Published in Bioinformatics on October 18, 2005
Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. PLoS One (2008) 2.09
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Aging mice show a decreasing correlation of gene expression within genetic modules. PLoS Genet (2009) 1.78
Differential dependency network analysis to identify condition-specific topological changes in biological networks. Bioinformatics (2008) 1.56
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. BMC Bioinformatics (2010) 1.53
Statistical methods for gene set co-expression analysis. Bioinformatics (2009) 1.47
Differential variability analysis of gene expression and its application to human diseases. Bioinformatics (2008) 1.46
Identifying set-wise differential co-expression in gene expression microarray data. BMC Bioinformatics (2009) 1.32
Characterizing disease states from topological properties of transcriptional regulatory networks. BMC Bioinformatics (2006) 1.27
DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data. Bioinformatics (2010) 1.23
Correlation network analysis applied to complex biofilm communities. PLoS One (2011) 1.21
Mining tissue specificity, gene connectivity and disease association to reveal a set of genes that modify the action of disease causing genes. BioData Min (2008) 1.21
Weighted frequent gene co-expression network mining to identify genes involved in genome stability. PLoS Comput Biol (2012) 1.19
Link-based quantitative methods to identify differentially coexpressed genes and gene pairs. BMC Bioinformatics (2011) 1.19
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Dissection of regulatory networks that are altered in disease via differential co-expression. PLoS Comput Biol (2013) 1.14
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Identification of genes associated with multiple cancers via integrative analysis. BMC Genomics (2009) 1.12
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Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor. BMC Genomics (2009) 0.99
A semi-parametric Bayesian model for unsupervised differential co-expression analysis. BMC Bioinformatics (2010) 0.98
Identification of markers associated with global changes in DNA methylation regulation in cancers. BMC Bioinformatics (2012) 0.97
A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinformatics (2009) 0.96
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Meta Analysis of Gene Expression Data within and Across Species. Curr Genomics (2008) 0.95
R/EBcoexpress: an empirical Bayesian framework for discovering differential co-expression. Bioinformatics (2012) 0.95
Whole miRNome-wide differential co-expression of microRNAs. Genomics Proteomics Bioinformatics (2012) 0.95
Differential coexpression analysis of obesity-associated networks in human subcutaneous adipose tissue. Int J Obes (Lond) (2011) 0.94
Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. Plant Physiol (2012) 0.94
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Functional categories associated with clusters of genes that are co-expressed across the NCI-60 cancer cell lines. PLoS One (2012) 0.94
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Extensive decoupling of metabolic genes in cancer. PLoS Comput Biol (2015) 0.91
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Differentially expressed genes in major depression reside on the periphery of resilient gene coexpression networks. Front Neurosci (2011) 0.88
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A stochastic model for identifying differential gene pair co-expression patterns in prostate cancer progression. BMC Genomics (2009) 0.85
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Loss of connectivity in cancer co-expression networks. PLoS One (2014) 0.85
Quantifying differential gene connectivity between disease states for objective identification of disease-relevant genes. BMC Syst Biol (2011) 0.84
Current challenges and future potential of tomato breeding using omics approaches. Breed Sci (2013) 0.83
Massive human co-expression network and its medical applications. Chem Biodivers (2012) 0.82
Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival. Artif Intell Med (2012) 0.82
DiME: a scalable disease module identification algorithm with application to glioma progression. PLoS One (2014) 0.82
Combining transcriptional datasets using the generalized singular value decomposition. BMC Bioinformatics (2008) 0.81
Noncoding RNAs and neurobehavioral mechanisms in psychiatric disease. Mol Psychiatry (2015) 0.81
Systematically characterizing and prioritizing chemosensitivity related gene based on Gene Ontology and protein interaction network. BMC Med Genomics (2012) 0.81
DECODE: an integrated differential co-expression and differential expression analysis of gene expression data. BMC Bioinformatics (2015) 0.81
Chapter 8: Biological knowledge assembly and interpretation. PLoS Comput Biol (2012) 0.80
Genetic architecture of gene expression in the chicken. BMC Genomics (2013) 0.80
Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation. BMC Genomics (2009) 0.80
Identification and optimization of classifier genes from multi-class earthworm microarray dataset. PLoS One (2010) 0.79
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle. BMC Bioinformatics (2011) 0.79
Functional Analysis and Characterization of Differential Coexpression Networks. Sci Rep (2015) 0.79
Gene differential coexpression analysis based on biweight correlation and maximum clique. BMC Bioinformatics (2014) 0.79
Comparative network analysis via differential graphlet communities. Proteomics (2014) 0.78
How to improve postgenomic knowledge discovery using imputation. EURASIP J Bioinform Syst Biol (2009) 0.78
UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets. BMC Bioinformatics (2015) 0.78
Inequalities and duality in gene coexpression networks of HIV-1 infection revealed by the combination of the double-connectivity approach and the Gini's method. J Biomed Biotechnol (2011) 0.78
RMaNI: Regulatory Module Network Inference framework. BMC Bioinformatics (2013) 0.77
Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression. BMC Bioinformatics (2015) 0.77
Gene set analysis using sufficient dimension reduction. BMC Bioinformatics (2016) 0.77
Identification of phenotype deterministic genes using systemic analysis of transcriptional response. Sci Rep (2014) 0.77
Module Based Differential Coexpression Analysis Method for Type 2 Diabetes. Biomed Res Int (2015) 0.76
Systematic identification of core transcription factors mediating dysregulated links bridging inflammatory bowel diseases and colorectal cancer. PLoS One (2013) 0.76
Coexpression Pattern Analysis of NPM1-Associated Genes in Chronic Myelogenous Leukemia. Biomed Res Int (2015) 0.76
A novel method to identify pathways associated with renal cell carcinoma based on a gene co-expression network. Oncol Rep (2015) 0.76
Network Topologies Decoding Cervical Cancer. PLoS One (2015) 0.76
A smoking-associated 7-gene signature for lung cancer diagnosis and prognosis. Int J Oncol (2012) 0.76
Identification of genes associated with renal cell carcinoma using gene expression profiling analysis. Oncol Lett (2016) 0.76
Voting-based cancer module identification by combining topological and data-driven properties. PLoS One (2013) 0.76
Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma. BMC Med Genomics (2015) 0.76
Hierarchical parallelization of gene differential association analysis. BMC Bioinformatics (2011) 0.76
Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection. Sci Rep (2016) 0.75
microRNAs' differential regulations mediate the progress of Human Papillomavirus (HPV)-induced Cervical Intraepithelial Neoplasia (CIN). BMC Syst Biol (2015) 0.75
Proteomics Discovery of Disease Biomarkers. Biomark Insights (2008) 0.75
Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds. Front Microbiol (2016) 0.75
Differentially correlated genes in co-expression networks control phenotype transitions. F1000Res (2016) 0.75
Co-Expression Analysis of Blood Cell Genome Expression to Preliminary Investigation of Regulatory Mechanisms in Uremia. Med Sci Monit (2017) 0.75
No3CoGP: non-conserved and conserved coexpressed gene pairs. BMC Res Notes (2014) 0.75
A methodology to infer gene networks from spatial patterns of expression--an application to fluorescence in situ hybridization images. Mol Biosyst (2013) 0.75
Exploring the Functional Disorder and Corresponding Key Transcription Factors in Intraductal Papillary Mucinous Neoplasms Progression. Int J Genomics (2015) 0.75
Pan- and core- network analysis of co-expression genes in a model plant. Sci Rep (2016) 0.75
Fusing Gene Interaction to Improve Disease Discrimination on Classification Analysis. Adv Genet Eng (2012) 0.75
Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer. PLoS One (2016) 0.75
Integrating multiple microarray data for cancer pathway analysis using bootstrapping K-S test. J Biomed Biotechnol (2009) 0.75
Differential co-expression analysis of venous thromboembolism based on gene expression profile data. Exp Ther Med (2016) 0.75
Identification of hub genes involved in the development of hepatocellular carcinoma by transcriptome sequencing. Oncotarget (2017) 0.75
Three-way interaction model to trace the mechanisms involved in Alzheimer's disease transgenic mice. PLoS One (2017) 0.75
Pathway-related modules involved in the application of sevoflurane or propofol in off-pump coronary artery bypass graft surgery. Exp Ther Med (2017) 0.75
PERIOD2::LUCIFERASE real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues. Proc Natl Acad Sci U S A (2004) 12.43
The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res (2009) 7.87
Mapping human genetic diversity in Asia. Science (2009) 7.40
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran. Cell (2007) 6.84
Impaired DNA damage response, genome instability, and tumorigenesis in SIRT1 mutant mice. Cancer Cell (2008) 5.11
Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. Nat Genet (2011) 4.50
Combining multiple microarray studies and modeling interstudy variation. Bioinformatics (2003) 4.38
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat Genet (2014) 4.13
Senescence, aging, and malignant transformation mediated by p53 in mice lacking the Brca1 full-length isoform. Genes Dev (2003) 2.78
A noncanonical E-box enhancer drives mouse Period2 circadian oscillations in vivo. Proc Natl Acad Sci U S A (2005) 2.67
BRCA1, histone H2AX phosphorylation, and male meiotic sex chromosome inactivation. Curr Biol (2004) 2.67
GSA-SNP: a general approach for gene set analysis of polymorphisms. Nucleic Acids Res (2010) 2.09
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
Structural diversity of the hagfish variable lymphocyte receptors. J Biol Chem (2006) 1.89
Integrative analysis of multiple gene expression profiles applied to liver cancer study. FEBS Lett (2004) 1.63
Conditional ablation of LYVE-1+ cells unveils defensive roles of lymphatic vessels in intestine and lymph nodes. Blood (2013) 1.60
Postnatal maturation of the red nucleus motor map depends on rubrospinal connections with forelimb motor pools. J Neurosci (2014) 1.48
Double antiangiogenic protein, DAAP, targeting VEGF-A and angiopoietins in tumor angiogenesis, metastasis, and vascular leakage. Cancer Cell (2010) 1.47
PSIbase: a database of Protein Structural Interactome map (PSIMAP). Bioinformatics (2005) 1.42
Remodeling of global transcription patterns of Cryptococcus neoformans genes mediated by the stress-activated HOG signaling pathways. Eukaryot Cell (2009) 1.40
Conformational flexibility in mammalian 15S-lipoxygenase: Reinterpretation of the crystallographic data. Proteins (2008) 1.40
ATM-Chk2-p53 activation prevents tumorigenesis at an expense of organ homeostasis upon Brca1 deficiency. EMBO J (2006) 1.38
Recapitulation of two genomewide association studies on blood pressure and essential hypertension in the Korean population. J Hum Genet (2010) 1.35
Immunosenescent CD8+ T cells and C-X-C chemokine receptor type 3 chemokines are increased in human hypertension. Hypertension (2013) 1.32
The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun (2013) 1.32
Gene expression profiling of human HBV- and/or HCV-associated hepatocellular carcinoma cells using expressed sequence tags. Int J Oncol (2006) 1.26
Adenovirus-mediated transfer of siRNA against PTTG1 inhibits liver cancer cell growth in vitro and in vivo. Hepatology (2006) 1.18
FESD: a Functional Element SNPs Database in human. Nucleic Acids Res (2005) 1.16
Impact of transcriptional properties on essentiality and evolutionary rate. Genetics (2006) 1.05
Identification of SNP markers for common CNV regions and association analysis of risk of subarachnoid aneurysmal hemorrhage in Japanese population. Biochem Biophys Res Commun (2008) 1.02
Bioinformatics in the post-genome era. J Biochem Mol Biol (2004) 1.01
CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes. Nucleic Acids Res (2012) 1.01
Crystal structure of Drosophila angiotensin I-converting enzyme bound to captopril and lisinopril. FEBS Lett (2003) 0.99
Crystal structure of the BAFF-BAFF-R complex and its implications for receptor activation. Nat Struct Biol (2003) 0.99
TO-GO: a Java-based Gene Ontology navigation environment. Bioinformatics (2005) 0.99
TAK1 regulates autophagic cell death by suppressing the phosphorylation of p70 S6 kinase 1. Sci Rep (2013) 0.98
Imaging fully hydrated whole cells by coherent x-ray diffraction microscopy. Phys Rev Lett (2013) 0.98
Prediction of protein-protein interaction types using association rule based classification. BMC Bioinformatics (2009) 0.96
Meta- and gene set analysis of stomach cancer gene expression data. Mol Cells (2007) 0.96
A large population of small chloroplasts in tobacco leaf cells allows more effective chloroplast movement than a few enlarged chloroplasts. Plant Physiol (2002) 0.90
Transcriptional regulation and life-span modulation of cytosolic aconitase and ferritin genes in C.elegans. J Mol Biol (2004) 0.90
CCCP induces autophagy in an AMPK-independent manner. Biochem Biophys Res Commun (2011) 0.89
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. Nucleic Acids Res (2006) 0.88
The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis or atopic dermatitis. Biochem Biophys Res Commun (2012) 0.86
Gene cataloging and expression profiling in human gastric cancer cells by expressed sequence tags. Genomics (2004) 0.85
A methodology for multivariate phenotype-based genome-wide association studies to mine pleiotropic genes. BMC Syst Biol (2011) 0.85
Transcriptome analysis of human gastric cancer. Mamm Genome (2005) 0.84
Feed-forward control of preshaping in the rat is mediated by the corticospinal tract. Eur J Neurosci (2010) 0.82
Feature genes of hepatitis B virus-positive hepatocellular carcinoma, established by its molecular discrimination approach using prediction analysis of microarray. Biochim Biophys Acta (2004) 0.82
Stage-dependent gene expression profiles during natural killer cell development. Genomics (2005) 0.82
DNA methylation analysis of CD4+ T cells in patients with psoriasis. Arch Dermatol Res (2013) 0.81
A new hepatocytic isoform of PLZF lacking the BTB domain interacts with ATP7B, the Wilson disease protein, and positively regulates ERK signal transduction. J Cell Biochem (2006) 0.81
GARNET--gene set analysis with exploration of annotation relations. BMC Bioinformatics (2011) 0.81
Antibody-secreting cells with a phenotype of Ki-67low, CD138high, CD31high, and CD38high secrete nonspecific IgM during primary hepatitis A virus infection. J Immunol (2013) 0.81
Performance Comparison of Two Gene Set Analysis Methods for Genome-wide Association Study Results: GSA-SNP vs i-GSEA4GWAS. Genomics Inform (2012) 0.80
The prolonged half-lives of new erythropoietin derivatives via peptide addition. Biochem Biophys Res Commun (2005) 0.80
Ethnic variability in the allelic distribution of pharmacogenes between Korean and other populations. Pharmacogenet Genomics (2012) 0.79
TFExplorer: integrated analysis database for predicted transcription regulatory elements. Bioinformatics (2004) 0.78
Partial AUC maximization for essential gene prediction using genetic algorithms. BMB Rep (2013) 0.77
Drop-on-demand patterning of bacterial cells using pulsed jet electrospraying. Anal Chem (2010) 0.77
Multifunctional drug delivery system using starch-alginate beads for controlled release. Biol Pharm Bull (2005) 0.77
Development of an adaptable coherent x-ray diffraction microscope with the emphasis on imaging hydrated specimens. Rev Sci Instrum (2013) 0.76
Pattern discovery of multivariate phenotypes by association rule mining and its scheme for genome-wide association studies. Int J Data Min Bioinform (2012) 0.76
A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis. BMC Bioinformatics (2010) 0.76
GoBean: a Java GUI application for visual exploration of GO term enrichments. BMB Rep (2012) 0.75
Gene set analyses of genome-wide association studies on 49 quantitative traits measured in a single genetic epidemiology dataset. Genomics Inform (2013) 0.75
Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble. BMC Bioinformatics (2010) 0.75
CysQ of Cryptosporidium parvum, a Protozoa, May Have Been Acquired from Bacteria by Horizontal Gene Transfer. Genomics Inform (2012) 0.75
Understanding Disease Susceptibility through Population Genomics. Genomics Inform (2012) 0.75
GS2PATH: a web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data. Bioinformation (2007) 0.75
Whole genome comparison of donor and cloned dogs. Sci Rep (2013) 0.75
Molecular phylogeny and geography of Korean medaka fish (Oryzias latipes). Mol Cells (2005) 0.75
Fabrication and Characteristics of High Mobility InSnZnO Thin Film Transistors. J Nanosci Nanotechnol (2016) 0.75
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Genome data mining for everyone. BMB Rep (2008) 0.75
Oxidation characteristics of airborne carbon nanoparticles by NO(2). Sci Total Environ (2008) 0.75
Analysis of the Electrical Properties of an Electron Injection Layer in Alq3-Based Organic Light Emitting Diodes. J Nanosci Nanotechnol (2016) 0.75
CONSORF: a consensus prediction system for prokaryotic coding sequences. Bioinformatics (2007) 0.75