James A. Fellows Yates

James A. Fellows Yates

Bioinformatician and Biomolecular Archaeologist

Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie Hans-Knöll-Institut


I am a biomolecular archaeologist and bioinformatician. I currently work between the Department of Palaeobiotechnology at the Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute and Max Planck Institute for Evolutionary Anthropology, while finishing up my my Ph.D. on ancient oral microbiomes .

I originally trained as an Archaeologist at the University of York, where I specialised in palaeoproteomics. After which I moved to the Universität Tübingen to study for an M.Sc. in Archaeological Sciences, specialising in palaeogenetics. During my time in Tübingen I also worked as a technician for a stable isotope lab. I worked for a short period for the Institut für Vor- und Frühgeschichtliche Archäologie and Provinzialrömische Archäologie at LMU München, developing strategies for authenticating ancient dietary DNA.

My current area of research is centred on the ancient DNA content of fossilised dental plaque, also known as dental calculus. My sample set includes individuals spanning from the Palaeolithic to modern day. I am primarily exploring how we can analyse and authenticate the complex genetic make-up of this material through shotgun metagenomics.

I am involved in the leading and developing of the open-source nexflow pipeline nf-core/eager (v2), which is intended to be a complete re-write and extension of the NGS processing pipeline for ancient DNA data EAGER (v1), to reach modern computational and palaeogenetic standards. I am developing and contributing to multiple open-source software focusing on ancient metagenomics (which can be seen on my github).

I also established an international community of researchers in ancient metagenomics, and ran the associated SPAAM2 round-table workshop, and I am also a core-team member of the nf-core initiative for best-practise Nextflow bioinformatic pipelines.

Previously, I have worked on Late Pleistocene woolly mammoth mitochondrial genomes, as well as testing collagen ‘fingerprinting’ methods (ZooMS) on burnt skeletal remains.

See my resumé.

  • Ancient Metagenomics
  • Bioinformatics
  • Ph.D. in Bioinformatics, 2021

    FSU Jena / MPI-SHH

  • M.Sc. in Naturwissenschaftliche Archäologie, 2015

    Eberhard Karls Universität Tübingen

  • BSc in Bioarchaeology, 2013

    University of York

Recent & Upcoming Talks

Introduction to Archaeogenetics
Invited Lecture
nf-core/eager: Reproducible, portable, and efficient ancient genome reconstruction
Conference Poster

Recent Publications

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