Published in BMC Bioinformatics on August 10, 2010
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Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res (2012) 2.54
Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis. PLoS One (2011) 1.53
INMEX--a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res (2013) 1.48
A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. Bioinformatics (2012) 1.05
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Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet (2001) 63.36
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics (2006) 22.61
ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia (2004) 17.08
ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res (2003) 15.48
Multiple-laboratory comparison of microarray platforms. Nat Methods (2005) 11.74
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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
Robust estimators for expression analysis. Bioinformatics (2002) 8.30
Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res (2002) 7.29
Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res (2008) 5.88
GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res (2003) 4.82
Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. Bioinformatics (2005) 4.80
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res (2008) 4.73
Expression Profiler: next generation--an online platform for analysis of microarray data. Nucleic Acids Res (2004) 4.21
Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics (2005) 3.93
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res (2007) 3.80
A gene expression signature predicts survival of patients with stage I non-small cell lung cancer. PLoS Med (2006) 3.37
Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med (2008) 3.31
Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biol (2008) 3.16
CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. Nucleic Acids Res (2006) 2.93
Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet (2003) 2.54
Centralization: a new method for the normalization of gene expression data. Bioinformatics (2001) 2.47
Celsius: a community resource for Affymetrix microarray data. Genome Biol (2007) 2.38
Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. BMC Bioinformatics (2005) 2.36
Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. Gene (2007) 2.16
Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers. J Clin Oncol (2006) 2.11
Merging two gene-expression studies via cross-platform normalization. Bioinformatics (2008) 1.93
Lack of correct data format and comparability limits future integrative microarray research. Nat Biotechnol (2006) 1.75
Large-scale integration of cancer microarray data identifies a robust common cancer signature. BMC Bioinformatics (2007) 1.74
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics (2008) 1.68
MDQC: a new quality assessment method for microarrays based on quality control reports. Bioinformatics (2007) 1.61
New normalization methods for cDNA microarray data. Bioinformatics (2003) 1.56
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. BMC Bioinformatics (2008) 1.52
Much room for improvement in deposition rates of expression microarray datasets. Nat Methods (2008) 1.51
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. BMC Bioinformatics (2009) 1.50
EzArray: a web-based highly automated Affymetrix expression array data management and analysis system. BMC Bioinformatics (2008) 1.42
Survival prediction of stage I lung adenocarcinomas by expression of 10 genes. J Clin Invest (2007) 1.41
Combining Affymetrix microarray results. BMC Bioinformatics (2005) 1.36
Using generalized procrustes analysis (GPA) for normalization of cDNA microarray data. BMC Bioinformatics (2008) 1.32
WebArrayDB: cross-platform microarray data analysis and public data repository. Bioinformatics (2009) 1.27
Statistical challenges in preprocessing in microarray experiments in cancer. Clin Cancer Res (2008) 1.19
Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions. BMC Bioinformatics (2006) 1.12
A 10-gene classifier for distinguishing head and neck squamous cell carcinoma and lung squamous cell carcinoma. Clin Cancer Res (2007) 1.10
Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. BMC Genomics (2008) 1.08
Power enhancement via multivariate outlier testing with gene expression arrays. Bioinformatics (2008) 1.02
Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations. BMC Bioinformatics (2009) 1.01
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data. Nucleic Acids Res (2008) 0.96
Randomization in laboratory procedure is key to obtaining reproducible microarray results. PLoS One (2008) 0.94
Genomic profiling of acquired resistance to apoptosis in cells derived from human atherosclerotic lesions: potential role of STATs, cyclinD1, BAD, and Bcl-XL. J Mol Cell Cardiol (2005) 0.92
GenMiner: mining non-redundant association rules from integrated gene expression data and annotations. Bioinformatics (2008) 0.92
A novel approach to detect differentially expressed genes from count-based digital databases by normalizing with housekeeping genes. Genomics (2009) 0.81
CleanEx: new data extraction and merging tools based on MeSH term annotation. Nucleic Acids Res (2009) 0.81
Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips. Nucleic Acids Res (2009) 0.78
dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res (2006) 2.28
MicroRNA-214 downregulation contributes to tumor angiogenesis by inducing secretion of the hepatoma-derived growth factor in human hepatoma. J Hepatol (2012) 2.03
A sense of danger from radiation. Radiat Res (2004) 2.02
Highly efficient classification and identification of human pathogenic bacteria by MALDI-TOF MS. Mol Cell Proteomics (2007) 1.73
Hepatic expression of HCV RNA-dependent RNA polymerase triggers innate immune signaling and cytokine production. Mol Cell (2012) 1.61
Defining the priority of using 18F-FDG PET for recurrent cervical cancer. J Nucl Med (2004) 1.58
Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis. PLoS One (2011) 1.53
Region-specific gene expression profiles in the left atria of patients with valvular atrial fibrillation. Heart Rhythm (2012) 1.47
Pre-radiotherapy PSA level as a predictor for biochemical control in prostate cancer patients receiving radiotherapy after radical prostatectomy. Biomed J (2013) 1.38
Randomized trial of surgical staging (extraperitoneal or laparoscopic) versus clinical staging in locally advanced cervical cancer. Gynecol Oncol (2003) 1.31
Macrophages from irradiated tumors express higher levels of iNOS, arginase-I and COX-2, and promote tumor growth. Int J Radiat Oncol Biol Phys (2007) 1.28
Functional network analysis of the transcriptomes of mesenchymal stem cells derived from amniotic fluid, amniotic membrane, cord blood, and bone marrow. Stem Cells (2007) 1.20
Delivery of a read-through inducing compound, TC007, lessens the severity of a spinal muscular atrophy animal model. Hum Mol Genet (2009) 1.19
Radiotherapy decreases vascular density and causes hypoxia with macrophage aggregation in TRAMP-C1 prostate tumors. Clin Cancer Res (2009) 1.19
Expression, purification, and characterization of two N,N-dimethyltransferases, tylM1 and desVI, involved in the biosynthesis of mycaminose and desosamine. Biochemistry (2002) 1.13
Irradiation promotes an m2 macrophage phenotype in tumor hypoxia. Front Oncol (2012) 1.12
Differentially expressed genes in radioresistant nasopharyngeal cancer cells: gp96 and GDF15. Mol Cancer Ther (2007) 1.11
Molecular characterization of adenocarcinoma and squamous carcinoma of the uterine cervix using microarray analysis of gene expression. Int J Cancer (2006) 1.11
Compartmental responses after thoracic irradiation of mice: strain differences. Int J Radiat Oncol Biol Phys (2005) 1.11
Decreased expression of microRNA-199b increases protein levels of SET (protein phosphatase 2A inhibitor) in human choriocarcinoma. Cancer Lett (2009) 1.10
Role of human papillomavirus genotype in prognosis of early-stage cervical cancer undergoing primary surgery. J Clin Oncol (2007) 1.10
Stress-induced phosphoprotein 1 as a secreted biomarker for human ovarian cancer promotes cancer cell proliferation. Mol Cell Proteomics (2010) 1.06
Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis. PLoS One (2011) 1.04
Segmentation of cDNA microarray images by kernel density estimation. J Biomed Inform (2008) 1.03
Impact of pretreatment body mass index on patients with head-and-neck cancer treated with radiation. Int J Radiat Oncol Biol Phys (2012) 1.02
Macrophage inflammatory protein-3alpha is a novel serum marker for nasopharyngeal carcinoma detection and prediction of treatment outcomes. Clin Cancer Res (2008) 1.01
Clinical behaviors and outcomes for adenocarcinoma or adenosquamous carcinoma of cervix treated by radical hysterectomy and adjuvant radiotherapy or chemoradiotherapy. Int J Radiat Oncol Biol Phys (2012) 1.00
Value of dual-phase 2-fluoro-2-deoxy-d-glucose positron emission tomography in cervical cancer. J Clin Oncol (2003) 1.00
Promoter polymorphisms of DNMT3B and the risk of head and neck squamous cell carcinoma in Taiwan: a case-control study. Oral Oncol (2006) 1.00
Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling. ScientificWorldJournal (2012) 0.99
Identification of candidate nasopharyngeal carcinoma serum biomarkers by cancer cell secretome and tissue transcriptome analysis: potential usage of cystatin A for predicting nodal stage and poor prognosis. Proteomics (2010) 0.99
Long-term outcome and prognostic factors for adenocarcinoma/adenosquamous carcinoma of cervix after definitive radiotherapy. Int J Radiat Oncol Biol Phys (2010) 0.98
Recurrence and poor prognosis following resection of small hepatitis B-related hepatocellular carcinoma lesions are associated with aberrant tumor expression profiles of glypican 3 and osteopontin. Ann Surg Oncol (2011) 0.98
Secreted stress-induced phosphoprotein 1 activates the ALK2-SMAD signaling pathways and promotes cell proliferation of ovarian cancer cells. Cell Rep (2012) 0.97
Usage of case-based reasoning, neural network and adaptive neuro-fuzzy inference system classification techniques in breast cancer dataset classification diagnosis. J Med Syst (2010) 0.97
Tumor-secreted SDF-1 promotes glioma invasiveness and TAM tropism toward hypoxia in a murine astrocytoma model. Lab Invest (2011) 0.96
Thyroid hormone receptor-dependent transcriptional regulation of fibrinogen and coagulation proteins. Endocrinology (2004) 0.96
Molecular epidemiology and clinical manifestations of viral gastroenteritis in hospitalized pediatric patients in Northern Taiwan. J Clin Microbiol (2007) 0.96
Population-based cohort study on the risk of malignancy in East Asian children with juvenile idiopathic arthritis. BMC Cancer (2014) 0.96
Functional phenotype of macrophages depends on assay procedures. Int Immunol (2007) 0.95
Molecular signature of clinical severity in recovering patients with severe acute respiratory syndrome coronavirus (SARS-CoV). BMC Genomics (2005) 0.95
Prenatally diagnosed balanced chromosome rearrangements: eight years' experience. J Reprod Med (2006) 0.95
Alkaline phosphatase: does it have a role in predicting hepatocellular carcinoma recurrence? J Gastrointest Surg (2011) 0.95
Global analyses of small interfering RNAs derived from Bamboo mosaic virus and its associated satellite RNAs in different plants. PLoS One (2010) 0.94
Does diabetes mellitus influence the efficacy of FDG-PET in the diagnosis of cervical cancer? Eur J Nucl Med Mol Imaging (2005) 0.94
Identification of prognostic factors in patients with cervical cancer and supraclavicular lymph node recurrence. Gynecol Oncol (2011) 0.94
Interleukin-1 receptor antagonist (IL-1RA) prevents apoptosis in ex vivo expansion of human limbal epithelial cells cultivated on human amniotic membrane. Stem Cells (2006) 0.94
High-temperature requirement protein A4 (HtrA4) suppresses the fusogenic activity of syncytin-1 and promotes trophoblast invasion. Mol Cell Biol (2012) 0.93
Radiation therapy-induced tumor invasiveness is associated with SDF-1-regulated macrophage mobilization and vasculogenesis. PLoS One (2013) 0.93
Gene selection for cancer identification: a decision tree model empowered by particle swarm optimization algorithm. BMC Bioinformatics (2014) 0.92
Hysteroscopic management of cesarean scar pregnancy after unsuccessful methotrexate treatment. J Minim Invasive Gynecol (2005) 0.92
Vasculatures in tumors growing from preirradiated tissues: formed by vasculogenesis and resistant to radiation and antiangiogenic therapy. Int J Radiat Oncol Biol Phys (2011) 0.92
Induction of radioprotective peroxiredoxin-I by ionizing irradiation. J Neurosci Res (2002) 0.92
Protection against radiation-induced bone marrow and intestinal injuries by Cordyceps sinensis, a Chinese herbal medicine. Radiat Res (2006) 0.91
Concurrent cisplatin, 5-fluorouracil, leucovorin, and radiotherapy for invasive bladder cancer. Int J Radiat Oncol Biol Phys (2003) 0.91
The concentration of inhibin B in follicular fluid: relation to oocyte maturation and embryo development. Hum Reprod (2002) 0.90
Potential ex vivo immunomodulatory effects of San-Huang-Xie-Xin-Tang and its component herbs on mice and humans. J Ethnopharmacol (2009) 0.90
DNA microarray analysis of the effect on inflammation in patients treated with acupuncture for allergic rhinitis. J Altern Complement Med (2008) 0.90
Honokiol inhibits LPS-induced maturation and inflammatory response of human monocyte-derived dendritic cells. J Cell Physiol (2011) 0.89
MicroRNA and messenger RNA analyses of mesenchymal stem cells derived from teeth and the Wharton jelly of umbilical cord. Stem Cells Dev (2011) 0.89
Change in amniotic fluid levels of multiple anti-angiogenic proteins before development of preeclampsia and intrauterine growth restriction. J Clin Endocrinol Metab (2010) 0.89
Intra- and inter-individual variance of gene expression in clinical studies. PLoS One (2012) 0.88
Meconium peritonitis in utero---the value of prenatal diagnosis in determining neonatal outcome. Taiwan J Obstet Gynecol (2008) 0.88
Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles. BMC Bioinformatics (2008) 0.88
Modeling neurogenesis impairment in Down syndrome with induced pluripotent stem cells from Trisomy 21 amniotic fluid cells. Exp Cell Res (2012) 0.87
Identification of differential gene expression between intestinal and diffuse gastric cancer using cDNA microarray. Oncol Rep (2006) 0.87
Clinical application of radiophotoluminescent glass dosimeter for dose verification of prostate HDR procedure. Med Phys (2008) 0.87
Tumor stress-induced phosphoprotein1 (STIP1) as a prognostic biomarker in ovarian cancer. PLoS One (2013) 0.87
Analyses of placental gene expression in pregnancy-related hypertensive disorders. Taiwan J Obstet Gynecol (2011) 0.87
Characterization of a de novo unbalanced Y;autosome translocation in a 45,X mentally retarded male and literature review. Fertil Steril (2008) 0.87
Analysis of functional groups of differentially expressed genes in the peripheral blood of patients with cervical cancer undergoing concurrent chemoradiation treatment. Radiat Res (2008) 0.87