Published in BMC Bioinformatics on February 08, 2007
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res (2009) 3.50
Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res (2011) 3.25
Mesenchymal differentiation mediated by NF-κB promotes radiation resistance in glioblastoma. Cancer Cell (2013) 2.98
Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function. Genome Res (2009) 1.83
Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes. Genome Med (2010) 1.64
GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics (2010) 1.52
Consistency analysis of redundant probe sets on affymetrix three-prime expression arrays and applications to differential mRNA processing. PLoS One (2009) 1.45
Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery. Genome Biol (2016) 1.43
Distinct perturbation of the translatome by the antidiabetic drug metformin. Proc Natl Acad Sci U S A (2012) 1.43
Widespread over-expression of the X chromosome in sterile F₁hybrid mice. PLoS Genet (2010) 1.32
Fibrotic myofibroblasts manifest genome-wide derangements of translational control. PLoS One (2008) 1.30
Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data. BMC Bioinformatics (2008) 1.29
Prioritizing genes for follow-up from genome wide association studies using information on gene expression in tissues relevant for type 2 diabetes mellitus. BMC Med Genomics (2009) 1.19
Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia. Genome Med (2010) 1.18
Thawing Frozen Robust Multi-array Analysis (fRMA). BMC Bioinformatics (2011) 1.13
Identification of novel type 1 diabetes candidate genes by integrating genome-wide association data, protein-protein interactions, and human pancreatic islet gene expression. Diabetes (2012) 1.09
Eukaryotic initiation factor 4E binding protein family of proteins: sentinels at a translational control checkpoint in lung tumor defense. Cancer Res (2009) 1.06
"Hook"-calibration of GeneChip-microarrays: chip characteristics and expression measures. Algorithms Mol Biol (2008) 1.05
Identification of differential translation in genome wide studies. Proc Natl Acad Sci U S A (2010) 1.05
Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements. BMC Bioinformatics (2010) 1.04
25-Hydroxycholesterol acts as an amplifier of inflammatory signaling. Proc Natl Acad Sci U S A (2014) 1.04
Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation. PLoS One (2009) 1.01
Physiology, pathology and relatedness of human tissues from gene expression meta-analysis. PLoS One (2008) 0.97
Estrogen receptor alpha drives proliferation in PTEN-deficient prostate carcinoma by stimulating survival signaling, MYC expression and altering glucose sensitivity. Oncotarget (2015) 0.94
A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data. BMC Genomics (2008) 0.94
miRNAs mediate SnRK1-dependent energy signaling in Arabidopsis. Front Plant Sci (2013) 0.93
AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. BMC Bioinformatics (2011) 0.93
Direct integration of intensity-level data from Affymetrix and Illumina microarrays improves statistical power for robust reanalysis. BMC Med Genomics (2012) 0.93
Salvaging Affymetrix probes after probe-level re-annotation. BMC Res Notes (2008) 0.92
Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis. PLoS One (2013) 0.92
Probiotic Lactobacillus rhamnosus downregulates FCER1 and HRH4 expression in human mast cells. World J Gastroenterol (2011) 0.89
Non-thermal plasma treatment altered gene expression profiling in non-small-cell lung cancer A549 cells. BMC Genomics (2015) 0.87
Small nucleolar RNAs as new biomarkers in chronic lymphocytic leukemia. BMC Med Genomics (2013) 0.87
Docetaxel-loaded solid lipid nanoparticles suppress breast cancer cells growth with reduced myelosuppression toxicity. Int J Nanomedicine (2014) 0.85
Integrative computational biology for cancer research. Hum Genet (2011) 0.85
Comparison of sepsis-induced transcriptomic changes in a murine model to clinical blood samples identifies common response patterns. Front Microbiol (2012) 0.85
Long Noncoding RNA Expression during Human B-Cell Development. PLoS One (2015) 0.84
Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome. BMC Bioinformatics (2010) 0.84
Circulating blood leukocyte gene expression profiles: effects of the Ames dwarf mutation on pathways related to immunity and inflammation. Exp Gerontol (2007) 0.84
Stable isotope labeling in zebrafish allows in vivo monitoring of cardiac morphogenesis. Mol Cell Proteomics (2013) 0.84
Suppression of the DHX9 helicase induces premature senescence in human diploid fibroblasts in a p53-dependent manner. J Biol Chem (2014) 0.84
Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees. BMC Bioinformatics (2009) 0.82
Arterial wall stress controls NFAT5 activity in vascular smooth muscle cells. J Am Heart Assoc (2014) 0.82
Transthyretin proteins regulate angiogenesis by conferring different molecular identities to endothelial cells. J Biol Chem (2013) 0.81
A Patient-Derived Xenograft Model of Parameningeal Embryonal Rhabdomyosarcoma for Preclinical Studies. Sarcoma (2015) 0.80
mTORC1 and CK2 coordinate ternary and eIF4F complex assembly. Nat Commun (2016) 0.80
An integrated transcriptomic and meta-analysis of hepatoma cells reveals factors that influence susceptibility to HCV infection. PLoS One (2011) 0.80
Gene profiling characteristics of radioadaptive response in AG01522 normal human fibroblasts. PLoS One (2015) 0.79
MERAV: a tool for comparing gene expression across human tissues and cell types. Nucleic Acids Res (2015) 0.78
Time since onset of disease and individual clinical markers associate with transcriptional changes in uncomplicated dengue. PLoS Negl Trop Dis (2015) 0.78
The expression of embryonic liver development genes in hepatitis C induced cirrhosis and hepatocellular carcinoma. Cancers (Basel) (2012) 0.77
FDR-FET: an optimizing gene set enrichment analysis method. Adv Appl Bioinform Chem (2011) 0.77
Genome-wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation. J Endocrinol (2011) 0.77
SCOREM: statistical consolidation of redundant expression measures. Nucleic Acids Res (2011) 0.77
A decision theory paradigm for evaluating identifier mapping and filtering methods using data integration. BMC Bioinformatics (2013) 0.77
Assessment of mTOR-Dependent Translational Regulation of Interferon Stimulated Genes. PLoS One (2015) 0.76
Staphylococcus epidermidis Biofilm-Released Cells Induce a Prompt and More Marked In vivo Inflammatory-Type Response than Planktonic or Biofilm Cells. Front Microbiol (2016) 0.75
ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs. BMC Bioinformatics (2011) 0.75
Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results. BMC Res Notes (2012) 0.75
Imputing Gene Expression to Maximize Platform Compatibility. Bioinformatics (2016) 0.75
Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization. BMC Genomics (2014) 0.75
System Level Meta-analysis of Microarray Datasets for Elucidation of Diabetes Mellitus Pathobiology. Curr Genomics (2017) 0.75
An Expanded Role for HLA Genes: HLA-B Encodes a microRNA that Regulates IgA and Other Immune Response Transcripts. Front Immunol (2017) 0.75
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
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
Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74
The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science (2005) 20.51
NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res (2005) 17.61
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res (2005) 17.58
Multiple-laboratory comparison of microarray platforms. Nat Methods (2005) 11.74
ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res (2005) 6.73
The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res (2005) 4.17
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics (2005) 3.66
Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics (2004) 3.56
Lack of correct data format and comparability limits future integrative microarray research. Nat Biotechnol (2006) 1.75
Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Res (2005) 1.42
Comparative microarray analysis. OMICS (2006) 1.30
Apoptosis resistance downstream of eIF4E: posttranscriptional activation of an anti-apoptotic transcript carrying a consensus hairpin structure. Nucleic Acids Res (2006) 1.27
The expression signature of in vitro senescence resembles mouse but not human aging. Genome Biol (2005) 1.03
mTORC1-mediated cell proliferation, but not cell growth, controlled by the 4E-BPs. Science (2010) 4.81
Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages. Proc Natl Acad Sci U S A (2007) 4.69
Conserved GU-rich elements mediate mRNA decay by binding to CUG-binding protein 1. Mol Cell (2008) 4.11
eIF4E phosphorylation promotes tumorigenesis and is associated with prostate cancer progression. Proc Natl Acad Sci U S A (2010) 3.13
Epigenetic activation of a subset of mRNAs by eIF4E explains its effects on cell proliferation. PLoS One (2007) 2.35
Translational control of the innate immune response through IRF-7. Nature (2008) 2.30
Hypoxia-independent angiogenesis in adipose tissues during cold acclimation. Cell Metab (2009) 2.11
Leishmania repression of host translation through mTOR cleavage is required for parasite survival and infection. Cell Host Microbe (2011) 2.01
mTORC1 controls mitochondrial activity and biogenesis through 4E-BP-dependent translational regulation. Cell Metab (2013) 1.91
Human muscle gene expression responses to endurance training provide a novel perspective on Duchenne muscular dystrophy. FASEB J (2005) 1.85
Lack of correct data format and comparability limits future integrative microarray research. Nat Biotechnol (2006) 1.75
Insulin receptor expression by human prostate cancers. Prostate (2009) 1.57
Fibrotic extracellular matrix activates a profibrotic positive feedback loop. J Clin Invest (2014) 1.54
p53-dependent translational control of senescence and transformation via 4E-BPs. Cancer Cell (2009) 1.51
The helicase protein DHX29 promotes translation initiation, cell proliferation, and tumorigenesis. Proc Natl Acad Sci U S A (2009) 1.34
PDGF-BB modulates hematopoiesis and tumor angiogenesis by inducing erythropoietin production in stromal cells. Nat Med (2011) 1.33
Altered regulation of the PINK1 locus: a link between type 2 diabetes and neurodegeneration? FASEB J (2007) 1.19
Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors. Proc Natl Acad Sci U S A (2012) 1.17
mTOR coordinates protein synthesis, mitochondrial activity and proliferation. Cell Cycle (2015) 1.11
A novel 4EHP-GIGYF2 translational repressor complex is essential for mammalian development. Mol Cell Biol (2012) 1.09
Effective small interfering RNAs and phosphorothioate antisense DNAs have different preferences for target sites in the luciferase mRNAs. Biochem Biophys Res Commun (2003) 1.06
Eukaryotic initiation factor 4E binding protein family of proteins: sentinels at a translational control checkpoint in lung tumor defense. Cancer Res (2009) 1.06
The expression signature of in vitro senescence resembles mouse but not human aging. Genome Biol (2005) 1.03
Tumour PDGF-BB expression levels determine dual effects of anti-PDGF drugs on vascular remodelling and metastasis. Nat Commun (2013) 0.98
RNAi screening uncovers Dhx9 as a modifier of ABT-737 resistance in an Eμ-myc/Bcl-2 mouse model. Blood (2013) 0.93
Functional comparison of single- and double-stranded siRNAs in mammalian cells. Biochem Biophys Res Commun (2004) 0.90
Regulatory element identification in subsets of transcripts: comparison and integration of current computational methods. RNA (2009) 0.89
Role of 3'UTRs in the translation of mRNAs regulated by oncogenic eIF4E--a computational inference. PLoS One (2009) 0.88
Hedgehog signaling is active in human prostate cancer stroma and regulates proliferation and differentiation of adjacent epithelium. Prostate (2013) 0.87
Correlation of regional emphysema and lung cancer: a lung tissue research consortium-based study. J Thorac Oncol (2014) 0.86
Distinct translational control in CD4+ T cell subsets. PLoS Genet (2013) 0.84
A pro-tumourigenic loop at the human prostate tumour interface orchestrated by oestrogen, CXCL12 and mast cell recruitment. J Pathol (2014) 0.83
A chemical genetic screen for mTOR pathway inhibitors based on 4E-BP-dependent nuclear accumulation of eIF4E. Chem Biol (2009) 0.80
Using functional genomics to study PINK1 and metabolic physiology. Methods Enzymol (2009) 0.79