Published in Environ Mol Mutagen on August 01, 2013
Biomarkers of coronary artery disease: the promise of the transcriptome. Curr Cardiol Rep (2014) 0.84
Application of toxicogenomic profiling to evaluate effects of benzene and formaldehyde: from yeast to human. Ann N Y Acad Sci (2014) 0.81
Techniques and Approaches to Genetic Analyses in Nephrological Disorders. J Pediatr Genet (2015) 0.75
Expression profile of ZFX isoform3/variant 5 in gastric cancer tissues and its association with tumor size. Iran J Basic Med Sci (2014) 0.75
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet (2001) 63.36
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
Random-effects models for longitudinal data. Biometrics (1982) 54.17
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
Why most published research findings are false. PLoS Med (2005) 41.68
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
Genetic analysis of genome-wide variation in human gene expression. Nature (2004) 27.28
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature (2010) 23.55
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics (2010) 19.86
NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res (2008) 17.35
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res (2012) 15.84
ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res (2003) 15.48
Transcriptome genetics using second generation sequencing in a Caucasian population. Nature (2010) 14.85
NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res (2010) 14.38
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
Non-coding RNAs in human disease. Nat Rev Genet (2011) 11.40
The genetic association database. Nat Genet (2004) 11.29
Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet (2007) 11.09
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18
DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics (2012) 9.31
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res (2010) 9.08
ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic Acids Res (2006) 8.92
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell (2010) 8.66
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
Host-gut microbiota metabolic interactions. Science (2012) 7.73
Differential expression in RNA-seq: a matter of depth. Genome Res (2011) 7.13
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
ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res (2005) 6.73
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol (2004) 6.67
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol (2011) 6.54
The impact of the gut microbiota on human health: an integrative view. Cell (2012) 6.01
Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol (2013) 5.89
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
Complementing the genome with an "exposome": the outstanding challenge of environmental exposure measurement in molecular epidemiology. Cancer Epidemiol Biomarkers Prev (2005) 5.51
Non-coding RNAs: regulators of disease. J Pathol (2010) 5.12
ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res (2012) 4.91
Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc Natl Acad Sci U S A (2004) 4.89
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res (2005) 4.86
Cell type-specific gene expression differences in complex tissues. Nat Methods (2010) 4.75
Epidemiology. Environment and disease risks. Science (2010) 4.64
Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer. Nat Med (2007) 4.63
Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol (2011) 4.57
Opinion: understanding 'global' systems biology: metabonomics and the continuum of metabolism. Nat Rev Drug Discov (2003) 4.46
Hematotoxicity in workers exposed to low levels of benzene. Science (2004) 4.19
A window into third-generation sequencing. Hum Mol Genet (2010) 4.07
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol (2012) 3.83
Estimation of direct causal effects. Epidemiology (2006) 3.78
Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics (2012) 3.74
Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet (2011) 3.73
A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood (2009) 3.63
PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol (2011) 3.57
Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol (2009) 3.30
Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell (2013) 3.26
MicroRNA responses to cellular stress. Cancer Res (2006) 3.13
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS One (2009) 2.98
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics (2010) 2.95
RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics (2012) 2.94
The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool. J Lab Clin Med (2006) 2.90
The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res (2012) 2.72
Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types. Pharmacogenomics J (2004) 2.60
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res (2012) 2.47
Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nat Genet (2009) 2.38
MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proc Natl Acad Sci U S A (2009) 2.37
Gene expression profiling of human lung tissue from smokers with severe emphysema. Am J Respir Cell Mol Biol (2004) 2.33
Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol (2010) 2.32
Effects of cigarette smoke on the human oral mucosal transcriptome. Cancer Prev Res (Phila) (2010) 2.30
Design and validation issues in RNA-seq experiments. Brief Bioinform (2011) 2.26
Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. Genome Biol (2007) 2.20
Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing. BMC Genomics (2012) 2.19
A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs. PLoS Genet (2008) 2.19
Smoking-induced gene expression changes in the bronchial airway are reflected in nasal and buccal epithelium. BMC Genomics (2008) 2.11
A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res (2010) 2.07
Disruption of microRNA expression in human airway cells by diesel exhaust particles is linked to tumorigenesis-associated pathways. Environ Health Perspect (2009) 1.98
Transcriptome analysis using next-generation sequencing. Curr Opin Biotechnol (2012) 1.97
Detection and removal of biases in the analysis of next-generation sequencing reads. PLoS One (2011) 1.91
Gene expression profiles in peripheral blood mononuclear cells can distinguish patients with non-small cell lung cancer from patients with nonmalignant lung disease. Cancer Res (2009) 1.86
CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Res (2007) 1.80
Role of human noncoding RNAs in the control of tumorigenesis. Proc Natl Acad Sci U S A (2009) 1.76
Between a chicken and a grape: estimating the number of human genes. Genome Biol (2010) 1.72
Genetic and environmental pathways to complex diseases. BMC Syst Biol (2009) 1.67
Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer. Nucleic Acids Res (2008) 1.63
Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq. Cancer Prev Res (Phila) (2011) 1.61
Down-regulation of the notch pathway in human airway epithelium in association with smoking and chronic obstructive pulmonary disease. Am J Respir Crit Care Med (2008) 1.57
Global gene expression profiling in whole-blood samples from individuals exposed to metal fumes. Environ Health Perspect (2005) 1.54
The Japanese toxicogenomics project: application of toxicogenomics. Mol Nutr Food Res (2010) 1.54
Global profiling and molecular characterization of alternative splicing events misregulated in lung cancer. Mol Cell Biol (2010) 1.53
An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs. PLoS One (2011) 1.53
The next-generation sequencing technology and application. Protein Cell (2010) 1.52
A highly standardized, robust, and cost-effective method for genome-wide transcriptome analysis of peripheral blood applicable to large-scale clinical trials. Genomics (2006) 1.51
Molecular signature of smoking in human lung tissues. Cancer Res (2012) 1.50
The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics. PLoS One (2012) 1.49
A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics (2010) 1.47
The dynamic epigenome and its implications in toxicology. Toxicol Sci (2007) 1.45
High-resolution transcriptome of human macrophages. PLoS One (2012) 1.42
Similarities and differences between smoking-related gene expression in nasal and bronchial epithelium. Physiol Genomics (2009) 1.42
Epidemiology. Environment and disease risks. Science (2010) 4.64
Epidemiology of myelodysplastic syndromes and chronic myeloproliferative disorders in the United States, 2001-2004, using data from the NAACCR and SEER programs. Blood (2008) 4.41
Hematotoxicity in workers exposed to low levels of benzene. Science (2004) 4.19
Genetic variation in TNF and IL10 and risk of non-Hodgkin lymphoma: a report from the InterLymph Consortium. Lancet Oncol (2006) 4.13
Tumor necrosis factor (TNF) and lymphotoxin-alpha (LTA) polymorphisms and risk of non-Hodgkin lymphoma in the InterLymph Consortium. Am J Epidemiol (2010) 2.86
Genetic variants at 6p21.33 are associated with susceptibility to follicular lymphoma. Nat Genet (2009) 2.73
Genome-wide association study of follicular lymphoma identifies a risk locus at 6p21.32. Nat Genet (2010) 2.37
Occupational exposure to formaldehyde, hematotoxicity, and leukemia-specific chromosome changes in cultured myeloid progenitor cells. Cancer Epidemiol Biomarkers Prev (2010) 2.34
An emerging role for epigenetic dysregulation in arsenic toxicity and carcinogenesis. Environ Health Perspect (2010) 2.16
Biological sample collection and processing for molecular epidemiological studies. Mutat Res (2003) 2.13
Polymorphisms and haplotypes in folate-metabolizing genes and risk of non-Hodgkin lymphoma. Blood (2004) 1.93
Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia. Nat Genet (2013) 1.85
Personalized exposure assessment: promising approaches for human environmental health research. Environ Health Perspect (2005) 1.83
Body mass index, leptin and leptin receptor polymorphisms, and non-hodgkin lymphoma. Cancer Epidemiol Biomarkers Prev (2004) 1.80
Research recommendations for selected IARC-classified agents. Environ Health Perspect (2010) 1.73
In utero origin of t(8;21) AML1-ETO translocations in childhood acute myeloid leukemia. Blood (2002) 1.71
Genetic and environmental pathways to complex diseases. BMC Syst Biol (2009) 1.67
Polymorphisms in the oxidative stress genes, superoxide dismutase, glutathione peroxidase and catalase and risk of non-Hodgkin's lymphoma. Haematologica (2006) 1.64
High-performance single cell genetic analysis using microfluidic emulsion generator arrays. Anal Chem (2010) 1.64
Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma. PLoS One (2008) 1.61
GWAS of follicular lymphoma reveals allelic heterogeneity at 6p21.32 and suggests shared genetic susceptibility with diffuse large B-cell lymphoma. PLoS Genet (2011) 1.58
Decreased urinary beta-defensin-1 expression as a biomarker of response to arsenic. Toxicol Sci (2008) 1.54
Functional FAS promoter polymorphisms are associated with increased risk of acute myeloid leukemia. Cancer Res (2003) 1.53
Critical windows of exposure to household pesticides and risk of childhood leukemia. Environ Health Perspect (2002) 1.52
Cytogenetics of Hispanic and White children with acute lymphoblastic leukemia in California. Cancer Epidemiol Biomarkers Prev (2006) 1.51
Accuracy of multiplexed Illumina platform-based single-nucleotide polymorphism genotyping compared between genomic and whole genome amplified DNA collected from multiple sources. Cancer Epidemiol Biomarkers Prev (2006) 1.45
Detailed exposure assessment for a molecular epidemiology study of benzene in two shoe factories in China. Ann Occup Hyg (2004) 1.44
Estimating the global public health implications of electricity and coal consumption. Environ Health Perspect (2011) 1.42
Using urinary biomarkers to elucidate dose-related patterns of human benzene metabolism. Carcinogenesis (2005) 1.37
Formaldehyde exposure and leukemia: a new meta-analysis and potential mechanisms. Mutat Res (2008) 1.36
Polymorphisms in the thymidylate synthase and serine hydroxymethyltransferase genes and risk of adult acute lymphocytic leukemia. Blood (2002) 1.34
Toxicogenomic profiling of chemically exposed humans in risk assessment. Mutat Res (2010) 1.30
Individual differences in arsenic metabolism and lung cancer in a case-control study in Cordoba, Argentina. Toxicol Appl Pharmacol (2010) 1.30
Formaldehyde in China: production, consumption, exposure levels, and health effects. Environ Int (2009) 1.28
Arsenic immunotoxicity: a review. Environ Health (2013) 1.27
Current understanding of the mechanism of benzene-induced leukemia in humans: implications for risk assessment. Carcinogenesis (2011) 1.26
Modeling human metabolism of benzene following occupational and environmental exposures. Cancer Epidemiol Biomarkers Prev (2006) 1.26
NQO1 polymorphisms and de novo childhood leukemia: a HuGE review and meta-analysis. Am J Epidemiol (2008) 1.25
Discovery of novel biomarkers by microarray analysis of peripheral blood mononuclear cell gene expression in benzene-exposed workers. Environ Health Perspect (2005) 1.24
The role of inflammation in age-related disease. Aging (Albany NY) (2013) 1.22
Reproductive and developmental toxicity of formaldehyde: a systematic review. Mutat Res (2011) 1.20
Aberrations in chromosomes associated with lymphoma and therapy-related leukemia in benzene-exposed workers. Environ Mol Mutagen (2007) 1.17
Site-specific translocation and evidence of postnatal origin of the t(1;19) E2A-PBX1 fusion in childhood acute lymphoblastic leukemia. Proc Natl Acad Sci U S A (2002) 1.16
Polymorphisms in innate immunity genes and risk of non-Hodgkin lymphoma. Br J Haematol (2006) 1.16
Polymorphisms in cytokine and cellular adhesion molecule genes and susceptibility to hematotoxicity among workers exposed to benzene. Cancer Res (2005) 1.16
Validation of an agricultural non-point source (AGNPS) pollution model for a catchment in the Jiulong River watershed, China. J Environ Sci (China) (2008) 1.15
Genetic variation in the folate metabolic pathway and risk of childhood leukemia. Blood (2010) 1.14
Household exposure to paint and petroleum solvents, chromosomal translocations, and the risk of childhood leukemia. Environ Health Perspect (2008) 1.13
Performance in omics analyses of blood samples in long-term storage: opportunities for the exploitation of existing biobanks in environmental health research. Environ Health Perspect (2013) 1.13
Acetylated H4K16 by MYST1 protects UROtsa cells from arsenic toxicity and is decreased following chronic arsenic exposure. Toxicol Appl Pharmacol (2009) 1.12
The nature of chromosomal aberrations detected in humans exposed to benzene. Crit Rev Toxicol (2002) 1.12
The flavoring agent dihydrocoumarin reverses epigenetic silencing and inhibits sirtuin deacetylases. PLoS Genet (2005) 1.12
Bone marrow injury induced via oxidative stress in mice by inhalation exposure to formaldehyde. PLoS One (2013) 1.11
Global gene expression profiling of a population exposed to a range of benzene levels. Environ Health Perspect (2010) 1.10
Occupational exposure to trichloroethylene is associated with a decline in lymphocyte subsets and soluble CD27 and CD30 markers. Carcinogenesis (2010) 1.10
Large-scale evaluation of candidate genes identifies associations between DNA repair and genomic maintenance and development of benzene hematotoxicity. Carcinogenesis (2008) 1.10
Ignoring and adding errors do not improve the science. Carcinogenesis (2013) 1.07
Formaldehyde and leukemia: epidemiology, potential mechanisms, and implications for risk assessment. Environ Mol Mutagen (2010) 1.07
Risk of non-Hodgkin lymphoma associated with polymorphisms in folate-metabolizing genes. Cancer Epidemiol Biomarkers Prev (2005) 1.06
Single-cell multiplex gene detection and sequencing with microfluidically generated agarose emulsions. Angew Chem Int Ed Engl (2011) 1.06
Association between mitochondrial DNA copy number, blood cell counts, and occupational benzene exposure. Environ Mol Mutagen (2008) 1.05
Improving prediction of chemical carcinogenicity by considering multiple mechanisms and applying toxicogenomic approaches. Mutat Res (2008) 1.05
A functional TNFRSF5 gene variant is associated with risk of lymphoma. Blood (2008) 1.04
Molecular biomarkers for the study of childhood leukemia. Toxicol Appl Pharmacol (2005) 1.04
Evidence that humans metabolize benzene via two pathways. Environ Health Perspect (2009) 1.03
IARC monographs: 40 years of evaluating carcinogenic hazards to humans. Environ Health Perspect (2015) 1.03
Low efficiency of the Moloney murine leukemia virus reverse transcriptase during reverse transcription of rare t(8;21) fusion gene transcripts. Biotechniques (2002) 1.03
Involvement of N-6 adenine-specific DNA methyltransferase 1 (N6AMT1) in arsenic biomethylation and its role in arsenic-induced toxicity. Environ Health Perspect (2010) 1.03
Chromosome-wide aneuploidy study (CWAS) in workers exposed to an established leukemogen, benzene. Carcinogenesis (2011) 1.03
Polymorphisms in genes involved in DNA double-strand break repair pathway and susceptibility to benzene-induced hematotoxicity. Carcinogenesis (2006) 1.02
Genetic polymorphisms and benzene metabolism in humans exposed to a wide range of air concentrations. Pharmacogenet Genomics (2007) 1.02
Decreased levels of CXC-chemokines in serum of benzene-exposed workers identified by array-based proteomics. Proc Natl Acad Sci U S A (2005) 1.02
Hypermethylation of the 5' CpG island of the FHIT gene is associated with hyperdiploid and translocation-negative subtypes of pediatric leukemia. Cancer Res (2004) 1.02