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Functional Genomics

Delivers tools and services for the submission, archiving, analysis and visualisation of functional genomics experiments

The Functional Genomics Team develops and maintains resources, tools, and workflows to support the submission, analysis, and visualisation of functional genomics data.

We lead the development of Expression Atlas, a flagship open-access resource integrating bulk and single-cell transcriptomics data across species, tissues, and conditions.

We promote FAIR data principles and support data reuse through the coordinated submission and expert curation of functional genomics datasets, ranging from bulk and single-cell RNA-Seq to epigenetic profiling technologies. Submissions are managed via the Annotare submission tool and archived in the BioStudies database as part of the ArrayExpress collection. Through standardised metadata capture, we ensure that submitted datasets are made discoverable, well-annotated, and ready for integration into downstream resources such as Expression Atlas.

With combined expertise in biology, bioinformatics, and software engineering, we focus on:

  • Metadata enrichment and quality control
  • Scalable, reproducible analysis pipelines
  • Accessible visualisations
  • Development of community standards and formats
  • Outreach and training to support open science

We also support the data infrastructure of the Human Cell Atlas (HCA) by maintaining the HCA Data Repository. We manage the ingest of new datasets through the HCA Data Contributor Portal, working with contributors and HCA bionetworks to ensure data are archived in the HCA Data Portal according to agreed metadata standards. We lead coordination efforts to evolve these standards in response to emerging technologies and the needs of integration teams building the atlases.

Data resources

Expression Atlas

Expression Atlas

The Expression Atlas is an added-value database based on re-analysis of (single cell/bulk RNA-seq and microarray) gene and protein expression data from EMBL-EBI’s ArrayExpress and PRIDE archives respectively, as well as from external sources. It shows you which genes/proteins are expressed under dif…

Annotare

Annotare

Annotare is a tool designed for submitting functional genomics data to the ArrayExpress collection in BioStudies. It supports a wide range of assays that profile different layers of gene regulation, including RNA-seq, single-cell RNA-seq, ChIP-seq, and related techniques. Adhering to high metadata s…

ArrayExpress Archive of Functional Genomics Data

ArrayExpress Archive of Functional Genomics Data

The ArrayExpress Archive is a database of functional genomics experiments, including gene expression, where you can query and download data collected to MIAME and MINSEQE standards. ArrayExpress is one of three internatinoal repositories recommended by many journals for microarray and RNAseq functio…

Latest EMBL-EBI Jobs

User Experience (UX) Designer

Technology in EMBL-EBI Hinxton

We are seeking a proactive and creative User Experience (UX) Designer to join our dynamic team. This role is ideal for a designer with experience in data-heavy environments who can craft intuitive, user-centric interfaces and workflows for complex scientific applications. If you are passionate about…

Closes on 12th January. Posted 8th December 2025

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