MED-BMS31
OMICS data analysis for systems biology
Course infoSchedule
Course moduleMED-BMS31
Credits (ECTS)3
CategoryMA (Master)
Language of instructionEnglish
Offered byRadboud University; Faculty of Medical Sciences; Biomedische wetenschappen;
Lecturer(s)
Contactperson for the course
prof. dr. M.A. Huijnen
Other course modules lecturer
Examiner
prof. dr. M.A. Huijnen
Other course modules lecturer
Academic year2022
Period
W48-B  (28/11/2022 to 31/08/2023)
Starting block
W48-B
Course mode
full-time
RemarksThursday and Friday for 4 weeks after the start of the period. Check schedule for exact test date (in case of resits).
Registration using OSIRISYes
Course open to students from other facultiesYes
Pre-registrationYes
Pre-registration openfrom 01/08/2022 up to and including 30/09/2022
Waiting listYes
Placement procedureDone manually by Back Office
ExplanationDone manually by Back Office
Aims
After completion of the course, students are able to:
 
  1. Work in Linux
  2. Explain what RNAseq and DNAsequencing reads look like and what they reflect
  3. Apply the most commonly used tools to process primary RNAseq and DNA sequencing data
  4. Distinguish neutral versus disease causing variants in DNA sequences and from sequencing errors
  5. Identify differentially expressed genes and pathways from RNAseq data
  6. Apply pattern recognition techniques to gene expression results from RNAseq data

 
Content
This course focuses on the analysis of the omics data: genomics and RNAseq, and how to translate the raw data into biologically and medically meaningful variables. The course will be a “hands-on” course. Students will get the data and learn to process them using the currently available programs and interpret the results. The programs are run in the Linux and Rstudio environments, and students will be made familiar with Linux to be able to work with it. The students will be able to interpret the results from the primary analyses. E.g. they will be able to interpret mutations into likely errors, neutral and disease causing mutations,  or, after converting RNAseq reads into gene expression values they will be able to call differentially expressed genes and interpret them into differentially regulated biological processes and pathways. In the last days of the course the students will do a research project using the skills they have learned during the course.

Intructional modes

Lectures and COOs

Required prior knowledge
Familiarity with Rstudio is useful.
Instructional modes
Working group

Tests
Written exam; open questions
Test weight75
Test typeWritten exam
OpportunitiesBlock W48-B, Block W48-B

Presentation
Test weight25
Test typePresentation
OpportunitiesBlock W48-B, Block W48-B