Published in BMC Genomics on May 04, 2005
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Res (2007) 2.39
The local and systemic inflammatory transcriptome after acute kidney injury. J Am Soc Nephrol (2008) 2.08
Epidermal growth factor receptor (EGFR) regulates mechanical ventilation-induced lung injury in mice. Transl Res (2008) 1.57
Genetic and pharmacologic evidence links oxidative stress to ventilator-induced lung injury in mice. Am J Respir Crit Care Med (2007) 1.41
Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results. BMC Genomics (2006) 1.40
Nuclear reprogramming in heterokaryons is rapid, extensive, and bidirectional. FASEB J (2009) 1.31
Identification of candidate genes in scleroderma-related pulmonary arterial hypertension. Transl Res (2008) 1.27
A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Res (2006) 1.17
Kidney ischemia-reperfusion injury induces caspase-dependent pulmonary apoptosis. Am J Physiol Renal Physiol (2009) 1.16
Cross-species analysis of gene expression in non-model mammals: reproducibility of hybridization on high density oligonucleotide microarrays. BMC Genomics (2007) 1.07
Cross-species hybridizations on a multi-species cDNA microarray to identify evolutionarily conserved genes expressed in oocytes. BMC Genomics (2006) 1.03
EGFR-activated signaling and actin remodeling regulate cyclic stretch-induced NRF2-ARE activation. Am J Respir Cell Mol Biol (2006) 1.02
Detection of transcriptional difference of porcine imprinted genes using different microarray platforms. BMC Genomics (2006) 0.95
Vaccinia virus-specific molecular signature in atopic dermatitis skin. J Allergy Clin Immunol (2010) 0.94
Single-species microarrays and comparative transcriptomics. PLoS One (2008) 0.86
Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection. BMC Genomics (2007) 0.85
Biomarker discovery in animal health and disease: the application of post-genomic technologies. Biomark Insights (2007) 0.81
Understanding mechanism of in vitro maturation, fertilization and culture of sheep embryoes through in silico analysis. Bioinformation (2012) 0.80
A Method to Detect Differential Gene expression in Cross-Species Hybridization Experiments at Gene and Probe Level. Biomed Inform Insights (2010) 0.77
Gene expression profiles in a rabbit model of systemic lupus erythematosus autoantibody production. J Immunol (2010) 0.76
A Method to Detect Differential Gene Expression in Cross-Species Hybridization Experiments at Gene and Probe Level. Biomed Inform Insights (2010) 0.75
Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array. Microarrays (Basel) (2014) 0.75
Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74
MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol (2003) 20.83
Concordance of the toxicity of pharmaceuticals in humans and in animals. Regul Toxicol Pharmacol (2000) 4.58
Probe selection for high-density oligonucleotide arrays. Proc Natl Acad Sci U S A (2003) 3.31
Pre-B-cell colony-enhancing factor as a potential novel biomarker in acute lung injury. Am J Respir Crit Care Med (2004) 3.19
Sphingosine 1-phosphate reduces vascular leak in murine and canine models of acute lung injury. Am J Respir Crit Care Med (2004) 2.73
A comparison of statistical methods for analysis of high density oligonucleotide array data. Bioinformatics (2003) 2.20
A novel animal model of sepsis after acute lung injury in sheep. Crit Care Med (2002) 1.95
Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations. Biotechniques (2002) 1.80
Orthologous gene-expression profiling in multi-species models: search for candidate genes. Genome Biol (2004) 1.77
A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucleic Acids Res (2004) 1.51
A road less travelled: large animal models in immunological research. Nat Rev Immunol (2003) 1.42
Cross-species hybridisation of pig RNA to human nylon microarrays. BMC Genomics (2002) 1.29
Microarray analysis of regional cellular responses to local mechanical stress in acute lung injury. Am J Physiol Lung Cell Mol Physiol (2006) 1.23
A strategy for oligonucleotide microarray probe reduction. Genome Biol (2002) 1.16
Inhibition of neuronal nitric oxide synthase by 7-nitroindazole attenuates acute lung injury in an ovine model. Am J Physiol Regul Integr Comp Physiol (2003) 1.10
Gene expression analysis of the acute phase response using a canine microarray. Toxicol Sci (2003) 1.05
Upregulation of collagens detected by gene array in a model of flow-induced pulmonary vascular remodeling. Am J Physiol Heart Circ Physiol (2002) 1.02
The predictivity of the toxicity of pharmaceuticals in humans from animal data--an interim assessment. Toxicol Lett (1998) 0.95
Endothelin receptor blockade in canine oleic acid-induced lung injury. Intensive Care Med (2003) 0.88
Cross-species application of cDNA microarrays to profile gene expression using UV-induced melanoma in Monodelphis domestica as the model system. Genomics (2004) 0.86
Study of direct lung injury by seawater in canine models. Di Yi Jun Yi Da Xue Xue Bao (2003) 0.80
The mature male sheep: a model to study the effects of nutrition on the reproductive axis. Reprod Suppl (2002) 0.80
Contribution of large animal models to the development of clinical intestinal transplantation. Acta Gastroenterol Belg (1999) 0.80
affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (2004) 32.08
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet (2010) 11.82
Multiple-laboratory comparison of microarray platforms. Nat Methods (2005) 11.74
Increased methylation variation in epigenetic domains across cancer types. Nat Genet (2011) 8.92
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics (2006) 7.53
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Intra-individual change over time in DNA methylation with familial clustering. JAMA (2008) 6.17
Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature (2010) 6.06
A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (2004) 5.99
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics (2014) 5.93
Transcriptional regulation of vascular endothelial cell responses to hypoxia by HIF-1. Blood (2004) 5.71
Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol (2005) 5.63
Frozen robust multiarray analysis (fRMA). Biostatistics (2010) 5.57
Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet (2009) 5.52
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics (2006) 5.20
Travelling waves in the occurrence of dengue haemorrhagic fever in Thailand. Nature (2004) 5.05
Preprocessing of oligonucleotide array data. Nat Biotechnol (2004) 4.70
Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci U S A (2009) 4.40
The External RNA Controls Consortium: a progress report. Nat Methods (2005) 4.24
A gene expression bar code for microarray data. Nat Methods (2007) 4.20
A framework for oligonucleotide microarray preprocessing. Bioinformatics (2010) 3.97
Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol (2014) 3.89
Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med (2010) 3.81
Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics (2012) 3.74
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol (2012) 3.62
Protective effects of sphingosine 1-phosphate in murine endotoxin-induced inflammatory lung injury. Am J Respir Crit Care Med (2004) 3.59
Activated protein C mediates novel lung endothelial barrier enhancement: role of sphingosine 1-phosphate receptor transactivation. J Biol Chem (2005) 3.54
Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Mol Cell (2006) 3.22
Sequencing technology does not eliminate biological variability. Nat Biotechnol (2011) 3.20
Pre-B-cell colony-enhancing factor as a potential novel biomarker in acute lung injury. Am J Respir Crit Care Med (2004) 3.19
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol (2012) 3.13
Magnitude-dependent regulation of pulmonary endothelial cell barrier function by cyclic stretch. Am J Physiol Lung Cell Mol Physiol (2003) 2.89
Sphingosine 1-phosphate reduces vascular leak in murine and canine models of acute lung injury. Am J Respir Crit Care Med (2004) 2.73
Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics (2010) 2.70
Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis. Am J Respir Crit Care Med (2008) 2.64
State of the Art. A structural and functional assessment of the lung via multidetector-row computed tomography: phenotyping chronic obstructive pulmonary disease. Proc Am Thorac Soc (2006) 2.60
Pulmonary endothelial cell barrier enhancement by sphingosine 1-phosphate: roles for cortactin and myosin light chain kinase. J Biol Chem (2004) 2.44
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res (2011) 2.42
Feature-level exploration of a published Affymetrix GeneChip control dataset. Genome Biol (2006) 2.39
SNP-specific array-based allele-specific expression analysis. Genome Res (2008) 2.30
Regulation of sphingosine 1-phosphate-induced endothelial cytoskeletal rearrangement and barrier enhancement by S1P1 receptor, PI3 kinase, Tiam1/Rac1, and alpha-actinin. FASEB J (2005) 2.29
Mitochondrial metabolism, redox signaling, and fusion: a mitochondria-ROS-HIF-1alpha-Kv1.5 O2-sensing pathway at the intersection of pulmonary hypertension and cancer. Am J Physiol Heart Circ Physiol (2007) 2.26
Relationship between dynamic respiratory mechanics and disease heterogeneity in sheep lavage injury. Crit Care Med (2007) 2.25
Differential regulation of pulmonary endothelial monolayer integrity by varying degrees of cyclic stretch. Am J Pathol (2006) 2.25
Association between the MUC5B promoter polymorphism and survival in patients with idiopathic pulmonary fibrosis. JAMA (2013) 2.20
Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods (2013) 2.19
Hyperoxia-induced NAD(P)H oxidase activation and regulation by MAP kinases in human lung endothelial cells. Am J Physiol Lung Cell Mol Physiol (2002) 2.18
Simvastatin attenuates vascular leak and inflammation in murine inflammatory lung injury. Am J Physiol Lung Cell Mol Physiol (2005) 2.13
Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics (2010) 2.11
DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity. Cancer Res (2008) 2.08
Characterization of the interstitial lung diseases via density-based and texture-based analysis of computed tomography images of lung structure and function. Acad Radiol (2003) 2.08
Role of Rho GTPases in thrombin-induced lung vascular endothelial cells barrier dysfunction. Microvasc Res (2004) 2.07
Consolidated strategy for the analysis of microarray spike-in data. Nucleic Acids Res (2008) 2.04
Ethnic differences and functional analysis of MET mutations in lung cancer. Clin Cancer Res (2009) 2.03
Redefining CpG islands using hidden Markov models. Biostatistics (2010) 2.03
In vitro and in vivo modulation of vascular barrier integrity by sphingosine 1-phosphate: mechanistic insights. Cell Signal (2005) 2.01
Novel role of microtubules in thrombin-induced endothelial barrier dysfunction. FASEB J (2004) 1.98
The role of the microtubules in tumor necrosis factor-alpha-induced endothelial cell permeability. Am J Respir Cell Mol Biol (2003) 1.93
Epoxycyclopentenone-containing oxidized phospholipids restore endothelial barrier function via Cdc42 and Rac. Circ Res (2004) 1.88
Novel polymorphisms in the myosin light chain kinase gene confer risk for acute lung injury. Am J Respir Cell Mol Biol (2006) 1.88
Hepatocyte growth factor enhances endothelial cell barrier function and cortical cytoskeletal rearrangement: potential role of glycogen synthase kinase-3beta. FASEB J (2002) 1.87
Use of consomic rats for genomic insights into ventilator-associated lung injury. Am J Physiol Lung Cell Mol Physiol (2007) 1.86
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. BMC Bioinformatics (2006) 1.85
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics (2009) 1.83
Global synthetic-lethality analysis and yeast functional profiling. Trends Genet (2005) 1.82
Peripheral blood mononuclear cell gene expression profiles predict poor outcome in idiopathic pulmonary fibrosis. Sci Transl Med (2013) 1.81
A variant in the promoter of MUC5B and idiopathic pulmonary fibrosis. N Engl J Med (2011) 1.81
Shear stress-mediated cytoskeletal remodeling and cortactin translocation in pulmonary endothelial cells. Am J Respir Cell Mol Biol (2002) 1.78
Orthologous gene-expression profiling in multi-species models: search for candidate genes. Genome Biol (2004) 1.77
Quantitative analysis of sphingoid base-1-phosphates as bisacetylated derivatives by liquid chromatography-tandem mass spectrometry. Anal Biochem (2005) 1.77
A multilevel model to address batch effects in copy number estimation using SNP arrays. Biostatistics (2010) 1.76
Lung endothelial heparan sulfates mediate cationic peptide-induced barrier dysfunction: a new role for the glycocalyx. Am J Physiol Lung Cell Mol Physiol (2003) 1.76
Overcoming bias and systematic errors in next generation sequencing data. Genome Med (2010) 1.75
Intracellular generation of sphingosine 1-phosphate in human lung endothelial cells: role of lipid phosphate phosphatase-1 and sphingosine kinase 1. J Biol Chem (2007) 1.74
Quantifying uncertainty in genotype calls. Bioinformatics (2009) 1.74
Significance analysis and statistical dissection of variably methylated regions. Biostatistics (2011) 1.74
Focal adhesions: paradigm for a signaling nexus. Circ Res (2006) 1.73
Endothelial cell barrier regulation by sphingosine 1-phosphate. J Cell Biochem (2004) 1.71
Microtubule disassembly induces cytoskeletal remodeling and lung vascular barrier dysfunction: role of Rho-dependent mechanisms. J Cell Physiol (2004) 1.70
Transactivation of sphingosine 1-phosphate receptors is essential for vascular barrier regulation. Novel role for hyaluronan and CD44 receptor family. J Biol Chem (2006) 1.67
A differentiation-dependent splice variant of myosin light chain kinase, MLCK1, regulates epithelial tight junction permeability. J Biol Chem (2004) 1.64
Role of sphingosine-1 phosphate in the enhancement of endothelial barrier integrity by platelet-released products. Am J Physiol Lung Cell Mol Physiol (2003) 1.64
Akt-mediated transactivation of the S1P1 receptor in caveolin-enriched microdomains regulates endothelial barrier enhancement by oxidized phospholipids. Circ Res (2009) 1.64
Tidal volume delivery during high-frequency oscillatory ventilation in adults with acute respiratory distress syndrome. Crit Care Med (2007) 1.64
DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci Transl Med (2013) 1.63
A novel molecular signature for elevated tricuspid regurgitation velocity in sickle cell disease. Am J Respir Crit Care Med (2012) 1.63
Differential effects of shear stress and cyclic stretch on focal adhesion remodeling, site-specific FAK phosphorylation, and small GTPases in human lung endothelial cells. Exp Cell Res (2004) 1.63