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Ancient DNA, Biomolecular Archaeology, Archaeogenetics, Bioinformatics, Metagenomics, Microbiome, Open Data, Open Source, Nextflow, Palaeogenetics
Germany, United Kingdom

Activities

Employment (5)

Max Planck Institute for Evolutionary Anthropology: Leipzig, DE

2021-09-01 to present | Scientific Researcher (Archaeogenetics)
Employment
Source: Self-asserted source
James A. Fellows Yates

Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV Hans-Knöll-Institut: Jena, Thüringen, DE

2021-09-01 to present | Scientific Researcher (Paleobiotechnology)
Employment
Source: Self-asserted source
James A. Fellows Yates

Ludwig-Maximilians-Universität München Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie: Munchen, Bayern, DE

2020-06-01 to 2021-08-31 | PhD Researcher
Employment
Source: Self-asserted source
James A. Fellows Yates

Max-Planck-Institut für Menschheitsgeschichte: Jena, Thüringen, DE

2015-10-01 to 2020-05-31 | PhD Student (Department of Archaeogenetics)
Employment
Source: Self-asserted source
James A. Fellows Yates

Eberhard Karls Universität Tübingen Fachbereich III Geowissenschaften: Tubingen, Baden-Württemberg, DE

2014-03-01 to 2015-03-01 | Research Assistant - Stable Isotopes (Biogeologie)
Employment
Source: Self-asserted source
James A. Fellows Yates

Education and qualifications (3)

Friedrich Schiller University Jena: Jena, Thüringen, DE

2015-10-01 to 2022-05-17 | Ph.D. (Archaeogenetics - MPI-SHH)
Education
Source: Self-asserted source
James A. Fellows Yates

Eberhard Karls Universität Tübingen: Tubingen, Baden-Württemberg, DE

2013-10-01 to 2015-08-31 | M.Sc. Naturwissenschaftliches Archäologie (Institute for Archaeological Sciences)
Education
Source: Self-asserted source
James A. Fellows Yates

University of York: York, York, GB

2010-10-01 to 2013-07-01 | B.Sc. Bioarchaeology (Archaeology)
Education
Source: Self-asserted source
James A. Fellows Yates

Professional activities (3)

International Society for Biomolecular Archaeology: London, GB

2022 to present | Board Member / Webmaster
Service
Source: Self-asserted source
James A. Fellows Yates

nf-core: Stockholm, SE

2020 to present | Core team member
Service
Source: Self-asserted source
James A. Fellows Yates

SPAAM Community: Jena, DE

2019 to present | Founder
Service
Source: Self-asserted source
James A. Fellows Yates

Funding (1)

Studienstipendien für Graduierte aller wissenschaftlichen Fächer

2014-10 to 2015-07 | Grant
Deutscher Akademischer Austauschdienst (Bonn, DE)
GRANT_NUMBER:

https://www.daad.de/deutschland/stipendium/datenbank/de/21148-stipendiendatenbank/?status=&origin=21&subjectGrps=&daad=1&q=&page=4&detail=5002620050026247

Source: Self-asserted source
James A. Fellows Yates

Works (35)

Empowering bioinformatics communities with Nextflow and nf-core

2024-05-14 | Preprint | Author
Contributors: Björn Langer; A J Amaral; Marie-Odile BAUDEMENT; Franziska Bonath; Mathieu Charles; PRAVEEN KRISHNA CHITNEEDI; Emily Louise Clark; Paolo Di Tommaso; Djebali S; Philip Ewels et al.
Source: Self-asserted source
James A. Fellows Yates

nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling

2023-10-23 | Preprint
Contributors: Sofia Stamouli; Moritz E. Beber; Tanja Normark; Thomas A. Christensen, II; Lili Andersson-Li; Maxime Borry; Mahwash Jamy; James A. Fellows Yates
Source: check_circle
Crossref

Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT

F1000Research
2023-08-02 | Journal article
Part of ISSN: 2046-1402
Contributors: Maxime Borry; Adrian Forsythe; Aida Andrades Valtueña; Alexander Hübner; Anan Ibrahim; Andrea Quagliariello; Anna E. White; Arthur Kocher; Åshild J. Vågene‬; Bjørn Peare Bartholdy et al.
Source: Self-asserted source
James A. Fellows Yates via Crossref Metadata Search

TAXPASTA: TAXonomic Profile Aggregation and STAndardisation

Journal of Open Source Software
2023-07-11 | Journal article
Contributors: Moritz E. Beber; Maxime Borry; Sofia Stamouli; James A. Fellows Yates
Source: check_circle
Crossref

Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic

Science
2023-05-12 | Journal article
Contributors: Martin Klapper; Alexander Hübner; Anan Ibrahim; Ina Wasmuth; Maxime Borry; Veit G. Haensch; Shuaibing Zhang; Walid K. Al-Jammal; Harikumar Suma; James A. Fellows Yates et al.
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species

Molecular Biology and Evolution
2022-12-05 | Journal article
Part of ISSN: 0737-4038
Part of ISSN: 1537-1719
Contributors: Markella Moraitou; Adrian Forsythe; James A Fellows Yates; Jaelle C Brealey; Christina Warinner; Katerina Guschanski
Source: Self-asserted source
James A. Fellows Yates

PRJEB34569

2021 | Dataset
OTHER-ID:

PRJEB34569

Source: check_circle
EMBL-EBI

Ancient Metagenomic Studies: Considerations for the Wider Scientific Community

mSystems
2021-12-21 | Journal article
Contributors: Clio Der Sarkissian; Irina M. Velsko; Anna K. Fotakis; Åshild J. Vågene; Alexander Hübner; James A. Fellows Yates; Jack A. Gilbert
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

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
2021-09-14 | Journal article
Contributors: Christina Warinner; Irina M. Velsko; James A. Fellows Yates
Source: check_circle
Crossref

A-Z of ancient DNA protocols for shotgun Illumina Next Generation Sequencing v2

2021-06-15 | Preprint
Contributors: James A Fellows Yates; Franziska Aron; Gunnar U Neumann; Irina Velsko; Eirini Skourtanioti; Eleftheria Orfanou; Zandra Fagernäs; Raphaela Stahl; Aida Andrades Valtuena; Christina Warinner et al.
Source: check_circle
Crossref

Laboratory Protocols for Ancient and Modern Dental Calculus DNA Processing (Fellows Yates et al. 2021) v3

2021-06-15 | Preprint
Contributors: James A Fellows Yates; Irina Velsko; Franziska Aron; Courtney Hofman; Christina Warinner
Source: check_circle
Crossref

The evolution and changing ecology of the African hominid oral microbiome

Proceedings of the National Academy of Sciences
2021-05-18 | Journal article
Contributors: James A. Fellows Yates; Irina M. Velsko; Franziska Aron; Cosimo Posth; Courtney A. Hofman; Rita M. Austin; Cody E. Parker; Allison E. Mann; Kathrin Nägele; Kathryn Weedman Arthur et al.
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

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

PeerJ
2021-03-16 | Journal article
Source: Self-asserted source
James A. Fellows Yates

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

Scientific Data
2021-01-26 | Journal article
Contributors: James A. Fellows Yates; Aida Andrades Valtueña; Åshild J. Vågene; Becky Cribdon; Irina M. Velsko; Maxime Borry; Miriam J. Bravo-Lopez; Antonio Fernandez-Guerra; Eleanor J. Green; Shreya L. Ramachandran et al.
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Laboratory Protocols for Ancient and Modern Dental Calculus DNA Processing (Fellows Yates et al. 2021) v2

2021-01-06 | Preprint
Contributors: James A Fellows Yates; Irina Velsko; Franziska Aron; Courtney Hofman; Christina Warinner
Source: check_circle
Crossref

Laboratory Protocols for Ancient and Modern Dental Calculus DNA Processing (Fellows Yates et al. 2021) v1

2020-12-23 | Preprint
Contributors: James A Fellows Yates; Irina Velsko; Franziska Aron; Courtney Hofman; Christina Warinner
Source: check_circle
Crossref

(Non-UDG treated) double-stranded modern dental calculus DNA library preparation for Illumina sequencing

protocols.io
2020-12-10 | Journal article | Author
Contributors: James A. Fellows Yates
Source: check_circle
protocols.io

Non-UDG treated double-stranded DNA library preparation for Illumina sequencing of ancient dental calculus 

protocols.io
2020-12-10 | Journal article | Author
Contributors: James A. Fellows Yates
Source: check_circle
protocols.io

Dental Calculus Field-Sampling Protocol (Warinner Version)

protocols.io
2020-12-08 | Journal article | Author
Contributors: James A. Fellows Yates
Source: check_circle
protocols.io
grade
Preferred source (of 2)‎

Dental Calculus Field-Sampling Protocol (Sabin version) v2

2020-12-04 | Preprint
Contributors: Susanna Sabin; James A Fellows Yates
Source: check_circle
Crossref

Full-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing

protocols.io
2020-12-04 | Journal article | Author
Contributors: James A. Fellows Yates
Source: check_circle
protocols.io

Half-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing

protocols.io
2020-12-04 | Journal article | Author
Contributors: James A. Fellows Yates
Source: check_circle
protocols.io

Tooth Sampling from the inner pulp chamber for ancient DNA Extraction

protocols.io
2020-12-04 | Journal article | Author
Contributors: James A. Fellows Yates
Source: check_circle
protocols.io
grade
Preferred source (of 2)‎

Tooth Sampling from the inner pulp chamber for ancient DNA Extraction

protocols.io
2020-12-04 | Journal article | Author
Contributors: James A. Fellows Yates
Source: check_circle
protocols.io
grade
Preferred source (of 2)‎

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

Quaternary International
2020-11 | Journal article
Part of ISSN: 1040-6182
Source: Self-asserted source
James A. Fellows Yates

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

2020-09-03 | Preprint
Contributors: James A. Fellows Yates; Aida Andrades Valtueña; Ashild J. Vågene; Becky Cribdon; Irina M. Velsko; Maxime Borry; Miriam J. Bravo-López; Antonio Fernandez-Guerra; Eleanor J. Green; Shreya L. Ramachandran et al.
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

A-Z of ancient DNA protocols for shotgun Illumina Next Generation Sequencing v1

2020-08-24 | Preprint
Contributors: James A Fellows Yates; Franziska Aron; Gunnar U Neumann; Irina Velsko; Eirini Skourtanioti; Eleftheria Orfanou; Zandra Fagernäs; Raphaela Stahl; Aida Andrades Valtuena; Christina Warinner et al.
Source: check_circle
Crossref

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

2020-06-12 | Preprint
Contributors: James A. Fellows Yates; Thiseas C. Lamnidis; Maxime Borry; Aida Andrades Valtueña; Zandra Fagernäs; Stephen Clayton; Maxime U. Garcia; Judith Neukamm; Alexander Peltzer
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Dental Calculus Field-Sampling Protocol (Sabin version) v1

2019-10-02 | Preprint
Contributors: Susanna Sabin; James A Fellows Yates
Source: check_circle
Crossref

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

BioScience
2019-10-02 | Journal article
Part of ISSN: 0006-3568
Part of ISSN: 1525-3244
Source: Self-asserted source
James A. Fellows Yates

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

Microbiome
2019-07-06 | Journal article
Part of ISSN: 2049-2618
Source: Self-asserted source
James A. Fellows Yates

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin

Scientific Reports
2018-06-29 | Journal article
Contributors: Allison E. Mann; Susanna Sabin; Kirsten Ziesemer; Åshild J. Vågene; Hannes Schroeder; Andrew T. Ozga; Krithivasan Sankaranarayanan; Courtney A. Hofman; James A. Fellows Yates; Domingo C. Salazar-García et al.
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

PRJEB21582

2017 | Dataset
OTHER-ID:

PRJEB21582

Source: check_circle
EMBL-EBI

Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes

Scientific Reports
2017-12-18 | Journal article
Contributors: James A. Fellows Yates; Dorothée G. Drucker; Ella Reiter; Simon Heumos; Frido Welker; Susanne C. Münzel; Piotr Wojtal; Martina Lázničková-Galetová; Nicholas J. Conard; Alexander Herbig et al.
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

A Robust Framework for Microbial Archaeology.

2017-04 | Journal article
Contributors: Warinner C; Herbig A; Mann A; Fellows Yates JA; Weiß CL; Burbano HA; Orlando L; Krause J
Source: Self-asserted source
James A. Fellows Yates via Europe PubMed Central

Peer review (5 reviews for 5 publications/grants)

Review activity for Bioinformatics (1)
Review activity for Environmental microbiology. (1)
Review activity for Evolution letters. (1)
Review activity for Journal of archaeological science. (1)
Review activity for Microbial genomics. (1)