Published in Bioinformatics on May 06, 2011
"Guilt by association" is the exception rather than the rule in gene networks. PLoS Comput Biol (2012) 1.45
Assessing identity, redundancy and confounds in Gene Ontology annotations over time. Bioinformatics (2013) 1.01
Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls. BMC Neurosci (2013) 0.90
Bias tradeoffs in the creation and analysis of protein-protein interaction networks. J Proteomics (2014) 0.88
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). BMC Bioinformatics (2013) 0.88
Influence of choice of null network on small-world parameters of structural correlation networks. PLoS One (2013) 0.85
Progress and challenges in the computational prediction of gene function using networks. F1000Res (2012) 0.84
TMA Navigator: Network inference, patient stratification and survival analysis with tissue microarray data. Nucleic Acids Res (2013) 0.83
FTO, obesity and the adolescent brain. Hum Mol Genet (2012) 0.83
KCTD8 gene and brain growth in adverse intrauterine environment: a genome-wide association study. Cereb Cortex (2011) 0.82
Stability indicators in network reconstruction. PLoS One (2014) 0.82
Exploiting single-cell expression to characterize co-expression replicability. Genome Biol (2016) 0.81
A vertex similarity-based framework to discover and rank orphan disease-related genes. BMC Syst Biol (2012) 0.81
Acquired dependence of acute myeloid leukemia on the DEAD-box RNA helicase DDX5. Cell Rep (2014) 0.78
Revealing molecular mechanisms by integrating high-dimensional functional screens with protein interaction data. PLoS Comput Biol (2014) 0.76
A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. PLoS Negl Trop Dis (2016) 0.76
Predicting gene function using similarity learning. BMC Genomics (2013) 0.75
Prediction of optimal gene functions for osteosarcoma using network-based- guilt by association method based on gene oncology and microarray profile. J Bone Oncol (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
The human genome browser at UCSC. Genome Res (2002) 168.23
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res (2002) 76.95
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
Hierarchical organization of modularity in metabolic networks. Science (2002) 22.47
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
The genetic landscape of a cell. Science (2010) 16.52
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res (2002) 15.70
The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol (2007) 10.46
A network of protein-protein interactions in yeast. Nat Biotechnol (2000) 10.31
Coexpression analysis of human genes across many microarray data sets. Genome Res (2004) 9.38
MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res (2006) 7.75
MINT, the molecular interaction database: 2009 update. Nucleic Acids Res (2009) 7.19
Online predicted human interaction database. Bioinformatics (2005) 6.83
Global protein function prediction from protein-protein interaction networks. Nat Biotechnol (2003) 6.28
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol (2008) 5.94
iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics (2008) 5.77
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol (2008) 4.61
Geometric interpretation of gene coexpression network analysis. PLoS Comput Biol (2008) 4.57
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
Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics (2007) 3.83
Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics (2007) 3.59
High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods (2008) 3.17
Assessment of prediction accuracy of protein function from protein--protein interaction data. Yeast (2001) 2.90
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics (2005) 2.83
Guilt-by-association goes global. Nature (2000) 2.62
Kernel-based data fusion and its application to protein function prediction in yeast. Pac Symp Biocomput (2004) 2.48
Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol (2009) 2.47
Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'. Trends Plant Sci (2007) 2.15
Prediction of protein function using protein-protein interaction data. J Comput Biol (2003) 2.15
Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol (2008) 1.95
The impact of multifunctional genes on "guilt by association" analysis. PLoS One (2011) 1.69
Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci U S A (2004) 1.67
Fast protein classification with multiple networks. Bioinformatics (2005) 1.63
Biomolecular interaction network database. Brief Bioinform (2005) 1.27
Predicting gene function using hierarchical multi-label decision tree ensembles. BMC Bioinformatics (2010) 1.19
Extreme self-organization in networks constructed from gene expression data. Phys Rev Lett (2002) 1.00
Local coherence in genetic interaction patterns reveals prevalent functional versatility. Bioinformatics (2008) 0.98
Rank-based edge reconstruction for scale-free genetic regulatory networks. BMC Bioinformatics (2008) 0.85
Searching the MINT database for protein interaction information. Curr Protoc Bioinformatics (2008) 0.83
Coexpression analysis of human genes across many microarray data sets. Genome Res (2004) 9.38
ErmineJ: tool for functional analysis of gene expression data sets. BMC Bioinformatics (2005) 4.98
Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res (2005) 4.41
Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model. Nat Genet (2008) 3.76
Zac1 regulates an imprinted gene network critically involved in the control of embryonic growth. Dev Cell (2006) 3.67
Hierarchical model of gene regulation by transforming growth factor beta. Proc Natl Acad Sci U S A (2003) 2.37
Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling. J Clin Oncol (2003) 2.18
Gene Ontology term overlap as a measure of gene functional similarity. BMC Bioinformatics (2008) 2.10
Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells. Cell Stem Cell (2009) 2.09
Molecular aging in human prefrontal cortex is selective and continuous throughout adult life. Biol Psychiatry (2005) 2.06
Classification and subtype prediction of adult soft tissue sarcoma by functional genomics. Am J Pathol (2003) 1.94
Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice. Nat Neurosci (2005) 1.91
Activation of MAPK pathways links LMNA mutations to cardiomyopathy in Emery-Dreifuss muscular dystrophy. J Clin Invest (2007) 1.87
Inducible enhancement of memory storage and synaptic plasticity in transgenic mice expressing an inhibitor of ATF4 (CREB-2) and C/EBP proteins. Neuron (2003) 1.80
The impact of multifunctional genes on "guilt by association" analysis. PLoS One (2011) 1.69
Subtype-specific peripheral blood gene expression profiles in recent-onset juvenile idiopathic arthritis. Arthritis Rheum (2009) 1.56
Sharing and reusing gene expression profiling data in neuroscience. Neuroinformatics (2007) 1.50
Relationships between gene expression and brain wiring in the adult rodent brain. PLoS Comput Biol (2011) 1.47
"Guilt by association" is the exception rather than the rule in gene networks. PLoS Comput Biol (2012) 1.45
Akt1 deficiency affects neuronal morphology and predisposes to abnormalities in prefrontal cortex functioning. Proc Natl Acad Sci U S A (2006) 1.44
Altered hippocampal transcript profile accompanies an age-related spatial memory deficit in mice. Learn Mem (2004) 1.43
beta-catenin/TCF/Lef controls a differentiation-associated transcriptional program in renal epithelial progenitors. Development (2007) 1.42
Activation of MAPK in hearts of EMD null mice: similarities between mouse models of X-linked and autosomal dominant Emery Dreifuss muscular dystrophy. Hum Mol Genet (2007) 1.38
Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction. BMC Bioinformatics (2003) 1.36
Cutting edge: STAT6 serves as a positive and negative regulator of gene expression in IL-4-stimulated B lymphocytes. J Immunol (2002) 1.35
Gene expression profiling of depression and suicide in human prefrontal cortex. Neuropsychopharmacology (2004) 1.33
Transcriptomes in healthy and diseased gingival tissues. J Periodontol (2008) 1.30
Diverse epigenetic strategies interact to control epidermal differentiation. Nat Cell Biol (2012) 1.29
Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. Bioinformatics (2012) 1.28
Gene function analysis in complex data sets using ErmineJ. Nat Protoc (2010) 1.16
Gene expression signatures in polyarticular juvenile idiopathic arthritis demonstrate disease heterogeneity and offer a molecular classification of disease subsets. Arthritis Rheum (2009) 1.15
Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis. Hum Mol Genet (2010) 1.14
A Mendelian locus on chromosome 16 determines susceptibility to doxorubicin nephropathy in the mouse. Proc Natl Acad Sci U S A (2005) 1.11
Understanding the impact of 1q21.1 copy number variant. Orphanet J Rare Dis (2011) 1.11
Genomic signatures predict migration and spawning failure in wild Canadian salmon. Science (2011) 1.10
Subgingival bacterial colonization profiles correlate with gingival tissue gene expression. BMC Microbiol (2009) 1.07
Neurocarta: aggregating and sharing disease-gene relations for the neurosciences. BMC Genomics (2013) 1.06
Assessing identity, redundancy and confounds in Gene Ontology annotations over time. Bioinformatics (2013) 1.01
Automated recognition of brain region mentions in neuroscience literature. Front Neuroinform (2009) 1.00
Informatics in neuroscience. Brief Bioinform (2007) 0.98
An ancestral haplotype defines susceptibility to doxorubicin nephropathy in the laboratory mouse. J Am Soc Nephrol (2006) 0.97
A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinformatics (2009) 0.96
Using text mining to link journal articles to neuroanatomical databases. J Comp Neurol (2012) 0.95
Pitfalls in the application of gene-set analysis to genetics studies. Trends Genet (2014) 0.95
Periodontal therapy alters gene expression of peripheral blood monocytes. J Clin Periodontol (2007) 0.93
Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration. Front Neuroinform (2011) 0.93
Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls. BMC Neurosci (2013) 0.90
Differential amplification of gene expression in lens cell lines conditioned to survive peroxide stress. Invest Ophthalmol Vis Sci (2002) 0.90
Gene expression signatures in chronic and aggressive periodontitis: a pilot study. Eur J Oral Sci (2004) 0.89
Application and evaluation of automated semantic annotation of gene expression experiments. Bioinformatics (2009) 0.89
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). BMC Bioinformatics (2013) 0.88
Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text. Bioinformatics (2012) 0.88
Prenatal alcohol exposure alters steady-state and activated gene expression in the adult rat brain. Alcohol Clin Exp Res (2015) 0.87
Decoding unattended fearful faces with whole-brain correlations: an approach to identify condition-dependent large-scale functional connectivity. PLoS Comput Biol (2012) 0.87
Meta-analysis of kindling-induced gene expression changes in the rat hippocampus. Front Neurosci (2009) 0.84
Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain. Front Neurosci (2013) 0.84
Consequences of high temperatures and premature mortality on the transcriptome and blood physiology of wild adult sockeye salmon (Oncorhynchus nerka). Ecol Evol (2012) 0.84
Copy number variants (CNVs) analysis in a deeply phenotyped cohort of individuals with intellectual disability (ID). BMC Med Genet (2014) 0.84
FTO, obesity and the adolescent brain. Hum Mol Genet (2012) 0.83
miRNA and miRNA target genes in copy number variations occurring in individuals with intellectual disability. BMC Genomics (2013) 0.82
KCTD8 gene and brain growth in adverse intrauterine environment: a genome-wide association study. Cereb Cortex (2011) 0.82
Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing. Neuroimage (2012) 0.82
Bioinformatics techniques in microarray research: applied microarray data analysis using R and SAS software. Methods Mol Biol (2010) 0.80
Microarray analysis of gene expression following the formalin test in the infant rat. Pain (2005) 0.78
Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. Cancer Inform (2009) 0.77
Expansion of the QARS deficiency phenotype with report of a family with isolated supratentorial brain abnormalities. Neurogenetics (2014) 0.77
The NeuroDevNet Neuroinformatics Core. Semin Pediatr Neurol (2011) 0.77
Cluster analysis of genes with significant change in expression in cells conditioned to survive TBOOH. Exp Eye Res (2004) 0.77
Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. Summit on Translat Bioinforma (2009) 0.75