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PhD course on Ancient Environmental Genomics
Provider: Faculty of Health and Medical Sciences

Activity no.: 3610-23-00-00There are no available seats 
Enrollment deadline: 01/09/2023
Date and time01.10.2023, at: 09:00 - 08.10.2023, at: 17:00
Regular seats20
Course fee7,440.00 kr.
LecturersMartin Sikora
Mikkel Winther Pedersen
ECTS credits5.00
Contact personIda Marie Bergman Rasmussen    E-mail address: ida.mbr@sund.ku.dk
Enrolment Handling/Course OrganiserPhD administration     E-mail address: phdkursus@sund.ku.dk

Aim and content

This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member universities. 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 universities. 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. Be familiar with the standard bioinformatic tools used for ancient eDNA analysis, command lines and pipelines. Able to set up virtual conda environments for the analysis.

2. Be able to 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 public according to standards.

6. Able to evaluate and authenticate ancient origin.

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 8 whole 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. Students should have some basic knowledge about command line data processing.


Relevance to graduate programmes

Biostatistics and Bioinformatics

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.

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.

Victor Moreno Mayar, Assistant professor, Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen.

Peter Heintzmann, Researcher and Wallenberg Academy Fellow, Centre for PaleoGenetics, Stockholm University.


Dates

1 - 8 October 2023.

All days – 09:00-17:00


Course location

Globe Institute, University of Copenhagen.


Registration

1 September 2023.


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.

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