SSB-51306 Introduction to Functional Genomics


Studiepunten 6.00

Problem-based learning
Course coordinator(s)dr. ir. LH de Graaff
Lecturer(s)dr. ir. P van Baarlen
dr. ir. GJEJ Hooiveld
dr. ir. LH de Graaff
dr. ir. EG Zoetendal
dr. ir. JE Wellink
Examiner(s)prof. dr. VAP Martins dos Santos

Language of instruction:


Assumed knowledge on:

Basic knowledge in biological sciences


Driven by the continuing and accelerating discoveries in ~omics technology, unique and exiting possibilities have emerged to perform genome-wide investigation of organisms and communities of organisms at the molecular level. As part of these developments the field of functional genomics is developing rapidly to contribute to the genome-wide models that are being constructed in Systems Biology. The area of functional genomics attempts to determine the function of genes and proteins based on high-throughput approaches. In this context, Systems Biology studies the mutual/reciprocal interactions between genes, proteins, metabolites to reveal the networks that underlie specific phenotypes.
In this introductory course, the students will learn the basic methodology and concepts used in Functional Genomics research. Methods that will be discussed include transposon mutant libraries, RNA silencing and gene knockout libraries and models. Their applications will be illustrated using examples from bacteria, fungi, plants, animals and humans.
Metagenomics approaches capitalize on the new generation technologies for sequencing nucleic acids and proteins, as well as on other high-throughput methodologies and are frequently used to explore complex microbial ecosystems. Advanced applications of functional metagenomics, including analyses through meta-proteomics, meta-transcriptomics and high-throughput metabolomics are used to address the microbial functions underlying microbiota in a wide range of environments, from acid mining lakes to the mammalian gut. Studies in Functional Genomics have an obvious impact in society. As a result, novel biotechnological products can be developed, environmental-control processes improved, health beneficial food products, and nutrition-based prevention and treatment strategies can be designed. The future outlook of these studies and their impact for society will be discussed during the course.

Learning outcomes:

After successful completion of this course students are able to:
- understand the concepts transcriptome, proteome and metabolome;
- understand the relations between transcriptome, proteome and metabolome;
- understand the high throughput methods applied in functional genomics;
- apply functional genomics approaches to simple research questions;
- nterpret data from functional genomics studies;
- integrate data from different levels (molecule-to-molecule and whole-genome levels);
- critically interpret relevant literature;
- design follow up experiments using literature data and electronic databases;
- interpret, present and describe results in an oral presentation and concisely in a written report.


Lectures and case studies. In the case studies the students will work in small groups on cases related to the different themes of the course.


Written examination (75%) and reports of the literature cases (25%).


A reader will be available.

Verplicht voor: WUMINBSc Minor Microbes Inside2AF
WUSYBBSc Minor Systems Biology2AF