Course Syllabus

Jump to Today

 

 

 DIS Logo

 

Semester & Location:

Fall 2025 - DIS Copenhagen
Type & Credits:

Elective Course - 3 credits
Major Disciplines: Biology, Chemistry / Biochemistry
Research Mentor:

Eske Willerslev, Professor, Thorfinn Sand Korneliussen

(current students please use the Canvas Inbox) 
Research Director:

Susana Dietrich - research@dis.dk
Senior Research Manager:

Jeanette Erbo Wern jwe@dis.dk 
Academic Support:

research@dis.dk
Time & Place:

See "Course Summary" below

Research Project Description

The Section for Geogenetics at the Globe Institute, University of Copenhagen, has a strong track record in generating and analyzing ancient DNA (aDNA). In this project, the focus is on the analysis and interpretation of aDNA from environmental samples and human remains, with the aim of reconstructing past ecosystems and human populations. By combining environmental and human genome analyses, this project will demonstrate how aDNA studies contribute to understanding evolutionary history, species adaptation, and human interactions with their environment.

Research Assistants (RAs) will work with existing unpublished datasets and not be directly involved in wetlab generation of new data. Instead, the project emphasizes hands-on experience with key techniques in ancient DNA research by handling, analyzing, and interpreting real aDNA dataset from sources such as sediment cores and archaeological skeletal material. RAs will learn how to critically assess DNA authenticity and interpret genetic data to reconstruct past environments and human populations. By the end of the project, RAs will understand both the scientific and methodological challenges of working with ancient genetic material.

Data Analysis and Interpretation of Ancient DNA

Sequencing Data and Preprocessing: The project will focus on the computational analysis of aDNA. RAs will become familiar with the structure and characteristics of short-read sequencing data (e.g., Illumina) commonly used in aDNA studies. The project includes preprocessing steps such as adapter trimming, quality filtering, and an introduction to how biochemical treatments like UDG (Uracil-DNA Glycosylase) impact data characteristics, although the RAs will not be directly involved in wet lab work.

Authentication and Quality Control: Ancient DNA presents unique challenges related to degradation and contamination. RAs will learn to authenticate aDNA sequences through read mapping, analysis of post-mortem damage patterns, and contamination screening. Tools such as mapDamage, MALT, and PALEOMIX will be used to verify data authenticity and assess the quality of the sequences.

Bioinformatics and Interpretation: Using established bioinformatics pipelines, RAs will apply population genetic methods such as principal component analysis (PCA), ADMIXTURE, and phylogenetic inference to investigate genetic diversity and population history. For environmental samples, metabarcoding and taxonomic assignment methods will be used to reconstruct past ecosystems. Emphasis will be placed on interpreting the results within ecological and evolutionary frameworks

References and Further Reading

Learning Objectives

The primary objective is for you to experience the world of research and gain skills that will prepare you for any future career you choose to pursue. By the end of the term, you will grasp the complexities of the research project and have made your own contribution to the project. You will have learned to communicate ideas and findings, both orally and in writing, to colleagues within your particular discipline, as well as peers from other disciplines.

Research Mentor

image.png

Thorfinn Sand Korneliussen, Associate professor computational biology

Eske Willerslev’s group (2015 – present) PhD Statistical methods for low coverage DNA, Natural History Museum, DK (2012 - 2015). MSc (Cand.Scient) (Bioinformatics), Dept of Biology, University of Copenhagen (2012)

Roles and Responsibilities of the Research Assistant

You are expected to spend a minimum of 10 hours per week on the project. The workload
may vary over the semester. If you are travelling to do field research in a different
location, additional time may be required.
As research assistant, you will engage in some or all of the following:
1. Participate in weekly meetings with your research mentor at a time set collectively at the beginning of the term.
2. Participate in a research orientation at the beginning of the semester 
3. Participate in two research workshops during the semester.
4. Write an assessment of your own strengths and weaknesses in the research
process at the beginning of the semester. Revisit at the end of the semester as part of an evaluation of your own participation in, and learning from, the research project.
5. Keep a research journal and submit it on canvas every week (or another specified interval) for your research mentor an DIS Research, describing the activities of the week, and outlining goals for the following week.
6. Conduct literature reviews.
7. Participate in carrying out the research project. This may include: familiarizing yourself with core concepts, prototyping, design testing, preliminary user studies. The specific responsibilities may vary depending on how the project progresses. Be prepared to contribute to tasks that may come up
during the semester. Research processes are not always predictable.
8. Present the relevance of the research and/or findings to peer(s) from other
disciplines at the DIS Festival.
9. Make a final oral and/or written presentation of the research you are involved in, depending on what is agreed with your research mentor.

Readings

The readings will be agreed upon with the Research Mentor at the beginning of the semester -
the exact content will differ depending on your background. You will receive guidance
concerning the basics of relevant concepts, study designs, methods of analysis, etc.

Evaluation and Grading

All research assistants are assessed on their participation, weekly status reports to the research mentor, self-evaluation and presentation to peers from other disciplines. Additional evaluation and grading depends on the individual research project and project phase and is outlined by the research mentor. It may include literature reviews, a poster presentation for an expert panel, a working paper, etc.

Participation*

10% of grade comprises attendance & active participation including homework in the research orientation, research workshops, and DIS Festival 

20%

Literature review

5%

Research Project Outline

10%

Presentation at DIS Festival

10%

Final Paper

55%

TOTAL

100%

Research Orientation & Workshops

Days and times are available in the Course Summary, below.

Field Research (if applicable)

Some research projects include field research. Expenses related to fieldwork will be
covered by a DIS travel grant. The fieldwork will be planned with the research
mentor at the beginning of the semester.

Approach to Mentoring

All DIS research mentors have been trained in mentoring students but their approach to
mentoring may differ. Mentoring is about engaging at a different - and often deeper -
level than what is typical in the class room. However, mentoring also comes with some
degree of ambiguity, which is important for you to expect. The research
mentor will work closely with you throughout the semester but part of the training is also
for you to use your own judgement, to make assessments and decisions. As part of
planning your tasks and responsibilities for the semester together, the research
mentor will talk to you about her/his approach to mentoring.

Expectations of the Research Assistant

The specific expectations of the individual research assistant are agreed upon at the
beginning of the semester. In general, a research assistant is expected to take initiative,
take ownership of the project and work independently. You must also be prepared for
meetings and be willing to part take in relevant discussions. In cases where more
research assistants are involved in the same project, you will be expected to engage in
some teamwork. Carrying out a research project is not a straightforward and
predictable process. This is part of what makes it exciting. It also means that
communication is crucial. You are expected to take responsibility for communicating
about problems or issues that arise.

Data

Note that many US colleges/universities require their students who are participating in research at home or abroad to acquire Institutional Review Board approval. Examples include:

  • Research involving human subjects
  • If the results of any research conducted during your semester with DIS involving human subjects are to be made public or published in the US

You are responsible for confirming whether home IRB-approval is required and, if so, for seeking the approval of your home schools IRB. In addition, all research conducted in Europe must adhere to GDPR regulations, as noted above.

Disability and Resource Statement

Any student who has a need for accommodation based on the impact of a disability should contact Academic Support in Copenhagen (acadsupp@dis.dk) or in Stockholm (academics@disstockholm.se), depending on the project location. In order to receive accommodations, students should inform the instructor of approved DIS accommodations within the first two weeks of classes.

Academic Regulations

Please make sure to read the Academic Regulations. on the DIS website. There you will find regulations on: 

Course Summary:

Course Summary
Date Details Due