James Yates
Scientific Researcher at Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute
Leipzig, Saxony, Germany
Summary
🤩
Rockstar🎓
Top SchoolJames Yates is a bioinformatician and scientific researcher with 10 years’ experience building scalable, community-driven open-source tooling for metagenomics, ancient DNA and microbiome analysis. He leads development of multiple nf-core Nextflow pipelines and core tools, shepherding international contributor teams and championing reproducible workflows used across the field. James created field-wide metadata standards and the AncientMetagenomeDir repository, helping curate >7,000 libraries and consulting with 100+ researchers to improve FAIR data practices. He has a strong software-engineering footprint—contributions to projects like MultiQC and bioconda plus backend work on nf-core/tools demonstrate full-stack and CI/build expertise. A PhD-trained bioinformatician who also co-organised a globally attended summer school and edited its textbook, he combines deep domain knowledge with community leadership and practical automation skills.
10 years of coding experience
1 year of employment as a software developer
Doctor of Philosophy - PhD, Bioinformatics, magna cum laude (1,1), Doctor of Philosophy - PhD, Bioinformatics, magna cum laude (1,1) at Friedrich Schiller University JenaMaster of Science - MSc, Naturwissenschaftliches Archäologie, Sehr-Gut, Master of Science - MSc, Naturwissenschaftliches Archäologie, Sehr-Gut at University of TübingenBachelor of Science - BSc, Bioarchaeology, First, Bachelor of Science - BSc, Bioarchaeology, First at University of YorkDoctor of Philosophy - PhD, Bioinformatics, magna cum laude (1,1), Doctor of Philosophy - PhD, Bioinformatics, magna cum laude (1,1) at Max Planck Institute for the Science of Human History
Github Skills (33)
website-development10
package-management10
python10
bash10
conda10
integrations10
nextflow10
e-mail10
automation10
php10
build-automation10
pipeline10
mu10
bioinformatics10
automations10
Programming languages (26)
Github contributions (5)
nf-core/website
Mar 2020 - Jan 2023
Code and files for the main nf-core website.
Role in this project:
Full-stack Developer
Full-stack DeveloperContributions:456 reviews, 308 commits, 277 PRs in 2 years 11 months
Contributions summary:James made several changes to the nf-core website, including updates to the PHP functions, header, and footer files. They restructured the tutorial storage and updated the tools documentation. They also implemented new features and content, such as adding a section for a new module and incorporating the Gather Town information on the join page, as well as fixing minor issues like the pipeline stats link.
nf-corenextflow
nf-core/tools
Jan 2020 - Jan 2023
Python package with helper tools for the nf-core community.
Role in this project:Back-end Developer
Back-end DeveloperContributions:96 reviews, 123 commits, 80 PRs in 3 years
Contributions summary:James primarily contributed to the enhancement of the `nf-core/tools` pipeline template, focusing on email notification features. They implemented the ability to attach MultiQC reports to emails, added conditional logic based on report size, and improved the email content type to ensure proper display. Further improvements involved refactoring the email command creation and updating the MultiQC versions and configurations used in the template.
nf-corelinterpythonpipelinelinting
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