Advanced Genomics Analysis

6 EC

Semester 1, period 3

5053ADGA6Y

Owner Bachelor Biomedische Wetenschappen
Coordinator prof. dr. A.D.J. van Dijk
Part of Minor Biomedical Sciences: From basic biology to booming business, Minor Molecular Life Sciences, year 1Bachelor Biology, year 3Bachelor Psychobiology, year 3Bachelor Bèta-gamma, major Biomedische Wetenschappen, year 3Bachelor Biomedical sciences, Frontiers in Medical Biology, year 3Bachelor Biomedical sciences, differentiation Patient Oriented Research, year 3Double Bachelor Biomedical Sciences and Medicine, year 3
Links Visible Learning Trajectories

Course manual 2024/2025

Objectives

  • Explain basic principles of transcriptomics technologies
  • Explain the (statistical) concepts and principles of selected bioinformatics methods required for analyzing and interpreting large scale omics data sets
  • Demonstrate advanced scripting skills for R and Linux command line
  • Demonstrate ability to use relevant transcriptomics bioinformatics methods and tools in a correct way, to answer biomedical research questions.
  • Formulate relevant omics data analysis questions, generate results, and critically interpret the results
  • Structure complex omics data and results in clear figures and tables

Teaching methods

  • Self-study
  • Laptop seminar
  • Lecture

Learning activities

Activity

Hours

Hoorcollege

25

Laptopcollege

110

Tentamen

3

Self study

30

Total

168

(6 EC x 28 uur)

Attendance

Programme's requirements concerning attendance (OER-B):

  • Participation in all practical sessions, computer sessions, and seminars in the curriculum is obligatory.

Additional requirements for this course:

Absence needs to be communicated to the course coordinator.

Assessment

Item and weight Details

Final grade

1 (50%)

Tentamen

1 (50%)

Project report

The exam is an open book exam (you can use the material provided throughout the course).

Inspection of assessed work

Announcement on canvas.

Assignments

In the third and fourth week of the course, during some of the laptop seminars you will work on a project to analyze a transcriptomics dataset. A small report on this has to be handed in Jan. 29 which will be graded. You will work on this project in pairs.

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Weeknummer Onderwerpen Studiestof
1  introduction RNA-sequencing lecture (slides)
2 data analysis for interpretating and integrating RNA-sequencing results lecture (slides)
3 biological interpretation of RNA-sequencing results project handout
4 self-study, report writing, exam  

Contact information

Coordinator

  • prof. dr. A.D.J. van Dijk