Published in BMC Biotechnol on March 08, 2004
Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities. Appl Environ Microbiol (2006) 1.17
Model selection and efficiency testing for normalization of cDNA microarray data. Genome Biol (2004) 1.10
Performance and clinical evaluation of the 92-gene real-time PCR assay for tumor classification. J Mol Diagn (2011) 1.08
Expression profiling of laser-microdissected intrapulmonary arteries in hypoxia-induced pulmonary hypertension. Respir Res (2005) 1.07
Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray. BMC Genomics (2006) 0.88
Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design. BMC Biotechnol (2016) 0.84
An adaptable method using human mixed tissue ratiometric controls for benchmarking performance on gene expression microarrays in clinical laboratories. BMC Biotechnol (2011) 0.83
Effects of scanning sensitivity and multiple scan algorithms on microarray data quality. BMC Bioinformatics (2010) 0.82
HspR mutations are naturally selected in Bifidobacterium longum when successive heat shock treatments are applied. J Bacteriol (2010) 0.81
RNA-seq as a powerful tool for penaeid shrimp genetic progress. Front Genet (2014) 0.81
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03
TM4: a free, open-source system for microarray data management and analysis. Biotechniques (2003) 38.02
Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol (2002) 4.67
TM4 microarray software suite. Methods Enzymol (2006) 13.78
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics (2003) 12.00
Multiple-laboratory comparison of microarray platforms. Nat Methods (2005) 11.74
Genesis: cluster analysis of microarray data. Bioinformatics (2002) 10.50
Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol (2007) 10.49
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics (2006) 7.53
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Independence and reproducibility across microarray platforms. Nat Methods (2005) 6.26
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics (2011) 5.45
Marked genomic differences characterize primary and secondary glioblastoma subtypes and identify two distinct molecular and clinical secondary glioblastoma entities. Cancer Res (2006) 4.80
Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol (2002) 4.67
Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature (2012) 4.35
Structural flexibility in the Burkholderia mallei genome. Proc Natl Acad Sci U S A (2004) 4.13
Standards for microarray data. Science (2002) 4.11
Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res (2002) 3.93
Open source software for the analysis of microarray data. Biotechniques (2003) 3.89
Submission of microarray data to public repositories. PLoS Biol (2004) 3.83
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol (2008) 3.43
Standards for microarray data: an open letter. Environ Health Perspect (2004) 3.15
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res (2003) 3.12
Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample. PLoS One (2008) 2.92
What would you do if you could sequence everything? Nat Biotechnol (2008) 2.89
Molecular staging for survival prediction of colorectal cancer patients. J Clin Oncol (2005) 2.88
A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Nature (2011) 2.82
HMGB1 promotes drug resistance in osteosarcoma. Cancer Res (2011) 2.82
The underlying principles of scientific publication. Bioinformatics (2002) 2.79
Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling. J Natl Cancer Inst (2002) 2.77
GeneSigDB--a curated database of gene expression signatures. Nucleic Acids Res (2009) 2.65
AAPM recommendations on dose prescription and reporting methods for permanent interstitial brachytherapy for prostate cancer: report of Task Group 137. Med Phys (2009) 2.62
Universal RNA reference materials for gene expression. Clin Chem (2004) 2.53
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet (2006) 2.48
A three-gene model to robustly identify breast cancer molecular subtypes. J Natl Cancer Inst (2012) 2.34
Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies. BMC Genomics (2005) 2.34
Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. PLoS One (2009) 2.21
Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Res (2003) 2.15
Multi-platform, multi-site, microarray-based human tumor classification. Am J Pathol (2004) 2.14
Functional classification analysis of somatically mutated genes in human breast and colorectal cancers. Genomics (2008) 2.11
Sub-telomere directed gene expression during initiation of invasive aspergillosis. PLoS Pathog (2008) 2.09
Selective sensitivity to carboxyamidotriazole by human tumor cell lines with DNA mismatch repair deficiency. Int J Cancer (2008) 2.09
Physiogenomic resources for rat models of heart, lung and blood disorders. Nat Genet (2006) 2.05
Voltage-gated Na+ channel SCN5A is a key regulator of a gene transcriptional network that controls colon cancer invasion. Cancer Res (2010) 2.01
Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome. Cancer Res (2008) 1.99
Uneven chromosome contraction and expansion in the maize genome. Genome Res (2006) 1.96
Unique cell surface expression of receptor tyrosine kinase ROR1 in human B-cell chronic lymphocytic leukemia. Clin Cancer Res (2008) 1.95
Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. Plant Physiol (2005) 1.94
Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biol (2003) 1.94
Comparative analyses of potato expressed sequence tag libraries. Plant Physiol (2003) 1.84
Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue. Breast Cancer Res Treat (2009) 1.83
Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol (2006) 1.82
Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database. Genome Biol (2003) 1.82
The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Proc Natl Acad Sci U S A (2003) 1.79
Orthologous gene-expression profiling in multi-species models: search for candidate genes. Genome Biol (2004) 1.77
Comparison and validation of genomic predictors for anticancer drug sensitivity. J Am Med Inform Assoc (2013) 1.73
Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes. BMC Genomics (2006) 1.73
Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinformatics (2009) 1.71
survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinformatics (2011) 1.70
Contribution of gene loss to the pathogenic evolution of Burkholderia pseudomallei and Burkholderia mallei. Infect Immun (2004) 1.70
Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2014) 1.63
A panel of urinary biomarkers to monitor reversibility of renal injury and a serum marker with improved potential to assess renal function. Nat Biotechnol (2010) 1.62
A pilot study to detect high mobility group box 1 and heat shock protein 72 in cerebrospinal fluid of pediatric patients with meningitis. Crit Care Med (2008) 1.62
E(mu)-TCL1 mice represent a model for immunotherapeutic reversal of chronic lymphocytic leukemia-induced T-cell dysfunction. Proc Natl Acad Sci U S A (2009) 1.61
Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. Proc Natl Acad Sci U S A (2011) 1.59
Polymorphisms of ERCC1 C118T/C8092A and MDR1 C3435T predict outcome of platinum-based chemotherapies in advanced non-small cell lung cancer: a meta-analysis. Arch Med Res (2011) 1.55
In vivo cancer diagnosis with optical spectroscopy and acoustically induced blood stasis using a murine MCa35 model. Med Phys (2006) 1.54
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res (2011) 1.54
Viral perturbations of host networks reflect disease etiology. PLoS Comput Biol (2012) 1.54
Variance of gene expression identifies altered network constraints in neurological disease. PLoS Genet (2011) 1.53
Standardizing the standards. Mol Syst Biol (2006) 1.49
Identification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer. Clin Cancer Res (2009) 1.48
Luffa echinata Roxb. induces human colon cancer cell (HT-29) death by triggering the mitochondrial apoptosis pathway. Molecules (2012) 1.48
Autophagy regulates myeloid cell differentiation by p62/SQSTM1-mediated degradation of PML-RARα oncoprotein. Autophagy (2011) 1.47
Response to Shields: 'MIAME, we have a problem'. Trends Genet (2006) 1.46
Molecular profiling of LGL leukemia reveals role of sphingolipid signaling in survival of cytotoxic lymphocytes. Blood (2008) 1.45
NOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML. Blood (2014) 1.44
An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). BMC Bioinformatics (2009) 1.43
PCB association with model phospholipid bilayers. Environ Sci Technol (2008) 1.42
Experimental and clinical observations of 99mTc-MIBI uptake correlate with P-glycoprotein expression in lung cancer. Nucl Med Commun (2007) 1.41
Transcriptional profiling identifies a role for BrlA in the response to nitrogen depletion and for StuA in the regulation of secondary metabolite clusters in Aspergillus fumigatus. Eukaryot Cell (2008) 1.41
Seeded Bayesian Networks: constructing genetic networks from microarray data. BMC Syst Biol (2008) 1.40
Vivo motion and force measurement of surgical needle intervention during prostate brachytherapy. Med Phys (2006) 1.36
The early stage of bacterial genome-reductive evolution in the host. PLoS Pathog (2010) 1.35
Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome. Clin Cancer Res (2012) 1.35
Hypoxia-induced down-regulation of microRNA-34a promotes EMT by targeting the Notch signaling pathway in tubular epithelial cells. PLoS One (2012) 1.34
RNA-Seq analysis in MeV. Bioinformatics (2011) 1.33
Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories. BMC Genomics (2008) 1.33
Data standards: a call to action. OMICS (2006) 1.31
Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer. PLoS One (2012) 1.31
Histone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction. J Clin Invest (2013) 1.29
Beta-TCP bone graft substitutes in a bilateral rabbit tibial defect model. Biomaterials (2008) 1.29
Microarray blob-defect removal improves array analysis. Bioinformatics (2007) 1.28
Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS (2006) 1.26