Jonathan Griffiths

Jonathan Griffiths

Computational Biologist

Altos Labs

Biography

I am a computational scientist motivated by solving challenging problems, whose solutions positively impact human health. I have extensive experience across biology, genomics, statistics, and machine learning domains, both in academic and commercial settings.

Currently, I am working at Altos Labs in the BioML team, working across genetics, -omics, and machine learning/AI to build powerful models of how the genome functions.

Previously, I worked in the therapeutics arm of Genomics plc. I applied my integrative set of skills to understand biological processes from a broad range of modern, high-throughput datasets (primarily genetic associations and genomics) to identify opportunities for therapeutic intervention, and guided the design of experiments to validate these stories.

During my PhD, I worked on methodology for analysing the first large-scale, droplet-based single-cell RNA-sequencing data. I applied these methods by leasing the analysis of a landmark scRNA-seq dataset of mouse embryonic development. My PhD was funded by Wellcome, in the Marioni lab (Cambridge UK).

Interests
  • Functional genomics
  • Human genetics
  • Machine learning
  • Single-cell data & methods
Education
  • PhD (Single-cell genomics), 2019

    Marioni lab, University of Cambridge

  • BSc (Natural Sciences), 2015

    University College London

Themes

Statistics & machine learning
Genomics & human genetics
Single-cell methods
Data sharing
R aficionado
Espresso

Career

 
 
 
 
 
Computational Biologist
Jul 2022 – Present Cambridge, UK
I am working with Thore Graepel in the AI/ML team combining human genetics, omics, and large-scale machine learning data in Altos to to drive development of disease-reversing therapeutic targets.
 
 
 
 
 
Senior Scientist
May 2021 – Jun 2022 Cambridge, UK
In addition to further developing my target-focused work, I: worked closely with experimental collaborators for target validation; benchmarked and improved internal genetic association tools; establish substantial expertise in our disease area (including individual-level analyses and evaluation of the therapeutic landscape); and identified and resolved various other research questions as necessary.
 
 
 
 
 
Scientist
May 2019 – Apr 2021 Cambridge, UK
I developed a range of tools and analyses to provide insight from functional genomic data, including end-to-end handling of single-cell RNA-seq datasets for work in Therapeutics, as well as improvements to the risk prediction tools for the Precision Health side of Genomics plc. Subsequently I moved into an internal therapeutics project, where I focused on the identification of new targets for therapeutic intervention, working from target ID through analyses to story-building and presentation.
 
 
 
 
 
PhD student
Sep 2015 – Sep 2019 University of Cambridge
I led analysis on a landmark atlas of mouse embryonic development and subsequently generated gene-knockout chimaeric embryos. In addition, I developed several tools for analysis of single-cell RNA-sequencing data, including estimation of ploidy and remval of barcode-swapping sequencing artefacts.

Training & consulting

APTS PhD statistics course
Four weeks of residential training in statistics and applied probability. Training is provided at a level suitable for mathematics and statistics PhD students.
Consultancy for Elpis Biomed
Provided analysis and interpretation of in-house RNA-sequencing data, including integration with public datasets.
Human Cell Atlas hackathon
Invited to a hackathon on how to cost-effectively generate data for the Human Cell Atlas.

Publications

(2021). Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nature Biotechnology.

PDF Cite DOI

(2021). Integrated Polygenic Tool Substantially Enhances Coronary Artery Disease Prediction. Circulation: Genomic and Precision Medicine.

PDF Cite DOI

(2020). Diverse Routes toward Early Somites in the Mouse Embryo. Developmental Cell.

PDF Cite DOI

(2019). A single-cell molecular map of mouse gastrulation and early organogenesis. Nature.

Cite DOI

(2018). Detection and removal of barcode swapping in single-cell RNA-seq data. Nature Communications.

PDF Cite DOI

Contact