Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray

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Serial Analysis of Gene Expression

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Gene expression informatics —it's all in your mine

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Using oligonucleotide probe arrays to access genetic diversity

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One-stop shop for microarray data

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Microarray gene expression database: progress towards an international repository of gene expression data.

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Unlimited Access—Limitless SuccessPreprint

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Inferring tumour purity and stromal and immune cell admixture from expression data

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Database resources of the National Center for Biotechnology Information: update

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NCBI GEO: archive for functional genomics data sets—update

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Scenic: single-cell regulatory network inference and clustering.

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A gene atlas of the mouse and human protein-encoding transcriptomes

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Gene set knowledge discovery with enrichr

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A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles

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DNA methylation-based biomarkers and the epigenetic clock theory of ageing

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miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

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Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

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Genomic responses in mouse models poorly mimic human inflammatory diseases

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Leukemic IDH1 and IDH2 Mutations Result in a Hypermethylation Phenotype, Disrupt TET2 Function, and Impair Hematopoietic Differentiation

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An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets

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The Gene Expression Omnibus Database

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GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox

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Standardization of sample collection, isolation and analysis methods in extracellular vesicle research

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Genomic analysis of reactive astrogliosis

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The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

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[9] TM4 Microarray Software Suite

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JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

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New tools for studying microglia in the mouse and human CNS

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Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

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Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

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PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data

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Role of PFKFB3-Driven Glycolysis in Vessel Sprouting

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NCBI GEO: mining tens of millions of expression profiles--database and tools update

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The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

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Challenges of Big Data analysis

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Artificial intelligence to deep learning: machine intelligence approach for drug discovery

Gupta, R., Srivastava, D., Sahu, M., Tiwari, S., Ambasta, R. K., & Kumar, P. (2021) · Molecular Diversity · doi:10.1007/s11030-021-10217-3 · Cited by 1,473 · see citing works

Global reconstruction of the human metabolic network based on genomic and bibliomic data

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Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB

Medina, D. L., Paola, S. D., Peluso, I., Armani, A., Stefani, D. D., Venditti, R., Montefusco, S., Rosato, A. S., Prezioso, C., Forrester, A. R., et al. (2015) · Nature Cell Biology · doi:10.1038/ncb3114 · Cited by 1,405 · see citing works

Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays

Johnson, J. M., Castle, J. C., Garrett-Engele, P. W., Kan, Z., Loerch, P., Armour, C. D., Santos, R., Schadt, E. E., Stoughton, R. B., & Shoemaker, D. D. (2003) · Science · doi:10.1126/science.1090100 · Cited by 1,418 · see citing works

Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

Bagaev, A., Kotlov, N., Nomie, K., Svekolkin, V., Gafurov, A., Isaeva, O., Osokin, N., Kozlov, I., Frenkel, F., Gancharova, O., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.04.014 · Cited by 1,302 · see citing works

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

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GMD@CSB.DB: the Golm Metabolome Database

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Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids

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Transcriptional landscape of the prenatal human brain

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Genomic and transcriptomic hallmarks of poorly differentiated and anaplastic thyroid cancers

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ChEA3: transcription factor enrichment analysis by orthogonal omics integration

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Cutoff Finder: A Comprehensive and Straightforward Web Application Enabling Rapid Biomarker Cutoff Optimization

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A translational profiling approach for the molecular characterization of CNS cell types

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Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses

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NCBI GEO: mining millions of expression profiles--database and tools

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Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells

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High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes

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Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

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Transcriptomics technologies

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

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NCBI GEO: archive for functional genomics data sets--10 years on

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Database resources of the National Center for Biotechnology

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Plant metabolomics: large-scale phytochemistry in the functional genomics era

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ArrayExpress--a public repository for microarray gene expression data at the EBI

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TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues

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Accounting for cellular heterogeneity is critical in epigenome-wide association studies

Jaffe, A. E., & Irizarry, R. A. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r31 · Cited by 1,067 · see citing works

NCBI GEO: archive for high-throughput functional genomic data

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Biological Network Exploration with Cytoscape 3

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Multiple common variants for celiac disease influencing immune gene expression

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TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop

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Organoids

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A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains

Hutchinson, J. N., Ensminger, A. W., Clemson, C., Lynch, C. R., Lawrence, J. B., & Chess, A. J. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-39 · Cited by 997 · see citing works

Distribution of miRNA expression across human tissues

Ludwig, N., Leidinger, P., Becker, K., Backes, C., Fehlmann, T., Pallasch, C., Rheinheimer, S., Meder, B., Stähler, C., Meese, E., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw116 · Cited by 968 · see citing works

The Connectivity Map: A new tool for biomedical research

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Deep learning in cancer diagnosis, prognosis and treatment selection

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A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study

den Boer, M. L., van Slegtenhorst, M., de Menezes, R. X., Cheok, M. H.-C., Buijs-Gladdines, J. G. C. A. M., Peters, S. T. C. J. M., van Zutven, L. J. C. M., Beverloo, H. B., van der Spek, P. J., Escherich, G., et al. (2009) · The Lancet Oncology · doi:10.1016/s1470-2045(08)70339-5 · Cited by 927 · see citing works

The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance

Li, W., Oono, Y., Zhu, J., He, X., Wu, J., Iida, K., Lu, X., Cui, X., Jin, H., & Zhu, J. (2008) · The Plant Cell · doi:10.1105/tpc.108.059444 · Cited by 917 · see citing works

Sharing Detailed Research Data Is Associated with Increased Citation Rate

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PREDICT: a method for inferring novel drug indications with application to personalized medicine

Gottlieb, A., Stein, G. Y., Ruppin, E., & Sharan, R. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.26 · Cited by 892 · see citing works

c-Jun overexpression in CAR T cells induces exhaustion resistance

Lynn, R. C., Weber, E. W., Sotillo, E., Gennert, D., Xu, P., Good, Z., Anbunathan, H., Lattin, J., Jones, R., Tieu, V., et al. (2019) · Nature · doi:10.1038/s41586-019-1805-z · Cited by 891 · see citing works

Swarm Learning for decentralized and confidential clinical machine learning

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Ten Simple Rules for Reproducible Computational Research

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In Vivo Imaging Reveals Extracellular Vesicle-Mediated Phenocopying of Metastatic Behavior

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Gateways to the FANTOM5 promoter level mammalian expression atlas

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High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation

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DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia

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