Published in Genome Biol on June 27, 2008
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature (2012) 14.76
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res (2010) 10.97
Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res (2011) 4.39
GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. Nat Genet (2013) 3.42
Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network. Cell (2013) 3.26
GeneMANIA prediction server 2013 update. Nucleic Acids Res (2013) 2.74
Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol (2012) 2.40
Chapter 2: Data-driven view of disease biology. PLoS Comput Biol (2012) 2.40
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics (2010) 2.39
Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinformatics (2010) 2.26
Visualizing multidimensional cancer genomics data. Genome Med (2013) 2.19
Relaxation response induces temporal transcriptome changes in energy metabolism, insulin secretion and inflammatory pathways. PLoS One (2013) 2.05
Understanding multicellular function and disease with human tissue-specific networks. Nat Genet (2015) 2.04
The impact of multifunctional genes on "guilt by association" analysis. PLoS One (2011) 1.69
It's the machine that matters: Predicting gene function and phenotype from protein networks. J Proteomics (2010) 1.57
FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res (2013) 1.56
"Guilt by association" is the exception rather than the rule in gene networks. PLoS Comput Biol (2012) 1.45
Web-queryable large-scale data sets for hypothesis generation in plant biology. Plant Cell (2009) 1.44
Gibbon genome and the fast karyotype evolution of small apes. Nature (2014) 1.43
Genome-wide association study of short-acting β2-agonists. A novel genome-wide significant locus on chromosome 2 near ASB3. Am J Respir Crit Care Med (2015) 1.42
Spliceosome SNRNP200 Promotes Viral RNA Sensing and IRF3 Activation of Antiviral Response. PLoS Pathog (2016) 1.39
How can functional annotations be derived from profiles of phenotypic annotations? BMC Bioinformatics (2017) 1.38
Perrault syndrome is caused by recessive mutations in CLPP, encoding a mitochondrial ATP-dependent chambered protease. Am J Hum Genet (2013) 1.37
Bayesian Markov Random Field analysis for protein function prediction based on network data. PLoS One (2010) 1.29
Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proc Natl Acad Sci U S A (2011) 1.27
Arabinogalactan-proteins and the research challenges for these enigmatic plant cell surface proteoglycans. Front Plant Sci (2012) 1.26
Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells. Mol Cell (2014) 1.22
Predicting gene function using hierarchical multi-label decision tree ensembles. BMC Bioinformatics (2010) 1.19
ePlant and the 3D data display initiative: integrative systems biology on the world wide web. PLoS One (2011) 1.16
Combining heterogeneous data sources for accurate functional annotation of proteins. BMC Bioinformatics (2013) 1.15
Dissection of regulatory networks that are altered in disease via differential co-expression. PLoS Comput Biol (2013) 1.14
Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nat Protoc (2011) 1.14
The influence of scaffold elasticity on germ layer specification of human embryonic stem cells. Biomaterials (2011) 1.13
The Disease and Gene Annotations (DGA): an annotation resource for human disease. Nucleic Acids Res (2012) 1.11
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Res (2011) 1.11
Metabolomics as a tool to investigate abiotic stress tolerance in plants. Int J Mol Sci (2013) 1.11
The role of indirect connections in gene networks in predicting function. Bioinformatics (2011) 1.10
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol (2013) 1.09
CDK6 as a key regulator of hematopoietic and leukemic stem cell activation. Blood (2014) 1.09
Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development. Nat Commun (2014) 1.08
Prediction and validation of gene-disease associations using methods inspired by social network analyses. PLoS One (2013) 1.05
FuncBase: a resource for quantitative gene function annotation. Bioinformatics (2010) 1.01
POLYGALACTURONASE INVOLVED IN EXPANSION1 functions in cell elongation and flower development in Arabidopsis. Plant Cell (2014) 0.99
Heme-oxygenase-1 implications in cell morphology and the adhesive behavior of prostate cancer cells. Oncotarget (2014) 0.98
Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge. PLoS One (2013) 0.97
Coregulation and modulation of NFκB-related genes in celiac disease: uncovered aspects of gut mucosal inflammation. Hum Mol Genet (2013) 0.97
Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources. Plant Physiol (2010) 0.96
A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinformatics (2009) 0.96
RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. Genome Biol (2012) 0.95
Rapid Inflammasome Activation following Mucosal SIV Infection of Rhesus Monkeys. Cell (2016) 0.94
Accurate evaluation and analysis of functional genomics data and methods. Ann N Y Acad Sci (2012) 0.94
Protein function prediction using text-based features extracted from the biomedical literature: the CAFA challenge. BMC Bioinformatics (2013) 0.94
Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation. Mol Biol Cell (2014) 0.93
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. Front Genet (2014) 0.92
Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. Genome Med (2015) 0.92
Review of biological network data and its applications. Genomics Inform (2013) 0.92
DNA methylation patterns in naïve CD4+ T cells identify epigenetic susceptibility loci for malar rash and discoid rash in systemic lupus erythematosus. Lupus Sci Med (2015) 0.91
Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data. Bioinformatics (2012) 0.91
Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold. Pac Symp Biocomput (2014) 0.90
Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks. Front Cell Dev Biol (2014) 0.90
A role for central spindle proteins in cilia structure and function. Cytoskeleton (Hoboken) (2011) 0.90
Multiple genetic interaction experiments provide complementary information useful for gene function prediction. PLoS Comput Biol (2012) 0.90
A race through the maze of genomic evidence. Genome Biol (2008) 0.89
Gene expression analysis uncovers novel hedgehog interacting protein (HHIP) effects in human bronchial epithelial cells. Genomics (2013) 0.89
Glucocorticoid receptor coordinates transcription factor-dominated regulatory network in macrophages. BMC Genomics (2014) 0.88
A genome-wide analysis of 'Bounty' descendants implicates several novel variants in migraine susceptibility. Neurogenetics (2012) 0.88
Autworks: a cross-disease network biology application for Autism and related disorders. BMC Med Genomics (2012) 0.88
In utero exposure to benzo(a)pyrene predisposes offspring to cardiovascular dysfunction in later-life. Toxicology (2012) 0.88
Genome-wide matching of genes to cellular roles using guilt-by-association models derived from single sample analysis. BMC Res Notes (2012) 0.88
Pathway network inference from gene expression data. BMC Syst Biol (2014) 0.88
Methods, challenges, and promise of next-generation sequencing in cancer biology. Yale J Biol Med (2011) 0.87
NUCLEAR FACTOR Y transcription factors have both opposing and additive roles in ABA-mediated seed germination. PLoS One (2013) 0.87
Robust PCA based method for discovering differentially expressed genes. BMC Bioinformatics (2013) 0.87
Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers. BMC Genomics (2013) 0.87
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst Biol (2012) 0.86
Antibody-mediated protection against SHIV challenge includes systemic clearance of distal virus. Science (2016) 0.86
Integration of molecular network data reconstructs Gene Ontology. Bioinformatics (2014) 0.85
Data- and knowledge-based modeling of gene regulatory networks: an update. EXCLI J (2015) 0.85
High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method. Nucleic Acids Res (2013) 0.85
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Brief Bioinform (2015) 0.84
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinformatics (2014) 0.84
Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish. Development (2014) 0.84
Inferring alterations in cell-to-cell communication in HER2+ breast cancer using secretome profiling of three cell models. Biotechnol Bioeng (2014) 0.84
Progress and challenges in the computational prediction of gene function using networks. F1000Res (2012) 0.84
The application of network label propagation to rank biomarkers in genome-wide Alzheimer's data. BMC Genomics (2014) 0.84
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development. Front Neurosci (2014) 0.84
cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Res (2015) 0.84
Hierarchical ensemble methods for protein function prediction. ISRN Bioinform (2014) 0.84
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists. Bioinform Biol Insights (2015) 0.84
Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. Nat Methods (2014) 0.84
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. BMC Syst Biol (2013) 0.84
Genome-wide analysis identifies 12 loci influencing human reproductive behavior. Nat Genet (2016) 0.84
Epigenome-guided analysis of the transcriptome of plaque macrophages during atherosclerosis regression reveals activation of the Wnt signaling pathway. PLoS Genet (2014) 0.84
Transcript co-variance with Nestin in two mouse genetic reference populations identifies Lef1 as a novel candidate regulator of neural precursor cell proliferation in the adult hippocampus. Front Neurosci (2014) 0.83
Common genes underlying asthma and COPD? Genome-wide analysis on the Dutch hypothesis. Eur Respir J (2014) 0.83
Plant systems biology: insights, advances and challenges. Planta (2014) 0.83
Parametric Bayesian priors and better choice of negative examples improve protein function prediction. Bioinformatics (2013) 0.83
Epigenetic profiling of ADHD symptoms trajectories: a prospective, methylome-wide study. Mol Psychiatry (2016) 0.83
Fyn-dependent gene networks in acute ethanol sensitivity. PLoS One (2013) 0.83
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 47.15
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A (1999) 22.80
Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A (2000) 19.39
A gene-coexpression network for global discovery of conserved genetic modules. Science (2003) 18.75
STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res (2006) 12.16
A combined algorithm for genome-wide prediction of protein function. Nature (1999) 9.99
Global protein function prediction from protein-protein interaction networks. Nat Biotechnol (2003) 6.28
Network-based prediction of protein function. Mol Syst Biol (2007) 6.13
The functional landscape of mouse gene expression. J Biol (2004) 5.65
Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput Chem (1996) 5.16
Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat Genet (1999) 5.06
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet (2002) 4.68
Discovery of biological networks from diverse functional genomic data. Genome Biol (2005) 3.73
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics (2005) 3.70
Predicting gene function from patterns of annotation. Genome Res (2003) 3.55
The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol (1999) 3.46
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol (2005) 2.68
Learning gene functional classifications from multiple data types. J Comput Biol (2002) 2.65
Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes. Genome Res (1999) 2.65
Kernel-based data fusion and its application to protein function prediction in yeast. Pac Symp Biocomput (2004) 2.48
An integrated probabilistic model for functional prediction of proteins. J Comput Biol (2004) 1.67
Fast protein classification with multiple networks. Bioinformatics (2005) 1.63
Automated discovery of 3D motifs for protein function annotation. Bioinformatics (2006) 1.60
Discovering functional relationships: biochemistry versus genetics. Trends Genet (2005) 1.31
Effective similarity measures for expression profiles. Bioinformatics (2006) 1.30
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure. Bioinformatics (2006) 1.27
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
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
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
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
Computational phenotyping of two-person interactions reveals differential neural response to depth-of-thought. PLoS Comput Biol (2012) 1.16
Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein. Genome Biol (2014) 1.15
In the mind of the market: theory of mind biases value computation during financial bubbles. Neuron (2013) 1.09
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
Designing of silver nanoparticles in gum arabic based semi-IPN hydrogel. Int J Biol Macromol (2010) 1.00
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
Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway. Mol Syst Biol (2009) 0.94
Global profiles of gene expression induced by adrenocorticotropin in Y1 mouse adrenal cells. Endocrinology (2006) 0.94
Jury remains out on simple models of transcription factor specificity. Nat Biotechnol (2011) 0.92
RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins. Nucleic Acids Res (2013) 0.87
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst Biol (2012) 0.86
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
Labeling nodes using three degrees of propagation. PLoS One (2012) 0.82
Microcapsules and transdermal patch: a comparative approach for improved delivery of antidiabetic drug. AAPS PharmSciTech (2009) 0.82
Predicting node characteristics from molecular networks. Methods Mol Biol (2011) 0.81
Mixture model for sub-phenotyping in GWAS. Pac Symp Biocomput (2012) 0.81
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
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
Chemistry of small organic molecules on snow grains: the applicability of artificial snow for environmental studies. Environ Sci Technol (2011) 0.76
Contributions of steroidogenic factor 1 to the transcription landscape of Y1 mouse adrenocortical tumor cells. Mol Cell Endocrinol (2010) 0.76
The biologic basis of clinical heterogeneity in juvenile idiopathic arthritis. Arthritis Rheumatol (2014) 0.76
Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction. Pac Symp Biocomput (2014) 0.75
Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors. Pac Symp Biocomput (2015) 0.75
Network news: functional modules revealed during early embryogenesis in C. elegans. Dev Cell (2005) 0.75
Characteristics of xanthan gum-based biodegradable superporous hydrogel. Int J Biol Macromol (2009) 0.75
REGULATORY RNA. Pac Symp Biocomput (2016) 0.75