limma: Linear Models for Microarray Data

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The Molecular Signature of Tissue Resident Memory CD8 T Cells Isolated from the Brain

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A Virulent Strain of Deformed Wing Virus (DWV) of Honeybees (Apis mellifera) Prevails after Varroa destructor-Mediated, or In Vitro, Transmission

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L1000CDS2: LINCS L1000 characteristic direction signatures search engine

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A general modular framework for gene set enrichment analysis

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Crosstalk Between the MSI Status and Tumor Microenvironment in Colorectal Cancer

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MicroRNA-regulated pathways associated with endometriosis

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Field-Caught Permethrin-Resistant Anopheles gambiae Overexpress CYP6P3, a P450 That Metabolises Pyrethroids

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Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination inArabidopsis

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Peripheral blood gene expression: it all boils down to the RNA collection tubes

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Déjà vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins

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microRNA‐101 is a potent inhibitor of autophagy

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Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens

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Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

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PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments

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The epigenetic modifier EZH2 controls melanoma growth and metastasis through silencing of distinct tumour suppressors

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Conserved epigenetic sensitivity to early life experience in the rat and human hippocampus

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Mutant huntingtin's effects on striatal gene expression in mice recapitulate changes observed in human Huntington's disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage

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Telomere position effect: regulation of gene expression with progressive telomere shortening over long distancesPreprint

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Expression differences for genes involved in lignin, glutathione and sulphate metabolism in response to cadmium in Arabidopsis thaliana and the related Zn/Cd‐hyperaccumulator Thlaspi caerulescens

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Rice MADS3 Regulates ROS Homeostasis during Late Anther Development

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Distinct signalling pathways and transcriptome response signatures differentiate ammonium- and nitrate-supplied plants

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Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

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Expression profiling in primates reveals a rapid evolution of human transcription factors

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Common patterns and disease-related signatures in tuberculosis and sarcoidosis

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High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

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The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions

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PERSISTENT TAPETAL CELL1 Encodes a PHD-Finger Protein That Is Required for Tapetal Cell Death and Pollen Development in Rice

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Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection

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Polyester : simulating RNA-seq datasets with differential transcript expression

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The signature of maternal rearing in the methylome in rhesus macaque prefrontal cortex and T cells

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Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle

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Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice

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Identification of Functional Heterogeneity of Carcinoma-Associated Fibroblasts with Distinct IL6-Mediated Therapy Resistance in Pancreatic Cancer

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The Hippo pathway transcriptional co-activator, YAP, is an ovarian cancer oncogene

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Changes in the Endometrial Transcriptome During the Bovine Estrous Cycle: Effect of Low Circulating Progesterone and Consequences for Conceptus Elongation

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Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection

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miRNA-mRNA Integrated Analysis Reveals Roles for miRNAs in Primary Breast Tumors

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Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients

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An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice

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Analysis of microarray experiments of gene expression profiling

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Multifaceted effects of oligodendroglial exosomes on neurons: impact on neuronal firing rate, signal transduction and gene regulation

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Mutations in the SIX1/2 Pathway and the DROSHA/DGCR8 miRNA Microprocessor Complex Underlie High-Risk Blastemal Type Wilms Tumors

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Ethylene Interacts with Abscisic Acid to Regulate Endosperm Rupture during Germination: A Comparative Approach Using Lepidium sativum and Arabidopsis thaliana

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Carryover effect of postpartum inflammatory diseases on developmental biology and fertility in lactating dairy cows

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BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud

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Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus

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A systematic evaluation of single-cell RNA-sequencing imputation methods

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IRF-3, IRF-5, and IRF-7 coordinately regulate the type I IFN response in myeloid dendritic cells downstream of MAVS signaling

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Histone Deacetylase Inhibitor Panobinostat Induces Clinical Responses with Associated Alterations in Gene Expression Profiles in Cutaneous T-Cell Lymphoma

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Genes Involved in Viral Carcinogenesis and Tumor Initiation in Hepatitis C Virus-Induced Hepatocellular Carcinoma

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Inflorescence Meristem Identity in Rice Is Specified by Overlapping Functions of Three AP1 / FUL -Like MADS Box Genes and PAP2 , a SEPALLATA MADS Box Gene

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Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression

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The HDAC inhibitor 4b ameliorates the disease phenotype and transcriptional abnormalities in Huntington's disease transgenic mice

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Delayed bactericidal response of Mycobacterium tuberculosis to bedaquiline involves remodelling of bacterial metabolism

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ABA‐Hypersensitive Germination1 encodes a protein phosphatase 2C, an essential component of abscisic acid signaling in Arabidopsis seed

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Defense‐related transcription factors WRKY 70 and WRKY 54 modulate osmotic stress tolerance by regulating stomatal aperture in A rabidopsis

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Erratum to: A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

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Effect of aspirin and NSAIDs on risk and survival from colorectal cancer

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A comparison of statistical methods for detecting differentially expressed genes from RNA‐seq data

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Differential Placental Gene Expression in Severe Preeclampsia

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Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

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Whole-cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum

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ATF4 is an oxidative stress–inducible, prodeath transcription factor in neurons in vitro and in vivo

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Major Cellular and Physiological Impacts of Ocean Acidification on a Reef Building Coral

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Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influencePreprint

Gordon, L., Joo, J. E., Powell, J. E., Ollikainen, M., Novakovic, B., Li, X., Andronikos, R. H., Cruickshank, M. N., Conneely, K. N., Smith, A. K., et al. (2012) · Genome Research · doi:10.1101/gr.136598.111 · Cited by 276

Broad defects in epidermal cornification in atopic dermatitis identified through genomic analysis

Guttman-Yassky, E., Suárez-Fariñas, M., Chiricozzi, A., Nograles, K. E., Shemer, A., Fuentes-Duculan, J., Cardinale, I., Lin, P., Bergman, R., Bowcock, A. M., et al. (2009) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2009.09.031 · Cited by 268

Aberrant global methylation patterns affect the molecular pathogenesis and prognosis of multiple myeloma

Walker, B. A., Wardell, C. P., Chiecchio, L., Smith, E. M., Boyd, K. D., Neri, A., Davies, F. E., Ross, F. M., & Morgan, G. J. (2011) · Blood · doi:10.1182/blood-2010-04-279539 · Cited by 267

MeV: MultiExperiment Viewer

Howe, E., Holton, K. M., Nair, S. J., Schlauch, D., Sinha, R., & Quackenbush, J. F. (2010) · Springer eBooks · doi:10.1007/978-1-4419-5714-6_15 · Cited by 270

The Arabidopsis MicroRNA396-GRF1/GRF3 Regulatory Module Acts as a Developmental Regulator in the Reprogramming of Root Cells during Cyst Nematode Infection

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Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets

Chawade, A., Alexandersson, E., & Levander, F. (2014) · Journal of Proteome Research · doi:10.1021/pr401264n · Cited by 264

Transcriptomic response of sea urchin larvaeStrongylocentrotus purpuratusto CO2-driven seawater acidification

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Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations

Yaari, G., Bolen, C. R., Thakar, J., & Kleinstein, S. H. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt660 · Cited by 269

Identification of differentially expressed genes between osteoblasts and osteocytes

Paić, F., Igwe, J. C., Nori, R., Kronenberg, M. S., Franceschetti, T., Harrington, P., Kuo, L., Shin, D., Rowe, D. W., Harris, S. E., et al. (2009) · Bone · doi:10.1016/j.bone.2009.06.010 · Cited by 271

Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children’s Environmental Health Studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group

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Cancer transcriptome profiling at the juncture of clinical translation

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Array-Based Gene Discovery with Three Unrelated Subjects Shows SCARB2/LIMP-2 Deficiency Causes Myoclonus Epilepsy and Glomerulosclerosis

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O-GlcNAc transferase (OGT) as a placental biomarker of maternal stress and reprogramming of CNS gene transcription in development

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Human MAIT and CD8αα cells develop from a pool of type-17 precommitted CD8+ T cells

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NuRD‐mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression

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Gene Expression Atlas at the European Bioinformatics Institute

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Different TCR-induced T lymphocyte responses are potentiated by stiffness with variable sensitivity

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Immuno-genomic landscape of osteosarcoma

Wu, C.-C., Beird, H. C., Andrew Livingston, J., Advani, S., Mitra, A., Cao, S., Reuben, A., Ingram, D., Wang, W.-L., Ju, Z., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14646-w · Cited by 251

Heavy metal‐associated isoprenylated plant protein ( HIPP ): characterization of a family of proteins exclusive to plants

Neto, J. B. D. A., Turchetto‐Zolet, A. C., de Oliveira, L. F. V., Zanettini, M. H. B., & Margis-Pinheiro, M. M. A. N. (2013) · FEBS Journal · doi:10.1111/febs.12159 · Cited by 250

Sex differences in the genome-wide DNA methylation pattern and impact on gene expression, microRNA levels and insulin secretion in human pancreatic islets

Hall, E., Volkov, P., Dayeh, T., Esguerra, J. L. S., Salö, S., Eliasson, L., Rönn, T., Bacos, K., & Ling, C. (2014) · Genome Biology · doi:10.1186/s13059-014-0522-z · Cited by 249

Durvalumab plus tremelimumab alone or in combination with low-dose or hypofractionated radiotherapy in metastatic non-small-cell lung cancer refractory to previous PD(L)-1 therapy: an open-label, multicentre, randomised, phase 2 trial

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Deep Learning Accurately Predicts Estrogen Receptor Status in Breast Cancer Metabolomics Data

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Small extracellular vesicles and their miRNA cargo are anti-apoptotic members of the senescence-associated secretory phenotype

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Evaluation of MicroRNA Expression Profiles That May Predict Recurrence of Localized Stage I Non–Small Cell Lung Cancer after Surgical Resection

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Siglec-1 Is a Novel Dendritic Cell Receptor That Mediates HIV-1 Trans-Infection Through Recognition of Viral Membrane Gangliosides

Izquierdo-Useros, N., Lorizate, M., Puertas, M. C., Rodriguez-Plata, M. T., Zangger, N., Erikson, E., Pino, M., Erkizia, I., Glass, B., Clotet, B., et al. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001448 · Cited by 244

Development and validation of a novel molecular biomarker diagnostic test for the early detection of sepsis

Sutherland, A. J., Thomas, M., Brandon, R. A., Brandon, R. B., Lipman, J., Tang, B. M. P., McLean, A. S., Pascoe, R., Price, G. R., Nguyen, T., et al. (2011) · Critical Care · doi:10.1186/cc10274 · Cited by 246

Venn diagrams in bioinformatics

Jia, A., Xu, L., & Wang, Y. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab108 · Cited by 249

Genome-wide DNA methylation levels and altered cortisol stress reactivity following childhood trauma in humans

Houtepen, L. C., Vinkers, C. H., Carrillo-Roa, T., Hiemstra, M., van Lier, P. A., Meeus, W., Branje, S., Heim, C. M., Nemeroff, C. B., Mill, J., et al. (2016) · Nature Communications · doi:10.1038/ncomms10967 · Cited by 242

Drug Target Prediction and Repositioning Using an Integrated Network-Based Approach

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Gene expression profiling in the adult Down syndrome brain

Lockstone, H. E., Harris, L. W., Swatton, J. E., Wayland, M. T., Holland, A. J., & Bahn, S. (2007) · Genomics · doi:10.1016/j.ygeno.2007.08.005 · Cited by 240

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

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Empirical array quality weights in the analysis of microarray data

Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic, A., Holloway, A., & Smyth, G. K. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-261 · Cited by 312

Examples

Yes, L. (2010)

LLAMA: AN ONLINE MICROARRAY LINEAR ANALYSIS TOOLPreprint

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