Published in BMC Bioinformatics on February 06, 2008
Biomarker discovery for Alzheimer's disease, frontotemporal lobar degeneration, and Parkinson's disease. Acta Neuropathol (2010) 1.38
Identification of differential gene pathways with principal component analysis. Bioinformatics (2009) 1.32
Pathway analysis using random forests with bivariate node-split for survival outcomes. Bioinformatics (2009) 1.04
Identification of cancer-associated gene clusters and genes via clustering penalization. Stat Interface (2009) 0.96
A survey of computational intelligence techniques in protein function prediction. Int J Proteomics (2014) 0.83
Random Effects Model for Multiple Pathway Analysis with Applications to Type II Diabetes Microarray Data. Stat Biosci (2014) 0.77
Stratified pathway analysis to identify gene sets associated with oral contraceptive use and breast cancer. Cancer Inform (2014) 0.77
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet (2005) 29.45
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet (2002) 14.69
An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A (2005) 13.54
Predicting the clinical status of human breast cancer by using gene expression profiles. Proc Natl Acad Sci U S A (2001) 13.30
Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics (2007) 9.87
Bias in random forest variable importance measures: illustrations, sources and a solution. BMC Bioinformatics (2007) 8.23
Gene expression predictors of breast cancer outcomes. Lancet (2003) 6.99
Estrogen-receptor status and outcomes of modern chemotherapy for patients with node-positive breast cancer. JAMA (2006) 6.45
Risk factors for breast cancer according to estrogen and progesterone receptor status. J Natl Cancer Inst (2004) 4.57
Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics (2007) 3.68
Levels of hypoxia-inducible factor-1alpha independently predict prognosis in patients with lymph node negative breast carcinoma. Cancer (2003) 3.47
A gene-expression signature to predict survival in breast cancer across independent data sets. Oncogene (2006) 3.21
PubMatrix: a tool for multiplex literature mining. BMC Bioinformatics (2003) 3.11
A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics (2006) 2.42
Tight clustering: a resampling-based approach for identifying stable and tight patterns in data. Biometrics (2005) 2.37
A consensus prognostic gene expression classifier for ER positive breast cancer. Genome Biol (2006) 2.17
Pathway analysis using random forests classification and regression. Bioinformatics (2006) 2.01
Combining serial analysis of gene expression and array technologies to identify genes differentially expressed in breast cancer. Cancer Res (1999) 1.74
Amplification and overexpression of peroxisome proliferator-activated receptor binding protein (PBP/PPARBP) gene in breast cancer. Proc Natl Acad Sci U S A (1999) 1.54
BRCA1 and FOXA1 proteins coregulate the expression of the cell cycle-dependent kinase inhibitor p27(Kip1). Oncogene (2006) 1.48
Differential recruitment of coregulator proteins steroid receptor coactivator-1 and silencing mediator for retinoid and thyroid receptors to the estrogen receptor-estrogen response element by beta-estradiol and 4-hydroxytamoxifen in human breast cancer. J Clin Endocrinol Metab (2004) 1.29
Targeting fatty acid synthase in breast and endometrial cancer: An alternative to selective estrogen receptor modulators? Endocrinology (2006) 1.17
Hypoxia-inducible factor 1 alpha in high-risk breast cancer: an independent prognostic parameter? Breast Cancer Res (2004) 1.14
BRCA1 modulates xenobiotic stress-inducible gene expression by interacting with ARNT in human breast cancer cells. J Biol Chem (2006) 1.10
Identification of carcinoma cells in peripheral blood samples of patients with advanced breast carcinoma using RT-PCR amplification of CK7 and MUC1. Breast (2004) 0.96
Immunohistochemical evaluation of immune response in invasive ductal breast cancer of not-otherwise-specified type. Breast (2003) 0.91
Circulating tumour markers in breast cancer. Eur J Nucl Med Mol Imaging (2004) 0.86
Expression of epithelial mucins Muc1, Muc2, and Muc3 in ductal carcinoma in situ of the breast. Breast J (2001) 0.84
Detection of hepatocyte growth factor/scatter factor receptor (c-Met) and MUC1 from the axillary fluid drainage in patients after breast cancer surgery. Isr Med Assoc J (2003) 0.77
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature (2012) 16.13
De novo mutations in histone-modifying genes in congenital heart disease. Nature (2013) 5.15
On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genet Epidemiol (2003) 4.67
Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell (2007) 4.13
Association mapping, using a mixture model for complex traits. Genet Epidemiol (2002) 3.95
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics (2003) 3.78
Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. Cancer Res (2004) 3.64
Serum protein markers for early detection of ovarian cancer. Proc Natl Acad Sci U S A (2005) 3.22
Inactivating E2f1 reverts apoptosis resistance and cancer sensitivity in Trp53-deficient mice. Nat Cell Biol (2003) 3.05
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res (2004) 2.69
Genetic analysis of variation in transcription factor binding in yeast. Nature (2010) 2.69
A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet (2009) 2.53
Strong association of the alcohol dehydrogenase 1B gene (ADH1B) with alcohol dependence and alcohol-induced medical diseases. Biol Psychiatry (2011) 2.45
A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics (2004) 2.23
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics (2004) 2.16
Genomewide linkage scan for opioid dependence and related traits. Am J Hum Genet (2006) 2.15
Information assessment on predicting protein-protein interactions. BMC Bioinformatics (2004) 2.14
Practical population group assignment with selected informative markers: characteristics and properties of Bayesian clustering via STRUCTURE. Genet Epidemiol (2005) 2.09
ras mutations are associated with aggressive tumor phenotypes and poor prognosis in thyroid cancer. J Clin Oncol (2003) 2.07
Haplotypes at the OPRM1 locus are associated with susceptibility to substance dependence in European-Americans. Am J Med Genet B Neuropsychiatr Genet (2003) 2.07
Pathway analysis using random forests classification and regression. Bioinformatics (2006) 2.01
Genetic variants of Nogo-66 receptor with possible association to schizophrenia block myelin inhibition of axon growth. J Neurosci (2008) 1.96
A cluster of metabolic defects caused by mutation in a mitochondrial tRNA. Science (2004) 1.95
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol (2014) 1.95
Bias detection and correction in RNA-Sequencing data. BMC Bioinformatics (2011) 1.93
Control of T helper 2 responses by transcription factor IRF4-dependent dendritic cells. Immunity (2013) 1.88
Organ-specific expression of Arabidopsis genome during development. Plant Physiol (2005) 1.83
Variant in the glucokinase regulatory protein (GCKR) gene is associated with fatty liver in obese children and adolescents. Hepatology (2011) 1.79
Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence. Biol Psychiatry (2011) 1.76
A common variant in the patatin-like phospholipase 3 gene (PNPLA3) is associated with fatty liver disease in obese children and adolescents. Hepatology (2010) 1.71
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res (2005) 1.71
Relay ring-closing metathesis (RRCM): a strategy for directing metal movement throughout olefin metathesis sequences. J Am Chem Soc (2004) 1.69
Modeling supravalvular aortic stenosis syndrome with human induced pluripotent stem cells. Circulation (2012) 1.69
Two-stage designs in case-control association analysis. Genetics (2006) 1.65
Glucocerebrosidase gene-deficient mouse recapitulates Gaucher disease displaying cellular and molecular dysregulation beyond the macrophage. Proc Natl Acad Sci U S A (2010) 1.60
Noninvasive analysis of the sputum transcriptome discriminates clinical phenotypes of asthma. Am J Respir Crit Care Med (2015) 1.58
Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. J Mol Biol (2004) 1.57
The meiosis-specific zip4 protein regulates crossover distribution by promoting synaptonemal complex formation together with zip2. Dev Cell (2006) 1.57
Rapid generation of maturationally synchronized human dendritic cells: contribution to the clinical efficacy of extracorporeal photochemotherapy. Blood (2010) 1.56
Association of haplotypic variants in DRD2, ANKK1, TTC12 and NCAM1 to alcohol dependence in independent case control and family samples. Hum Mol Genet (2007) 1.55
Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem (2004) 1.55
Haplotype-association analysis. Adv Genet (2008) 1.55
The impacts of errors in individual genotyping and DNA pooling on association studies. Genet Epidemiol (2004) 1.52
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. BMC Bioinformatics (2003) 1.52
Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell (2002) 1.52
Regulation of a transient receptor potential (TRP) channel by tyrosine phosphorylation. SRC family kinase-dependent tyrosine phosphorylation of TRPV4 on TYR-253 mediates its response to hypotonic stress. J Biol Chem (2003) 1.50
Comparisons of multi-marker association methods to detect association between a candidate region and disease. Genet Epidemiol (2010) 1.50
Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q. Neuropsychopharmacology (2011) 1.50
Susceptibility loci for murine HIV-associated nephropathy encode trans-regulators of podocyte gene expression. J Clin Invest (2009) 1.49
FTO gene SNPs associated with extreme obesity in cases, controls and extremely discordant sister pairs. BMC Med Genet (2008) 1.48
Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proc Natl Acad Sci U S A (2003) 1.46
Trans-heterozygous Pkd1 and Pkd2 mutations modify expression of polycystic kidney disease. Hum Mol Genet (2002) 1.44
A comparison of several methods for haplotype frequency estimation and haplotype reconstruction for tightly linked markers from general pedigrees. Genet Epidemiol (2006) 1.43
Molecular architecture of the chick vestibular hair bundle. Nat Neurosci (2013) 1.43
Finding genetic contributions to sporadic disease: a recessive locus at 12q24 commonly contributes to patent ductus arteriosus. Proc Natl Acad Sci U S A (2002) 1.42
Human impacts have shaped historical and recent evolution in Aedes aegypti, the dengue and yellow fever mosquito. Evolution (2013) 1.42
Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis. Plant J (2002) 1.40
VitaPad: visualization tools for the analysis of pathway data. Bioinformatics (2004) 1.39
Fine mapping of a seizure susceptibility locus on mouse Chromosome 1: nomination of Kcnj10 as a causative gene. Mamm Genome (2004) 1.39
Analytical and clinical validity of whole-genome oligonucleotide array comparative genomic hybridization for pediatric patients with mental retardation and developmental delay. Am J Med Genet A (2008) 1.39
Impaired interferon signaling in dendritic cells from older donors infected in vitro with West Nile virus. J Infect Dis (2011) 1.38
Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Development (2003) 1.38
Detection of DNA copy number alterations using penalized least squares regression. Bioinformatics (2005) 1.38
Macrophage migration inhibitory factor promoter polymorphisms and the clinical expression of scleroderma. Arthritis Rheum (2006) 1.35
Pumilio 1 suppresses multiple activators of p53 to safeguard spermatogenesis. Curr Biol (2012) 1.34
Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics (2005) 1.33
On the use of DNA pooling to estimate haplotype frequencies. Genet Epidemiol (2003) 1.33
A genome-wide association study on obesity and obesity-related traits. PLoS One (2011) 1.33
Genome-wide association study identifies new susceptibility loci for posttraumatic stress disorder. Biol Psychiatry (2013) 1.32
PSMIX: an R package for population structure inference via maximum likelihood method. BMC Bioinformatics (2006) 1.32
Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray. Plant Mol Biol (2004) 1.32
Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans. RNA (2011) 1.31
COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. Bioinformatics (2011) 1.29
Haplotype block structures show significant variation among populations. Genet Epidemiol (2004) 1.28
Improved risk prediction for Crohn's disease with a multi-locus approach. Hum Mol Genet (2011) 1.28
A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol (2003) 1.27
Aminopyridine-based c-Jun N-terminal kinase inhibitors with cellular activity and minimal cross-kinase activity. J Med Chem (2006) 1.26
False Discovery Rate Control With Groups. J Am Stat Assoc (2010) 1.23
Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline. EMBO J (2013) 1.22
Haplotypic variants in DRD2, ANKK1, TTC12, and NCAM1 are associated with comorbid alcohol and drug dependence. Alcohol Clin Exp Res (2008) 1.22
Interacting genetic loci on chromosomes 20 and 10 influence extreme human obesity. Am J Hum Genet (2002) 1.21
Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genet (2005) 1.20
Gene expression in temporal lobe epilepsy is consistent with increased release of glutamate by astrocytes. Mol Med (2007) 1.19
A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study. PLoS One (2011) 1.19
Handling multiple testing while interpreting microarrays with the Gene Ontology Database. BMC Bioinformatics (2004) 1.19
Quantitative trait loci in Anopheles gambiae controlling the encapsulation response against Plasmodium cynomolgi Ceylon. BMC Genet (2003) 1.19
A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell (2005) 1.18
Dual macrolactonization/pyran-hemiketal formation via acylketenes: applications to the synthesis of (-)-callipeltoside A and a lyngbyaloside B model system. Angew Chem Int Ed Engl (2008) 1.17
Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis. J Biomed Inform (2007) 1.16
Evidence for association between multiple complement pathway genes and AMD. Genet Epidemiol (2007) 1.15
A comparison of methods for clustering 16S rRNA sequences into OTUs. PLoS One (2013) 1.15
Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. Bioinformatics (2007) 1.15
Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment. BMC Genet (2005) 1.15
A biphasic pattern of gene expression during mouse retina development. BMC Dev Biol (2006) 1.14
Pathway analysis comparison using Crohn's disease genome wide association studies. BMC Med Genomics (2010) 1.13
Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Comput Biol Chem (2005) 1.13
On optimal pooling designs to identify rare variants through massive resequencing. Genet Epidemiol (2011) 1.12
Incorporating biological pathways via a Markov random field model in genome-wide association studies. PLoS Genet (2011) 1.12
Parametric and nonparametric FDR estimation revisited. Biometrics (2006) 1.11
Integrating GWASs and human protein interaction networks identifies a gene subnetwork underlying alcohol dependence. Am J Hum Genet (2013) 1.10