Published in Bioinformatics on March 23, 2007
Sex-specific and lineage-specific alternative splicing in primates. Genome Res (2009) 3.61
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
Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet (2008) 1.86
Large scale comparison of global gene expression patterns in human and mouse. Genome Biol (2010) 1.77
Optimization of gene expression by natural selection. Proc Natl Acad Sci U S A (2009) 1.50
Cross species analysis of microarray expression data. Bioinformatics (2009) 1.47
Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species. BMC Genomics (2008) 1.47
On the relation between promoter divergence and gene expression evolution. Mol Syst Biol (2008) 1.43
Characterizing natural variation using next-generation sequencing technologies. Trends Genet (2009) 1.39
Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy. Genome Biol (2008) 1.38
Cell proliferation and interleukin-6-type cytokine signaling are implicated by gene expression responses in early optic nerve head injury in rat glaucoma. Invest Ophthalmol Vis Sci (2011) 1.35
An evolutionarily conserved sexual signature in the primate brain. PLoS Genet (2008) 1.21
A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway. PLoS One (2008) 1.08
Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment. BMC Plant Biol (2010) 1.04
Using high-density exon arrays to profile gene expression in closely related species. Nucleic Acids Res (2009) 0.98
Genome-wide gene expression analysis reveals a dynamic interplay between luteotropic and luteolytic factors in the regulation of corpus luteum function in the bonnet monkey (Macaca radiata). Endocrinology (2008) 0.94
Evolution of primate gene expression: drift and corrective sweeps? Genetics (2008) 0.93
Preferential gene expression in the limbus of the vervet monkey. Mol Vis (2008) 0.92
A comprehensive analysis of gene expression evolution between humans and mice. Evol Bioinform Online (2009) 0.92
Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma. Proc Biol Sci (2013) 0.87
Single-species microarrays and comparative transcriptomics. PLoS One (2008) 0.86
Profile of whole blood gene expression following immune stimulation in a wild passerine. BMC Genomics (2014) 0.85
Gene expression profiling of preovulatory follicle in the buffalo cow: effects of increased IGF-I concentration on periovulatory events. PLoS One (2011) 0.84
Association between levels of coding sequence divergence and gene misregulation in Drosophila male hybrids. J Mol Evol (2007) 0.84
Gene expression analysis of the ovary of hybrid females of Xenopus laevis and X. muelleri. BMC Evol Biol (2008) 0.83
Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol (2008) 0.82
Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees. BMC Bioinformatics (2009) 0.82
In vitro homology search array comprehensively reveals highly conserved genes and their functional characteristics in non-sequenced species. BMC Genomics (2010) 0.82
Profiling of luteal transcriptome during prostaglandin F2-alpha treatment in buffalo cows: analysis of signaling pathways associated with luteolysis. PLoS One (2014) 0.81
Population transcriptomics: insights from Drosophila simulans, Drosophila sechellia and their hybrids. Genetica (2011) 0.81
Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors. Funct Integr Genomics (2010) 0.81
Comparative genomic analysis of light-regulated transcripts in the Solanaceae. BMC Genomics (2009) 0.81
Kernel density weighted loess normalization improves the performance of detection within asymmetrical data. BMC Bioinformatics (2011) 0.79
What to compare and how: Comparative transcriptomics for Evo-Devo. J Exp Zool B Mol Dev Evol (2015) 0.78
A Method to Detect Differential Gene expression in Cross-Species Hybridization Experiments at Gene and Probe Level. Biomed Inform Insights (2010) 0.77
Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi. BMC Evol Biol (2012) 0.77
A Method to Detect Differential Gene Expression in Cross-Species Hybridization Experiments at Gene and Probe Level. Biomed Inform Insights (2010) 0.75
Bioinformatic Analysis Identifies Three Potentially Key Differentially Expressed Genes in Peripheral Blood Mononuclear Cells of Patients with Takayasu's Arteritis. Cell J (2017) 0.75
Social regulation of the lymph node transcriptome in rhesus macaques (Macaca mulatta). Psychoneuroendocrinology (2016) 0.75
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (2009) 67.17
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
Moderated statistical tests for assessing differences in tag abundance. Bioinformatics (2007) 22.87
Generation of a functional mammary gland from a single stem cell. Nature (2006) 18.30
Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics (2007) 18.19
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers. Nat Med (2009) 10.88
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics (2013) 9.98
High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet (2008) 9.68
Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol (2010) 9.15
ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays. J Immunol Methods (2009) 9.00
A comparison of background correction methods for two-colour microarrays. Bioinformatics (2007) 8.59
voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol (2014) 8.13
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res (2012) 7.52
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol (2011) 6.48
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics (2004) 6.04
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics (2009) 5.62
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res (2010) 5.40
Control of mammary stem cell function by steroid hormone signalling. Nature (2010) 5.38
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res (2013) 4.45
Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature (2006) 4.26
Sex-specific genetic architecture of human disease. Nat Rev Genet (2008) 4.01
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc (2013) 4.00
Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors. Proc Natl Acad Sci U S A (2005) 3.66
Sex-specific and lineage-specific alternative splicing in primates. Genome Res (2009) 3.61
Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics (2006) 3.54
The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells. Nat Immunol (2011) 3.44
Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics (2009) 3.41
Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways. Breast Cancer Res (2010) 3.40
Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet (2010) 3.19
Identification of genetic variants that affect histone modifications in human cells. Science (2013) 3.11
ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics (2010) 2.86
Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science (2012) 2.79
affylmGUI: a graphical user interface for linear modeling of single channel microarray data. Bioinformatics (2006) 2.74
Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes. Genome Biol (2007) 2.68
Genomics: ENCODE explained. Nature (2012) 2.62
Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Res (2012) 2.57
Dissecting the regulatory architecture of gene expression QTLs. Genome Biol (2012) 2.51
The transcription factor IRF4 is essential for TCR affinity-mediated metabolic programming and clonal expansion of T cells. Nat Immunol (2013) 2.48
Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips. Nucleic Acids Res (2010) 2.47
Pro-inflammatory CD11c+CD206+ adipose tissue macrophages are associated with insulin resistance in human obesity. Diabetes (2010) 2.35
Aire regulates the transfer of antigen from mTECs to dendritic cells for induction of thymic tolerance. Blood (2011) 2.25
Statistical modeling of sequencing errors in SAGE libraries. Bioinformatics (2004) 2.25
Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol (2004) 2.22
Primate transcript and protein expression levels evolve under compensatory selection pressures. Science (2013) 2.18
Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics (2008) 2.14
Controls of nucleosome positioning in the human genome. PLoS Genet (2012) 2.14
Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn. Stat Appl Genet Mol Biol (2010) 2.13
Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Stat Appl Genet Mol Biol (2012) 2.13
Different noses for different people. Nat Genet (2003) 2.10
Histone deacetylase inhibitor panobinostat induces clinical responses with associated alterations in gene expression profiles in cutaneous T-cell lymphoma. Clin Cancer Res (2008) 1.94
A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genet (2011) 1.92
Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet (2008) 1.86
False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics (2011) 1.85
Microarray background correction: maximum likelihood estimation for the normal-exponential convolution. Biostatistics (2008) 1.84
Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet (2012) 1.79
Platelets kill intraerythrocytic malarial parasites and mediate survival to infection. Science (2009) 1.74
Targeting BCL-2 with the BH3 mimetic ABT-199 in estrogen receptor-positive breast cancer. Cancer Cell (2013) 1.74
The effects of EBV transformation on gene expression levels and methylation profiles. Hum Mol Genet (2011) 1.74
Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. Proc Natl Acad Sci U S A (2012) 1.73
Genomic-scale capture and sequencing of endogenous DNA from feces. Mol Ecol (2010) 1.71
Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells. Blood (2010) 1.71
Array-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosis. Am J Hum Genet (2008) 1.69
Erg is required for self-renewal of hematopoietic stem cells during stress hematopoiesis in mice. Blood (2011) 1.69
Social environment is associated with gene regulatory variation in the rhesus macaque immune system. Proc Natl Acad Sci U S A (2012) 1.63
Deregulation of MYCN, LIN28B and LET7 in a molecular subtype of aggressive high-grade serous ovarian cancers. PLoS One (2011) 1.57
Expression quantitative trait loci detected in cell lines are often present in primary tissues. Hum Mol Genet (2009) 1.57
Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray. Genome Biol (2007) 1.56
Nonequivalent gene expression and copy number alterations in high-grade serous ovarian cancers with BRCA1 and BRCA2 mutations. Clin Cancer Res (2013) 1.54
Amplicon-dependent CCNE1 expression is critical for clonogenic survival after cisplatin treatment and is correlated with 20q11 gain in ovarian cancer. PLoS One (2010) 1.54
Polycomb repressive complex 2 (PRC2) restricts hematopoietic stem cell activity. PLoS Biol (2008) 1.53
Copy number analysis identifies novel interactions between genomic loci in ovarian cancer. PLoS One (2010) 1.50
Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons. Protein Sci (2004) 1.48
Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS One (2013) 1.46
Sensitization of BCL-2-expressing breast tumors to chemotherapy by the BH3 mimetic ABT-737. Proc Natl Acad Sci U S A (2011) 1.45
Evolution of bitter taste receptors in humans and apes. Mol Biol Evol (2004) 1.45
Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). PLoS Genet (2009) 1.43
Id2 expression delineates differential checkpoints in the genetic program of CD8α+ and CD103+ dendritic cell lineages. EMBO J (2011) 1.41
Disruption of the histone acetyltransferase MYST4 leads to a Noonan syndrome-like phenotype and hyperactivated MAPK signaling in humans and mice. J Clin Invest (2011) 1.39
Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis. BMC Bioinformatics (2006) 1.39
Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res (2011) 1.36
Targeting antigen to mouse dendritic cells via Clec9A induces potent CD4 T cell responses biased toward a follicular helper phenotype. J Immunol (2011) 1.33
Global changes in the mammary epigenome are induced by hormonal cues and coordinated by Ezh2. Cell Rep (2013) 1.33
Aire-deficient C57BL/6 mice mimicking the common human 13-base pair deletion mutation present with only a mild autoimmune phenotype. J Immunol (2009) 1.32
Gata-3 negatively regulates the tumor-initiating capacity of mammary luminal progenitor cells and targets the putative tumor suppressor caspase-14. Mol Cell Biol (2011) 1.29
Identification of Pax5 target genes in early B cell differentiation. J Immunol (2008) 1.28
The molecular signature of CD8+ T cells undergoing deletional tolerance. Blood (2009) 1.27
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet (2012) 1.25
Gene expression profiling of esophageal cancer: comparative analysis of Barrett's esophagus, adenocarcinoma, and squamous cell carcinoma. Int J Cancer (2007) 1.24
An evolutionarily conserved sexual signature in the primate brain. PLoS Genet (2008) 1.21
The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity. J Exp Med (2014) 1.21
Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics (2011) 1.20
Maximal killing of lymphoma cells by DNA damage-inducing therapy requires not only the p53 targets Puma and Noxa, but also Bim. Blood (2010) 1.19
Fas-mediated neutrophil apoptosis is accelerated by Bid, Bak, and Bax and inhibited by Bcl-2 and Mcl-1. Proc Natl Acad Sci U S A (2011) 1.18
Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees. Genetics (2007) 1.18
The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. Hum Mol Genet (2012) 1.18
The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease. RNA (2013) 1.16