Published in BMC Bioinformatics on February 27, 2013
Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee. Proc Natl Acad Sci U S A (2014) 1.02
Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line. Cell Stress Chaperones (2015) 0.85
Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus. BMC Evol Biol (2015) 0.81
Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq. BMC Genomics (2016) 0.79
Current transcriptomics in pig immunity research. Mamm Genome (2014) 0.78
A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor. Bioinform Biol Insights (2015) 0.77
Cross-species gene expression analysis of species specific differences in the preclinical assessment of pharmaceutical compounds. PLoS One (2014) 0.77
Rethinking Meta-Analysis: Applications for Air Pollution Data and Beyond. Risk Anal (2015) 0.76
Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds. BMC Genomics (2015) 0.75
Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies. Cell Syst (2017) 0.75
Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol (2004) 101.91
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03
OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res (2003) 33.03
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
A gene-coexpression network for global discovery of conserved genetic modules. Science (2003) 18.75
Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet (2006) 16.12
NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res (2010) 14.38
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res (2006) 11.43
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science (2010) 11.37
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics (2006) 11.33
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2010) 10.97
An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet (2004) 10.92
Heat-shock proteins, molecular chaperones, and the stress response: evolutionary and ecological physiology. Annu Rev Physiol (1999) 9.95
Noise in gene expression: origins, consequences, and control. Science (2005) 9.64
The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J (2007) 8.09
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res (2010) 7.67
Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell (2003) 6.04
Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One (2007) 5.62
Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS One (2007) 5.03
From signatures to models: understanding cancer using microarrays. Nat Genet (2005) 4.29
InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res (2007) 4.15
The heat shock response: life on the verge of death. Mol Cell (2010) 3.71
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol (2006) 3.68
Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics (2009) 3.50
Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med (2008) 3.31
Differences between human and mouse embryonic stem cells. Dev Biol (2004) 3.30
L2L: a simple tool for discovering the hidden significance in microarray expression data. Genome Biol (2005) 3.27
The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res (2010) 3.15
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc Natl Acad Sci U S A (2010) 2.85
The altered evolutionary trajectories of gene duplicates. Trends Genet (2004) 2.81
Vitellogenesis as a biomarker for estrogenic contamination of the aquatic environment. Environ Health Perspect (1995) 2.67
Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res (2012) 2.54
Duplicate genes increase gene expression diversity within and between species. Nat Genet (2004) 2.40
Stress-activated genomic expression changes serve a preparative role for impending stress in yeast. Mol Biol Cell (2008) 2.27
How confident can we be that orthologs are similar, but paralogs differ? Trends Genet (2009) 2.21
Computational methods for Gene Orthology inference. Brief Bioinform (2011) 2.16
A new type of stochastic dependence revealed in gene expression data. Stat Appl Genet Mol Biol (2006) 2.15
Meta-analysis of microarray data on pancreatic cancer defines a set of commonly dysregulated genes. Oncogene (2005) 1.89
Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res (2004) 1.88
Prediction of human disease genes by human-mouse conserved coexpression analysis. PLoS Comput Biol (2008) 1.81
Wild intersex roach (Rutilus rutilus) have reduced fertility. Biol Reprod (2002) 1.69
Full genome gene expression analysis of the heat stress response in Drosophila melanogaster. Cell Stress Chaperones (2005) 1.63
Toxicogenomic profiling of the hepatic tumor promoters indole-3-carbinol, 17beta-estradiol and beta-naphthoflavone in rainbow trout. Toxicol Sci (2005) 1.57
List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists. Gene (2005) 1.53
Comparison study of microarray meta-analysis methods. BMC Bioinformatics (2010) 1.49
Gene expression responses of European flounder (Platichthys flesus) to 17-beta estradiol. Toxicol Lett (2006) 1.37
Pharmaceutical industry effluent diluted 1:500 affects global gene expression, cytochrome P450 1A activity, and plasma phosphate in fish. Environ Toxicol Chem (2009) 1.29
Genome-wide survey and expression profiling of heat shock proteins and heat shock factors revealed overlapped and stress specific response under abiotic stresses in rice. Plant Sci (2009) 1.27
Eggshell and egg yolk proteins in fish: hepatic proteins for the next generation: oogenetic, population, and evolutionary implications of endocrine disruption. Comp Hepatol (2003) 1.20
Gene Aging Nexus: a web database and data mining platform for microarray data on aging. Nucleic Acids Res (2006) 1.14
Combined analysis reveals a core set of cycling genes. Genome Biol (2007) 1.10
Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. BMC Genomics (2008) 1.08
Weighted analysis of general microarray experiments. BMC Bioinformatics (2007) 1.03
Mercury-induced hepatotoxicity in zebrafish: in vivo mechanistic insights from transcriptome analysis, phenotype anchoring and targeted gene expression validation. BMC Genomics (2010) 1.03
Meta-analysis of genome-wide gene expression differences in onset and maintenance phases of genetic hypertension. Hypertension (2010) 1.02
The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data. PLoS Comput Biol (2012) 1.02
Identifying cycling genes by combining sequence homology and expression data. Bioinformatics (2006) 0.97
Microarray analysis in the zebrafish (Danio rerio) liver and telencephalon after exposure to low concentration of 17alpha-ethinylestradiol. Aquat Toxicol (2007) 0.96
Transcriptional profiles of human epithelial cells in response to heat: computational evidence for novel heat shock proteins. Shock (2008) 0.90
Cross-species queries of large gene expression databases. Bioinformatics (2010) 0.89
Sensitive and robust gene expression changes in fish exposed to estrogen--a microarray approach. BMC Genomics (2007) 0.89
Role of pituitary hormones on 17alpha-ethinylestradiol-induced cholestasis in rat. J Pharmacol Exp Ther (2006) 0.89
A comparison of parametric versus permutation methods with applications to general and temporal microarray gene expression data. Bioinformatics (2003) 0.88
Weighted analysis of paired microarray experiments. Stat Appl Genet Mol Biol (2005) 0.88
Quality optimised analysis of general paired microarray experiments. Stat Appl Genet Mol Biol (2006) 0.87
A cross-species analysis of the rodent uterotrophic program: elucidation of conserved responses and targets of estrogen signaling. Physiol Genomics (2005) 0.87
Analysis of the heat shock response in mouse liver reveals transcriptional dependence on the nuclear receptor peroxisome proliferator-activated receptor alpha (PPARalpha). BMC Genomics (2010) 0.86
An integrated transcriptomic and proteomic approach characterizing estrogenic and metabolic effects of 17 alpha-ethinylestradiol in zebrafish (Danio rerio). Gen Comp Endocrinol (2010) 0.85
Exposure to xenobiotic compounds: looking for new biomarkers. Gen Comp Endocrinol (2003) 0.84
Dynamics of estrogen biomarker responses in rainbow trout exposed to 17beta-estradiol and 17alpha-ethinylestradiol. Environ Toxicol Chem (2003) 0.81
Gene expression profiling identifies key estradiol targets in the frontal cortex of the rat. Endocrinology (2010) 0.80
Cross species expression analysis of innate immune response. J Comput Biol (2010) 0.77
High-resolution yeast phenomics resolves different physiological features in the saline response. Proc Natl Acad Sci U S A (2003) 2.85
Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS One (2011) 1.74
Effluent from bulk drug production is toxic to aquatic vertebrates. Environ Toxicol Chem (2009) 1.67
The scourge of antibiotic resistance: the important role of the environment. Clin Infect Dis (2013) 1.64
Contamination of surface, ground, and drinking water from pharmaceutical production. Environ Toxicol Chem (2009) 1.61
Expression profiling of GIST: CD133 is associated with KIT exon 11 mutations, gastric location and poor prognosis. Int J Cancer (2011) 1.59
Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics (2009) 1.48
Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment. Environ Health Perspect (2013) 1.42
Pharmaceuticals and personal care products in the environment: what are the big questions? Environ Health Perspect (2012) 1.38
BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Res (2013) 1.35
Pharmaceutical industry effluent diluted 1:500 affects global gene expression, cytochrome P450 1A activity, and plasma phosphate in fish. Environ Toxicol Chem (2009) 1.29
PROPHECY--a database for high-resolution phenomics. Nucleic Acids Res (2005) 1.26
Evolutionary conservation of human drug targets in organisms used for environmental risk assessments. Environ Sci Technol (2008) 1.25
mRNA stability changes precede changes in steady-state mRNA amounts during hyperosmotic stress. RNA (2009) 1.25
Human Health Risk Assessment (HHRA) for environmental development and transfer of antibiotic resistance. Environ Health Perspect (2013) 1.13
Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiol Genomics (2007) 1.12
Influence of humans on evolution and mobilization of environmental antibiotic resistome. Emerg Infect Dis (2013) 1.10
Genetic basis of arsenite and cadmium tolerance in Saccharomyces cerevisiae. BMC Genomics (2009) 1.07
Weighted analysis of general microarray experiments. BMC Bioinformatics (2007) 1.03
Diclofenac in fish: blood plasma levels similar to human therapeutic levels affect global hepatic gene expression. Environ Toxicol Chem (2011) 1.01
Genome-scale modeling of the protein secretory machinery in yeast. PLoS One (2013) 0.96
Distribution and hormonal regulation of membrane progesterone receptors beta and gamma in ciliated epithelial cells of mouse and human fallopian tubes. Reprod Biol Endocrinol (2009) 0.96
Distinct cytoplasmic and nuclear functions of the stress induced protein DDIT3/CHOP/GADD153. PLoS One (2012) 0.95
Progesterone-receptor antagonists and statins decrease de novo cholesterol synthesis and increase apoptosis in rat and human periovulatory granulosa cells in vitro. Biol Reprod (2004) 0.93
PROPHECY--a yeast phenome database, update 2006. Nucleic Acids Res (2006) 0.93
Evolutionary forces act on promoter length: identification of enriched cis-regulatory elements. Mol Biol Evol (2009) 0.93
A treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi-drug resistant integron-bearing bacteria. PLoS One (2013) 0.93
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals. BMC Genomics (2005) 0.93
Fluoroquinolones and qnr genes in sediment, water, soil, and human fecal flora in an environment polluted by manufacturing discharges. Environ Sci Technol (2014) 0.92
Sensitive and robust gene expression changes in fish exposed to estrogen--a microarray approach. BMC Genomics (2007) 0.89
Rapid effects of progesterone on ciliary beat frequency in the mouse fallopian tube. Reprod Biol Endocrinol (2010) 0.88
Weighted analysis of paired microarray experiments. Stat Appl Genet Mol Biol (2005) 0.88
Membrane progesterone receptor gamma: tissue distribution and expression in ciliated cells in the fallopian tube. Mol Reprod Dev (2007) 0.87
A metabolomics approach to elucidate effects of food deprivation in juvenile rainbow trout (Oncorhynchus mykiss). Am J Physiol Regul Integr Comp Physiol (2010) 0.87
Using NMR metabolomics to identify responses of an environmental estrogen in blood plasma of fish. Aquat Toxicol (2006) 0.87
Quality optimised analysis of general paired microarray experiments. Stat Appl Genet Mol Biol (2006) 0.87
Acquired genetic mechanisms of a multiresistant bacterium isolated from a treatment plant receiving wastewater from antibiotic production. Appl Environ Microbiol (2013) 0.87
Genetic pleiotropy in Saccharomyces cerevisiae quantified by high-resolution phenotypic profiling. Mol Genet Genomics (2006) 0.87
Anaerobic α-amylase production and secretion with fumarate as the final electron acceptor in Saccharomyces cerevisiae. Appl Environ Microbiol (2013) 0.87
Therapeutic levels of levonorgestrel detected in blood plasma of fish: results from screening rainbow trout exposed to treated sewage effluents. Environ Sci Technol (2010) 0.86
GC-MS analysis and ecotoxicological risk assessment of triclosan, carbamazepine and parabens in Indian rivers. J Hazard Mater (2010) 0.86
The impact of temperature on the metabolome and endocrine metabolic signals in Atlantic salmon (Salmo salar). Comp Biochem Physiol A Mol Integr Physiol (2012) 0.85
Octopamine receptors from the barnacle balanus improvisus are activated by the alpha2-adrenoceptor agonist medetomidine. Mol Pharmacol (2010) 0.85
Reproducible (1)H NMR-based metabolomic responses in fish exposed to different sewage effluents in two separate studies. Environ Sci Technol (2011) 0.84
Dominant role of nuclear progesterone receptor in the control of rat periovulatory granulosa cell apoptosis. Biol Reprod (2009) 0.83
Transcriptional and metabolic data integration and modeling for identification of active pathways. Biostatistics (2012) 0.83
Predicted critical environmental concentrations for 500 pharmaceuticals. Regul Toxicol Pharmacol (2010) 0.83
A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences. BMC Genomics (2012) 0.82
Variations in bioconcentration of human pharmaceuticals from sewage effluents into fish blood plasma. Environ Toxicol Pharmacol (2007) 0.81
Oral exposure to industrial effluent with exceptionally high levels of drugs does not indicate acute toxic effects in rats. Environ Toxicol Chem (2013) 0.80
Contributions from metabolomics to fish research. Mol Biosyst (2008) 0.80
The classical progesterone receptor mediates the rapid reduction of fallopian tube ciliary beat frequency by progesterone. Reprod Biol Endocrinol (2013) 0.80
Management of the endoplasmic reticulum stress by activation of the heat shock response in yeast. FEMS Yeast Res (2013) 0.80
Effluent from drug manufacturing affects cytochrome P450 1 regulation and function in fish. Chemosphere (2012) 0.80
Transcriptional effects of progesterone receptor antagonist in rat granulosa cells. Mol Cell Endocrinol (2009) 0.80
Non-steroidal anti-inflammatory drugs in Indian rivers. Environ Sci Pollut Res Int (2013) 0.79
Hepatic transcriptome profiling indicates differential mRNA expression of apoptosis and immune related genes in eelpout (Zoarces viviparus) caught at Göteborg harbor, Sweden. Aquat Toxicol (2012) 0.79
GC-MS determination of bisphenol A and alkylphenol ethoxylates in river water from India and their ecotoxicological risk assessment. Ecotoxicol Environ Saf (2013) 0.79
The outcome spectrum of multiple sclerosis: disability, mortality, and a cluster of predictors from onset. J Neurol (2015) 0.78
Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae. BMC Syst Biol (2014) 0.78
Antimicrobial activity of filamentous fungi isolated from highly antibiotic-contaminated river sediment. Infect Ecol Epidemiol (2012) 0.77
Underappreciated role of regionally poor water quality on globally increasing antibiotic resistance. Environ Sci Technol (2014) 0.77
Does waterborne citalopram affect the aggressive and sexual behaviour of rainbow trout and guppy? J Hazard Mater (2011) 0.77
Aqueous and lipid nuclear magnetic resonance metabolomic profiles of the earthworm Aporrectodea caliginosa show potential as an indicator species for environmental metabolomics. Environ Toxicol Chem (2014) 0.77
Upper Respiratory Infections and MRI Activity in Relapsing-Remitting Multiple Sclerosis. Neuroepidemiology (2015) 0.76
Fish models in toxicology. Zebrafish (2007) 0.76
Changes in HbA1c and frequency of measuring HbA1c and adjusting glucose-lowering medications in the 10 years following diagnosis of type 2 diabetes: a population-based study in the UK. Diabetologia (2014) 0.76
Does ketoprofen or diclofenac pose the lowest risk to fish? J Hazard Mater (2012) 0.76
Apoptotic effects of a progesterone receptor antagonist on rat granulosa cells are not mediated via reduced protein isoprenylation. Mol Reprod Dev (2007) 0.76
Urinary detection times and metabolite/parent compound ratios after a single dose of buprenorphine. J Anal Toxicol (2008) 0.75
Testing of chromosomal clumping of gene properties. Stat Appl Genet Mol Biol (2009) 0.75
[Cheaper drugs without environmental considerations can cost us dearly. Sweden proposes tightening of international regulations to reduce emissions]. Lakartidningen (2012) 0.75
Physiology and mRNA expression in rainbow trout (Oncorhynchus mykiss) after long-term exposure to the new antifoulant medetomidine. Comp Biochem Physiol C Toxicol Pharmacol (2011) 0.75
Global hepatic gene expression in rainbow trout exposed to sewage effluents: a comparison of different sewage treatment technologies. Sci Total Environ (2012) 0.75
[Good drugs at the wrong place can affect nature and lead to resistance]. Lakartidningen (2014) 0.75
[Systems biology can radically change health care. Basis for individualized prediction, prevention and treatment]. Lakartidningen (2007) 0.75