Dr. rer. nat. James A. Fellows Yates
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Dr. rer. nat. James A. Fellows Yates

Dr. rer. nat. James A. Fellows Yates

Bioinformatician and Biomolecular Archaeologist

English, German

Background


About

About

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.

Work Experience

Work Experience

Projects Experience

Projects Experience

  • nf-core/eager

    - Present

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline.

  • nf-core/taxprofiler

    - Present

    Highly parallelised multi-taxonomic profiling of shotgun metagenomic data.

  • nf-core/funcscan

    - Present

    Screening of functional components and natural products from assembled contigs

  • cuperdec

    - Present

    R library to generate 'Cumulative Percent Decay' curves for microbial taxonomic profiles

  • AncientMetagenomeDir

    - Present

    Repository containing lists of all published ancient metagenome samples (and related)

  • BareBonesBash

    - Present

    Walkthroughs and presentations for a gentle gif-filled introduction to using bash

  • MEx-IPA

    - Present

    Interactive results viewer for maltExtract

Skills

Skills

  • Linux

    Installation

    Administration

    Ubuntu

  • Nextflow

    Pipeline development

    DSL1

    Genomics

  • R

    Tidyverse

    Packages

    Shiny

  • Shell

    Bash

    File management

    File modification

    sed

    vim

  • Conda

    bioconda

    recipes

    environments

  • Git

    GitHub

    GitHub Actions

Education

Education

  • Bioinformatics, Ph.D., Friedrich-Schiller-Universität Jena (Jena, Germany) / Max Planck Institute for the Science of Human History (Jena, Germany) / Max Planck Institute for Evolutionary Anthropology (Leipzig, Germany)

    Oct, 2015 - May, 2022

  • Paläogenetik; Naturwissenschaftliche Archäologie, M.Sc., Eberhard Karls Universität Tübingen

    Oct, 2013 - Sep, 2015

  • Bioarchaeology, B.Sc. Hons., University of York

    Oct, 2010 - Sep, 2013

Awards

Awards

  • 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]

Volunteer Work

Volunteer Work

  • 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

Publications

Publications

  • Ancient Metagenomic Studies: Considerations for the Wider Scientific Community , mSystems

    Published on: Dec 21, 2021

    Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions & Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.

  • 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.

  • Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager , PeerJ

    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

  • Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir , Scientific Data

    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.

  • Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus , Quaternary International

    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.

  • Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir , bioRxiv

    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.

  • Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager , bioRxiv

    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.

  • Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene , BioScience

    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.

  • Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage , Microbiome

    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.

  • Differential preservation of endogenous human and microbial DNA in dental calculus and dentin , Scientific Reports

    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.

  • Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes , Scientific Reports

    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.