Detection of functional modules from protein interaction networks.

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A core-attachment based method to detect protein complexes in PPI networks. BMC Bioinformatics (2009) 2.10

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Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PLoS Comput Biol (2012) 1.54

Revealing static and dynamic modular architecture of the eukaryotic protein interaction network. Mol Syst Biol (2007) 1.53

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In search of the biological significance of modular structures in protein networks. PLoS Comput Biol (2007) 1.38

Protein complex identification by supervised graph local clustering. Bioinformatics (2008) 1.32

Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. BMC Bioinformatics (2007) 1.30

A novel functional module detection algorithm for protein-protein interaction networks. Algorithms Mol Biol (2006) 1.25

Growing functional modules from a seed protein via integration of protein interaction and gene expression data. BMC Bioinformatics (2007) 1.13

The function of communities in protein interaction networks at multiple scales. BMC Syst Biol (2010) 1.07

Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics (2006) 1.05

Protein interaction networks--more than mere modules. PLoS Comput Biol (2010) 1.05

Detecting uber-operons in prokaryotic genomes. Nucleic Acids Res (2006) 1.04

A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae. Genome Res (2005) 1.04

Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network. BMC Syst Biol (2010) 1.03

Identifying functional modules in interaction networks through overlapping Markov clustering. Bioinformatics (2012) 1.03

A critical and integrated view of the yeast interactome. Comp Funct Genomics (2004) 1.02

From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization. PLoS Comput Biol (2013) 0.98

An in silico method for detecting overlapping functional modules from composite biological networks. BMC Syst Biol (2008) 0.98

Metabolic engineering in the -omics era: elucidating and modulating regulatory networks. Microbiol Mol Biol Rev (2005) 0.97

Jerarca: efficient analysis of complex networks using hierarchical clustering. PLoS One (2010) 0.94

Pathway and network analysis in proteomics. J Theor Biol (2014) 0.93

Discover protein complexes in protein-protein interaction networks using parametric local modularity. BMC Bioinformatics (2010) 0.90

Yeast Protein Interactome topology provides framework for coordinated-functionality. Nucleic Acids Res (2006) 0.90

Systems biology in the context of big data and networks. Biomed Res Int (2014) 0.90

Protein complex prediction based on k-connected subgraphs in protein interaction network. BMC Syst Biol (2010) 0.89

Protein interaction networks in plants. Planta (2006) 0.89

Cluster-based assessment of protein-protein interaction confidence. BMC Bioinformatics (2012) 0.87

Identifying protein complexes directly from high-throughput TAP data with Markov random fields. BMC Bioinformatics (2007) 0.87

Clustering under the line graph transformation: application to reaction network. BMC Bioinformatics (2004) 0.86

Discovery of protein complexes with core-attachment structures from Tandem Affinity Purification (TAP) data. J Comput Biol (2011) 0.86

Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme. BMC Bioinformatics (2011) 0.86

Comparative evolutionary analysis of protein complexes in E. coli and yeast. BMC Genomics (2010) 0.86

A protein interaction map of the LSU processome. Genes Dev (2015) 0.85

Protein function assignment through mining cross-species protein-protein interactions. PLoS One (2008) 0.85

Disentangling function from topology to infer the network properties of disease genes. BMC Syst Biol (2013) 0.85

Joint clustering of protein interaction networks through Markov random walk. BMC Syst Biol (2014) 0.84

BicNET: Flexible module discovery in large-scale biological networks using biclustering. Algorithms Mol Biol (2016) 0.84

Identifying protein complexes based on density and modularity in protein-protein interaction network. BMC Syst Biol (2013) 0.84

Differential evolutionary conservation of motif modes in the yeast protein interaction network. BMC Genomics (2006) 0.84

POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. J R Soc Interface (2008) 0.83

Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs. BMC Bioinformatics (2010) 0.83

Massive human co-expression network and its medical applications. Chem Biodivers (2012) 0.82

Diffusion model based spectral clustering for protein-protein interaction networks. PLoS One (2010) 0.82

A novel function prediction approach using protein overlap networks. BMC Syst Biol (2013) 0.81

Inferring functional modules of protein families with probabilistic topic models. BMC Bioinformatics (2011) 0.81

Network analysis reveals distinct clinical syndromes underlying acute mountain sickness. PLoS One (2014) 0.81

CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions. BMC Bioinformatics (2008) 0.81

Benchmarking human protein complexes to investigate drug-related systems and evaluate predicted protein complexes. PLoS One (2013) 0.81

Discovering protein complexes in protein interaction networks via exploring the weak ties effect. BMC Syst Biol (2012) 0.80

Ontology integration to identify protein complex in protein interaction networks. Proteome Sci (2011) 0.80

Predicting protein complex in protein interaction network - a supervised learning based method. BMC Syst Biol (2014) 0.79

Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology. BMC Bioinformatics (2010) 0.79

Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test. BMC Syst Biol (2010) 0.79

The human plasma membrane peripherome: visualization and analysis of interactions. Biomed Res Int (2014) 0.78

Two-layer modular analysis of gene and protein networks in breast cancer. BMC Syst Biol (2014) 0.76

Functional consequences of necdin nucleocytoplasmic localization. PLoS One (2012) 0.76

A multiobjective approach for identifying protein complexes and studying their association in multiple disorders. Algorithms Mol Biol (2015) 0.75

IRES-dependent translated genes in fungi: computational prediction, phylogenetic conservation and functional association. BMC Genomics (2015) 0.75

C-element: a new clustering algorithm to find high quality functional modules in PPI networks. PLoS One (2013) 0.75

PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks. BMC Genomics (2013) 0.75

A NEW CLUSTERING METHOD AND ITS APPLICATION TO PROTEOMIC PROFILING FOR COLON CANCER. IASTED Int Conf Comput Syst Biol (2006) (2006) 0.75

A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae. BMC Syst Biol (2016) 0.75

Investigating topological and functional features of multimodular proteins. J Biomed Biotechnol (2009) 0.75

Quantitative assessment of gene expression network module-validation methods. Sci Rep (2015) 0.75

MAE-FMD: multi-agent evolutionary method for functional module detection in protein-protein interaction networks. BMC Bioinformatics (2014) 0.75

Discovering Distinct Functional Modules of Specific Cancer Types Using Protein-Protein Interaction Networks. Biomed Res Int (2015) 0.75

Protein complexes predictions within protein interaction networks using genetic algorithms. BMC Bioinformatics (2016) 0.75

Increasing the precision of orthology-based complex prediction through network alignment. PeerJ (2014) 0.75

Genome composition and phylogeny of microbes predict their co-occurrence in the environment. PLoS Comput Biol (2017) 0.75

Characterization of known protein complexes using k-connectivity and other topological measures. F1000Res (2013) 0.75

Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms. BMC Bioinformatics (2015) 0.75

miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25

miRBase: tools for microRNA genomics. Nucleic Acids Res (2007) 38.61

Human MicroRNA targets. PLoS Biol (2004) 34.51

Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science (2006) 18.14

Requirement of bic/microRNA-155 for normal immune function. Science (2007) 16.24

Identification of virus-encoded microRNAs. Science (2004) 12.56

MicroRNAs regulate brain morphogenesis in zebrafish. Science (2005) 11.16

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13

microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells. Immunity (2007) 6.72

A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway. Genes Dev (2007) 4.69

RNA editing of human microRNAs. Genome Biol (2006) 4.16

Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics (2002) 4.12

Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods (2008) 3.41

An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. Nat Genet (2009) 3.05

Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res (2004) 2.86

Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol (2007) 2.73

Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res (2004) 2.66

Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc (2009) 2.66

Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (2003) 2.66

The miR-144/451 locus is required for erythroid homeostasis. J Exp Med (2010) 2.54

Prediction of microRNA targets. Drug Discov Today (2007) 2.46

The balance of driving forces during genome evolution in prokaryotes. Genome Res (2003) 2.39

Computational prediction of protein-protein interactions. Mol Biotechnol (2007) 2.35

The net of life: reconstructing the microbial phylogenetic network. Genome Res (2005) 2.31

Protein families and TRIBES in genome sequence space. Nucleic Acids Res (2003) 2.27

BioLayout(Java): versatile network visualisation of structural and functional relationships. Appl Bioinformatics (2005) 2.26

Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction. Circulation (2012) 2.14

Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A (2003) 2.08

Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods (2013) 1.92

The phylogenetic extent of metabolic enzymes and pathways. Genome Res (2003) 1.92

Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes Dev (2009) 1.84

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements. Nature (2011) 1.77

COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics (2003) 1.77

Myriads of protein families, and still counting. Genome Biol (2003) 1.75

RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73

Transcription regulation and environmental adaptation in bacteria. Trends Microbiol (2003) 1.63

Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res (2005) 1.61

Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets. Cancer Res (2010) 1.59

Annotation of mammalian primary microRNAs. BMC Genomics (2008) 1.53

Classification schemes for protein structure and function. Nat Rev Genet (2003) 1.52

A logic-based diagram of signalling pathways central to macrophage activation. BMC Syst Biol (2008) 1.49

MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells. J Biol Chem (2012) 1.43

Efficient inhibition of miR-155 function in vivo by peptide nucleic acids. Nucleic Acids Res (2010) 1.41

MagicMatch--cross-referencing sequence identifiers across databases. Bioinformatics (2005) 1.34

Highly consistent patterns for inherited human diseases at the molecular level. Bioinformatics (2005) 1.33

An exponential core in the heart of the yeast protein interaction network. Mol Biol Evol (2004) 1.31

Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis. Mol Cell (2013) 1.29

Structural and functional properties of genes involved in human cancer. BMC Genomics (2006) 1.29

Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PLoS Genet (2012) 1.28

The phylogenetic diversity of eukaryotic transcription. Nucleic Acids Res (2003) 1.28

Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28

Percolation of annotation errors through hierarchically structured protein sequence databases. Math Biosci (2005) 1.27

Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. EMBO Rep (2005) 1.25

Functional evolution of the yeast protein interaction network. Mol Biol Evol (2004) 1.25

GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics (2003) 1.23

Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs. Proc Natl Acad Sci U S A (2010) 1.20

Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis. BMC Genomics (2010) 1.20

From genes to genomes: universal scale-invariant properties of microbial chromosome organisation. J Mol Biol (2003) 1.15

MapMi: automated mapping of microRNA loci. BMC Bioinformatics (2010) 1.15

Probabilistic annotation of protein sequences based on functional classifications. BMC Bioinformatics (2005) 1.12

Automated metabolic reconstruction for Methanococcus jannaschii. Archaea (2004) 1.07

SylArray: a web server for automated detection of miRNA effects from expression data. Bioinformatics (2010) 1.07

Beyond 100 genomes. Genome Biol (2003) 1.06

MiR-25 regulates Wwp2 and Fbxw7 and promotes reprogramming of mouse fibroblast cells to iPSCs. PLoS One (2012) 0.99

Genetic variation between Helicobacter pylori strains: gene acquisition or loss? Trends Microbiol (2002) 0.98

Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia. Mol Cancer (2014) 0.98

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation. BMC Genomics (2009) 0.96

MiR-221 influences effector functions and actin cytoskeleton in mast cells. PLoS One (2011) 0.95

The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression. Mol Cancer (2010) 0.94

LIN28 Expression in malignant germ cell tumors downregulates let-7 and increases oncogene levels. Cancer Res (2013) 0.92

Robustness of metabolic map reconstruction. J Bioinform Comput Biol (2004) 0.91

The properties of protein family space depend on experimental design. Bioinformatics (2005) 0.91

Metabolic database systems for the analysis of genome-wide function. Biotechnol Bioeng (2003) 0.91

Clustering the annotation space of proteins. BMC Bioinformatics (2005) 0.91

Denoising inferred functional association networks obtained by gene fusion analysis. BMC Genomics (2007) 0.90

Genome-wide expression patterns in physiological cardiac hypertrophy. BMC Genomics (2010) 0.89

Enhanced susceptibility to Citrobacter rodentium infection in microRNA-155-deficient mice. Infect Immun (2012) 0.89

CoGenT++: an extensive and extensible data environment for computational genomics. Bioinformatics (2005) 0.89

miR-221 affects multiple cancer pathways by modulating the level of hundreds messenger RNAs. Front Genet (2013) 0.89

CORRIE: enzyme sequence annotation with confidence estimates. BMC Bioinformatics (2007) 0.87

Transcriptome classification reveals molecular subtypes in psoriasis. BMC Genomics (2012) 0.87

Metabolic innovations towards the human lineage. BMC Evol Biol (2008) 0.85

Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification. PLoS One (2011) 0.85

Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data. Hum Genet (2011) 0.85

Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks. BMC Res Notes (2011) 0.85

Messenger RNA and microRNA profiling during early mouse EB formation. Gene Expr Patterns (2011) 0.84

Depletion of HPV16 early genes induces autophagy and senescence in a cervical carcinogenesis model, regardless of viral physical state. J Pathol (2013) 0.83

Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. Brief Bioinform (2012) 0.83

Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion. BMC Evol Biol (2011) 0.81

Gene network and proteomic analyses of cardiac responses to pathological and physiological stress. Circ Cardiovasc Genet (2013) 0.81

Large-scale analysis of microRNA evolution. BMC Genomics (2012) 0.81

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines. PLoS One (2012) 0.80

Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles. PLoS One (2013) 0.80