James is a biomolecular archaeologist turned bioinformatician. His work currently focuses on the development of pipelines and tools for high-throughput analysis of next generation sequencing data of ancient metagenomics. He leads the development and is a contributor to a range of open-source metagenomics Nextflow pipelines and as well as tools in written in in R and Shiny. He is a core member of the nf-core bioinformatics pipeline initiative and the founder of the SPAAM community of ancient metagenomics researchers, the latter of which he runs a collaborative project improving access to ancient metagenomic data via metadata standardisation. He also has a passion for open science, spanning open-data, open-software, and open-protocols.
Post Doctoral Researcher
Development and training of/in metagenomic bioinformatic tools and pipelines. Sample and Next Generation Sequencing Data and project management and organisation. Establishment, organisation and teaching of/at a graduate-level summer school. Supervision of graduate students.
Development of approaches and tools for novel archaeological metagenomic data for an ERC project.
- Sample preparation and logging
- Collagen extraction
- Data digitalisation and cleaning
A list of the main set of projects I am currently working on or have developed.
See Projects. All projects contributed to date are OSS.
My publications and preprints
"> Conferences and Invited Talks
SedaDNA Society, Pacific Seminar Series, October 2022, Online
Nextflow Summit, October 2022, Barcelona Spain
Standards Precautions, and Advances in Ancient Metagenomics 2022 (SPAAM4), October 2022, Online
Applied Hologenomics, October 2022, Bilbao, Spain (Presented by supervisor due to sickness)
Palaeoproteomics Section, GLOBE Institute, Copenhagen, Denmark, Apr 2022, Online
Series: NGI Sweden Outreach (Ancient DNA), November 2021, Online
Standards Precautions, and Advances in Ancient Metagenomics 2021 (SPAAM3), September 2021, Online
International Symposium for Biomolecular Archaeology (ISBA9), June 2021, Online
Wellcome Trust Connecting Science - Ancient Biomolecules of Plants, Animals, and Microbes, March 2021, Online
Standards Precautions, and Advances in Ancient Metagenomics 2020 (SPAAM2), September 2020, Online
International Symposium for Biomolecular Archaeology (ISBA8), September 2018, Jena, Germany
Annual Meeting of the European Association for Archaeologists (EAA 2018), September 2018, Barcelona, Spain
Society for Molecular Biology and Evolution (SMBE18), July 2018, Yokohama, Japan
Megafauna and Methods Workshop, February 2017, Jena, Germany
Workshop ‘All About Teeth’, July 2019, EVEREST graduate school, University of Tübingen, Germany
Archaeological Science workshop ‘Palaeodiet’, July 2018, Institute for Archaeological Sciences, University of Tübingen, Germany
International Symposium for Biomolecular Archaeology (ISBA7), September 2016, Oxford, United Kingdom
"> Funding and Grants
Graduate Scholarship for studying at a German institution. €7860
Postgraduate scholarship for studying at the University of Oxford. £1000 [Declined]
Skills & Proficiency
These are my blog posts
- 2020-03-17: All Possible NCBI Taxonomy Ranks
- 2020-03-17: Gentle introduction to nf-core/eager
- 2019-06-18: pvclust Node Values In ggtree
- 2019-05-03: 'Tidy' Pop-Gen PCA plotting in R
- 2017-10-08: Updating a Github Pages Theme Through a Repo Merge
- 2017-08-03: How-to: Sequin Submission to Genbank Tutorial
- 2017-05-28: How-to: Simple 'change over time' maps in R
- 2017-05-28: How-to: cancel a MrBayes run early