Published in Bioinformatics on August 25, 2007
limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res (2015) 14.81
Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res (2008) 6.15
Control of mammary stem cell function by steroid hormone signalling. Nature (2010) 5.38
Statistical issues in the analysis of Illumina data. BMC Bioinformatics (2008) 3.66
Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways. Breast Cancer Res (2010) 3.40
Diagnostic microRNA profiling in cutaneous T-cell lymphoma (CTCL). Blood (2011) 2.96
Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet (2011) 2.68
Genome-wide analysis of long noncoding RNA stability. Genome Res (2012) 2.49
Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips. Nucleic Acids Res (2010) 2.47
Hepatic gene expression profiles differentiate presymptomatic patients with mild versus severe nonalcoholic fatty liver disease. Hepatology (2013) 2.42
BM mesenchymal stromal cell-derived exosomes facilitate multiple myeloma progression. J Clin Invest (2013) 2.34
Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res (2013) 2.19
Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types. Clin Cancer Res (2010) 2.15
Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology. Nucleic Acids Res (2008) 2.11
Swift: primary data analysis for the Illumina Solexa sequencing platform. Bioinformatics (2009) 2.03
Statistical methods of background correction for Illumina BeadArray data. Bioinformatics (2009) 1.99
Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial. PLoS One (2013) 1.94
Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet (2008) 1.86
Microarray background correction: maximum likelihood estimation for the normal-exponential convolution. Biostatistics (2008) 1.84
Discovery of somatic STAT5b mutations in large granular lymphocytic leukemia. Blood (2013) 1.80
The histone variant macroH2A is an epigenetic regulator of key developmental genes. Nat Struct Mol Biol (2009) 1.75
Patterns of microRNA expression in normal and early Alzheimer's disease human temporal cortex: white matter versus gray matter. Acta Neuropathol (2010) 1.71
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res (2010) 1.71
Major cellular and physiological impacts of ocean acidification on a reef building coral. PLoS One (2012) 1.70
MicroRNAs control hepatocyte proliferation during liver regeneration. Hepatology (2010) 1.64
Role of miR-34c microRNA in the late steps of spermatogenesis. RNA (2010) 1.60
The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics (2009) 1.55
Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes. PLoS One (2013) 1.52
Let-7, mir-98 and mir-183 as biomarkers for cancer and schizophrenia [corrected]. PLoS One (2015) 1.48
KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming. Genes Dev (2010) 1.48
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
Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genet (2009) 1.46
The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry (2013) 1.44
Long-lived Indy induces reduced mitochondrial reactive oxygen species production and oxidative damage. Proc Natl Acad Sci U S A (2009) 1.42
Retracted Investigation of the hub genes and related mechanism in ovarian cancer via bioinformatics analysis. J Ovarian Res (2013) 1.42
Natural Variation in plep-1 Causes Male-Male Copulatory Behavior in C. elegans. Curr Biol (2015) 1.41
Comparison of small n statistical tests of differential expression applied to microarrays. BMC Bioinformatics (2009) 1.40
Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy. Genome Biol (2008) 1.38
Global transcriptome analysis in influenza-infected mouse lungs reveals the kinetics of innate and adaptive host immune responses. PLoS One (2012) 1.37
Interplay between HIV-1 infection and host microRNAs. Nucleic Acids Res (2011) 1.36
Genetic architecture of microRNA expression: implications for the transcriptome and complex traits. Am J Hum Genet (2012) 1.36
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. Nucleic Acids Res (2010) 1.35
Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence (2011) 1.35
Host responses to melioidosis and tuberculosis are both dominated by interferon-mediated signaling. PLoS One (2013) 1.35
Population differences in microRNA expression and biological implications. RNA Biol (2011) 1.33
Exprtarget: an integrative approach to predicting human microRNA targets. PLoS One (2010) 1.31
Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach. BMC Bioinformatics (2010) 1.30
Genome-wide microRNA profiling of human temporal lobe epilepsy identifies modulators of the immune response. Cell Mol Life Sci (2012) 1.30
Genomic analyses of musashi1 downstream targets show a strong association with cancer-related processes. J Biol Chem (2009) 1.29
Short-term calorie restriction in male mice feminizes gene expression and alters key regulators of conserved aging regulatory pathways. PLoS One (2009) 1.28
Elevated levels of circulating microRNA-200 family members correlate with serous epithelial ovarian cancer. BMC Cancer (2012) 1.27
Up-regulation of microRNAs in brain of human alcoholics. Alcohol Clin Exp Res (2011) 1.26
Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile. Nucleic Acids Res (2012) 1.25
Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog (2009) 1.24
Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data. Nucleic Acids Res (2009) 1.24
Genomic analyses of the RNA-binding protein Hu antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites. J Biol Chem (2011) 1.24
A Novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network. PLoS One (2012) 1.23
Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae. PLoS One (2010) 1.21
Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies. Mol Cell Proteomics (2010) 1.21
miR-135a contributes to paclitaxel resistance in tumor cells both in vitro and in vivo. Oncogene (2011) 1.20
The microbe-derived short chain fatty acid butyrate targets miRNA-dependent p21 gene expression in human colon cancer. PLoS One (2011) 1.20
Reversible antibiotic tolerance induced in Staphylococcus aureus by concurrent drug exposure. MBio (2015) 1.19
Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat Commun (2012) 1.19
Ecologically appropriate xenobiotics induce cytochrome P450s in Apis mellifera. PLoS One (2012) 1.19
Deep sequencing reveals novel microRNAs and regulation of microRNA expression during cell senescence. PLoS One (2011) 1.18
Human bronchial epithelial cells exposed in vitro to cigarette smoke at the air-liquid interface resemble bronchial epithelium from human smokers. Am J Physiol Lung Cell Mol Physiol (2013) 1.18
'Bois noir' phytoplasma induces significant reprogramming of the leaf transcriptome in the field grown grapevine. BMC Genomics (2009) 1.17
Seasonal differences of gene expression profiles in song sparrow (Melospiza melodia) hypothalamus in relation to territorial aggression. PLoS One (2009) 1.16
MicroRNAs show mutually exclusive expression patterns in the brain of adult male rats. PLoS One (2009) 1.16
The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease. RNA (2013) 1.16
Control of reproductive floral organ identity specification in Arabidopsis by the C function regulator AGAMOUS. Plant Cell (2013) 1.15
Aneuploid chromosomes are highly unstable during DNA transformation of Candida albicans. Eukaryot Cell (2009) 1.15
Estimating the proportion of microarray probes expressed in an RNA sample. Nucleic Acids Res (2010) 1.14
MicroRNA expression profiles of whole blood in lung adenocarcinoma. PLoS One (2012) 1.13
Making informed choices about microarray data analysis. PLoS Comput Biol (2010) 1.13
An RNAi screen reveals intestinal regulators of branching morphogenesis, differentiation, and stem cell proliferation in planarians. Dev Cell (2012) 1.12
miR-210 has an antiapoptotic effect in pulmonary artery smooth muscle cells during hypoxia. Am J Physiol Lung Cell Mol Physiol (2012) 1.09
Gene expression during Drosophila melanogaster egg development before and after reproductive diapause. BMC Genomics (2009) 1.07
Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses. BMC Genomics (2011) 1.07
MicroRNA signatures in tumor tissue related to angiogenesis in non-small cell lung cancer. PLoS One (2012) 1.07
Reprogramming of the microRNA transcriptome mediates resistance to rapamycin. J Biol Chem (2013) 1.06
MicroRNA-33a mediates the regulation of high mobility group AT-hook 2 gene (HMGA2) by thyroid transcription factor 1 (TTF-1/NKX2-1). J Biol Chem (2013) 1.06
Comparative transcript profiling of Candida albicans and Candida dubliniensis identifies SFL2, a C. albicans gene required for virulence in a reconstituted epithelial infection model. Eukaryot Cell (2009) 1.05
Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. Nucleic Acids Res (2011) 1.05
A dual-species co-cultivation system to study the interactions between Roseobacters and dinoflagellates. Front Microbiol (2014) 1.04
Fis is essential for capsule production in Pasteurella multocida and regulates expression of other important virulence factors. PLoS Pathog (2010) 1.03
How microRNA and transcription factor co-regulatory networks affect osteosarcoma cell proliferation. PLoS Comput Biol (2013) 1.03
Stone formation in peach fruit exhibits spatial coordination of the lignin and flavonoid pathways and similarity to Arabidopsis dehiscence. BMC Biol (2010) 1.03
Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Mol Biosyst (2013) 1.02
Transcriptomic analyses during the transition from biomass production to lipid accumulation in the oleaginous yeast Yarrowia lipolytica. PLoS One (2011) 1.02
Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. Mol Cell Proteomics (2010) 1.02
RNA helicase DDX5 regulates microRNA expression and contributes to cytoskeletal reorganization in basal breast cancer cells. Mol Cell Proteomics (2011) 1.01
miR-142-3p balances proliferation and differentiation of mesenchymal cells during lung development. Development (2014) 1.01
HPV-related methylation signature predicts survival in oropharyngeal squamous cell carcinomas. J Clin Invest (2013) 1.01
Early changes in gene expression induced by tobacco smoke: Evidence for the importance of estrogen within lung tissue. Cancer Prev Res (Phila) (2010) 1.01
COLOMBOS: access port for cross-platform bacterial expression compendia. PLoS One (2011) 1.00
Transcriptional profiling of chondrodysplasia growth plate cartilage reveals adaptive ER-stress networks that allow survival but disrupt hypertrophy. PLoS One (2011) 1.00
Separate-channel analysis of two-channel microarrays: recovering inter-spot information. BMC Bioinformatics (2013) 1.00
Thrombospondin 1 promotes an aggressive phenotype through epithelial-to-mesenchymal transition in human melanoma. Oncotarget (2014) 0.99
Interspecific Y chromosome introgressions disrupt testis-specific gene expression and male reproductive phenotypes in Drosophila. Proc Natl Acad Sci U S A (2011) 0.99
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (2009) 67.17
Moderated statistical tests for assessing differences in tag abundance. Bioinformatics (2007) 22.87
A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol (2010) 22.10
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
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
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
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
limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics (2004) 6.04
Control of mammary stem cell function by steroid hormone signalling. Nature (2010) 5.38
SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol (2012) 4.99
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
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
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
ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics (2010) 2.86
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
Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Res (2012) 2.57
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
ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res (2011) 2.23
Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics (2008) 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
Bpipe: a tool for running and managing bioinformatics pipelines. Bioinformatics (2012) 2.09
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
Natural selection on gene expression. Trends Genet (2006) 1.90
Terminal osteoblast differentiation, mediated by runx2 and p27KIP1, is disrupted in osteosarcoma. J Cell Biol (2004) 1.88
Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet (2008) 1.86
Microarray background correction: maximum likelihood estimation for the normal-exponential convolution. Biostatistics (2008) 1.84
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
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
Deregulation of MYCN, LIN28B and LET7 in a molecular subtype of aggressive high-grade serous ovarian cancers. PLoS One (2011) 1.57
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
Using DNA microarrays to study gene expression in closely related species. Bioinformatics (2007) 1.50
Copy number analysis identifies novel interactions between genomic loci in ovarian cancer. PLoS One (2010) 1.50
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
The comparative roles of suppressor of cytokine signaling-1 and -3 in the inhibition and desensitization of cytokine signaling. J Biol Chem (2006) 1.45
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
Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing. J Pathol (2013) 1.38
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
Gene expression profiling of esophageal cancer: comparative analysis of Barrett's esophagus, adenocarcinoma, and squamous cell carcinoma. Int J Cancer (2007) 1.24
The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity. J Exp Med (2014) 1.21
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
A 10-step guide to party conversation for bioinformaticians. Genome Biol (2013) 1.17
The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease. RNA (2013) 1.16
Estimating the proportion of microarray probes expressed in an RNA sample. Nucleic Acids Res (2010) 1.14
Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. Genome Biol (2009) 1.14
DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging. Genome Biol (2014) 1.12
Corset: enabling differential gene expression analysis for de novo assembled transcriptomes. Genome Biol (2014) 1.12
Regulation of hematopoietic stem cells by their mature progeny. Proc Natl Acad Sci U S A (2010) 1.09
A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway. PLoS One (2008) 1.08
Illumina WG-6 BeadChip strips should be normalized separately. BMC Bioinformatics (2009) 1.08
Segmental duplications contribute to gene expression differences between humans and chimpanzees. Genetics (2009) 1.06
Effective adjunctive therapy by an innate defense regulatory peptide in a preclinical model of severe malaria. Sci Transl Med (2012) 1.05
Condensin I associates with structural and gene regulatory regions in vertebrate chromosomes. Nat Commun (2013) 1.02
RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome. Genome Biol (2013) 1.02
Genome-wide DNA methylation analysis identifies hypomethylated genes regulated by FOXP3 in human regulatory T cells. Blood (2013) 1.01
Fine mapping of Leishmania major susceptibility Locus lmr2 and evidence of a role for Fli1 in disease and wound healing. Infect Immun (2010) 1.00
Implementing prenatal diagnosis based on cell-free fetal DNA: accurate identification of factors affecting fetal DNA yield. PLoS One (2011) 0.99
Deaf-1 regulates epithelial cell proliferation and side-branching in the mammary gland. BMC Dev Biol (2008) 0.98
Description of an early intervention to prevent substance abuse and psychopathology in recent rape victims. Behav Modif (2005) 0.95
Murine hematopoietic blast colony-forming cells and their progeny have distinctive membrane marker profiles. Proc Natl Acad Sci U S A (2009) 0.94
Functional transcriptome analysis of the postnatal brain of the Ts1Cje mouse model for Down syndrome reveals global disruption of interferon-related molecular networks. BMC Genomics (2014) 0.93
Spatiotemporal regulation of multiple overlapping sense and novel natural antisense transcripts at the Nrgn and Camk2n1 gene loci during mouse cerebral corticogenesis. Cereb Cortex (2010) 0.93
Gene network disruptions and neurogenesis defects in the adult Ts1Cje mouse model of Down syndrome. PLoS One (2010) 0.92
Women in science. Genome Biol (2012) 0.92
Detection of gene expression in an individual cell type within a cell mixture using microarray analysis. PLoS One (2009) 0.92