the measure of man 蛋白 Proteome Analysis Database- online application of InterPro and CluSTr for the functional classification of proteins in whole genomes The utility of different representations of protein sequence for predicting functional class TargetDB- a database of peptides targeting proteins to subcellular locations ARED= human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins The RESID Database of protein structure modifications and the NRL-3D Sequence¨CStructure Database Protein Information Resource- a community resource for expert annotation of protein data A Java applet for visualizing protein?§Cprotein interaction STRAP- editor for STRuctural Alignments of Proteins A collection of well characterised integral membrane proteins Predicting protein?§Cprotein interactions from primary structure A genetic algorithm for designing gene- the G protein-coupled receptor protein superfamily The MetaFam Server- a comprehensive protein family resource A simple probabilistic scoring method for protein domain identification a software tool for low complexity proteins and protein domains trEST, trGEN and Hits- access to databases of predicted protein sequences The COG database- new developments in phylogenetic classification of proteins from complete genomes A fully automatic evolutionary classification of protein folds Accommodating Protein Flexibility in Computational Drug Design The mouse SWISS-2D PAGE database- a tool for proteomics study of diabetes and obesity BioMolQuest- integrated database-based retrieval of protein structural and functional information VARSPLIC- alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL TRITON- in silico construction of protein mutants and prediction of their activities The protein kinase resource and other bioinformation resources ProDDO- a database of disordered proteins from the Protein Data Bank a database of protein structural domains The SBASE protein domain library PDB-REPRDB- a database of representative protein chains from the Protein Data Bank TIGRFAMs- a protein family resource for the functional identification of proteins NIFAS- visual analysis of domain evolution in proteins PALI- a database of alignments and phylogeny of homologous protein structures Bioanalytical characterization of proteins The InterPro database, an integrated documentation resource for protein families, domains and functional sites Multi-class protein fold recognition using support vector machines and neural networks ToothPrint, a proteomic database for dental tissues Mining literature for protein?§Cprotein interactions Estimating 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 sequences Identification of novel multi-transmembrane proteins from genomic databases Prediction 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 -database CluSTr- a database of clusters of SWISS-PROT+TrEMBL proteins DIP- The Database of Interacting Proteins-2001 update Iterative sequence-secondary structure search for protein homologs Protein-protein interaction map inference using interacting domain profile pairs DaliLite workbench for protein structure comparison MASIA- recognition of common patterns and properties in multiple aligned protein sequences Clustering of highly homologous sequences to reduce the size of large protein databases On the trail of protein sequences Analysis of conservation and substitutions of secondary structure elements within protein superfamilies FORESST- fold recognition from secondary structure predictions of proteins MetaFam- a unified classification of protein families-1 Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database GlycoSuiteDB- a new curated relational database of glycoprotein glycan structures and their biological sources PALI?aa database of Phylogeny and ALIgnment of homologous protein structures ProtEST- protein multiple sequence alignments from expressed sequence tags MetaFam- a unified classification of protein families. II MaxSub- 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 literature PANAL- an integrated resource for Protein sequence ANALysis An Expressed Sequence Tag EST- Discovery of New G-Protein Coupled Receptors 核酸 ODNBase?aa web database for antisense oligonucleotide effectiveness studies NTDB- Thermodynamic Database for Nucleic Acids The EMBL nucleotide sequence database 数据库 Kabat Database and its applications- future directions PromEC- An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites PLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes PlasmoDB- An integrative database of the Plasmodium falciparum genome PlantsP- a functional genomics database for plant phosphorylation OrCGDB- a database of genes involved in oral cancer BBID- the biological biochemical image database The 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 names B-SPID- An object-relational database architecture to store, retrieve, and manipulate neuroimaging data Database of Structural Motifs in Proteins Mendel, a database of nomenclature for sequenced plant genes Development of the receptor database (RDB)- application to the endocrine disruptor problem LIGAND- chemical database for enzyme reactions Disperse- a simple and efficient approach to parallel database searching A National Cardiac Surgery Database IMGT-HLA Database?aa sequence database for the human major histocompatibility complex DRAGON- Database Referencing of Array Genes Online IMGT, the international ImMunoGeneTics database ICB database- the gyrB database for identification and classification of bacteria HyPaLib- a database of RNAs and RNA structural elements defined by hybrid patterns HUNT- launch of a full-length cDNA database from the Helix Research Institute GABAagent- a system for integrating data on GABA receptors-1 HC Forum- a web site based on an international human cytogenetic database GOBASE- the organelle genome database Genomes OnLine Database (GOLD)- a monitor of genome projects world-wide GenMapDB- a database of mapped human BAC clones FULL-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 resources LGICdb- the ligand-gated ion channel database STRBase- a short tandem repeat DNA database for the human identity testing community The Molecular Biology Database Collection- an updated compilation of biological database resources The Mouse Gene Expression Database The Mouse Genome Database (MGD)- integration nexus for the laboratory mouse The RDP-II (Ribosomal Database Project) The Stanford Microarray Database The KMDB-MutationView- a mutation database for human disease genes The 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 database The Homeodomain Resource- sequences, structures, DNA binding sites and genomic information The EMOTIF database Organelle genome resources at NCBI RECODE- a database of frameshifting, bypassing and codon redefinition utilized for gene expression rSNP_Guide, a database system for analysis of transcription factor binding to target sequences- application to SNPs and site-directed mutations BLAST Search Updater- a notification system for new database matches Semi-automated update and cleanup of structural RNA alignment databases Viral Genome DataBase RefSeq and LocusLink- NCBI gene-centered resources RHdb- the Radiation Hybrid database The ARKdb- genome databases for farmed and other animals rrndb- the Ribosomal RNA Operon Copy Number Database The Arabidopsis Information Resource (TAIR) Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data Database verification studies of SWISS-PROT and GenBank Searching Expressed Sequence Tag Databases SpliceDB- database of canonical and non-canonical mammalian splice sites SRPDB (Signal Recognition Particle Database) TreeGeneBrowser- phylogenetic data mining of gene sequences from public databases RISSC- a novel database for ribosomal 16S¨C23S RNA genes spacer regions ACTIVITY- a database on DNA-RNA sites activity adapted to apply sequence-activity relationships from one system to another DBTBS- a database of Bacillus subtilis promoters and transcription factors Viral Genome DataBase Updated database of patterns used to detect local similarities Pathway analysis in metabolic databases via differential metabolic display Database resources of the National Center for Biotechnology Information A rapid classification protocol for the CATH Domain Database to support structural genomics PIR- a new resource for bioinformatics dbSNP- the NCBI database of genetic variation ALFRED- an allele frequency database for diverse populations and DNA polymorphisms The Human Transcript Database- a catalogue of full length cDNA inserts Aminoacyl-tRNA synthetases database CKAAPs DB- a conserved key amino acid positions database MethDB?aa public database for DNA methylation data BIND?aThe Biomolecular Interaction Network Database Comprehensive Microbial Resource The mouse SWISS-2D PAGE database A comprehensive BAC resource European Large Subunit Ribosomal RNA Database MView- a web-compatible database search 算法 biotech-Plant biotechnology web alert A new approach to sequence comparison The non-coding RNAs as riboregulators Compositional symmetries in complete genomes Comparison of genomic DNA sequences- solved and unsolved problems Mathematical simulation and analysis of cellular metabolism and regulation Automated image analysis for array hybridization experiments A Bayesian framework for the analysis of microarray expression data Mathematica packages for simulation of experimental genetics Genview 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 symbols GENIES- a natural-language processing system for the extraction of molecular pathways from journal articles XML, bioinformatics and data integration Finding pathogenicity islands and gene transfer events in genome data Frequency-domain analysis of biomolecular sequences Analysis of temporal gene expression profiles PhyloBLAST- facilitating phylogenetic analysis of BLAST results Optimizing reduced-space sequence analysis Validating clustering for gene expression data Efficient large-scale sequence comparison by locality-sensitive hashing Circles- automating the comparative analysis of RNA secondary structure Biochemical systems analysis of genome-wide expression data MIPSIM- similarity analysis of molecular interaction potentials Strategies for the development of a peptide computer BAliBASE (Benchmark Alignment dataBASE)- enhancements for repeats, transmembrane sequences and circular permutations Designing fast converging phylogenetic methods A comparison of signal sequence prediction methods using a test set of signal peptides AMADA- analysis of microarray data POWER_SAGE- comparing statistical tests for SAGE experiments J-Express- exploring gene expression data using Java An algorithm for finding signals of unknown length in DNA sequences A new approach to sequence comparison- normalized sequence alignment Alignment of 3D structures of macromolecular assemblies CAST- an iterative algorithm for the complexity analysis of sequence tracts ASAP- analysis of peptide composition Missing value estimation methods for DNA microarrays Mocca- semi-automatic method for domain hunting a new method for the normalization of gene expression data MutaProt- a web interface for structural analysis of point mutations DNA Sequence Analysis and Comparative Sequencing TRES- comparative promoter sequence analysis 模型 A knowledge model for analysis and simulation of regulatory networks Variations on probabilistic suffix trees- statistical modeling and prediction of protein families Rich probabilistic models for gene expression A numerical model of acid-base transport in rat distal tubule Web-based access to mouse models of human cancers a phase-orientated computational model of oncogenesis YPDTM, PombePDTM and WormPDTM- model organism volumes of the BioKnowledgeTM Library, an integrated resource for protein information SCORE- predicting the core of protein models A computer model to simulate family history of breast-ovarian cancer Conceptual 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 networks Quality control in mutation analysis- the European Molecular Genetics Quality Network (EMQN) Inferring qualitative relations in genetic networks and metabolic pathways Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network Neural network schemes for detecting rare events in human genomic DNA Dynamic simulation of the human red blood cell metabolic network T-REX- reconstructing and visualizing phylogenetic trees and reticulation networks Using a Neural Network to Screen a Population for Asthma hierarchical unsupervised growing neural network for clustering gene expression patterns Computational expansion of genetic networks WormBase- network access to the genome and biology of Caenorhabditis elegans Using a Neural Network to Screen a Population for Asthma Developing networks play a similar melody Genetic network inference- from co-expression clustering to reverse engineering 应用 bioinfor-Metabolic flux balance analysis and the in silico analysis Atlas of Genetics and Cytogenetics in Oncology and Haematology PDBsum- summaries and analyses of PDB structures RegulonDB (version 3 BodyMap incorporated PCR-based expression profiling data and a gene ranking system REBASE?arestriction enzymes and methylases PseudoBase- structural information on RNA pseudoknots Collecting and harvesting biological data- the GPCRDB and NucleaRDB information systems Efficient primer design algorithms GlycoMod - A software tool for determining glycosylation compositions Genetic Simulation Library GeneRAGE- a robust algorithm for sequence clustering and domain detection Gene recognition based on DAG shortest paths Functional and structural genomics using PEDANT Automatic discovery of regulatory in promoter regions based on whole cell expression data and functional Feature selection for DNA methylation based cancer classification PASS- prediction of activity spectra for biologically active substances E-CELL- software environment for whole-cell simulation DNAssist- the integrated editing and analysis of molecular biology sequences in Windows DNA structure for sequences and repeats of all lengths Uniform integration of genome mapping data using intersection graphs Digital reviews in molecular biology- approaches to structured digital publication The TIGR Gene Indices- analysis of gene transcript sequences in highly sampled eukaryotic species Flexibility of the genetic code with respect to DNA structure RDP- detection of recombination amongst aligned sequences A relational schema for both array-based and SAGE gene expression experiments A graph layout algorithm for drawing metabolic pathways Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles Virtual PCR The massively parallel genetic algorithm for RNA folding TAMBIS- Transparent Access to Multiple Bioinformatics Information Sources Integrating genomic homology into gene structure prediction Saturated BLAST- an automated multiple intermediate sequence search used to detect distant homology Molecular classification of multiple tumor types PSEUDOEXONS AND REGULATORY ELEMENTS IN THE GENOMIC SEQUENCE OF THE -CHEMOKINE Processing and quality control of DNA array hybridization data Predicting the oxidation state of cysteines by multiple sequence alignment Physical mapping with automatic capture of hybridization data PHAT- a transmembrane-specific substitution matrix Detection of a surface-exposed PEST like sequence in the metabotropic glutamate receptor mGluR1 Support vector machine classification and validation of cancer tissue samples Visualization of expression clusters using Sammon??￥s non-linear mapping Construction of DNA restriction maps based on a simplified experiment Evaluation of methods for the prediction of membrane spanning regions ExScript- AN EX-CENTRIC APPROACH TO THE DESCRIPTION OF TRANSCRIPT DIVERSITY biotech-Immobilized RNA switches for the analysis of complex chemical and biological mixtures Identifying target sites for cooperatively binding factors biotech-The Internet in clinical trials Identifying the 3-terminal exon in human DNA MEDUSA-large scale automatic selection and visual assessment of PCR primer pairs An integrated system for high throughput TaqManTM based SNP genotyping Prediction of quaternary structure from primary structure GABAagent- a system for integrating data on GABA receptors A systematic approach to dynamic programming in bioinformatics The TRANSFAC system on gene expression regulation BIOINFORMATICS TOOLS FOR WHOLE GENOMES Visual Cloning 2000 A Web interface generator for molecular biology programs in Unix A plant calmodulin-binding motor is part kinesin and part myosin A computer-driven approach to PCR-based differential screening, alternative to differential display A Bayesian framework for the analysis of microarray expression data Identification and analysis of eukaryotic promoters 其它 Ontology for immunogenetics- the IMGT-ONTOLOGY STACK- Sequence Tag Alignment and Consensus Knowledgebase Legal ethical and risk issues in telemedicine University bioinformatics programs on the rise LDB2000- sequence-based integrated maps of the human genome biotech-web-Chemical biotechnology Pharmaceutical biotechnology A browser for expression data biotech-Monitor- molecules and profiles Clinical websites are currently dangerous to health The PDB data uniformity project The retrieval effectiveness of medical information on the web