Selected

A single-cell molecular map of mouse gastrulation and early organogenesis
Blanca Pijuan-Sala*, Jonathan A. Griffiths*, Carolina Guibentif*, Tom W. Hiscock, Wajid Jawaid, Fernando J. Calero-Nieto, Carla Mulas, Ximena Ibarra-Soria, Richard C. V. Tyser, Debbie Lee Lian Ho, Wolf Reik, Shankar Srinivas, Benjamin D. Simons, Jennifer Nichols, John C. Marioni, Berthold Göttgens Nature, 2019 https://doi.org/10.1038/s41586-019-0933-9.

I presented this work (as a younger version of myself!) at Biology of Genomes 2018.

Detection and removal of barcode swapping in single-cell RNA-seq data
Jonathan A. Griffiths, Arianne C. Richard, Karsten Bach, Aaron T. L. Lun, John C. Marioni Nature Communications, 2018 https://doi.org/10.1038/s41467-018-05083-x

Using single-cell genomics to understand developmental processes and cell fate decisions
Jonathan A. Griffiths, Antonio Scialdone, John C. Marioni Molecular Systems Biology, 2018 https://doi.org/10.15252/msb.20178046

Others

2025

A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space
Luke TG Harland, Tim Lohoff, Noushin Koulena, Nico Pierson, Constantin Pape, Farhan Ameen, Jonathan A. Griffiths, Bart Theeuwes, Nicola K Wilson, Anna Kreshuk, Wolf Reik, Jennifer Nichols, Long Cai, John C Marioni, Berthold Göttgens, Shila Ghazanfar

2021

Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
Tim Lohoff, Shila Ghazanfar, Alsu Missarova, Noushin Koulena, Nico Pierson, Jonathan A Griffiths, Evan S Bardot, C-HL Eng, Richard CV Tyser, Ricard Argelaguet, Carolina Guibentif, Shankar Srinivas, James Briscoe, Benjamin D Simons, Anna-Katerina Hadjantonakis, Berthold Göttgens, Wolf Reik, Jennifer Nichols, Long Cai, JC Marioni Nature Biotechnology, 2021 https://doi.org/10.1038/s41587-021-01006-2

Integrated Polygenic Tool Substantially Enhances Coronary Artery Disease Prediction
Fernando Riveros-Mckay, Michael E. Weale, Rachel Moore, Saskia Selzam, Eva Krapohl, R. Michael Sivley, William A. Tarran, Peter Sørensen, Alexander S. Lachapelle, Jonathan A. Griffiths, Ayden Saffari, John Deanfield, Chris C.A. Spencer, Julia Hippisley-Cox, David J. Hunter, Jack W. O’Sullivan, Euan A. Ashley, Vincent Plagnol, Peter Donnelly Circulation: Genomic and Precision Medicine, 2021 https://doi.org/10.1161/CIRCGEN.120.003304

2020

Diverse Routes toward Early Somites in the Mouse Embryo
Carolina Guibentif*, Jonathan A. Griffiths*, Ivan Imaz-Rosshandler, Shila Ghazanfar, Jennifer Nichols, Valerie Wilson, Berthold Göttgens, John C. Marioni Developmental Cell, 2020 https://doi.org/10.1016/j.devcel.2020.11.013

2017

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data
Jonathan A. Griffiths, Antonio Scialdone, John C. Marioni BMC Genomics, 2017 https://doi.org/10.1186/s12864-017-4253-x