Duration
20h Th, 16h Pr, 4h AUTR
Number of credits
| Master in bio-informatics and modelling (120 ECTS) | 3 crédits | |||
| Master in biochemistry and molecular and cell biology (120 ECTS) | 3 crédits |
Lecturer
Denis Baurain, Franck Dequiedt, Marc Hanikenne, Patrick Meyer
Coordinator
Language(s) of instruction
French language
Organisation and examination
Teaching in the first semester, review in January
Schedule
Units courses prerequisite and corequisite
Prerequisite or corequisite units are presented within each program
Learning unit contents
Recent technological innovations (high-throughput sequencing and genotyping, genome editing, etc.) have led to a major boom in nucleic acid analyses. These make it possible to decipher the sequence, structure, content and evolution of genomes, as well as to analyse gene expression and regulation. Genetic engineering, via molecular cloning and genome editing techniques, then makes it possible to manipulate the function of these genes. They also make it possible to describe genomic variations, which in turn underlie phenotypic variations (e.g. diseases, adaptations to a particular environment).
These approaches require a combination of tools for generating large experimental datasets, analysing them bioinformatically and making them available in databases. They can be used to examine fundamental research questions in biology, and can also be applied to biomedical research and environmental issues.
In this context, the aim of this toolbox is to introduce concepts, both theoretical and methodological, that are useful for understanding and implementing genomic, bioinformatics and genetic engineering approaches. These concepts will then be used in different thematic modules (Evolution, Adaptation, Diversity; Development from the cell to the organism; Responses to the environment).
Table of contents of theoretical courses
Partim I. Genomics (M. Hanikenne/D. Baurain/P. Meyer)
- Nature of the genome
- Sequencing and assembly strategies
- Sequencing technologies, including high-throughput sequencing
- Computer modelling of sequences, sequencing coverage and assembly
- Databases, gene prediction, BLAST algorithm and HMM principle
- Transcriptomics and regulation
- Genomic variation
- Inference of gene expression networks
- Molecular biology techniques: cloning, PCR, qPCR, etc.
- Gene inactivation techniques: Crispr editing, siRNA transfection, degron AID system
Table of contents for practical and practical work
- Bioinfo work: Sequence modelling, coverage and assembly
- Bioinfo work: Databases, gene prediction, BLAST and HMM
- Bioinfo lab: Primer design and cloning strategy exercises
- Bioinfo lab: Inference of gene expression networks
Learning outcomes of the learning unit
By the end of the "Toolbox: Nucleic Acid Analysis" module, students will have :
- Acquired a good understanding of the concepts and methods of genomics and genetic engineering,
- Discovered illustrations of basic bioinformatics approaches,
- Acquired the keys to understanding the sustained pace of innovation and development in these disciplines, which now play a major role in all aspects of biology.
Prerequisite knowledge and skills
The notions of genetics, molecular biology, mathematics and R acquired on completion of the Biological Science Bachelor degree will be sufficient to tackle the course.
Planned learning activities and teaching methods
The theory sessions (2 hours) will take place in a classroom. They will mostly consist of ex cathedra lectures with active participation from the students, through solving small challenges in groups and watching and discussing short illustrative videos. The pooling of research by groups will provide an opportunity to debate and summarise the concepts covered.
Students are strongly encouraged to attend the course and take notes to supplement the material shown. The essential concepts to be mastered will be specified during the course.
The practical sessions will be mainly computer-based and will put into practice the theoretical concepts covered in the course.
Mode of delivery (face to face, distance learning, hybrid learning)
Face-to-face course
Additional information:
Presential
Recommended or required readings
Powerpoints and TP/DD notes will be made available on ecampus.
Exam(s) in session
Any session
- In-person
oral exam
Additional information:
The toolbox will be assessed by means of an integrative oral examination (face-to-face), with prior written preparation, in the presence of the 4 module teachers. Students will be assessed on their understanding of the concepts covered and their application, as well as their ability to integrate the information covered in the various parts of the course. The concepts covered during the practical sessions are likely to form part of the assessment.
Work placement(s)
Organisational remarks and main changes to the course
Practical and/or practical work is compulsory. Any absence must be justified and, where appropriate, students are required to put their work in order. If a report is required, it must be completed even in the event of absence. In the event of unjustified absence, the student may not be admitted to the examination.
Contacts
Module coordinator
Prof. Marc HANIKENNE
Tel. 04/366.38.44
email: marc.hanikenne@uliege.be
Co-Titulars
Prof. Denis BAURAIN, denis.baurain@uliege.be
Prof. Franck DEQUIEDT, fdequiedt@uliege.be
Prof. Patrick MEYER, patrick.meyer@uliege.be