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James Fellows Yates

Gast

Abteilung für Archäogenetik
Max-Planck-Institut für evolutionäre Anthropologie
Deutscher Platz 6
04103 Leipzig

E-Mail: james_fellows_yates@[>>> Please remove the text! <<<]eva.mpg.de

personal webpage   GitHub   Twitter  

Main Focus

James is a bioinformatician and aiomolecular archaeologist post-doc researcher workingly jointly between Max Planck Institute for Evolutionary Anthropology and the Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute. Originally with a background in archaeology, he has traversed disciplines from proteomic-based identification of burnt remains, to population genetics of Mammoths, to characteristing ancient oral microbiomes,  and is now specialising in bioinformatics of ancient metagenomics.

He is a founder of the SPAAM community of ancient metagenomics researchers, and serves on the core-team of the nf-core initiative of Nextflow bioinformatic pipelines.

With a passion for open-science and collaborative projects, his current work focuses on improving through-put and expanding on the types of analyses that can be performed on (ancient) metagenomic data. He is the lead developer and contributor to a range of best-practise Nextflow pipelines for both ancient and modern sequencing data (nf-core/eager,nf-core/taxprofiler, nf-core/funcscan, nf-core/mag). He has also developed tools for assisting in assessment ancient microbiome preservation, such as a CRAN-hosted R package (cuperdec), and a Shiny (R) interactive visualisation tool (MEx-IPA). He also spearheaded an iniative to transfer department internal wet-lab protocols onto the online open-repository protocols.io.

He currently also leads community-ran intiatives to improve domain-specific data access such as AncientMetagenomeDir (a standardised repository of all public ancient metagenomic data), as well as co-leading the MInAS project to standardise metadata reporting within ancient metagenomics and the wider ancient DNA field.

Keywords:

  • Ancient DNA
  • Palaeogenomics
  • Metagenomics
  • Microbiomes
  • Nextflow
  • Pipelines
  • R
  • Metadata
  • Standardisation
  • Community Projects
  • Open Source
  • Open Science

Curriculum Vitae

My CV can be viewed here.

Publications

2021

Warinner, C. G., Velsko, I. M., & Fellows Yates, J. A. (2021). Reply to Ben-Dor et al.: Oral bacteria of Neanderthals and modern humans exhibit evidence of starch adaptation. Proceedings of the National Academy of Sciences, 118: e2112526118.
DOI    BibTeX   Endnote   

Fellows Yates, J. A., Lamnidis, T. C., Borry, M., Andrades Valtueña, A., Fagernäs, Z., Clayton, S., Garcia, M. U., Neukamm, J., & Peltzer, A. (2021). Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ, 9: e10947.
Open Access    DOI    BibTeX   Endnote   

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., Díaz-Zorita Bonilla, M., Díez Fernández-Lomana, J. C., Drucker, D. G., Escribano Escrivá, E., Francken, M., Gibbon, V. E., González Morales, M. R., Grande Mateu, A., Harvati, K., Henry, A. G., Humphrey, L., Menéndez, M., Mihailović, D., Peresani, M., Rodríguez Moroder, S., Roksandic, M., Rougier, H., Sázelová, S., Stock, J. T., Straus, L. G., Svoboda, J., Teßmann, B., Walker, M. J., Power, R. C., Lewis, C. M., Sankaranarayanan, K., Guschanski, K., Wrangham, R. W., Dewhirst, F. E., Salazar-García, D. C., Krause, J., Herbig, A., & Warinner, C. G. (2021). The evolution and changing ecology of the African hominid oral microbiome. Proceedings of the National Academy of Sciences, 118(20): e2021655118.
Open Access    DOI    BibTeX   Endnote   

Sarkissian, C. D., Velsko, I. M., Fotakis, A. K., Vågene, Å. J., Hübner, A., & Fellows Yates, J. A. (2021). Ancient metagenomic studies: Considerations for the wider scientific community. mSystems, 6(6), e01315-e01321.
Open Access    DOI    BibTeX   Endnote   

2020

Mann, A. E., Fellows Yates, J. A., Fagernäs, Z., Austin, R. M., Nelson, E. A., & Hofman, C. A. (2020). Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus (advance online). Quaternary International.
Open Access    DOI    BibTeX   Endnote   

Fellows Yates, J. A., Andrades Valtueña, 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. G. (2020). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data, 8: 31.
Open Access    DOI    BibTeX   Endnote   

2019

Velsko, I. M., Fellows Yates, J. A., Aron, F., Hagan, R., Frantz, L. A. F., Loe, L., Martinez, J. B. R., Chaves, E., Gosden, C., Larson, G., & Warinner, C. G. (2019). Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage. Microbiome, 7(1): 102.
Open Access    DOI    BibTeX   Endnote   

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., Wood, R., Petraglia, M. D., Boivin, N. L., & Roberts, P. (2019). Micro methods for megafauna: novel approaches to late quaternary extinctions and their contributions to faunal conservation in the anthropocene. Bioscience, 69(11): biz105, pp. 877-887.
Open Access    DOI    BibTeX   Endnote   

2018

Mann, A., 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., Krause, J., Hofman, C., Bos, K. I., & Warinner, C. G. (2018). Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Scientific Reports, 8(1): 9822.
Open Access    DOI    BibTeX   Endnote   

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. (2017). Central European Woolly Mammoth population dynamics: Insights from Late Pleistocene Mitochondrial Genomes. Scientific Reports, 7: 17714.
Open Access    DOI    BibTeX   Endnote   

Warinner, C. G., Herbig, A., Mann, A., Fellows Yates, J. A., Weiß, C. L., Burbano, H. A., Orlando, L., & Krause, J. (2017). A robust framework for microbial archaeology. Annual Review of Genomics and Human Genetics, 18, 321-356.
Open Access    DOI    BibTeX   Endnote   

Conferences and Workshops

Organised

Fellows Yates, J.A. “AncientMetagenomeDir Metadatathon - Ancient Metagenomic Library Metadata Extension”, April 2022, Online, (Organised, Presented, Taught). Website: https://spaam-community.github.io/#/events/metadatathon-dec2021/README

nf-core core team “nf-core pipeline hackathon” March 2022, Online (Organised, Participated). Website: https://nf-co.re/events/2022/hackathon-march-2022

Fellows Yates, J.A. “AncientMetagenomeDir Metadatathon - Ancient Metagenomic Library Metadata Extension”, November/December 2021, Online, (Organised, Presented, Taught). Website: https://spaam-community.github.io/#/events/metadatathon-dec2021/README

nf-core core team “nf-core pipeline hackathon” October 2021, Online (Organised, Participated). Website: https://nf-co.re/events/2021/hackathon-october-2021

nf-core core team “nf-core pipeline hackathon”, March 2021, Online (Organised, Participated). Website: https://nf-co.re/events/2021/hackathon-march-2021

Fellows Yates. J.A.; Der Sarkissian, C; Fotakis, A; Hübner, A;  Vågene, Å. “SPAAM2: Standards, Precautions, and Advances in Ancient Metagenomics”, Satellite Conference to (postponed) ISBA9, September 2020, Online. (Organised, Chaired and Presented). Website: https://spaam-community.github.io/#/spaam2/README.

Presented

Fellows Yates, J.A. “Open Science Initiatives in Ancient (Meta)genomics” Invited Talk, Palaeoproteomics Section, GLOBE Institute, Copenhagen, Denmark, Apr 2022, Online

Fellows Yates, J.A. “How to use Inkscape & creating pipeline diagrams in Inkscape” Presentation, nf-core hackathon March 2022, Online

Fellows Yates, J.A.,Lamnidis, T.C., Borry, M., Andrades Valtueña, A., Fagernäs, Z., Clayton, S., Garcia M.U, Neukamm, J., Peltzer, A. “nf-core/eager: Reproducible, portable, and efficient ancient genome reconstruction” Conference poster, International Symposium for Biomolecular Archaeology (ISBA9), June 2021, Online
pdf: https://github.com/jfy133/jfy133.github.io/blob/main/uploads/FELLOWSYATES_James_abstract1517_poster84_ISBA9-Poster.pdf

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. Conference poster. “Improving access to ancient metagenomic data with the community-curated metadata repository AncientMetagenomeDir”. Wellcome Trust Connecting Science - Ancient Biomolecules of Plants, Animals, and Microbes, March 2021, Online
pdf: https://github.com/jfy133/jfy133.github.io/raw/main/uploads/AncientBiomolecules2021_FellowsYates.pdf

Fellows Yates. J.A.; Fernandez Guerra, A. “Towards standards in metadata reporting in ancient metagenomic studies: experiences from AncientMetagenomeDir” Conference presentation, Standards Precautions, and Advances in Ancient Metagenomics 2020 (SPAAM2), September 2020, Online 
doi: dx.doi.org/10.5281/zenodo.4109609

Fellows Yates. J.A. et al. "Reconstruction of Oral Microbiomes from Extinct and Extant Anthropoids through ancient DNA" Conference presentation, International Symposium for Biomolecular Archaeology (ISBA8), September 2018, Jena, Germany

Fellows Yates, J.A. et al. "Palaeogenomic Investigation Of 50,000 Years Of The Human Oral Microbiome In The Iberian Mediterranean" Conference presentation, Annual Meeting of the European Association for Archaeologists (EAA 2018), September 2018, Barcelona, Spain

Fellows Yates. J.A.; et al. "Reconstruction of Oral Microbiomes from Extinct and Extant Anthropoids through ancient DNA" Conference poster Society for Molecular Biology and Evolution (SMBE18), July 2018, Yokohama, Japan

Fellows Yates et al. (2017) "Central European Late Pleistocene Woolly Mammoths: Insights from ZooMS, Stable Isotope and aDNA data" Workshop presentation, Megafauna and Methods Workshop, Max Planck Institute for the Science of Human History, Jena, Germany

Fellows Yates et al. (2016) "Full Mitochondrial Genomes of Central European Upper Palaeolithic Woolly Mammoths (Mammuthus primigenius)" Conference Poster, International Symposium for Biomolecular Archaeology (ISBA7), University of Oxford, Oxford, United Kingdom
doi: dx.doi.org/10.13140/RG.2.2.33453.28648

Education

2015 - 2022

Ph.D. Bioinformatics, Faculty of Biology, Friedrich-Schiller-Universität Jena & MPI for the Science of Human History, Jena / MPI for Evolutionary Anthropology, Leipzig
Thesis: Evolution of the Human Oral Microbiome and Resource Development for Ancient Metagenomics

2013-2015

M.Sc. Naturwissenschaftliches Archäologie / Archaeological Sciences, Universität Tübingen (DE)
Thesis: Full Mitochondrial Genomes of Upper Palaeolithic Central EUropean Woolly Mammoths (Mammuthus primigenius)

2010-2013B.Sc. Bioarchaeology, University of York (UK)
Thesis: “It Will Not Be Possible To Use Zooarchaeology By Mass Spectrometry (ZooMS) To Identify Species In Samples Of Cremated Bone That Have Been Burnt Higher Than 155oC”

Additional

2020-2021

Researcher - Ludwig-Maximilians-Universität München
FoodTransforms Project - genetic-based bioinformatic food identifiication from ancient dental calculus 

2014-2015Stable Isotopes Student Research Assistant - Universität Tübingen
AG Biogeologie - sample preparation, collagen extraction, data curation

Teaching Experience

2022 Mar Intro to nf-core/eager (online intro eager2 pipeline), GLOBE Institute, Copenhagen DK,

2021 Dec Intro to nf-core/eager (online intro to eager2 pipeline), ECOBIOP, INRAE, FR

2021 Aug Intro to Archaeogenetics (Lecture), MPI-SHH SummerSchool, Online, MPI-SHH, Jena, DE

2021 Intro to NGS data processing (Lecture), MPI-SHH SummerSchool, Online, MPI-SHH, Jena, DE

2021 Aug Byteize Git (6 session workshop), MPI-EVA, Leipzig, DE

2021- Scripts and bytes (weekly computational drop-in surgery), MPI-EVA, Leipzig, DE

2021 Jan Intro to nf-core/eager (online intro to eager2 pipeline), GLOBE Institute, Copenhagen, DK

2020 Dec Intro to nf-core/eager (online intro to eager2 pipeline), Public (Multiple)

2020 Nov Intro to nf-core/eager (online intro to eager2 pipeline), LIIGH, Querétaro, MX

2020 Oct Intro to nf-core/eager (online intro to eager2 pipeline), MPI-SHH, Jena, DE

2019 - Scripts and bytes (weekly computational drop-in surgery), MPI-SHH, Jena, DE

2018 Dec Palaeowikithon (day-long internal wiki updating event), MPI-SHH, Jena, DE
Jun BareBonesBash (intro to bash programming workshop), MPI-SHH, Jena, DE

2017 Sept Introduction to Ancient Dietary Metagenomes, Universität Tübingen, Tübingen, DE

2017 May Methods Bootcamp workshop: Mapping, MPI-SHH, Jena, DE

2017 MarIntroduction to SLURM workshop, MPI-SHH, Jena, DE

2016 Jul EAGER-MALT Crash Course workshop, MPI-SHH, Jena, DE