limma: Linear Models for Microarray Data

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

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Variance stabilization applied to microarray data calibration and to the quantification of differential expression

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Identifying differentially expressed genes using false discovery rate controlling procedures

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Use of within-array replicate spots for assessing differential expression in microarray experiments

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Statistical Issues in cDNA Microarray Data Analysis

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Parameter estimation for the calibration and variance stabilization of microarray data

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Design and analysis of comparative microarray experiments

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limma powers differential expression analyses for RNA-sequencing and microarray studies

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Differential expression analysis for sequence count data

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Predicting effective microRNA target sites in mammalian mRNAs

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Gene ontology analysis for RNA-seq: accounting for selection bias

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Scenic: single-cell regulatory network inference and clustering.

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voom: precision weights unlock linear model analysis tools for RNA-seq read counts

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GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

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BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc

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Epithelial-to-mesenchymal transition is dispensable for metastasis but induces chemoresistance in pancreatic cancer

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A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

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Enhancing CD8 T-cell memory by modulating fatty acid metabolism

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N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells

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A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

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A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment

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A data-driven approach to preprocessing Illumina 450K methylation array data

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Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

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Perturbation-response genes reveal signaling footprints in cancer gene expression

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A novel signaling pathway impact analysis

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Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility

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Early T-cell precursor leukaemia: a subtype of very high-risk acute lymphoblastic leukaemia

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ChAMP: 450k Chip Analysis Methylation Pipeline

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Apoptotic Caspases Suppress mtDNA-Induced STING-Mediated Type I IFN Production

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Epithelial-to-mesenchymal transition induces cell cycle arrest and parenchymal damage in renal fibrosis

Lovisa, S., LeBleu, V. S., Tampe, B., Sugimoto, H., Vadnagara, K., Carstens, J. L., Wu, C.-C., Hagos, Y., Burckhardt, B. C., Pentcheva‐Hoang, T., et al. (2015) · Nature Medicine · doi:10.1038/nm.3902 · Cited by 995

De novo identification of differentially methylated regions in the human genome

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NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data

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A comparison of background correction methods for two-colour microarrays

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Virus-Plus-Susceptibility Gene Interaction Determines Crohn's Disease Gene Atg16L1 Phenotypes in Intestine

Cadwell, K., Patel, K., Maloney, N. S., Liu, T., Ng, A., Storer, C. E., Head, R. D., Xavier, R. J., Stappenbeck, T. S., & Virgin, H. W. (2010) · Cell · doi:10.1016/j.cell.2010.05.009 · Cited by 927

Camera: a competitive gene set test accounting for inter-gene correlation

Wu, D., & Smyth, G. K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks461 · Cited by 901

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target

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Circulating tumour DNA methylation markers for diagnosis and prognosis of hepatocellular carcinoma

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Ballgown bridges the gap between transcriptome assembly and expression analysis

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SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

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Type 2 Innate Signals Stimulate Fibro/Adipogenic Progenitors to Facilitate Muscle Regeneration

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The multiMiR R package and database: integration of microRNA–target interactions along with their disease and drug associations

Ru, Y., Kechris, K. J., Tabakoff, B., Hoffman, P. L., Radcliffe, R. A., Bowler, R. P., Mahaffey, S. B., Rossi, S., Călin, G. A., Bemis, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku631 · Cited by 805

BM mesenchymal stromal cell–derived exosomes facilitate multiple myeloma progression

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Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

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Intestinal label-retaining cells are secretory precursors expressing Lgr5

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The Arabidopsis Cold-Responsive Transcriptome and Its Regulation by ICE1

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Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms.

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Generation of Isogenic Pluripotent Stem Cells Differing Exclusively at Two Early Onset Parkinson Point Mutations

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Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women

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Testing significance relative to a fold-change threshold is a TREAT

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Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

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Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression

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Intimate bacterial–fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans

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hsa-miR-210 Is Induced by Hypoxia and Is an Independent Prognostic Factor in Breast Cancer

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Relationship between differentially expressed mRNA and mRNA-protein correlations in a xenograft model system

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Induction of a common microglia gene expression signature by aging and neurodegenerative conditions: a co-expression meta-analysis

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A pan-cancer proteomic perspective on The Cancer Genome Atlas

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Inactivation of CDK12 Delineates a Distinct Immunogenic Class of Advanced Prostate Cancer

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Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

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Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses

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Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles

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Patterns of Rare and Abundant Marine Microbial Eukaryotes

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Large Expression Differences in Genes for Iron and Zinc Homeostasis, Stress Response, and Lignin Biosynthesis Distinguish Roots of Arabidopsis thaliana and the Related Metal Hyperaccumulator Thlaspi caerulescens

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BET inhibitor resistance emerges from leukaemia stem cells

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Target analysis by integration of transcriptome and ChIP-seq data with BETA

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Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

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svaseq: removing batch effects and other unwanted noise from sequencing data

Leek, J. T. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku864 · Cited by 551

In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning

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Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor

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Incidence, Risk Factors, and Attributable Mortality of Secondary Infections in the Intensive Care Unit After Admission for Sepsis

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PresenceAbsence : An R Package for Presence Absence Analysis

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Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors

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Lactobacillus plantarum MB452 enhances the function of the intestinal barrier by increasing the expression levels of genes involved in tight junction formation

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Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development

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Selective enhancement of endothelial BMPR-II with BMP9 reverses pulmonary arterial hypertension

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Activation of HIV Transcription with Short-Course Vorinostat in HIV-Infected Patients on Suppressive Antiretroviral Therapy

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The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

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Studying and modelling dynamic biological processes using time-series gene expression data

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A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

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The Transcription Factors WRKY11 and WRKY17 Act as Negative Regulators of Basal Resistance inArabidopsis thaliana

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beadarray: R classes and methods for Illumina bead-based data

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Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements

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Auto-Antigenic Protein-DNA Complexes Stimulate Plasmacytoid Dendritic Cells to Promote Atherosclerosis

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Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

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A Spatio-Temporal Understanding of Growth Regulation during the Salt Stress Response in Arabidopsis

Geng, Y., Wu, R., Wee, C. W., Xie, F., Wei, X., Chan, P. M. Y., Tham, C., Duan, L., & Dinneny, J. R. (2013) · The Plant Cell · doi:10.1105/tpc.113.112896 · Cited by 456

FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar

Hsu, C., Adams, J. P., Kim, H.-J., No, K., Ma, C., Strauss, S. H., Drnevich, J. M., Vandervelde, L., Ellis, J. D., Rice, B., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1104713108 · Cited by 460

NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration

Xia, J., Benner, M. J., & Hancock, R. E. W. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku443 · Cited by 460

The landscape of histone modifications across 1% of the human genome in five human cell linesPreprint

Koch, C. M., Andrews, R., Flicek, P., Dillon, S. C., Karaöz, U., Clelland, G., Wilcox, S., Beare, D. M., Fowler, J. C., Couttet, P., et al. (2007) · Genome Research · doi:10.1101/gr.5704207 · Cited by 460

Reproducible RNA-seq analysis using recount2

Collado‐Torres, L., Nellore, A., Kammers, K., Ellis, S., Taub, M. A., Hansen, K. D., Jaffe, A. E., Langmead, B., & Leek, J. T. (2017) · Nature Biotechnology · doi:10.1038/nbt.3838 · Cited by 448

Induction and transcriptional regulation of the co-inhibitory gene module in T cells

Chihara, N., Madi, A., Kondo, T., Zhang, H., Acharya, N., Singer, M., Nyman, J., Marjanovic, N. D., Kowalczyk, M. S., Wang, C., et al. (2018) · Nature · doi:10.1038/s41586-018-0206-z · Cited by 438

Foxp3+ T cells expressing RORγt represent a stable regulatory T-cell effector lineage with enhanced suppressive capacity during intestinal inflammation

Yang, B.-H., Hagemann, S., Mamareli, P., Lauer, U., Hoffmann, U., Beckstette, M., Föhse, L., Prinz, I., Pezoldt, J., Suerbaum, S., et al. (2015) · Mucosal Immunology · doi:10.1038/mi.2015.74 · Cited by 447

A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium

Sinha, A., Hughes, K. R., Modrzynska, K., Otto, T. D., Pfander, C., Dickens, N. J., Religa, A. A., Bushell, E., Graham, A., Cameron, R., et al. (2014) · Nature · doi:10.1038/nature12970 · Cited by 435

Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis

Sweeney, T. E., Braviak, L., Tato, C. M., & Khatri, P. (2016) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(16)00048-5 · Cited by 435

Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers

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A critical developmental switch defines the kinetics of kidney cyst formation after loss of Pkd1

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T-Cell Infiltration and Signaling in the Adult Dorsal Spinal Cord Is a Major Contributor to Neuropathic Pain-Like Hypersensitivity

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DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients

Volkmar, M., Dedeurwaerder, S., Cunha, D. A., Ndlovu, M. N., Defrance, M., Deplus, R., Calonne, E., Volkmar, U., Igoillo‐Esteve, M., Naamane, N., et al. (2012) · The EMBO Journal · doi:10.1038/emboj.2011.503 · Cited by 420

Gene expression divergence recapitulates the developmental hourglass model

Kalinka, A. T., Varga, K. M., Gerrard, D. T., Preibisch, S., Corcoran, D. L., Jarrells, J., Ohler, U., Bergman, C., & Tomančák, P. (2010) · Nature · doi:10.1038/nature09634 · Cited by 415

Associations with early-life socio-economic position in adult DNA methylation

Borghol, N., Suderman, M. J., McArdle, W. L., Racine, A., Hallett, M. T., Pembrey, M. E., Hertzman, C., Power, C., & Szyf, M. (2011) · International Journal of Epidemiology · doi:10.1093/ije/dyr147 · Cited by 429

Citrullination regulates pluripotency and histone H1 binding to chromatin

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ROCK and JAK1 Signaling Cooperate to Control Actomyosin Contractility in Tumor Cells and Stroma

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Myocardin-related transcription factors and SRF are required for cytoskeletal dynamics and experimental metastasis

Medjkane, S., Pérez-Sánchez, C., Gaggioli, C., Sahai, E. A., & Treisman, R. (2009) · Nature Cell Biology · doi:10.1038/ncb1833 · Cited by 407

Long-term forest soil warming alters microbial communities in temperate forest soils

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Mutant IDH1 regulates the tumor-associated immune system in gliomasPreprint

Amankulor, N., Kim, Y., Arora, S., Kargl, J., Szulzewsky, F., Hanke, M. L., Margineantu, D. H., Rao, A., Bolouri, H., Delrow, J. J., et al. (2017) · Genes & Development · doi:10.1101/gad.294991.116 · Cited by 411

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

Shao, Z., Zhang, Y., Yuan, G., Orkin, S. H., & Waxman, D. J. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r16 · Cited by 410

An Antioxidant Response Phenotype Shared between Hereditary and Sporadic Type 2 Papillary Renal Cell Carcinoma

Ooi, A., Wong, J.-C., Petillo, D., Roossien, D., Perrier-Trudova, V., Whitten, D., Min, B. W. H., Tan, M.-H., Zhang, Z., Yang, X. J., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.08.024 · Cited by 401

Induction of a Human Pluripotent State with Distinct Regulatory Circuitry that Resembles Preimplantation Epiblast

Chan, Y.-S., Göke, J., Ng, J.-H., Lu, X., Gonzales, K. A. U., Tan, C.-P., Tng, W. J., Hong, Z.-Z., Lim, Y. S., & Ng, H. (2013) · Cell stem cell · doi:10.1016/j.stem.2013.11.015 · Cited by 392

Limma: linear models for microarray data. In Bioinformatics and computational biology solutions using R and Bioconductor

Smyth, G. K. (2013)

limmaGUI: A graphical user interface for linear modeling of microarray data

Wettenhall, J. M., & Smyth, G. K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth449 · Cited by 720

Empirical array quality weights in the analysis of microarray data

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Examples

Yes, L. (2010)

LLAMA: AN ONLINE MICROARRAY LINEAR ANALYSIS TOOLPreprint

Routley, B. S., & Muldoon, M. R. (2005) · MIMS EPrints (University of Southampton)