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