clusterMaker: a multi-algorithm clustering plugin for Cytoscape

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clusterMaker: a multi-algorithm clustering plugin for Cytoscape is …
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scholarly articleQ13442814

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P8978DBLP publication IDjournals/bmcbi/MorrisANBWSBF11
P6179Dimensions Publication ID1033062809
P356DOI10.1186/1471-2105-12-436
P932PMC publication ID3262844
P698PubMed publication ID22070249
P5875ResearchGate publication ID51787251

P50authorAaron M. NewmanQ30347612
John H MorrisQ106637257
Thomas E FerrinQ37391597
Gary D. BaderQ37393655
Jan BaumbachQ43680418
P2093author name stringGang Su
Tobias Wittkop
Leonard Apeltsin
P2860cites workExploration of uncharted regions of the protein universeQ21092729
An automated method for finding molecular complexes in large protein interaction networksQ21284295
Markov clustering versus affinity propagation for the partitioning of protein interaction graphsQ21284364
Finding and evaluating community structure in networksQ21563748
Cytoscape: a software environment for integrated models of biomolecular interaction networksQ24515682
Cluster analysis and display of genome-wide expression patternsQ24644463
Expression analysis of G Protein-Coupled Receptors in mouse macrophagesQ24650905
Basic local alignment search toolQ25938991
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resourcesQ27860739
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiaeQ27860755
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometryQ27861116
Proteome survey reveals modularity of the yeast cell machineryQ27929510
Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteinsQ27932356
A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicingQ27932638
Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profileQ27935813
Global landscape of protein complexes in the yeast Saccharomyces cerevisiaeQ27938796
The genetic landscape of a cellQ28131628
An efficient algorithm for large-scale detection of protein familiesQ28131838
Integration of biological networks and gene expression data using CytoscapeQ28681323
Java Treeview--extensible visualization of microarray dataQ29547226
TM4: a free, open-source system for microarray data management and analysisQ29547339
BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networksQ29547427
Discovering regulatory and signalling circuits in molecular interaction networksQ29614951
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiaeQ29615775
TM4 microarray software suiteQ29618829
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction mapQ29618911
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editingQ30480876
A mouse protein interactome through combined literature mining with multiple sources of interaction evidenceQ51802930
Using support vector machines to distinguish enzymes: approached by incorporating wavelet transformQ51861300
GeneRAGE: a robust algorithm for sequence clustering and domain detectionQ52077020
Sequence clustering strategies improve remote homology recognitions while reducing search timesQ56979236
Superparamagnetic clustering of dataQ74567124
A split-ubiquitin-based assay detects the influence of mutations on the conformational stability of the p53 DNA binding domain in vivoQ78477022
Exploring expression data: identification and analysis of coexpressed genesQ30584655
Clustering by passing messages between data pointsQ31091773
Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model ExplorerQ33380438
AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster numberQ33536850
SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scaleQ33538869
Improving the quality of protein similarity network clustering algorithms using the network edge weight distributionQ33759251
GLay: community structure analysis of biological networksQ33760198
Clustering of highly homologous sequences to reduce the size of large protein databasesQ33941836
Mechanistic diversity in a metalloenzyme superfamilyQ34081644
Clustering and analysis of protein familiesQ34282435
PIRSF: family classification system at the Protein Information ResourceQ34284552
Modular organization of cellular networksQ34329388
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage databaseQ34496170
Homology-free prediction of functional class of proteins and peptides by support vector machinesQ37108573
Identification of protein functions using a machine-learning approach based on sequence-derived propertiesQ37316390
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteinsQ38661398
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomesQ38661643
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to proteinQ39524339
ProtoMap: automatic classification of protein sequences and hierarchy of protein familiesQ39541528
ProtoNet: hierarchical classification of the protein spaceQ39790583
jClust: a clustering and visualization toolboxQ42540306
Comprehensive cluster analysis with Transitivity ClusteringQ44615124
Partitioning biological data with transitivity clusteringQ45786159
Protein complex prediction via cost-based clusteringQ47387430
Clustering of proximal sequence space for the identification of protein familiesQ48628372
P275copyright licenseCreative Commons Attribution 2.0 GenericQ19125117
P6216copyright statuscopyrightedQ50423863
P4510describes a project that usesCytoscapeQ3699942
P433issue1
P407language of work or nameEnglishQ1860
P921main subjectCytoscapeQ3699942
P304page(s)436
P577publication date2011-11-09
P1433published inBMC BioinformaticsQ4835939
P1476titleclusterMaker: a multi-algorithm clustering plugin for Cytoscape
P478volume12

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