Published in BMC Bioinformatics on August 30, 2006
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
Dystrophin-deficient cardiomyopathy in mouse: expression of Nox4 and Lox are associated with fibrosis and altered functional parameters in the heart. Neuromuscul Disord (2008) 1.52
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. BMC Bioinformatics (2008) 1.52
Statistical challenges in preprocessing in microarray experiments in cancer. Clin Cancer Res (2008) 1.19
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
Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle. BMC Genomics (2008) 1.17
Dysferlin deficiency shows compensatory induction of Rab27A/Slp2a that may contribute to inflammatory onset. Am J Pathol (2008) 1.12
Microarray analysis of the temporal response of skeletal muscle to methylprednisolone: comparative analysis of two dosing regimens. Physiol Genomics (2007) 1.10
SRY-box containing gene 17 regulates the Wnt/β-catenin signaling pathway in oligodendrocyte progenitor cells. J Neurosci (2011) 1.10
Molecular signatures of prostate stem cells reveal novel signaling pathways and provide insights into prostate cancer. PLoS One (2009) 1.08
Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements. BMC Bioinformatics (2010) 1.04
Novel transcriptional profile in wrist muscles from cerebral palsy patients. BMC Med Genomics (2009) 1.01
Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations. BMC Bioinformatics (2009) 1.01
Infection and genotype remodel the entire soybean transcriptome. BMC Genomics (2009) 0.98
Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling. Genome Biol (2007) 0.98
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
Asynchronous remodeling is a driver of failed regeneration in Duchenne muscular dystrophy. J Cell Biol (2014) 0.92
Molecular signatures of the primitive prostate stem cell niche reveal novel mesenchymal-epithelial signaling pathways. PLoS One (2010) 0.92
Expression profiling of inflammatory mediators in pediatric sinus mucosa. Arch Otolaryngol Head Neck Surg (2009) 0.92
Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips. BMC Bioinformatics (2007) 0.89
Gene expression profiling in the rhesus macaque: methodology, annotation and data interpretation. Methods (2009) 0.89
Differential gene expression and a functional analysis of PCB-exposed children: understanding disease and disorder development. Environ Int (2011) 0.86
Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection. BMC Genomics (2007) 0.85
Nitric oxide inhibits the accumulation of CD4+CD44hiTbet+CD69lo T cells in mycobacterial infection. Eur J Immunol (2012) 0.84
Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation. BMC Genomics (2014) 0.84
Genes and biochemical pathways in human skeletal muscle affecting resting energy expenditure and fuel partitioning. J Appl Physiol (1985) (2010) 0.84
Gene expression changes in the septum: possible implications for microRNAs in sculpting the maternal brain. PLoS One (2012) 0.83
Is GSN significant for hip BMD in female Caucasians? Bone (2014) 0.82
A white-box approach to microarray probe response characterization: the BaFL pipeline. BMC Bioinformatics (2009) 0.81
Cardiovascular genomics: a biomarker identification pipeline. IEEE Trans Inf Technol Biomed (2012) 0.81
Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq. Methods (2013) 0.81
QServer: a biclustering server for prediction and assessment of co-expressed gene clusters. PLoS One (2012) 0.78
Transcriptional profiling and biological pathway analysis of human equivalence PCB exposure in vitro: indicator of disease and disorder development in humans. Environ Res (2015) 0.76
Transcriptome profiling of human ulcerative colitis mucosa reveals altered expression of pathways enriched in genetic susceptibility loci. PLoS One (2014) 0.75
Crucial genes associated with diabetic nephropathy explored by microarray analysis. BMC Nephrol (2016) 0.75
Global gene expression profiling in R155H knock-in murine model of VCP disease. Clin Transl Sci (2014) 0.75
Identification of genes associated with tongue cancer in patients with a history of tobacco and/or alcohol use. Oncol Lett (2016) 0.75
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
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
Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol (2005) 5.63
Effects of filtering by Present call on analysis of microarray experiments. BMC Bioinformatics (2006) 3.86
An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics (2006) 2.62
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
Nuclear envelope dystrophies show a transcriptional fingerprint suggesting disruption of Rb-MyoD pathways in muscle regeneration. Brain (2006) 2.22
Approximate variance-stabilizing transformations for gene-expression microarray data. Bioinformatics (2003) 2.20
How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results. BMC Bioinformatics (2006) 2.13
Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays. Bioinformatics (2004) 1.98
Experimental design and low-level analysis of microarray data. Int Rev Neurobiol (2004) 1.73
Embryonic myogenesis pathways in muscle regeneration. Dev Dyn (2004) 1.57
Variance-stabilizing transformations for two-color microarrays. Bioinformatics (2004) 1.14
At what scale should microarray data be analyzed? Am J Pharmacogenomics (2004) 1.14
Comparison of preprocessing procedures for oligo-nucleotide micro-arrays by parametric bootstrap simulation of spike-in experiments. Methods Inf Med (2004) 0.97
Improved parameter estimation for variance-stabilizing transformation of gene-expression microarray data. J Bioinform Comput Biol (2004) 0.83
Glucose restriction inhibits skeletal myoblast differentiation by activating SIRT1 through AMPK-mediated regulation of Nampt. Dev Cell (2008) 5.51
Genomics, intellectual disability, and autism. N Engl J Med (2012) 3.74
Elevated stearoyl-CoA desaturase-1 expression in skeletal muscle contributes to abnormal fatty acid partitioning in obese humans. Cell Metab (2005) 3.47
An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics (2006) 2.62
Sources of variability and effect of experimental approach on expression profiling data interpretation. BMC Bioinformatics (2002) 2.31
Nuclear envelope dystrophies show a transcriptional fingerprint suggesting disruption of Rb-MyoD pathways in muscle regeneration. Brain (2006) 2.22
Preclinical drug trials in the mdx mouse: assessment of reliable and sensitive outcome measures. Muscle Nerve (2009) 2.19
Changes in ubiquitin proteasome pathway gene expression in skeletal muscle with exercise and statins. Arterioscler Thromb Vasc Biol (2005) 2.12
Osteopontin promotes fibrosis in dystrophic mouse muscle by modulating immune cell subsets and intramuscular TGF-beta. J Clin Invest (2009) 2.10
Gene profiling in spinal cord injury shows role of cell cycle in neuronal death. Ann Neurol (2003) 2.06
SLC30A8 nonsynonymous variant is associated with recovery following exercise and skeletal muscle size and strength. Diabetes (2013) 2.05
Calorie-related rapid onset of alveolar loss, regeneration, and changes in mouse lung gene expression. Am J Physiol Lung Cell Mol Physiol (2003) 2.04
Secreted proteome profiling in human RPE cell cultures derived from donors with age related macular degeneration and age matched healthy donors. J Proteome Res (2006) 2.04
Deacetylase inhibitors increase muscle cell size by promoting myoblast recruitment and fusion through induction of follistatin. Dev Cell (2004) 2.01
Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays. Bioinformatics (2004) 1.98
Variability in muscle size and strength gain after unilateral resistance training. Med Sci Sports Exerc (2005) 1.95
ACE ID genotype and the muscle strength and size response to unilateral resistance training. Med Sci Sports Exerc (2006) 1.86
Loss of emerin at the nuclear envelope disrupts the Rb1/E2F and MyoD pathways during muscle regeneration. Hum Mol Genet (2006) 1.85
Gene expression profiling in DQA1*0501+ children with untreated dermatomyositis: a novel model of pathogenesis. J Immunol (2002) 1.83
Tissue-specific alternative splicing of TCF7L2. Hum Mol Genet (2009) 1.80
The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators of MyoD and skeletal muscle differentiation. Dev Cell (2006) 1.78
Constitutive activation of MAPK cascade in acute quadriplegic myopathy. Ann Neurol (2004) 1.77
GRB14, GPD1, and GDF8 as potential network collaborators in weight loss-induced improvements in insulin action in human skeletal muscle. Physiol Genomics (2006) 1.67
Dysferlin deficiency enhances monocyte phagocytosis: a model for the inflammatory onset of limb-girdle muscular dystrophy 2B. Am J Pathol (2008) 1.65
ACTN3 genotype is associated with increases in muscle strength in response to resistance training in women. J Appl Physiol (1985) (2005) 1.57
Embryonic myogenesis pathways in muscle regeneration. Dev Dyn (2004) 1.57
Differential dependency network analysis to identify condition-specific topological changes in biological networks. Bioinformatics (2008) 1.56
Microtubules underlie dysfunction in duchenne muscular dystrophy. Sci Signal (2012) 1.54
Dystrophin-deficient cardiomyopathy in mouse: expression of Nox4 and Lox are associated with fibrosis and altered functional parameters in the heart. Neuromuscul Disord (2008) 1.52
ACTN3 and MLCK genotype associations with exertional muscle damage. J Appl Physiol (1985) (2005) 1.52
Functional characteristics of dystrophic skeletal muscle: insights from animal models. J Appl Physiol (1985) (2002) 1.50
Slug is a novel downstream target of MyoD. Temporal profiling in muscle regeneration. J Biol Chem (2002) 1.50
Functional polymorphisms associated with human muscle size and strength. Med Sci Sports Exerc (2004) 1.49
The cooperative international neuromuscular research group Duchenne natural history study--a longitudinal investigation in the era of glucocorticoid therapy: design of protocol and the methods used. Muscle Nerve (2013) 1.48
Proteomics and systems biology in exercise and sport sciences research. Exerc Sport Sci Rev (2007) 1.43
Inflammasome up-regulation and activation in dysferlin-deficient skeletal muscle. Am J Pathol (2010) 1.41
Patterns of global gene expression in rat skeletal muscle during unloading and low-intensity ambulatory activity. Physiol Genomics (2003) 1.41
The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface. Nucleic Acids Res (2004) 1.40
Rare missense and synonymous variants in UBE1 are associated with X-linked infantile spinal muscular atrophy. Am J Hum Genet (2008) 1.39
A web-accessible complete transcriptome of normal human and DMD muscle. Neuromuscul Disord (2002) 1.38
Bodywide skipping of exons 45-55 in dystrophic mdx52 mice by systemic antisense delivery. Proc Natl Acad Sci U S A (2012) 1.32
Skipping toward personalized molecular medicine. N Engl J Med (2007) 1.30
Response of rat muscle to acute resistance exercise defined by transcriptional and translational profiling. J Physiol (2002) 1.29
Integrated DNA, cDNA, and protein studies in Becker muscular dystrophy show high exception to the reading frame rule. Hum Mutat (2008) 1.29
Canine models of Duchenne muscular dystrophy and their use in therapeutic strategies. Mamm Genome (2012) 1.28
Losartan decreases cardiac muscle fibrosis and improves cardiac function in dystrophin-deficient mdx mice. J Cardiovasc Pharmacol Ther (2011) 1.28
Fgfr4 is required for effective muscle regeneration in vivo. Delineation of a MyoD-Tead2-Fgfr4 transcriptional pathway. J Biol Chem (2005) 1.27
VBP15, a novel anti-inflammatory and membrane-stabilizer, improves muscular dystrophy without side effects. EMBO Mol Med (2013) 1.22
Balancing muscle hypertrophy and atrophy. Nat Med (2004) 1.22
Novel CLCN1 mutations with unique clinical and electrophysiological consequences. Brain (2002) 1.22
A randomized clinical trial to assess the effect of statins on skeletal muscle function and performance: rationale and study design. Prev Cardiol (2010) 1.21
In vivo and in vitro characterization of novel neuronal plasticity factors identified following spinal cord injury. J Biol Chem (2004) 1.20
Olfactory biopsies demonstrate a defect in neuronal development in Rett's syndrome. Ann Neurol (2003) 1.19
Gene expression profiling of experimental traumatic spinal cord injury as a function of distance from impact site and injury severity. Physiol Genomics (2005) 1.19
An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss. Genome Biol (2015) 1.19
Proteome analysis of skeletal muscle from obese and morbidly obese women. Diabetes (2005) 1.18
In vivo filtering of in vitro expression data reveals MyoD targets. C R Biol (2004) 1.18
Expression profiling reveals metabolic and structural components of extraocular muscles. Physiol Genomics (2002) 1.17
Molecular responses of human muscle to eccentric exercise. J Appl Physiol (1985) (2003) 1.17
Importance of SPP1 genotype as a covariate in clinical trials in Duchenne muscular dystrophy. Neurology (2012) 1.17
Direct analysis of lipids and small metabolites in mouse brain tissue by AP IR-MALDI and reactive LAESI mass spectrometry. Analyst (2010) 1.17
Skeletal muscle dictates the fibrinolytic state after exercise training in overweight men with characteristics of metabolic syndrome. J Physiol (2003) 1.15
Expression of two temporally distinct microglia-related gene clusters after spinal cord injury. Glia (2006) 1.14
Dysferlin deficiency shows compensatory induction of Rab27A/Slp2a that may contribute to inflammatory onset. Am J Pathol (2008) 1.12
A renaissance for antisense oligonucleotide drugs in neurology: exon skipping breaks new ground. Arch Neurol (2009) 1.11
Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data. Bioinformatics (2006) 1.11
Microarray analysis of the temporal response of skeletal muscle to methylprednisolone: comparative analysis of two dosing regimens. Physiol Genomics (2007) 1.10
Glucocorticoid-treated mice are an inappropriate positive control for long-term preclinical studies in the mdx mouse. PLoS One (2012) 1.10
Metabolic remodeling agents show beneficial effects in the dystrophin-deficient mdx mouse model. Skelet Muscle (2012) 1.10
Neuronal plasticity after spinal cord injury: identification of a gene cluster driving neurite outgrowth. FASEB J (2004) 1.09
Functional and molecular effects of arginine butyrate and prednisone on muscle and heart in the mdx mouse model of Duchenne Muscular Dystrophy. PLoS One (2010) 1.09
Asthmatic airway epithelium is intrinsically inflammatory and mitotically dyssynchronous. Am J Respir Cell Mol Biol (2010) 1.09
Sphingosine-1-phosphate enhances satellite cell activation in dystrophic muscles through a S1PR2/STAT3 signaling pathway. PLoS One (2012) 1.06
The paradox of muscle hypertrophy in muscular dystrophy. Phys Med Rehabil Clin N Am (2012) 1.06
In vivo multi-tissue corticosteroid microarray time series available online at Public Expression Profile Resource (PEPR). Pharmacogenomics (2003) 1.06
A C-terminal skeletal muscle sodium channel mutation associated with myotonia disrupts fast inactivation. J Physiol (2005) 1.05
Differential expression of immunoregulatory genes in male and female Norway rats following infection with Seoul virus. J Med Virol (2004) 1.05
Identification of disease specific pathways using in vivo SILAC proteomics in dystrophin deficient mdx mouse. Mol Cell Proteomics (2013) 1.05
Definition of the unique human extraocular muscle allotype by expression profiling. Physiol Genomics (2005) 1.04
Targeted mutation of mouse skeletal muscle sodium channel produces myotonia and potassium-sensitive weakness. J Clin Invest (2008) 1.03
Genome-wide identification of significant aberrations in cancer genome. BMC Genomics (2012) 1.03
Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. BMC Syst Biol (2014) 1.02
Time series proteome profiling to study endoplasmic reticulum stress response. J Proteome Res (2008) 1.02
Genetic modifiers of ambulation in the Cooperative International Neuromuscular Research Group Duchenne Natural History Study. Ann Neurol (2015) 1.01
Characterization of dysferlin deficient SJL/J mice to assess preclinical drug efficacy: fasudil exacerbates muscle disease phenotype. PLoS One (2010) 1.01
Prednisolone-induced changes in dystrophic skeletal muscle. FASEB J (2005) 1.00
MyoD acetylation influences temporal patterns of skeletal muscle gene expression. J Biol Chem (2007) 1.00
Skeletal muscle gene expression in response to resistance exercise: sex specific regulation. BMC Genomics (2010) 0.99
Membrane sealant Poloxamer P188 protects against isoproterenol induced cardiomyopathy in dystrophin deficient mice. BMC Cardiovasc Disord (2011) 0.99
Proteomic responses of skeletal and cardiac muscle to exercise. Expert Rev Proteomics (2011) 0.99
CCL2 and CCR2 polymorphisms are associated with markers of exercise-induced skeletal muscle damage. J Appl Physiol (1985) (2010) 0.99
PPARalpha L162V underlies variation in serum triglycerides and subcutaneous fat volume in young males. BMC Med Genet (2007) 0.99
Integrin alpha 7 beta 1 in muscular dystrophy/myopathy of unknown etiology. Am J Pathol (2002) 0.98
Genetic and clinical heterogeneity in eIF2B-related disorder. J Child Neurol (2008) 0.98
Interleukin-15 and interleukin-15R alpha SNPs and associations with muscle, bone, and predictors of the metabolic syndrome. Cytokine (2008) 0.98
Decreased asialotransferrin in cerebrospinal fluid of patients with childhood-onset ataxia and central nervous system hypomyelination/vanishing white matter disease. Clin Chem (2005) 0.98
Exercise training increases electron and substrate shuttling proteins in muscle of overweight men and women with the metabolic syndrome. J Appl Physiol (1985) (2004) 0.98
Relationships between circadian rhythms and modulation of gene expression by glucocorticoids in skeletal muscle. Am J Physiol Regul Integr Comp Physiol (2008) 0.98
Sexual dimorphism in immune response genes as a function of puberty. BMC Immunol (2006) 0.98