SSB-30306 Molecular Systems Biology

Course

Credits 6.00

Teaching methodContact hours
Lecture12
Practical65
Group work8
Course coordinator(s)dr. M Suarez Diez
Lecturer(s)dr. M Suarez Diez
prof. dr. SC de Vries
dr. ir. CA Maliepaard
prof. dr. ir. D de Ridder
dr. E Saccenti
Examiner(s)dr. M Suarez Diez

Language of instruction:

English

Assumed knowledge on:

Basic knowledge of statistics, Molecular Biology and Bioinformation Technology.

Continuation courses:

Toolbox Systems@work, Toolbox Molecular Biology, Advanced Systems Biology

Contents:

Nowadays increasing numbers of complete genomic sequences are available and methods have been developed to study system wide gene expression, protein interaction and metabolite formation. Systems biology integrates the results of the different omics techniques in order to understand how they work together by using special analysis and visualization techniques to extract relevant information for elucidating the function of genes, proteins and metabolites, to signify interactions between these molecules and to study the underlying regulatory mechanisms. The course is modular and focuses on data generation, mining, analysis and data integration and visualization.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- explain variation control and experimental design used in the generation of omics datasets;
- apply relevant univariate and multivariate statistical methods for analysis of omics data;
- compare these statistical methods with each other and explain which method is applied for which type of biological question;
- interpret mass spectrometry datasets of proteins;
- construct, enhance and mine biological networks of molecular interactions from omics data;
- analyse network topology using precise mathematical definitions, R and Cytoscape;
- construct protein classes based upon network properties;
- evaluate 'omics' information with respect to the biological questions.

Activities:

- hands on course;
- lectures;
- training and study of relevant literature;
- programming in R.

Examination:

Written report on assignment (20%), + written exam (80%) with open and closed questions with closed book. Minimum Mark for assignment: 5.0; Minimum Mark for written exam: 5.0.

Literature:

During the course, literature and exercises will be available in Brightspace.

ProgrammePhaseSpecializationPeriod
Compulsory for: MBFBioinformaticsMSc3WD
Restricted Optional for: MPBPlant BiotechnologyMScA: Functional Plant Genomics3WD
MinorPeriod
Compulsory for: WUSYBBSc Minor Systems Biology3WD