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Dr. James A. Fellows Yates

Bioinformatician

Education

PhD in Bioinformatics

Friedrich-Schiller-Universität Jena (Max Planck Institute for the Science of Human History / Max Planck Institute for Evolutionary Anthropology, 🇩🇪)
2015 - 2022

MSc in Naturwissenschaftliches Archäologie

Eberhard-Karls-Universität Tübingen (🇩🇪)
2013 - 2015

BSc (Hons) in Biomolecular Archaeology

University of York (🇬🇧)
2010 - 2013

Languages

  • English (Native)
  • German (B2)
  • Spanish (Basic)
  • Catalan (Basic)

Career Profile

James is a biomolecular archaeologist turned bioinformatician. His work currently focuses on the development of pipelines and tools for high-throughput analysis of next generation sequencing data of ancient metagenomics. He leads the development and is a contributor to a range of open-source metagenomics Nextflow pipelines and as well as tools in written in in 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, the latter of which he runs a collaborative project improving access to ancient metagenomic data via metadata standardisation. He also has a passion for open science, spanning open-data, open-software, and open-protocols.

Post Doctoral Researcher

Post Doctoral Researcher

2021 - Present
Department of Palaeobiotechnology, Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie Hans-Knöll-Institut / Microbiome Sciences Group, Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology

Development and training of/in metagenomic bioinformatic tools and pipelines. Sample and Next Generation Sequencing Data and project management and organisation. Establishment, organisation and teaching of/at a graduate-level summer school. Supervision of graduate students.

Scientific Researcher

2020-2021
Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München

Development of approaches and tools for novel archaeological metagenomic data for an ERC project.

Research Assistance

2015
AG Biogeologie, Biogeologie, Eberhard Karls Universität Tübingen

Data processing:

  • Sample preparation and logging
  • Collagen extraction
  • Data digitalisation and cleaning

Projects

A list of the main set of open source projects I am currently working on or have developed.

AncientMetagenomeDir - Community-curated repository of standardised metadata and download information for all publically available ancient (microbial) (meta)genome
MInAS - The MInAS project aims to develop standardised metadata reporting schemes of ancient DNA samples and sequencing data via community-based consensus and training.
Introduction to Ancient Metagenomics (SPAAM Summer School and Textbook) - A yearly practical summer school/block course introducting graduate and doctoral students to the basic bioinformatic workflows ancient metagenomics. All teaching material is dervied on a community curated textbook
Little Book of Smiley Plots - A light-hearted reference book of ancient DNA damage plots and their causes

OSS Contributions

See Projects. All projects contributed to date are OSS.

nf-core/eager - Lead developer of a fully reproducible and state-of-the-art Nextflow ancient DNA analysis pipeline for genomic analysis and pathogen screening.
nf-core/taxprofiler - Lead developer of a Nextflow pipeline for simultaenous multi-taxonomic profiling of shotgun metagenomic data.
nf-core/funcscan - Senior developer of a Nextflow pipeline for the screening of functional components and natural products from assembled contigs.
nf-core/mag - Regular contributor to a metagenomic _de novo_ assembly and binning pipeline written in Nextflow.
cuperdec - R Package for calculating and visualising cumulative percent 'decay' curves (a method I developed during my PhD), which are typically calculated from metagenomic taxonomic profiles. Available on CRAN.
MEx-IPA - This R shiny app is a modified implementation of the metric visualisation script of the HOPS pipeline, with additional interactive plot functionality.

Publications

My publications and preprints

  • Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
    • Borry, M., Forsythe, A., Valtueña Andrades, A., Hübner, A.,; Ibrahim, A., Quagliariello, A., White, A. E., Kocher, A., Vågene‬, Å. J., Bartholdy, B. P., Spurīte, D., Ponce-Soto, Gabriel Y.,; Neumann, G., Huang, I-T., Light, I., Velsko, I. M., Jackson, I., Frangenberg, J., Serrano, J. G., Fumey, J., Özdoğan, K. T.; Blevins, K. E., Daly, K. G., Lopopolo, M., Moraitou, M., Michel, M., van Os, M., Bravo-Lopez, M. J., Sarhan, M. S., Dagtas, N. D., Oskolkov, N., Smith, O. S., Lebrasseur, O., Rozwalak, P., Eisenhofer, R., Wasef, S., Ramachandran, S. L., Vanghi, V., Warinner, C., Fellows Yates, J. A.
    (2023) F1000
  • TAXPASTA: TAXonomic Profile Aggregation and STAndardisation
    • Beber, M. E., Borry, M., Stamouli, S., Fellows Yates, J. A.
    (2023) Journal of Open Source Software.
  • Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic
    • Klapper, M., Hübner, A., Ibrahim, A., Wasmuth, I., Borry, M., Haensch, V. G., Zhang, S., Al-Jammal, W. K., Suma, H., Fellows Yates, J. A., Frangenberg, J., Velsko, I. M., Chowdhury, S., Herbst, R., Bratovanov, E. V., Dahse, H.-M., Horch, T., Hertweck, C., González Morales, M. R., Straus, L.G., Vilotijevic, I., Warinner, C., Stallforth, P.
    (2023) Science.
  • Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species.
    • Moraitou, M., Forsythe, A., Fellows Yates, J. A., Brealey, J. C., Warinner, C., & Guschanski, K.
    (2022). Molecular Biology and Evolution, 39(12).
  • Ecology, not host phylogeny, shapes the oral microbiome in closely related species of gorillas.
    • Moraitou, M., Forsythe, A., Fellows Yates, J. A., Brealey, J. C., Warinner, C., & Guschanski, K.
    (2022). bioRxiv (p. 2022.06.06.494923).
  • Ancient Metagenomic Studies: Considerations for the Wider Scientific Community.
    • Der Sarkissian, C., Velsko, I. M., Fotakis, A. K., Vågene, Å. J., Hübner, A., & Fellows Yates, J. A.
    (2021). mSystems, 6(6), e0131521.
  • The evolution and changing ecology of the African hominid oral microbiome.
    • Fellows Yates, J. A., Velsko, I. M., Aron, F., Posth, C., Hofman, C. A., Austin, R. M., Parker, C. E., Mann, A. E., Nägele, K., Arthur, K. W., Arthur, J. W., Bauer, C. C., Crevecoeur, I., Cupillard, C., Curtis, M. C., Dalén, L., Bonilla, M. D.-Z., Carlos Díez Fernández-Lomana, J., Drucker, D. G., … Warinner, C.
    (2021). PNAS 118(20), e2021655118.
  • Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.
    • Fellows Yates, J. A., Lamnidis, T. C., Borry, M., Andrades Valtueña, A., Fagernäs, Z., Clayton, S., Garcia, M. U., Neukamm, J., & Peltzer, A.
    (2021). PeerJ, 9, e10947.
  • Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.
    • Fellows Yates, J. A., Andrades Valtueña, A., Vågene, Å. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-Lopez, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., Zaro, V., & Warinner, C.
    (2021). Scientific Data, 8(1), 31.
  • Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus.
    • Mann, A. E., Fellows Yates, J. A., Fagernäs, Z., Austin, R. M., Nelson, E. A., & Hofman, C. A.
    (2020). Quaternary International
  • Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.
    • Fellows Yates, J. A., Lamnidis, T. C., Borry, M., Andrades Valtueña, A., Fagernäs, Z., Clayton, S., Garcia, M. U., Neukamm, J., & Peltzer, A.
    (2020). bioRxiv (p. 2020.06.11.145615).
  • Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.
    • Fellows Yates, J. A., Valtueña, A. A., Vågene, A. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-López, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., & Warinner, C.
    (2020). bioRxiv (p. 2020.09.02.279570).
  • Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene.
    • Swift, J. A., Bunce, M., Dortch, J., Douglass, K., Faith, J. T., Fellows Yates, J. A., Field, J., Haberle, S. G., Jacob, E., Johnson, C. N., Lindsey, E., Lorenzen, E. D., Louys, J., Miller, G., Mychajliw, A. M., Slon, V., Villavicencio, N. A., Waters, M. R., Welker, F., … Roberts, P.
    (2019). Bioscience, 69(11), 877-887.
  • Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage.
    • Velsko, I. M., Fellows Yates, J. A., Aron, F., Hagan, R. W., Frantz, L. A. F., Loe, L., Martinez, J. B. R., Chaves, E., Gosden, C., Larson, G., & Warinner, C.
    (2019). Microbiome, 7(1), 102.
  • Differential preservation of endogenous human and microbial DNA in dental calculus and dentin.
    • Mann, A. E., Sabin, S., Ziesemer, K., Vågene, Å. J., Schroeder, H., Ozga, A. T., Sankaranarayanan, K., Hofman, C. A., Fellows Yates, J. A., Salazar-García, D. C., Frohlich, B., Aldenderfer, M., Hoogland, M., Read, C., Milner, G. R., Stone, A. C., Lewis, C. M., Jr, Krause, J., Hofman, C., Bos, K.I., Warinner, C.
    (2018). Scientific Reports, 8(1), 9822.
  • Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes.
    • Fellows Yates, J. A., Drucker, D. G., Reiter, E., Heumos, S., Welker, F., Münzel, S. C., Wojtal, P., Lázničková-Galetová, M., Conard, N. J., Herbig, A., Bocherens, H., & Krause, J.
    (2017) Scientific Reports, 7(1), 17714
  • A Robust Framework for Microbial Archaeology
    • Warinner, C., Herbig, A., Mann, A., Fellows Yates, J. A., Weiß, C. L., Burbano, H. A., Orlando, L., & Krause, J.
    (2017) Annual Review of Genomics and Human Genetics, 18, 321-356

    "> Conferences and Invited Talks

    Invited Talk: Bioinformatic Resources for (Ancient) Metagenomics

    2023
    Fellows Yates, J. A.,

    sedaDNA Society Yearly Meeting, June 2023, Tübingen, Germany

    Invited Talk: Community-curated NGS analysis pipelines

    2023
    Fellows Yates, J. A.,

    Next Generation Sequencing Competence Network Yearly Workshop (Germany), April 2023, Tübingen, Germany

    Invited Talk: Introduction to the SPAAM community and open-science initiatives

    2022
    Fellows Yates, J. A.,

    SedaDNA Society, Pacific Seminar Series, October 2022, Online

    Conference Poster: Efficient parallel taxonomic profiling for metagenomics with nf-core/taxprofiler

    2022
    Fellows Yates, J. A., Beber, M. E., Stamouli, S., Mesilaakso, L., Normark, T., Ou, J., Christensen, T.A., Jamy, M., Borry, M., Stępień, R, & nf-core community

    Nextflow Summit, October 2022, Barcelona Spain

    Conference Talk: cuperdec: assessing endogenous community preservation in (ancient) microbiome samples through cumulative percent decay

    2022
    Fellows Yates, J. A.

    Standards Precautions, and Advances in Ancient Metagenomics 2022 (SPAAM4), October 2022, Online

    Conference Poster: Improving accessiblity to ancient microbiome data beyond palaeogenomics

    2022
    Fellows Yates, J. A., SPAAM community, & nf-core Community

    Applied Hologenomics, October 2022, Bilbao, Spain (Presented by supervisor due to sickness)

    Invited Talk: Open Science Initiatives in Ancient (Meta)genomics

    2022
    Fellows Yates, J.A.

    Palaeoproteomics Section, GLOBE Institute, Copenhagen, Denmark, Apr 2022, Online

    Invited Talk: nf-core/eager: High-throughput and scalable palaeogenomics using nf-core/eager

    2021
    Fellows Yates, J.A.,

    Series: NGI Sweden Outreach (Ancient DNA), November 2021, Online

    Conference Talk: High-throughput and scalable ancient metagenomic analysis using nf-core/eager

    2021
    Fellows Yates, J.A.

    Standards Precautions, and Advances in Ancient Metagenomics 2021 (SPAAM3), September 2021, Online

    Conference Poster: nf-core/eager: Reproducible, portable, and efficient ancient genome reconstruction

    2021
    Fellows Yates, J.A., Lamnidis, T.C., Borry, M., Andrades Valtueña, A., Fagernäs, Z., Clayton, S., Garcia M.U, Neukamm, J., Peltzer, A.

    International Symposium for Biomolecular Archaeology (ISBA9), June 2021, Online

    Conference Poster: Improving access to ancient metagenomic data with the community-curated metadata repository AncientMetagenomeDir

    2021
    Fellows Yates, J. A., Andrades Valtueña, A., Vågene, Å. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-Lopez, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., Zaro, V., & Warinner, C.

    Wellcome Trust Connecting Science - Ancient Biomolecules of Plants, Animals, and Microbes, March 2021, Online

    Conference Talk: Towards standards in metadata reporting in ancient metagenomic studies: experiences from AncientMetagenomeDir

    2020
    Towards standards in metadata reporting in ancient metagenomic studies: experiences from AncientMetagenomeDir

    Standards Precautions, and Advances in Ancient Metagenomics 2020 (SPAAM2), September 2020, Online

    Conference Talk: Reconstruction of Oral Microbiomes from Extinct and Extant Anthropoids through ancient DNA

    2018
    Fellows Yates. J.A.; Aron, F.; Velsko, I.; Arthur, J.; Austin, R.M.; Crevecoeur, I.; Dalén, L.; Gonzalez Morales M.R.; Guschanski K.; Henry, A.G.; Hofman, C.A.; Humphrey, L.T.; Lewis, C.M.; Mann, A.E.; Nägele, K.; Parker, C.E.; Posth, C.; Rougier, H.; Sankaranarayan, K.; Semal, P., Stock, J.; Strauss, L.G.; Weedman Arthur, K.; Wrangham, R.W; Curtis, M.C; Diez, J.C.; Gibbon, V.E.; Menedez, M.; Peresani, M.; Roksandic, M.; Walker, M.J.; Power, R.C.; Salazar-Garcia, D.C.; Krause, J; Herbig, A.; Warinner. C.

    International Symposium for Biomolecular Archaeology (ISBA8), September 2018, Jena, Germany

    Conference Talk: Palaeogenomic Investigation Of 50,000 Years Of The Human Oral Microbiome In The Iberian Mediterranean

    2018
    Fellows Yates, J.A.; Salazar-García D.C.; Hofman, C.A.; Aron, F.; Power, R.C.; Benítez de Lugo Enrich, L.; Haber, M.; García Atiénzar, G.;Oms, X.; Benito, M.; Avilés Fernández, A.; Sanz, M.; Barciela González, V.; Valero Tévar, M.A.; Gallego Valle D.; Zarzalejos Prieto, M.; Giner Iranzo D.;Hevia Gómez P.; Peña Ruiz, C.; Esteban Borrajo, G.; Molero García, J.; Díez, J.C.; Daura, J.; Lomba-Maurandi, J.; Menéndez M.; Hernández Pérez, M.; Villaverde Bonilla, V.; Krause, J; Herbig, A.; Warinner, C.

    Annual Meeting of the European Association for Archaeologists (EAA 2018), September 2018, Barcelona, Spain

    Conference Poster: Reconstruction of Oral Microbiomes from Extinct and Extant Anthropoids through ancient DNA

    2018
    Fellows Yates. J.A.; Aron, F.; Velsko, I.; Arthur, J.; Austin, R.M.; Crevecoeur, I.; Dalén, L.; Gonzalez Morales M.R.; Guschanski K.; Henry, A.G.; Hofman, C.A.; Humphrey, L.T.; Lewis, C.M.; Mann, A.E.; Nägele, K.; Parker, C.E.; Posth, C.; Rougier, H.; Sankaranarayan, K.; Semal, P., Stock, J.; Strauss, L.G.; Weedman Arthur, K.; Wrangham, R.W; Curtis, M.C; Diez, J.C.; Gibbon, V.E.; Menedez, M.; Peresani, M.; Roksandic, M.; Walker, M.J.; Power, R.C.; Salazar-Garcia, D.C.; Krause, J; Herbig, A.; Warinner. C.

    Society for Molecular Biology and Evolution (SMBE18), July 2018, Yokohama, Japan

    Workshop Presentation: Central European Late Pleistocene Woolly Mammoths: Insights from ZooMS, Stable Isotope and aDNA data

    2017
    Fellows Yates, J.A.; Drucker, D.G.; Reiter, E.; Heumos, S.; Welker, F.; Münzel, S.C;; Wojtal, P.; Lázničková-Galetová, M.; Conard, N.J.; Herbig, A.; Bocherens, H.,; Krause, J.

    Megafauna and Methods Workshop, February 2017, Jena, Germany

    Invited Talk: Palaeomicrobiology of Teeth

    2019
    Fellows Yates, J. A.

    Workshop ‘All About Teeth’, July 2019, EVEREST graduate school, University of Tübingen, Germany

    Invited Talk: Introduction to Dietary Metagenomes

    2017
    Fellows Yates, J. A.

    Archaeological Science workshop ‘Palaeodiet’, July 2018, Institute for Archaeological Sciences, University of Tübingen, Germany

    Conference Poster: Full Mitochondrial Genomes of Central European Upper Palaeolithic Woolly Mammoths (Mammuthus primigenius) (Conference Poster)

    2016
    Fellows Yates, J. A.; Drucker, D.G.; Herbig, A.; Münzel, S.C.; Bocherens, H.; Krause, J.

    International Symposium for Biomolecular Archaeology (ISBA7), September 2016, Oxford, United Kingdom

    "> Funding and Grants

    Studienstipendien für Graduierte aller wissenschaftlichen Fächer

    2014 - 2015
    DAAD - Deutscher Akademischer Austauschdienst

    Graduate Scholarship for studying at a German institution. €7860

    Edward Hall Memorial Fund

    2013 - 2014
    Research Laboratory for Archaeology and the History of Art - University of Oxford

    Postgraduate scholarship for studying at the University of Oxford. £1000 [Declined]

    Skills & Proficiency

    Nextflow

    R

    Conda

    HPCs

    Bash

    Linux

    Git

    Blog

    These are my blog posts