Research directions
Big data on ageing
Extract answers from open data. Cell atlases let us select a tissue, cell type and gene, compare groups and identify a pattern to test.

What can be extracted from the data
Ageing and lifespan
- Open Genes
Ageing genes and the experiments in which changing their activity altered lifespan or age-related traits.
- GenAge
Genes linked to human ageing and genes that change lifespan in model organisms.
- AnAge
Maximum lifespan, body mass and age at maturity for more than 4,000 animal species.
- DrugAge
Compounds that extended lifespan in model organisms, with dose, species and effect size.
- GenDR
Genes on which lifespan extension by dietary restriction depends.
- CellAge
Genes that drive or inhibit cellular senescence.
- LongevityMap
Genetic variants tested for association with human longevity, negative results included.
- SynergyAge
Lifespan of model organisms under combinations of genetic interventions.
- Aging Atlas
Gene activity, epigenetic and protein data on ageing collected from many studies.
- Interventions Testing Program
Compounds tested for lifespan effects in genetically diverse mice at three sites in parallel.
- Mouse Phenome Database
Lifespan and traits of mouse strains, including raw Interventions Testing Program data.
- ClockBase
Biological age of human and mouse samples from public DNA methylation data, computed with many epigenetic clocks.
- Human Mortality Database
Mortality and life expectancy by country, year, sex and age.
- International Database on Longevity
Validated ages of people who lived to 105, 110 and beyond.
Cells, tissues and molecules
- Tabula Muris Senis
Single-cell gene activity in 23 mouse tissues and organs at ages from 1 to 30 months.
- Tabula Sapiens
Cell-type atlas of many organs sampled from the same donors.
- Human Cell Atlas
Single-cell data on human tissues from the international consortium's projects.
- CZ CELLxGENE Discover
Standardised single-cell datasets for comparing a gene across tissues, cell types and donor groups.
- GTEx
Gene activity in 54 tissues from nearly 1,000 donors aged 20 to 79, and the genetic variants that change it.
- Human Protein Atlas
Where each human protein is found across tissues, cells and subcellular structures.
- GEO
Archive of gene-activity and epigenetic experiments, including many young-versus-old comparisons.
- ArrayExpress
European archive of functional genomics experiments with sample descriptions.
- SRA
Raw sequencing reads for reprocessing.
- PRIDE
Raw data from proteomics experiments.
- MetaboLights
Raw data from metabolomics experiments.
- HMDB
Human metabolites and their concentrations in blood, urine and tissues.
Human genomes and cohorts
- UK Biobank
Genomes, blood tests, plasma proteins, imaging and health records of 500,000 people, by application.
- NHANES
Examinations and lab tests of US residents linked to mortality records; the PhenoAge clock was trained on them.
- Health and Retirement Study
Long-term follow-up of health, income and cognition in Americans over 50, including DNA methylation.
- Baltimore Longitudinal Study of Aging
Repeated examinations of the same people since 1958, by application.
- All of Us
Genomes, health records and wearable data from hundreds of thousands of US residents.
- FinnGen
Associations of genetic variants with thousands of diagnoses in Finland; summary results are open.
- GWAS Catalog
Published associations of genetic variants with traits, including lifespan and parental longevity.
- gnomAD
Variant frequencies across hundreds of thousands of people and how well each gene tolerates loss of function.
- ClinVar
Clinical significance of human genetic variants.
- dbGaP
Individual-level data from large cohorts such as the Framingham Heart Study, by application.
Proteins, structures and pathways
- UniProt
Protein functions, domains, modifications and variants.
- AlphaFold DB
Predicted structures of more than 200 million proteins.
- RCSB PDB
Experimentally determined structures of proteins and their complexes with small molecules.
- STRING
Known and predicted protein interactions.
- Reactome
Human signalling and metabolic pathways, reaction by reaction.
- KEGG
Metabolic and signalling pathway maps across many organisms.
- Gene Ontology
Gene functions in a shared vocabulary for enrichment analysis.
Compounds, drugs and trials
- ChEMBL
Measured activity of millions of compounds against protein targets.
- DrugBank
Approved and experimental drugs with their targets, metabolism and interactions.
- PubChem
Chemical compounds, their properties and biological screening results.
- Connectivity Map (LINCS)
Gene-activity changes in cells exposed to thousands of compounds; used to find compounds that shift cells towards a younger profile.
- Open Targets
Evidence linking targets to diseases from genetics, experiments and literature.
- FAERS
Adverse drug event reports submitted to the US Food and Drug Administration.
- ClinicalTrials.gov
Registered clinical trials with design, status and results.
- WHO ICTRP
Trials from national registries worldwide in one World Health Organization search.
Model organisms and species comparison
- WormBase
Genes, mutants and phenotypes of the nematode Caenorhabditis elegans, including lifespan.
- FlyBase
Genes, strains and phenotypes of the fruit fly Drosophila melanogaster.
- MGI
Mouse genes and phenotypes of knockout lines.
- SGD
Genes and phenotypes of baker's yeast, including replicative lifespan.
- Ensembl
Vertebrate genomes and gene correspondences across species for comparing long- and short-lived animals.
Publications, grants and patents
- PubMed
Abstracts and records of more than 37 million biomedical publications.
- PubMed Central
Full texts of open-access articles.
- Europe PMC
Full texts and preprints with genes, diseases and compounds tagged automatically.
- bioRxiv
Biology preprints before peer review.
- medRxiv
Medical and clinical preprints before peer review.
- OpenAlex
Links between papers, authors, institutions, citations and funders.
- NIH RePORTER
Projects funded by the US National Institutes of Health, with amounts, investigators and publications.
- The Lens
Patents and scholarly articles with the links between them.
From a cell atlas to a research answer
Research can begin with data already collected. Cell atlases describe the cells in a tissue and the genes they express. Selecting age, tissue and cell type can test a hypothesis, reveal an unusual cell population or suggest an experimental target. The database brings together atlases with their uses, limitations and links to original measurements.
Evidence to build on
Tabula Muris Senis profiled more than 350,000 cells from 23 mouse tissues and organs across age groups. The atlas helps distinguish changes within a cell type from shifts in the proportions of cell types. Those two processes can look similar in measurements averaged over an entire tissue.
What remains unresolved
A large number of cells can come from a small number of animals. Apparent precision at the cell level therefore needs checks at the level of independent organisms, and transfer to humans requires its own validation.
The next useful experiment
Choose an age-associated signal in an open atlas, reproduce it in a separate dataset and test whether changing the implicated process alters tissue function.
Proposed experimentsThe wider strategy
The presentation links progress to cheaper measurements, automation and reusable biological data. This approach asks how those resources can produce reliable, testable knowledge.
The Death-Fighting Spectrum presentation