Labeling nodes using three degrees of propagation.

PubWeight™: 0.82‹?›

🔗 View Article (PMC 3532359)

Published in PLoS One on December 28, 2012

Authors

Sara Mostafavi1, Anna Goldenberg, Quaid Morris

Author Affiliations

1: Department of Computer Science, Stanford University, Palo Alto, CA, USA. saram@cs.stanford.edu

Articles citing this

GeneMANIA prediction server 2013 update. Nucleic Acids Res (2013) 2.74

Compact Integration of Multi-Network Topology for Functional Analysis of Genes. Cell Syst (2016) 0.76

Articles cited by this

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52

Collective dynamics of 'small-world' networks. Nature (1998) 98.45

The spread of obesity in a large social network over 32 years. N Engl J Med (2007) 34.75

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29

BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41

Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77

Modularity and community structure in networks. Proc Natl Acad Sci U S A (2006) 17.97

The genetic landscape of a cell. Science (2010) 16.52

Dynamic spread of happiness in a large social network: longitudinal analysis over 20 years in the Framingham Heart Study. BMJ (2008) 10.80

A combined algorithm for genome-wide prediction of protein function. Nature (1999) 9.99

Interactome networks and human disease. Cell (2011) 7.16

Mixing patterns in networks. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 6.48

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol (2008) 5.94

Universal behavior of load distribution in scale-free networks. Phys Rev Lett (2001) 5.64

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78

Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res (2011) 4.39

Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics (2006) 3.94

Transitive functional annotation by shortest-path analysis of gene expression data. Proc Natl Acad Sci U S A (2002) 3.93

Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol (2003) 3.80

A statistical framework for genomic data fusion. Bioinformatics (2004) 3.64

Finding function: evaluation methods for functional genomic data. BMC Genomics (2006) 3.10

Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet (2009) 1.90

Distribution of node characteristics in complex networks. Proc Natl Acad Sci U S A (2007) 1.79

Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci U S A (2004) 1.67

Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res (2008) 1.61

It's the machine that matters: Predicting gene function and phenotype from protein networks. J Proteomics (2010) 1.57

Articles by these authors

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res (2010) 10.97

Cytoscape Web: an interactive web-based network browser. Bioinformatics (2010) 10.03

Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol (2008) 5.94

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell (2006) 5.72

Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol (2009) 5.41

Exploration of essential gene functions via titratable promoter alleles. Cell (2004) 5.21

Probing microRNAs with microarrays: tissue specificity and functional inference. RNA (2004) 4.91

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol (2009) 3.44

A panoramic view of yeast noncoding RNA processing. Cell (2003) 3.11

GeneMANIA prediction server 2013 update. Nucleic Acids Res (2013) 2.74

RBPDB: a database of RNA-binding specificities. Nucleic Acids Res (2010) 2.42

Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet (2005) 2.26

Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinformatics (2010) 2.26

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Mol Cell (2012) 1.93

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. RNA (2010) 1.87

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics (2007) 1.86

RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput Biol (2010) 1.78

iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res (2012) 1.63

Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment. Cell Stem Cell (2007) 1.56

Transcriptional networks: reverse-engineering gene regulation on a global scale. Curr Opin Microbiol (2004) 1.54

Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res (2010) 1.46

Essential role of complex II of the respiratory chain in hypoxia-induced ROS generation in the pulmonary vasculature. Am J Physiol Lung Cell Mol Physiol (2003) 1.25

ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. Bioinformatics (2009) 1.22

PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions. PLoS Comput Biol (2012) 1.18

PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biol (2015) 1.17

Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein. Genome Biol (2014) 1.15

Rapamycin attenuates hypoxia-induced pulmonary vascular remodeling and right ventricular hypertrophy in mice. Respir Res (2007) 1.15

Combining many interaction networks to predict gene function and analyze gene lists. Proteomics (2012) 1.09

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. Genome Med (2013) 1.05

Hypoxic vasoconstriction of partial muscular intra-acinar pulmonary arteries in murine precision cut lung slices. Respir Res (2006) 1.03

Intermedin/adrenomedullin-2 is a hypoxia-induced endothelial peptide that stabilizes pulmonary microvascular permeability. Am J Physiol Lung Cell Mol Physiol (2009) 0.98

Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. PLoS One (2011) 0.96

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. BMC Genomics (2012) 0.96

Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells. Genome Biol (2012) 0.95

Global profiles of gene expression induced by adrenocorticotropin in Y1 mouse adrenal cells. Endocrinology (2006) 0.94

Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway. Mol Syst Biol (2009) 0.94

Jury remains out on simple models of transcription factor specificity. Nat Biotechnol (2011) 0.92

Mitochondrial complex II is essential for hypoxia-induced ROS generation and vasoconstriction in the pulmonary vasculature. Adv Exp Med Biol (2003) 0.88

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins. Nucleic Acids Res (2013) 0.87

A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. Bioinformatics (2013) 0.87

Hypoxia-induced increase of endostatin in murine aorta and lung. Histochem Cell Biol (2006) 0.86

Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst Biol (2012) 0.86

Mitochondrial complex II is essential for hypoxia-induced pulmonary vasoconstriction of intra- but not of pre-acinar arteries. Cardiovasc Res (2012) 0.85

RNA-protein interactions: an overview. Methods Mol Biol (2014) 0.85

Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish. Development (2014) 0.84

Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization. Pac Symp Biocomput (2009) 0.81

A genome-wide assessment of adrenocorticotropin action in the Y1 mouse adrenal tumor cell line. Mol Cell Endocrinol (2007) 0.81

Mixture model for sub-phenotyping in GWAS. Pac Symp Biocomput (2012) 0.81

Predicting node characteristics from molecular networks. Methods Mol Biol (2011) 0.81

An efficient algorithm to integrate network and attribute data for gene function prediction. Pac Symp Biocomput (2014) 0.80

PLIDA: cross-platform gene expression normalization using perturbed topic models. Bioinformatics (2013) 0.78

Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression. PLoS One (2013) 0.78

Videomorphometric analysis of hypoxic pulmonary vasoconstriction of intra-pulmonary arteries using murine precision cut lung slices. J Vis Exp (2014) 0.77

The biologic basis of clinical heterogeneity in juvenile idiopathic arthritis. Arthritis Rheumatol (2014) 0.76

Contributions of steroidogenic factor 1 to the transcription landscape of Y1 mouse adrenocortical tumor cells. Mol Cell Endocrinol (2010) 0.76

Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction. Pac Symp Biocomput (2014) 0.75

Role of ROS and NO in hypoxia-induced increase in tyrosine hydroxylase-messenger RNA in PC12 cells. Adv Exp Med Biol (2003) 0.75

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun (2016) 0.75

Network news: functional modules revealed during early embryogenesis in C. elegans. Dev Cell (2005) 0.75

VENOUS THROMBOEMBOLISM AFTER MAJOR VENOUS INJURIES: COMPETING PRIORITIES. J Trauma Acute Care Surg (2017) 0.75

REGULATORY RNA. Pac Symp Biocomput (2016) 0.75

Systemic intraoperative anticoagulation during arterial injury repair: Implications for patency and bleeding. J Trauma Acute Care Surg (2017) 0.75

Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors. Pac Symp Biocomput (2015) 0.75