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Gene regulation in primates evolves under tissue-specific selection pressuresBioconductor: open software development for computational biology and bioinformaticsDeaf-1 regulates epithelial cell proliferation and side-branching in the mammary glandId2 expression delineates differential checkpoints in the genetic program of CD8α+ and CD103+ dendritic cell lineagesStatistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basisLinear models and empirical bayes methods for assessing differential expression in microarray experimentsedgeR: a Bioconductor package for differential expression analysis of digital gene expression dataOrchestrating high-throughput genomic analysis with BioconductorNormalization of cDNA microarray dataArray-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosisExpression profiling in primates reveals a rapid evolution of human transcription factorsProteomic and metabolomic analyses of mitochondrial complex I-deficient mouse model generated by spontaneous B2 short interspersed nuclear element (SINE) insertion into NADH dehydrogenase (ubiquinone) Fe-S protein 4 (Ndufs4) geneLung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining PathwayCount-based differential expression analysis of RNA sequencing data using R and BioconductorGeneration of a functional mammary gland from a single stem celllimma powers differential expression analyses for RNA-sequencing and microarray studiesFas-mediated neutrophil apoptosis is accelerated by Bid, Bak, and Bax and inhibited by Bcl-2 and Mcl-1Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates.Statistical issues in cDNA microarray data analysis.De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly.Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling.csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows.Empirical array quality weights in the analysis of microarray dataFrom reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq dataStatistical modeling of sequencing errors in SAGE libraries.limmaGUI: a graphical user interface for linear modeling of microarray data.A systematic approach for comprehensive T-cell epitope discovery using peptide libraries.affylmGUI: a graphical user interface for linear modeling of single channel microarray data.Signal regulatory protein molecules are differentially expressed by CD8- dendritic cells.Proximal genomic localization of STAT1 binding and regulated transcriptional activityGene expression changes during step-wise differentiation of embryonic stem cells along the inner ear hair cell pathway.Small-sample estimation of negative binomial dispersion, with applications to SAGE data.Moderated statistical tests for assessing differences in tag abundance.Polycomb repressive complex 2 (PRC2) restricts hematopoietic stem cell activityMolecular dissection of the pea shoot apical meristem.Integrative analysis of RUNX1 downstream pathways and target genes.Detection of gene expression in an individual cell type within a cell mixture using microarray analysis.Illumina WG-6 BeadChip strips should be normalized separatelyRNA-seq mixology: designing realistic control experiments to compare protocols and analysis methodsThe BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity.
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