Course Syllabus

 

 

Semester & Location:	Spring 2025 - DIS Copenhagen
Type & Credits:	Elective Course - 3 credits
Major Disciplines:	Biology, Biophysics, Biomedicine/Biotechnology
Research Mentor:	Christian Code, Ph.D (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

Dianox develops novel oligonucleotides called chemical antibodies or aptamers that can bind to proteins, small molecules, or cells with high affinity. We have developed a proprietary database and machine learning platform to create new aptamers targeting various molecules. The research project will involve testing the binding of aptamers to surface proteins related to cancer, utilizing techniques like fluorescence assays on proteins or cancer cell lines. Throughout the term, the research assistant will submit weekly one-pagers and culminate their work with a research paper.  The student will learn about aptamers, perform in silico rending and docking, and perform in vitro techniques in the laboratory. The aptamer can be used either as a drug or as a novel diagnostic.  The student will write a paper based on this work.

 Research Mentor bibliography:

•  Jahromi, B. Rezai, et al. "Contrast labeled immunoliposomes for detecting rupture prone aneurysms." Brain and Spine 2 (2022): 101411. 
• da Silva, Amanda Gabrielle, et al. "Development of a Molecular Aptamer Beacon Applied to Magnetic-Assisted RNA Extraction for Detection of Dengue and Zika Viruses Using Clinical Samples." International Journal of Molecular Sciences 23.22 (2022): 13866. 
• Morsch, Flemming, Iswarya Lalitha Umasankar, Lys Sanz Moreta, Paridhi Latawa, Danny B. Lange, Jesper Wengel, Huram Konjen, and Christian Code. "AptaBERT: Predicting aptamer binding interactions." bioRxiv (2023): 2023-11.

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.

Project-Specific Objectives Include:

Relevant literature search, data analysis including risk calculations, written discussion about the results of the data analysis and a summary report of the findings.

Research Mentor

Christian Code, PhD, has 10+ years of experience in developing new biotechnology products. Christian Code has developed three marketed liposomal cancer drugs. He has worked with a number of biophysical tools from fluorescence to mass spectrometry. His research has namely been with lipids (lipid protein, lipid-lipid, lipid oligonucleotide, drug) interactions. Currently, he is researching aptamers as novel therapeutics. 

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 in person or via email every week (or another specified interval) to your research mentor, 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 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 Enrollment and Grading.  
• Academic Expectations and Honor Code.