|
|
MODELTEST: testing the model of DNA substitution (1998)
|
9679
|
|
|
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment (2004)
|
6684
|
|
|
MrBayes 3: Bayesian phylogenetic inference under mixed models (2003)
|
5600
|
|
|
MRBAYES: Bayesian inference of phylogenetic trees (2001)
|
5007
|
|
|
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium (2000)
|
4930
|
|
|
Molecular classification of cancer: {C}lass discovery and class prediction by gene expression monitoring (1999)
|
4729
|
|
|
TreeView: an application to display phylogenetic trees on personal computers (1996)
|
4313
|
|
|
Inference of Population Structure Using Multilocus Genotype Data (2004)
|
3981
|
|
|
Haploview: analysis and visualization of LD and haplotype maps (2005)
|
3891
|
|
|
MEGA2: molecular evolutionary genetics analysis software (2001)
|
3853
|
|
|
VMD: Visual molecular dynamics (1996)
|
3446
|
|
|
MOLMOL: A program for display and analysis of macromolecular structures (1996)
|
2669
|
|
|
A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins (1970)
|
2642
|
|
|
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling (2000)
|
2641
|
|
|
DnaSP, DNA polymorphism analyses by the coalescent and other methods (2003)
|
2618
|
|
|
PAML: a program package for phylogenetic analysis by maximum likelihood (1997)
|
2575
|
|
|
Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization
|
2358
|
|
|
Designing the user interface strategies for effective human-computer interaction (1987)
|
2015
|
|
|
Amino acid substitution matrices from protein blocks (1992)
|
1901
|
|
|
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias (2003)
|
1716
|
|
|
Profile hidden Markov models (1998)
|
1714
|
|
|
Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays (1999)
|
1571
|
|
|
Gene Selection for Cancer Classification using Support Vector Machines (2002)
|
1518
|
|
|
Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation (1999)
|
1482
|
|
|
The rapid generation of mutation data matrices from protein sequences (1992)
|
1464
|
|
|
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (1998)
|
1427
|
|
|
Network Motifs: Simple Building Blocks of Complex Networks (2002)
|
1367
|
|
|
DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis (1999)
|
1308
|
|
|
Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer (1994)
|
1228
|
|
|
CLUSTAL V: improved software for multiple sequence alignment (1992)
|
1226
|
|
|
WHAT IF: A molecular modeling and drug design program (1990)
|
1194
|
|
|
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)
|
1182
|
|
|
Knowledge-based Analysis of Microarray Gene Expression Data By Using Support Vector Machines (2000)
|
1181
|
|
|
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models (2006)
|
1149
|
|
|
Using Bayesian Networks to Analyze Expression Data (2000)
|
1091
|
|
|
TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment (1994)
|
1042
|
|
|
Detecting subtle sequence signals: a gibbs sampling strategy for multiple alignment (1993)
|
995
|
|
|
The PSIPRED protein structure prediction server (2000)
|
970
|
|
|
SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny (1996)
|
952
|
|
|
The COG database: an updated version includes eukaryotes (2003)
|
952
|
|
|
Comparative assessment of large-scale data sets of protein-protein interactions (2002)
|
924
|
|
|
A model of evolutionary change in proteins (1978)
|
923
|
|
|
Monte carlo strategies in scientific computing (2001)
|
912
|
|
|
Multiclass cancer diagnosis using tumor gene expression signatures (2001)
|
855
|
|
|
Support vector machine classification and validation of cancer tissue samples using microarray expression data (2000)
|
845
|
|
|
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review (2002)
|
840
|
|
|
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles (1999)
|
835
|
|
|
A method of measuring eye movement using a scleral search coil in a magnetic field (1963)
|
826
|
|
|
Using Information Content to Evaluate Semantic Similarity in a Taxonomy (1995)
|
820
|
|
|
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models (2003)
|
799
|
|
|
Missing value estimation methods for DNA microarrays (2001)
|
789
|
|
|
Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data (2002)
|
764
|
|
|
Analysis of Variance for Gene Expression Microarray Data (2000)
|
760
|
|
|
A Real Time QRS Detection Algorithm (1985)
|
746
|
|
|
Singular value decomposition for genome-wide expression data processing and modeling (2000)
|
720
|
|
|
Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits (2003)
|
720
|
|
|
ProtTest: selection of best-fit models of protein evolution (2005)
|
717
|
|
|
MUSCLE: a multiple sequence alignment method with reduced time and space complexity (2004)
|
715
|
|
|
Methods for Assessing the Statistical Significance of Molecular Sequence Features by Using General Scoring Schemes (1990)
|
709
|
|
|
ESPript: analysis of multiple sequence alignments in PostScript (1999)
|
697
|
|
|
Hidden Markov Models in Computational Biology Applications to Protein Modeling (1994)
|
685
|
|
|
Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)
|
679
|
|
|
Artemis: sequence visualization and annotation (2000)
|
679
|
|
|
A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes (2001)
|
657
|
|
|
A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences (1998)
|
657
|
|
|
Hidden Markov models for detecting remote protein homologies (1998)
|
654
|
|
|
SOSUI: classification and secondary structure prediction system for membrane proteins (1998)
|
652
|
|
|
Biclustering of Expression Data (2000)
|
648
|
|
|
The Jalview Java alignment editor (2004)
|
648
|
|
|
Classification and diagnostic prediction of pediatric cancers using gene expression profiling and artificial neural networks (2002)
|
630
|
|
|
Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models (2001)
|
627
|
|
|
Fast and sensitive multiple sequence alignments on a microcomputer (1989)
|
621
|
|
|
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences (1999)
|
620
|
|
|
Clustal W and Clustal X version 2.0 (2007)
|
615
|
|
|
Genome-wide analysis of DNA copy-number changes using cDNA microarrays (1999)
|
611
|
|
|
A Greedy Algorithm for Aligning DNA Sequences (2000)
|
603
|
|
|
Classication and Diagnostic Prediction of Cancers using Gene Expression Proling and Articial Neural Networks
|
601
|
|
|
fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood (1994)
|
596
|
|
|
Variance stabilization applied to microarray data calibration and to the quantification of differential expression (2002)
|
595
|
|
|
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling (2006)
|
595
|
|
|
CONSEL: for assessing the confidence of phylogenetic tree selection (2001)
|
590
|
|
|
Generating samples under a Wright-Fisher neutral model of genetic variation (2002)
|
589
|
|
|
Biclustering Algorithms for Biological Data Analysis: A Survey (2004)
|
573
|
|
|
An efficient algorithm for large-scale detection of protein families (2002)
|
566
|
|
|
ADE4: a multivariate analysis and graphical display software (1997)
|
563
|
|
|
InterProScan - an integration platform for the signature-recognition methods in InterPro (2001)
|
548
|
|
|
DNA binding sites: representation and discovery (2000)
|
548
|
|
|
Specificity and Stability in Topology of Protein Networks (2002)
|
543
|
|
|
Using Bayesian Networks to Analyze Expression Data (1999)
|
538
|
|
|
GOLD-Graphical Overview of Linkage Disequilibrium (2000)
|
535
|
|
|
Optimal alignments in linear space (1988)
|
534
|
|
|
JPred: a consensus secondary structure prediction server (1998)
|
534
|
|
|
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees (1997)
|
528
|
|
|
Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data (1995)
|
528
|
|
|
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences (2008)
|
520
|
|
|
The Unified Medical Language System (1993)
|
516
|
|
|
A Bayesian Networks Approach for Predicting Protein-Protein Interactionsfrom Genomic Data (2003)
|
514
|
|
|
Protein interaction maps for complete genomes based on gene fusion events (1999)
|
500
|
|
|
RDP2: recombination detection and analysis from sequence alignments (2005)
|
498
|
|
|
affy - analysis of Affymetrix GeneChip data at the probe level (2004)
|
497
|