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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

Postdoctoral Fellow – Pandemic-scale Phylodynamics

Science, research and training in EMBL-EBI Hinxton

Your groupThe Goldman group at EMBL-EBI (https://www.ebi.ac.uk/research/goldman/) develops methods for improving sequencing technologies and bioinformatics analyses. We often devise new algorithms, mathematical models, and approximations, and use them to process large genomic datasets. The group is…

Closes on 19th January. Posted 23rd December 2025

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