生物信息学必读100篇论文

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