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Posts

All Possible NCBI Taxonomy Ranks

3 minute read

Published:

It was bothering me that nowhere on the NCBI website are all possible taxonomic ‘ranks’ actually described.

pvclust Node Values In ggtree

3 minute read

Published:

I recently was using the R package pvclust to test the ‘robusticity’ of clusters in a microbiome-related clustering analysis. While pvclust provides it’s own plots via plot() on a pvclust object, this plots the dendrogram in base R. For readability and customisability reasons I prefer using the packages ggplot2 and ggtree for making my figures. However, I was having a hard time to extract the node uncertainty values from the pvclust object and integrate them into a generic R phylo object for plotting the dendrogram in ggtree.

‘Tidy’ Pop-Gen PCA plotting in R

less than 1 minute read

Published:

Many people in the human population-genetics groups in my department at MPI-SHH use a propetiary Mac specific program to make their figures of PCAs (principle component analysis). Some of the members of these groups however do not have Macs and were struggling to recreate some of the plots their collegues were making.

Updating a Github Pages Theme Through a Repo Merge

1 minute read

Published:

I am new to Git and Github, and so I am still very much learning on the fly. Today I noticed the original repository for the theme of this website had added updates, so I thought to apply them to my own repository.

Sequin Submission to Genbank Tutorial

5 minute read

Published:

As I came to the end of my M.Sc. and writing the corresponding journal article, one thing I was aware of was that all previous papers on woolly mammoth mitchondrial genomes to NCBI’s GenBank database. To continue with this established ‘tradition’, I decided to investigate how to do this. Worringly, most people I spoke to didn’t have very positive views on this procdure, saying that it was complicated, error prone and badly documented and that it wasn’t worth my time. In fact, with a bit of help from the authors of some of the previous papers and with NCBI itself, the overall task ended up being easier than expected (admittedly after a considerable bit of trial and error).

How-to: Simple ‘change over time’ maps in R

4 minute read

Published:

In Archaeology, or other disciplines that looking through deep time, you often want to represent change through time. A simple example of this, is representing the location different archaeological sites through different cultural periods.

How-to: cancel a MrBayes run early

2 minute read

Published:

During my M.Sc. thesis I started to use the Bayesian phylogenetic MrBayes on clusters that do not make it feasible to keep open a terminal window. This meant I had to use ‘batch mode’, meaning I could only follow the status of the MrBayes run through the log files.

portfolio

publications

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

Published in Scientific Reports, 2017

Recommended citation: 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, K (2017). "Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes" Sci. Rep. 7(1):17714 (OPEN ACCESS) https://doi.org/10.1038/s41598-017-17723-1

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

Published in Scientific Reports, 2018

Recommended citation: 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 Jr., C.M; Krause, J; Hofman, C; Bos, K.I.; Warinner, C (2018) "Differential preservation of endogenous human and microbial DNA in dental calculus and dentin" Sci. Rep. 8(1) 8922 (OPEN ACCESS) https://doi.org/10.1038/s41598-018-28091-9

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

Published in Microbiome, 2019

Recommended citation: 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) "Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage" Microbiome 7(1) 102 (OPEN ACCESS) https://doi.org/10.1186/s40168-019-0717-3

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

Published in Bioscience, 2019

Recommended citation: 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.; Boivin, N.; Roberts, P. (2019) "Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene" Bioscience (OPEN ACCESS) https://doi.org/10.1093/biosci/biz105

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

Published in bioRxiv, 2020

Recommended citation: Fellows Yates, J. A., Valtueña, A. A., Vågene, Å. 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". In bioRxiv (p. 2020.09.02.279570). https://doi.org/10.1101/2020.09.02.279570 https://doi.org/10.1101/2020.09.02.279570

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

Published in Quaternary International, 2020

Recommended citation: 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. Quaternary International. DOI:https://doi.org/10.1016/j.quaint.2020.11.019 https://doi.org/10.1016/j.quaint.2020.11.019

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

Published in Scientific Data, 2021

Recommended citation: 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). "Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir". Scientific Data, 8(1), 31. https://doi.org/10.1038/s41597-021-00816-y https://doi.org/10.1038/s41597-021-00816-y

talks

Introduction to Ancient Dietary Metagenomes

Published:

Palaeodietary Workshop: I gave a lecture to masters and PhD students at the University of Tübingen on the challenges of using ancient DNA to study diet in the past, in particular focusing on our ability to authenticate these signals in dental calculus and palaeofaeces. I also presented a brief set of guidelines aimed at archaeologists, on what to look for when reading an ancient DNA paper in this context. The slides from this talk can found on Google Drive here, made avaliable under a CC-NC-SA 4.0 License.

Palaeomicrobiology of Teeth

Published:

EVEREST Workshop: All About Teeth: I gave a lecture to the EVEREST Graduate School at the University of Tübingen on what we can learn about human (pre)history in the context of the microbial remains of ancient teeth.

Standards Precautions and Advances in Ancient Metagenomics (SPAAM2)

Published:

SPAAM2: Standards Precautions and Advances in Ancient Metagenomics: I established, co-organised, chaired and also presented at the SPAAM2 round-table discussion workshop. Involving 80 ancient metagenomic researchers from around the world, we discussed a wide range of topics spanning the challenges of ancient microbiome, pathogenomic and environmental DNA reconstruction. In particular to co-chairing the large session entitled “Authentication, standards, and reproducibility in ancient metagenomic research.”, I gave a presentation entitled “Towards standards in metadata reporting in ancient metagenomic studies: experiences from AncientMetagenomeDir”, co-written with Antonio Fernandez Guerra. More information on SPAAM2 can be found on the SPAAM community website.

teaching

EAGER-MALT Crash Course Workshop

Workshop, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, 2016

The aim of this crash course was to get those new to the MPI-SHH up to speed with some of the core tools that we are using in the institute, particularly for those working on pathogens. The workshop began with showing where to find internal documentation about the computing infrastructure and also how to access said infrastructure. Then, three (and a half) different programs were introduced and short practical examples given. The three programs discussed was - EAGER: our specialized pipeline for ancient DNA sequencing data pre-processing to genome reconstruction; MALT: a super-fast HTS read aligner used here currently for bacterial DNA screening; and MEGAN: a visualisation and analysis program for MALT results.

Introduction to SLURM Workshop

Workshop, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, 2017

This mini-workshop was given in March 2017 as an practical introduction on how to use SLURM on the MPI-SHH DAG computing infrastructure.

Methods Bootcamp Workshop: Mapping

Workshop, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, 2017

This workshop was a part of the MPI-SHH ‘Methods Bootcamp’ seminar series, given by James A. Fellows Yates and Ron Huebler. This session introduced the basic concepts behind alignment, mapping of next generation sequencing DNA data and common programs used. We also gave practical examples of how different data compression techniques worked in these concepts.

BareBonesBash

Tutorial, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, 2018

Alongside Thiseas Lamnidis, we wrote a tutorial to give a very gentle introduction (with many terrible jokes) to how to use the bash terminal for people with little- to no experience of the command line. While we wrote this in the context of bioinformatics at the MPI-SHH, we feel parts to all of it is generally applicable to all newcomers to the terminal.

Palaeowikithon 2018

Workshop, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, 2018

With co-organiser Maxime Borry, we set up and guided a wikithon for Department of Archaeogenetics (MPI-SHH) internal wiki. This involved teaching members of the department how to use dokuwiki, organised and distributed tasks and teams, as well as a review process.