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James A. Fellows Yates

James A. Fellows Yates

Bioinformatician and Biomolecular Archaeologist

Leipzig, Sachsen, DE
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.

  • 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)

    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

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