PhD course on Ancient Environmental Genomics
Graduate School of Health and Medical Sciences at University of Copenhagen
This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee.
Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.
Learning objectives
A student who has met the objectives of the course will be able to:
1. Use standard bioinformatic tools for ancient eDNA analysis, command lines and workflows. Able to set up virtual conda environment on their own machines to perform the analysis.
2. Perform taxonomic profiling and identify taxa from complex metagenomes and achieve more complex phylogenetic placements and genome-wide analysis of all organisms including microbes, plants, animals and humans.
3. Be familiar with what requires prokaryotic, eukaryotic and viral-specific analysis.
4. Documenting and reporting each step in the bioinformatic process.
5. How to make data publicly available according to standards.
6. Able to evaluate and authenticate ancient origin given the standards within the field.
7. Review literature and data from a critical angle.
Skills
By the end of the course, you will be able to:
• Extract and build databases
• Confidently and autonomously use the latest bioinformatic tools
• Characterise and quantify the DNA damage and build damage/depth or age profiles.
• Assess the validity of read classifications
• Perform taxonomic profiling of eukaryotes and prokaryotes.
• Assemble environmental genomes
• Perform phylogenetic placements
Competencies
By the end of the course, you will be able to:
• Select the best approach to process high-throughput sequence data.
• Analyse ancient metagenomes and perform phylogenetic placement and interpretation for all kingdoms of life.
• Evaluate the robustness and reliability of the taxa identified, by authenticating ancient DNA origin and more.
• Environmental genome assembly.
• Review literature and data from a critical angle
Content
The ancient environmental genomics course is an intensive 6 day course that will provide a detailed introduction to the latest advances in analytical tools for analysing shotgun-sequenced (captured and non-captured) ancient environmental DNA. While the focus here will be on geological (permafrost soils, lake and marine sediments) and archaeological temporal archives, the competencies gained are not restricted to these. They can be used generally across any ancient environmental DNA such as dental calculus, coprolites, ice-cores, stalagmites and more. The aim is to equip the participants with the analytical capabilities to robustly profile and identify taxa from complex metagenomes and perform more complex phylogenetic placements and genome-wide analyses of all organisms including microbes, plants, animals and humans. Finally, we will also aim to guide and explain standards and best practices for documenting and reporting analysis and results and eventually making these publicly available.
Participants
This course is targeted student who work within the field of molecular biology, archaeology, geology and environmental sciences who is working with or has interest in ancient DNA from environmental/cultural contexts. However, it may also be relevant to forensic students and other students working with other degraded genetic data. Students should have a basic knowledge about command line data processing.
Relevance to graduate programmes
Biostatistics and Bioinformatics
Oral Sciences, Forensic Medicine and Bioanthropology
Life, Earth and Environmental Sciences graduate programme
It will also be relevant to student at the Biological institute, Geological Institute, Geography Institute at Science and the Archaeological Institute at HUM.
Language
English
Form
Lectures, discussions, exercises in R and the Unix/linux environments.
Course director
Martin Sikora, Associate professor, Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen.
Mikkel Winther Pedersen, Tenure-track assistant professor, Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen.
Teachers
Mikkel Winther Pedersen, Tenure-track assistant professor, Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen.
Pete Heintzman, Stockholm University
Benjamin Vernot, Max Planck Institute, Leipzig.
Thorfinn Korneliussen, Tenure-track assistant professor, Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen.
Karina K. Sand, Associate professor, Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen.
Antonio Guerra-Fernandez, Tenure-track assistant professor, Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen.
Martin Sikora, Associate professor, Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen.
Dates
September 21st - 26th 2025.
All days – 09:00-17:00
Course location
Globe Institute, University of Copenhagen.
Registration
July 1st 2025.
Expected frequency
Yearly.
Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules.
Applications from other participants will be considered after the last day of enrolment.
Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.