Required in stage
Second term
Both terms
Not organised
This year
Next year
Alternating years
External
Prerequisites
Identical coursesBioinformatics and Systems Biology: Expression, Regulation and Networks (B-KUL-E02N4A)
Cannot be taken as part of an examination contract
Demeulemeester Jonas (coordinator) | Demeulemeester Jonas | Lutsik Pavlo | N. | Fiers Mark (substitute) Aims
In this course, you will acquire a global view of how complex biological systems can be understood in terms of biological networks and how multiple types of high throughput omics data can be integrated to unravel biological networks. You will also develop insight into how the analysis strategies for high-throughput data work, what their main parameters are, and how to manage the complexity of the data analysis. Furthermore, you will use software applications to analyse multiple types of genomic data and to integrate those results to formulate biological hypotheses (e.g., identify biological processes active in a given biological system, identify new candidates for a biological pathway, etc.).
Previous knowledge
Given the interactive course format, there is a maximum number of students in this course. Students from a Faculty or programme other than Biomedical Sciences can submit a request to take this course.
Students from another program can only be admitted if the maximum number of students has not yet been reached.
* You need to have knowledge of molecular genetics (DNA, RNA, and protein structure and function; genome organisation and variation).
* You need to have a basic knowledge of bioinformatics databases and tools, sequence alignment, and basic linux experience. This introduction is given in the course "E06E3a Bioinformatica".
Order of Enrolment
Mixed prerequisite:
You may only take this course if you comply with the prerequisites. Prerequisites can be strict or flexible, or can imply simultaneity. A degree level can be also be a prerequisite.
Explanation:
STRICT: You may only take this course if you have passed or applied tolerance for the courses for which this condition is set.
FLEXIBLE: You may only take this course if you have previously taken the courses for which this condition is set.
SIMULTANEOUS: You may only take this course if you also take the courses for which this condition is set (or have taken them previously).
DEGREE: You may only take this course if you have obtained this degree level.
FLEXIBLE(E02N3A)
The codes of the course units mentioned above correspond to the following course descriptions:
E02N3A : Bioinformatics and Systems Biology: Sequence, Structure and Evolution
Is included in these courses of study
- Master of Statistics and Data Science (on campus) (Leuven) (Statistics and Data Science for Biometrics) 120 ects.
- Master of Biomedical Sciences (Leuven) 120 ects.
- Master in de biomedische wetenschappen (Leuven) (Afstudeerrichting Biomedisch basis- en translationeel onderzoek) 120 ects.
Activities
4 ects. Bioinformatics and Systems Biology: Expression, Regulation and Networks (B-KUL-E02N4a)
EnglishFormat: Practical
26 
First termDemeulemeester Jonas | Lutsik Pavlo | N. | Fiers Mark (substitute) Content
The following topics will be discussed:
Bulk RNA-seq analysis: normalisation, differential expression, functional analysis such as GO enrichment
Single-cell RNA-seq analysis (Seurat and/or Scanpy)
ChIP-seq analysis (read mapping, peak calling, motif analysis, links to genes)
Chromatin accessibility (e.g., ATAC-seq) and histone modifications
Single-cell ATAC-seq and multi-ome analysis
Regulatory sequence analysis: motif discovery and motif predictions
Gene regulatory network inference (e.g., iRegulon/SCENIC)
Evaluation
Evaluation: Bioinformatics and Systems Biology: Expression, Regulation and Networks (B-KUL-E22N4a)
Explanation
Assignment: The assignment is a team work, where you will analyse publicly available data sets (this includes the identification of relevant data sets). One or more of the sessions (part of the contact hours) can be used to work on this project, to discuss your progress with the teachers, and to receive feedback.
Students will have to do a peer assessment of their group and a peer review of other groups and they will have to motivate their review during an oral exam.
More information about the evaluation can be found on Toledo and will be given during class.
Information about retaking exams
Identical, but individual work