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.
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
We analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison.
We present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data.
AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories.
We demonstrate the challenges associated with accurate taxonomic identification and authentication of dietary taxa in ancient DNA data using both synthetic and ancient dental calculus datasets
AncientMetagenomeDir is a collection of indices of published genetic data deriving from ancient microbial samples that provides basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories.
We present nf-core/eager, an advanced and entirely redesigned pipeline for the analysis of ancient genomic data
In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena.
Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.
In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach.
We use a multi-method approach utilising proteomic, stable isotope and genetic techniques to identify and generate twenty woolly mammoth mitochondrial genomes, and associated dietary stable isotopic data, from highly fragmentary Late Pleistocene material from central Europe.