Published in BMC Bioinformatics on February 24, 2010
The signal transducers Stat1 and Stat3 and their novel target Jmjd3 drive the expression of inflammatory genes in microglia. J Mol Med (Berl) (2013) 1.64
Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis. PLoS One (2011) 1.04
Evidence for the complexity of microRNA-mediated regulation in ovarian cancer: a systems approach. PLoS One (2011) 1.02
Molecular markers and mechanisms of stroke: RNA studies of blood in animals and humans. J Cereb Blood Flow Metab (2011) 1.01
Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays. Nucleic Acids Res (2011) 0.98
Chronic alcohol exposure alters gene expression in HepG2 cells. Alcohol Clin Exp Res (2011) 0.95
The effects of MicroRNA transfections on global patterns of gene expression in ovarian cancer cells are functionally coordinated. BMC Med Genomics (2012) 0.90
A global insight into a cancer transcriptional space using pancreatic data: importance, findings and flaws. Nucleic Acids Res (2011) 0.90
Identification of pathway deregulation--gene expression based analysis of consistent signal transduction. PLoS One (2012) 0.84
Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation. BMC Genomics (2014) 0.84
The LO-BaFL method and ALS microarray expression analysis. BMC Bioinformatics (2012) 0.80
Down-regulation of IKKβ expression in glioma-infiltrating microglia/macrophages is associated with defective inflammatory/immune gene responses in glioblastoma. Oncotarget (2015) 0.79
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. Int Rev Neurobiol (2012) 0.77
A decision theory paradigm for evaluating identifier mapping and filtering methods using data integration. BMC Bioinformatics (2013) 0.77
SCOREM: statistical consolidation of redundant expression measures. Nucleic Acids Res (2011) 0.77
ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs. BMC Bioinformatics (2011) 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
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
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
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
Ensembl 2009. Nucleic Acids Res (2008) 25.38
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res (2005) 17.58
Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol (2001) 15.02
Comparison of Affymetrix GeneChip expression measures. Bioinformatics (2006) 7.49
ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res (2005) 6.73
Preprocessing of oligonucleotide array data. Nat Biotechnol (2004) 4.70
Social regulation of gene expression in human leukocytes. Genome Biol (2007) 4.65
Effects of filtering by Present call on analysis of microarray experiments. BMC Bioinformatics (2006) 3.86
Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics (2006) 3.44
Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. BMC Bioinformatics (2006) 2.35
Filtering for increased power for microarray data analysis. BMC Bioinformatics (2009) 2.30
Improved precision and accuracy for microarrays using updated probe set definitions. BMC Bioinformatics (2007) 2.17
How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results. BMC Bioinformatics (2006) 2.13
Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study. BMC Genomics (2008) 1.99
Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data. BMC Bioinformatics (2005) 1.96
Sources of variation in Affymetrix microarray experiments. BMC Bioinformatics (2005) 1.94
Probe set algorithms: is there a rational best bet? BMC Bioinformatics (2006) 1.53
Morphine effects on striatal transcriptome in mice. Genome Biol (2007) 1.02
Methods for evaluating gene expression from Affymetrix microarray datasets. BMC Bioinformatics (2008) 0.94
Three clinical variants of gastroesophageal reflux disease form two distinct gene expression signatures. J Mol Med (Berl) (2006) 0.90
Novel proteins regulated by mTOR in subependymal giant cell astrocytomas of patients with tuberous sclerosis complex and new therapeutic implications. Am J Pathol (2010) 0.90
AAindex: amino acid index database, progress report 2008. Nucleic Acids Res (2007) 4.21
Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet (2003) 2.54
Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics (2004) 1.68
The signal transducers Stat1 and Stat3 and their novel target Jmjd3 drive the expression of inflammatory genes in microglia. J Mol Med (Berl) (2013) 1.64
Coordinated and widespread expression of gamma-secretase in vivo: evidence for size and molecular heterogeneity. Neurobiol Dis (2004) 1.56
Epileptogenesis-related genes revisited. Prog Brain Res (2006) 1.04
LEF1/beta-catenin complex regulates transcription of the Cav3.1 calcium channel gene (Cacna1g) in thalamic neurons of the adult brain. J Neurosci (2010) 0.98
Molecular definition of the pro-tumorigenic phenotype of glioma-activated microglia. Glia (2013) 0.93
Prolonged activation of ERK triggers glutamate-induced apoptosis of astrocytes: neuroprotective effect of FK506. J Neurochem (2010) 0.92
Novel proteins regulated by mTOR in subependymal giant cell astrocytomas of patients with tuberous sclerosis complex and new therapeutic implications. Am J Pathol (2010) 0.90
Distance matrix-based approach to protein structure prediction. J Struct Funct Genomics (2009) 0.89
Early steps of microglial activation are directly affected by neuroprotectant FK506 in both in vitro inflammation and in rat model of stroke. J Mol Med (Berl) (2012) 0.88
Signal transducer and activator of transcription 1 (Stat1) maintains basal mRNA expression of pro-survival stat3-target genes in glioma C6 cells. J Cell Biochem (2011) 0.84
Gng12 is a novel negative regulator of LPS-induced inflammation in the microglial cell line BV-2. Inflamm Res (2009) 0.83
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition. Biopolymers (2003) 0.82
Novel β-catenin target genes identified in thalamic neurons encode modulators of neuronal excitability. BMC Genomics (2012) 0.82
Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs. Database (Oxford) (2013) 0.81
Novel higher-order epigenetic regulation of the Bdnf gene upon seizures. J Neurosci (2013) 0.79
Tuberous sclerosis complex inactivation disrupts melanogenesis via mTORC1 activation. J Clin Invest (2016) 0.75