Published in BMC Bioinformatics on February 10, 2005
Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. BMC Bioinformatics (2006) 2.35
Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons. Nucleic Acids Res (2006) 2.24
Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia. Cancer Prev Res (Phila) (2008) 2.04
Sources of variation in Affymetrix microarray experiments. BMC Bioinformatics (2005) 1.94
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. BMC Bioinformatics (2006) 1.85
Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell (2010) 1.81
The transcriptome of human oocytes. Proc Natl Acad Sci U S A (2006) 1.70
Comparison of small n statistical tests of differential expression applied to microarrays. BMC Bioinformatics (2009) 1.40
Differential expression of GADD45beta in normal and osteoarthritic cartilage: potential role in homeostasis of articular chondrocytes. Arthritis Rheum (2008) 1.33
DNA methylation inhibition increases T cell KIR expression through effects on both promoter methylation and transcription factors. Clin Immunol (2008) 1.21
Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte. Genome Biol (2007) 1.20
The end of the microarray Tower of Babel: will universal standards lead the way? J Biomol Tech (2006) 1.11
Constant p53 pathway inactivation in a large series of soft tissue sarcomas with complex genetics. Am J Pathol (2010) 1.09
IRS1 regulation by Wnt/beta-catenin signaling and varied contribution of IRS1 to the neoplastic phenotype. J Biol Chem (2009) 1.05
Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements. BMC Bioinformatics (2010) 1.04
Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray. Plant Methods (2010) 1.02
Molecular markers and mechanisms of stroke: RNA studies of blood in animals and humans. J Cereb Blood Flow Metab (2011) 1.01
Induction of immune mediators in glioma and prostate cancer cells by non-lethal photodynamic therapy. PLoS One (2011) 0.96
Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine. BMC Genomics (2007) 0.95
Methods for evaluating gene expression from Affymetrix microarray datasets. BMC Bioinformatics (2008) 0.94
Expectations, validity, and reality in gene expression profiling. J Clin Epidemiol (2010) 0.93
SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data. BMC Genomics (2009) 0.91
In praise of arrays. Pediatr Nephrol (2008) 0.91
Robust computational reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell fractions. BMC Bioinformatics (2006) 0.89
The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. BMC Bioinformatics (2006) 0.89
Identification of stem cell transcriptional programs normally expressed in embryonic and neural stem cells in alloreactive CD8+ T cells mediating graft-versus-host disease. Biol Blood Marrow Transplant (2010) 0.88
Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution. Biol Direct (2006) 0.86
Characterization of a genetic mouse model of lung cancer: a promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers. BMC Genomics (2014) 0.86
Reprogrammed transcriptome in rhesus-bovine interspecies somatic cell nuclear transfer embryos. PLoS One (2011) 0.86
An adaptation of the LMS method to determine expression variations in profiling data. Nucleic Acids Res (2007) 0.84
Different normalization strategies for microarray gene expression traits affect the heritability estimation. BMC Proc (2007) 0.82
LTR: Linear Cross-Platform Integration of Microarray Data. Cancer Inform (2010) 0.81
The path to routine use of genomic biomarkers in the cancer clinic. Genome Res (2015) 0.81
Genome-wide expression analysis of a spinal muscular atrophy model: towards discovery of new drug targets. PLoS One (2008) 0.80
Bcl6 is expressed in neuroblastoma: tumor cell type-specific expression predicts outcome. Transl Oncol (2009) 0.80
Analysis of gene expression data from non-small cell lung carcinoma cell lines reveals distinct sub-classes from those identified at the phenotype level. PLoS One (2012) 0.78
Gene expression profiling of granulosa cells from PCOS patients following varying doses of human chorionic gonadotropin. J Assist Reprod Genet (2013) 0.78
CLU blocks HDACI-mediated killing of neuroblastoma. Tumour Biol (2010) 0.77
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinformatics (2014) 0.76
Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A (2001) 68.44
Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74
A model of molecular interactions on short oligonucleotide microarrays. Nat Biotechnol (2003) 9.98
Robust estimators for expression analysis. Bioinformatics (2002) 8.30
A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (2004) 5.99
Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis. Cancer Res (2001) 2.90
Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biol (2002) 2.64
A comparison of statistical methods for analysis of high density oligonucleotide array data. Bioinformatics (2003) 2.20
Organ-specific molecular classification of primary lung, colon, and ovarian adenocarcinomas using gene expression profiles. Am J Pathol (2001) 1.95
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
A genome-wide association study of global gene expression. Nat Genet (2007) 22.98
Global quantification of mammalian gene expression control. Nature (2011) 22.36
Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med (2002) 21.28
The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature (2002) 18.30
ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia (2004) 17.08
EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci U S A (2003) 13.68
Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature (2009) 12.58
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia (2007) 10.74
Prevalence of chronic kidney disease in China: a cross-sectional survey. Lancet (2012) 10.53
Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol (2008) 10.17
Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med (2008) 10.12
A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat Genet (2007) 9.47
Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A (2004) 9.42
Autoantibody signatures in prostate cancer. N Engl J Med (2005) 7.56
SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet (2009) 7.48
Pooled analysis of fluorouracil-based adjuvant therapy for stage II and III colon cancer: who benefits and by how much? J Clin Oncol (2004) 7.36
Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res (2002) 7.29
Childhood adiposity, adult adiposity, and cardiovascular risk factors. N Engl J Med (2011) 7.16
Heterogeneity in cancer: cancer stem cells versus clonal evolution. Cell (2009) 7.09
Cubic AgPb(m)SbTe(2+m): bulk thermoelectric materials with high figure of merit. Science (2004) 7.07
p53-mediated activation of miRNA34 candidate tumor-suppressor genes. Curr Biol (2007) 6.87
Statins and the risk of colorectal cancer. N Engl J Med (2005) 6.86
Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat Genet (2008) 6.75
Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev (2007) 6.71
The SLUG zinc-finger protein represses E-cadherin in breast cancer. Cancer Res (2002) 6.47
Altered histone acetylation is associated with age-dependent memory impairment in mice. Science (2010) 6.38
Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell (2005) 6.04
Androgen-independent prostate cancer is a heterogeneous group of diseases: lessons from a rapid autopsy program. Cancer Res (2004) 5.88
A human snoRNA with microRNA-like functions. Mol Cell (2008) 5.84
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res (2011) 5.83
Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Transl Med (2011) 5.82
EGFR, p16, HPV Titer, Bcl-xL and p53, sex, and smoking as indicators of response to therapy and survival in oropharyngeal cancer. J Clin Oncol (2008) 5.46
Incidence of initial local therapy among men with lower-risk prostate cancer in the United States. J Natl Cancer Inst (2006) 5.42
A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet (2002) 5.38
Comparative genome hybridization suggests a role for NRXN1 and APBA2 in schizophrenia. Hum Mol Genet (2007) 5.28
EML4-ALK fusion lung cancer: a rare acquired event. Neoplasia (2008) 5.22
Refining the complex rheumatoid arthritis phenotype based on specificity of the HLA-DRB1 shared epitope for antibodies to citrullinated proteins. Arthritis Rheum (2005) 5.18
alpha-Methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer. JAMA (2002) 5.07
A powerful and flexible multilocus association test for quantitative traits. Am J Hum Genet (2008) 4.96
Childhood cardiovascular risk factors and carotid vascular changes in adulthood: the Bogalusa Heart Study. JAMA (2003) 4.88
Deep sequencing reveals 50 novel genes for recessive cognitive disorders. Nature (2011) 4.85
Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev Cell (2005) 4.83
Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med (2010) 4.81
Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet (2007) 4.69
Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics (2007) 4.66
Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics (2002) 4.56
A Wnt-Axin2-GSK3beta cascade regulates Snail1 activity in breast cancer cells. Nat Cell Biol (2006) 4.55
Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer. Cancer Cell (2007) 4.43
Adenoma-linked barrier defects and microbial products drive IL-23/IL-17-mediated tumour growth. Nature (2012) 4.41
Sequence and analysis of rice chromosome 4. Nature (2002) 4.39
Prediction of germline mutations and cancer risk in the Lynch syndrome. JAMA (2006) 4.34
Ligand configurational entropy and protein binding. Proc Natl Acad Sci U S A (2007) 4.33
Molecular profiling of pancreatic adenocarcinoma and chronic pancreatitis identifies multiple genes differentially regulated in pancreatic cancer. Cancer Res (2003) 4.30
Transmit and receive transmission line arrays for 7 Tesla parallel imaging. Magn Reson Med (2005) 4.25
Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase. Science (2011) 4.16
Statins and cancer prevention. Nat Rev Cancer (2005) 4.12
Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res (2006) 4.11
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature (2012) 4.00
Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nat Genet (2010) 3.99
Probabilistic model of the human protein-protein interaction network. Nat Biotechnol (2005) 3.99
Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics (2009) 3.87
A biomarker panel for acute graft-versus-host disease. Blood (2008) 3.83
A polycomb repression signature in metastatic prostate cancer predicts cancer outcome. Cancer Res (2007) 3.82
Seven new loci associated with age-related macular degeneration. Nat Genet (2013) 3.81
Frequency and spectrum of cancers in the Peutz-Jeghers syndrome. Clin Cancer Res (2006) 3.81
Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. Clin Cancer Res (2005) 3.79
A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet (2008) 3.71
Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC Bioinformatics (2008) 3.70
MicroRNA miR-34 inhibits human pancreatic cancer tumor-initiating cells. PLoS One (2009) 3.66
Gene expression in ovarian cancer reflects both morphology and biological behavior, distinguishing clear cell from other poor-prognosis ovarian carcinomas. Cancer Res (2002) 3.62
Chemoselection as a strategy for organ preservation in advanced oropharynx cancer: response and survival positively associated with HPV16 copy number. J Clin Oncol (2008) 3.55
Intradiscal injection therapy for degenerative chronic discogenic low back pain with end plate Modic changes. Spine J (2010) 3.55
Array CGH identifies reciprocal 16p13.1 duplications and deletions that predispose to autism and/or mental retardation. Hum Mutat (2007) 3.52
A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration. Proc Natl Acad Sci U S A (2007) 3.50
Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet (2007) 3.39
The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet (2013) 3.39
Meta-analysis for surrogacy: accelerated failure time models and semicompeting risks modeling. Biometrics (2011) 3.38
Small changes in expression affect predisposition to tumorigenesis. Nat Genet (2001) 3.37
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. Nat Genet (2010) 3.37
Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer. Mod Pathol (2007) 3.37