Marioni Group | Single cell genomics
John Marioni's group develop computational and statistical tools to exploit high-throughput genomics data to understand the regulation of gene expression and to model developmental and evolutionary processes. His team has pioneered approaches for analysing single-cell transcriptomics data and, together with four colleagues, he co-ordinates the Sanger Institute-EBI Single-Cell Genomics Centre.
Key Projects, Collaborations, Tools & Data
Research Programmes and Faciltites
Partners and Funders
Resolving the fibrotic niche of human liver cirrhosis at single-cell level.
PUBMED: 31597160; DOI: 10.1038/s41586-019-1631-3
IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response.
EMBO reports 2019;
PUBMED: 31283095; DOI: 10.15252/embr.201847379
A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans.
Science advances 2019;5;7;
PUBMED: 31392275; PMC: 6669018; DOI: 10.1126/sciadv.aax0396; URL:
Challenges in measuring and understanding biological noise.
Nature reviews. Genetics 2019
PUBMED: 31114032; DOI: 10.1038/s41576-019-0130-6
Identification of a regeneration-organizing cell in the Xenopus tail.
Science (New York, N.Y.) 2019;364;6441;
PUBMED: 31097661; DOI: 10.1126/science.aav9996
EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.
Genome biology 2019;20;1;
PUBMED: 30902100; PMC: 6431044; DOI: 10.1186/s13059-019-1662-y
Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis.
Nature communications 2019;10;1;
PUBMED: 30890697; DOI: 10.1038/s41467-019-09182-1
Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias.
PUBMED: 30373720; DOI: 10.7554/eLife.36278
COMRADES determines in vivo RNA structures and interactions.
Nature methods 2018
PUBMED: 30202058; DOI: 10.1038/s41592-018-0121-0
CTCF maintains regulatory homeostasis of cancer pathways.
Genome biology 2018;19;1;
PUBMED: 30086769; DOI: 10.1186/s13059-018-1484-3
T cell cytolytic capacity is independent of initial stimulation strength.
Nature immunology 2018
PUBMED: 30013148; DOI: 10.1038/s41590-018-0160-9
Detection and removal of barcode swapping in single-cell RNA-seq data.
Nature communications 2018;9;1;
PUBMED: 29991676; PMC: 6039488; DOI: 10.1038/s41467-018-05083-x
CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.
Genome biology 2018;19;1;
PUBMED: 29945659; DOI: 10.1186/s13059-018-1461-x
Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.
Molecular systems biology 2018;14;6;
PUBMED: 29925568; PMC: 6010767
Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.
Nucleic acids research 2018
PUBMED: 29860520; DOI: 10.1093/nar/gky437
Using single-cell genomics to understand developmental processes and cell fate decisions.
Molecular systems biology 2018;14;4;
Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Nature biotechnology 2018
PUBMED: 29608177; DOI: 10.1038/nbt.4091
Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens.
Frontiers in immunology 2018;9;
PUBMED: 30692988; PMC: 6340304; DOI: 10.3389/fimmu.2018.02902
SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.
Cell discovery 2018;4;
PUBMED: 29928511; PMC: 6006335; DOI: 10.1038/s41421-018-0032-3