Sep, 2021 - Present
James is a biomolecular archaeologist turned bioinformatician. His research is currently the metagenomic analysis of next generation sequencing data of ancient microbiomes. He leads the development of a range of open-source tools including the nextflow best-practices pipeline nf-core/eager, as well as packages in R and 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.
Sep, 2021 - Present
Scientific Researcher, Department of Archaeogenetics, Max-Planck-Institut für evolutionäre Anthropologie
Jan, 2021 - Present
Jun, 2020 - Aug, 20211 year 3 months
PhD Student Researcher, Department of Archaeogenetics, Max-Planck-Institut für Menschheitsgeschichte
Oct, 2015 - May, 20204 years 8 months
Mar, 2015 - Sep, 20157 months
Research Assistant, AG Biogeologie, Biogeologie, Eberhard Karls Universität Tübingen
Mar, 2015 - Sep, 20157 months
Sample preparation and logging
Data digitalisation and cleaning
Bioinformatics, Ph.D., Friedrich-Schiller-Universität Jena (Jena Germany) / Max Planck Institute for the Science of Human History (Jena, Germany)
Oct, 2015 - Present
Paläogenetik; Naturwissenschaftliche Archäologie, M.Sc., Eberhard Karls Universität Tübingen
Oct, 2013 - Sep, 2015
Bioarchaeology, B.Sc. Hons., University of York
Oct, 2010 - Sep, 2013
Studienstipendien für Graduierte aller wissenschaftlichen Fächer , DAAD - Deutscher Akademischer Austauschdienst
Awarded on: Oct 01, 2014
Scholarship for studying at a German institution. €7860
Edward Hall Memorial Fund [Declined] , Research Laboratory for Archaeology and the History of Art - University of Oxford
Awarded on: Oct 01, 2013
Postgraduate scholarship for studying at the University of Oxford. £1000 [Declined]
Founder, SPAAM Community (Standards, Precautions and Adbances in Ancient Metagenomics)
Jan, 2020 - Present
Grass roots community of early career researchers in ancient metagenomics, aiming promote collaboration and knowledge sharing the field.
Founder of the organisation
Lead organiser the SPAAM2 workshop (2021)
Leader of first SPAAM collaborative project - AncientMetagenomeDir
Core team member, nf-core
Aug, 2020 - Present
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Developed initiative wide documentation
Co-organised and ran hackathons
Provided general training and support
The evolution and changing ecology of the African hominid oral microbiome , Proceedings of the National Academy of Sciences
Published on: May 18, 2021
The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, 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.
Published on: Mar 16, 2021
We present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices
Published on: Jan 26, 2021
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.
Published on: Nov 19, 2020
We highlight common errors and sources of contamination across ancient DNA datasets, provide recommendations for dietary DNA validation, and call for caution in the interpretation of diet from dental calculus and other archaeological microbiome substrates.
Published on: Sep 03, 2020
[Preprint] AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) 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.
Published on: Jun 12, 2020
[Preprint] In the context of this heterogeneous landscape, we present nf-core/eager, an advanced and entirely redesigned pipeline for the analysis of ancient genomic data. nf-core/eager builds on existing ideas and concepts introduced in the original EAGER pipeline, and improves various aspects of the analysis procedure by employing computational frameworks such as Nextflow and nf-core.
Published on: Oct 02, 2019
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.
Published on: Jul 06, 2019
Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.
Published on: Jun 29, 2018
Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach.
Published on: Dec 18, 2017
Here, 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.
A Robust Framework for Microbial Archaeology , A Robust Framework for Microbial Archaeology
Published on: Apr 26, 2017
Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples.