Graduate School of health and Medical Sciences

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

Activity no.: 3610-23-00-00	There are no available seats
	Enrollment deadline: 01/09/2023

Date and time	01.10.2023, at: 09:00 - 08.10.2023, at: 17:00
Regular seats	20
Course fee	7,440.00 kr.
Lecturers	Martin Sikora Mikkel Winther Pedersen
ECTS credits	5.00

Contact person	Ida Marie Bergman Rasmussen E-mail address: ida.mbr@sund.ku.dk

Enrolment Handling/Course Organiser	PhD 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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