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• 4DXpress: a database for cross-species expression pattern comparisons
• A CD8+ T cell transcription signature predicts prognosis in autoimmune disease.
• A General Framework for Interrogation of mRNA Stability Programs Identifies RNA-Binding Proteins that Govern Cancer Transcriptomes.
• A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters
• A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.
• A System for Information Management in BioMedical Studies--SIMBioMS.
• A call for public archives for biological image data.
• A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.
• A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.
• A global map of human gene expression.
• A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.
• A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.
• A pipeline for RNA-seq data processing and quality assessment.
• A proteomics sample metadata representation for multiomics integration and big data analysis.
• A proteomics sample metadata representation for multiomics integration, and big data analysis.
• A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
• A user's guide to the encyclopedia of DNA elements (ENCODE).
• Aberration hubs in protein interaction networks highlight actionable targets in cancer.
• An integrated encyclopedia of DNA elements in the human genome.
• An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures
• An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures.
• An integrated landscape of protein expression in human cancer
• An integrated landscape of protein expression in human cancer.
• Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.
• Approaches to the automatic discovery of patterns in biosequences.
• ArrayExpress service for reviewers/editors of DNA microarray papers.
• ArrayExpress update - from bulk to single-cell expression data.
• ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.
• ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.
• ArrayExpress update--trends in database growth and links to data analysis tools.
• ArrayExpress update-simplifying data submissions.
• ArrayExpress--a public database of microarray experiments and gene expression profiles.
• ArrayExpress--a public repository for microarray gene expression data at the EBI.
• ArrayExpress--a public repository for microarray gene expression data at the EBI.
• ArrayExpress: a public database of gene expression data at EBI.
• Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
• Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
• BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
• Blood transcriptome profile induced by an efficacious vaccine formulated with salivary antigens from cattle ticks.
• Blood transcriptome profile induced by an efficacious vaccine formulated with salivary antigens from cattle ticks.
• Building and analysing genome-wide gene disruption networks.
• Cellular phenotype database: a repository for systems microscopy data.
• Chip technology
• ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.
• Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity.
• Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
• Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer
• Contributions of the EMERALD project to assessing and improving microarray data quality.
• Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.
• Current approaches to gene regulatory network modelling.
• Data storage and analysis in ArrayExpress and Expression Profiler.
• Data storage and analysis in ArrayExpress.
• Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.
• Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).
• Discovering unbounded unions of regular pattern languages from positive examples
• Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications.
• Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ.
• Dysregulation at multiple points of the kynurenine pathway is a ubiquitous feature of renal cancer: implications for tumour immune evasion.
• Efficient algorithm for learning simple regular expressions from noisy examples
• Efficient learning of regular expressions from good examples
• Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
• Expression Atlas update: from tissues to single cells.
• Expression Atlas update: gene and protein expression in multiple species.
• Expression Atlas: gene and protein expression across multiple studies and organisms.
• Expression Profiler
• Expression and Genetic Variation Databases for Cancer Research
• Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.
• From ArrayExpress to BioStudies.
• From gene networks to gene function.
• Funding high-throughput data sharing.
• Fusing microarray experiments with multivariate regression.
• Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci.
• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.
• Gene expression atlas at the European bioinformatics institute.
• Gene expression data analysis.
• Gene expression data analysis.
• Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
• Genomic basis for RNA alterations in cancer.
• Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
• Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.
• Germline determinants of the somatic mutation landscape in 2,642 cancer genomes
• Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.
• Global transcriptional responses of fission yeast to environmental stress.
• Guidelines for reporting single-cell RNA-seq experiments.
• HMGB1 binds to the rs7903146 locus in TCF7L2 in human pancreatic islets.
• HSM - a hybrid system based approach for modelling intracellular networks.
• High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
• Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
• Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.
• Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing.
• Impact of Alternative Splicing on the Human Proteome.
• Importing ArrayExpress datasets into R/Bioconductor.
• Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
• Inductive synthesis of dot expressions
• Integrating sequence, evolution and functional genomics in regulatory genomics.
• International network of cancer genome projects.
• Large scale comparison of global gene expression patterns in human and mouse.
• Learning about gene regulatory networks from gene deletion experiments.
• Learning of regular expressions by pattern matching
• Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma.
• MGED standards: work in progress.
• MageComet--web application for harmonizing existing large-scale experiment descriptions.
• Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.
• Meta-analysis reveals consistent immune response patterns in COVID-19 infected patients at single-cell resolution
• Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.
• Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
• Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
• Modeling sample variables with an Experimental Factor Ontology.
• Modelling gene networks at different organisational levels.
• Modelling in molecular biology: describing transcription regulatory networks at different scales.
• Modelling-based experiment retrieval: a case study with gene expression clustering.
• Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myocarditis.
• On the importance of standardisation in life sciences.
• One-stop shop for microarray data.
• Orchestrating differential data access for translational research: a pilot implementation.
• PASSIM--an open source software system for managing information in biomedical studies.
• Pan-cancer analysis of whole genomes.
• Pattern discovery in biosequences
• Periodic gene expression program of the fission yeast cell cycle.
• Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.
• Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes.
• Predicting gene regulatory elements in silico on a genomic scale.
• Prediction of gene expression in embryonic structures of Drosophila melanogaster.
• Probabilistic retrieval and visualization of biologically relevant microarray experiments.
• Probabilistic retrieval and visualization of biologically relevant microarray experiments.
• Proceedings of the 6th Asia-Pacific Bioinformatics Conference: Kyoto, Japan, 14-17 January 2008
• Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
• Protein interaction verification and functional annotation by integrated analysis of genome-scale data.
• Publisher Correction: Image Data Resource: a bioimage data integration and publication platform.
• Putative cell type discovery from single-cell gene expression data.
• REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.
• RNA-Seq gene profiling--a systematic empirical comparison.
• Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.
• Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
• Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.
• Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008).
• Report on the thirteenth international workshop on the identification and functional, evolutionary and expression analysis of transcribed sequences: comparative and functional genomics workshop.
• Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
• Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
• Reuse of public genome-wide gene expression data.
• SAIL--a software system for sample and phenotype availability across biobanks and cohorts.
• SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.
• SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.
• Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.
• Sex differences in oncogenic mutational processes.
• Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
• Standards for microarray data.
• Standards for systems biology.
• Submission of microarray data to public repositories.
• Subtype-specific micro-RNA expression signatures in breast cancer progression.
• Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.
• The ArrayExpress gene expression database: a software engineering and implementation perspective.
• The BREW workshop series: a stimulating experience in PhD education.
• The BioImage Archive - home of life-sciences microscopy data
• The BioSample Database (BioSD) at the European Bioinformatics Institute.
• The BioStudies database-one stop shop for all data supporting a life sciences study.
• The BioStudies database.
• The European Bioinformatics Institute's data resources.
• The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
• The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
• The Image Data Resource: A Bioimage Data Integration and Publication Platform.
• The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.
• The PRIDE database and related tools and resources in 2019: improving support for quantification data.
• The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.
• The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.
• The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".
• The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.
• The underlying principles of scientific publication.
• Tools for mapping high-throughput sequencing data.
• Top-down standards will not serve systems biology.
• Towards reconstruction of gene networks from expression data by supervised learning.
• Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.
• Transcriptome and genome sequencing uncovers functional variation in humans.
• Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing
• Transparency and reproducibility in artificial intelligence.
• Tumour gene expression signature in primary melanoma predicts long-term outcomes.
• Tumour gene expression signature in primary melanoma predicts long-term outcomes: A prospective multicentre study
• Updates to BioSamples database at European Bioinformatics Institute.
• Urinary metabolic phenotyping for Alzheimer's disease.
• Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes.
• User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.
• Using Deep Learning to Extrapolate Protein Expression Measurements.
• Variation in genomic landscape of clear cell renal cell carcinoma across Europe.
• Visualization of large microarray experiments with space maps.
• Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements
• Wrestling with SUMO and bio-ontologies.
• clustComp, a bioconductor package for the comparison of clustering results.