Marioni Group | Single cell genomics

Marioni Group | Single cell genomics

Marioni Group


Marioni, John
Dr John Marioni
Group Leader

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

Programmes, Associate Research Programmes and Facilities

Partners and Funders

Internal Partners


  • Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels.

    Morgan MD, Patin E, Jagla B, Hasan M, Quintana-Murci L and Marioni JC

    PLoS genetics 2020;16;3;e1008686

  • Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.

    Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ et al.

    Nature communications 2020;11;1;810

  • Eleven grand challenges in single-cell data science.

    Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC et al.

    Genome biology 2020;21;1;31

  • Expression Atlas update: from tissues to single cells.

    Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N et al.

    Nucleic acids research 2020;48;D1;D77-D83

  • Toward a Common Coordinate Framework for the Human Body.

    Rood JE, Stuart T, Ghazanfar S, Biancalani T, Fisher E et al.

    Cell 2019;179;7;1455-1467

  • Multi-omics profiling of mouse gastrulation at single-cell resolution.

    Argelaguet R, Clark SJ, Mohammed H, Stapel LC, Krueger C et al.

    Nature 2019;576;7787;487-491

  • Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis.

    Dobie R, Wilson-Kanamori JR, Henderson BEP, Smith JR, Matchett KP et al.

    Cell reports 2019;29;7;1832-1847.e8

  • Resolving the fibrotic niche of human liver cirrhosis at single-cell level.

    Ramachandran P, Dobie R, Wilson-Kanamori JR, Dora EF, Henderson BEP et al.

    Nature 2019;575;7783;512-518

  • The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

    HuBMAP Consortium

    Nature 2019;574;7777;187-192

  • Challenges in measuring and understanding biological noise.

    Eling N, Morgan MD and Marioni JC

    Nature reviews. Genetics 2019;20;9;536-548

  • IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response.

    Chen HC, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V et al.

    EMBO reports 2019;e47379

  • A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans.

    Saraiva LR, Riveros-McKay F, Mezzavilla M, Abou-Moussa EH, Arayata CJ et al.

    Science advances 2019;5;7;eaax0396

  • Identification of a regeneration-organizing cell in the Xenopus tail.

    Aztekin C, Hiscock TW, Marioni JC, Gurdon JB, Simons BD and Jullien J

    Science (New York, N.Y.) 2019;364;6441;653-658

  • EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.

    Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T et al.

    Genome biology 2019;20;1;63

  • Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis.

    Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC and Odom DT

    Nature communications 2019;10;1;1251

  • Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias.

    Laumer CE, Gruber-Vodicka H, Hadfield MG, Pearse VB, Riesgo A et al.

    eLife 2018;7

  • COMRADES determines in vivo RNA structures and interactions.

    Ziv O, Gabryelska MM, Lun ATL, Gebert LFR, Sheu-Gruttadauria J et al.

    Nature methods 2018;15;10;785-788

  • CTCF maintains regulatory homeostasis of cancer pathways.

    Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C et al.

    Genome biology 2018;19;1;106

  • T cell cytolytic capacity is independent of initial stimulation strength.

    Richard AC, Lun ATL, Lau WWY, Göttgens B, Marioni JC and Griffiths GM

    Nature immunology 2018;19;8;849-858

  • Detection and removal of barcode swapping in single-cell RNA-seq data.

    Griffiths JA, Richard AC, Bach K, Lun ATL and Marioni JC

    Nature communications 2018;9;1;2667

  • Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.

    Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V et al.

    Nucleic acids research 2018;46;12;5950-5966

  • CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.

    Morgan MD and Marioni JC

    Genome biology 2018;19;1;81

  • Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

    Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T et al.

    Molecular systems biology 2018;14;6;e8124

  • Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.

    Haghverdi L, Lun ATL, Morgan MD and Marioni JC

    Nature biotechnology 2018;36;5;421-427

  • Using single-cell genomics to understand developmental processes and cell fate decisions.

    Griffiths JA, Scialdone A and Marioni JC

    Molecular systems biology 2018;14;4;e8046

  • Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens.

    Fergusson JR, Morgan MD, Bruchard M, Huitema L, Heesters BA et al.

    Frontiers in immunology 2018;9;2902

  • SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.

    Do DV, Strauss B, Cukuroglu E, Macaulay I, Wee KB et al.

    Cell discovery 2018;4;33

  • Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.

    Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I et al.

    Cell reports 2017;20;5;1215-1228

  • Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

    Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A et al.

    Cell 2016;165;1;61-74

  • BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.

    Vallejos CA, Marioni JC and Richardson S

    PLoS computational biology 2015;11;6;e1004333

  • High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.

    Achim K, Pettit JB, Saraiva LR, Gavriouchkina D, Larsson T et al.

    Nature biotechnology 2015;33;5;503-9

  • Computational and analytical challenges in single-cell transcriptomics.

    Stegle O, Teichmann SA and Marioni JC

    Nature reviews. Genetics 2015;16;3;133-45

  • Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

    Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A et al.

    Nature biotechnology 2015;33;2;155-60

  • High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

    Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ et al.

    Genome research 2014;24;11;1797-807

  • Accounting for technical noise in single-cell RNA-seq experiments.

    Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X et al.

    Nature methods 2013;10;11;1093-5

  • Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

    Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E et al.

    Genome research 2012;22;12;2376-84