Posts by Collection

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; Bocheres, H; Krause, K (2017). "Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes" Sci. Rep. 7(1):17714. DOI: http://doi.org/10.1038/s41598-017-17723-1 https://doi.org/10.1038/s41598-017-17723-1

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.

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.