Bioinformatics

Teacher(s)

Dupont Pierre;

Language

English

Main themes

• Introduction to molecular biology
• Searching methods in biological databases
• Sequence comparisons, sequence alignment algorithms
• Motif search
• Hidden Markov models
• Gene expression measurement technology
• Transcriptome analysis methods
• Inference of interaction networks
• Phylogeny

Aims

At the end of this learning unit, the student is able to :
1	With respect to the AA referring system defined for  the Master in biomedical engineering, the course contributes to the development, mastery and assessment of the following skills : AA1.1, AA1.2, AA1.3 AA2.2, AA2.4 AA4.3 AA5.3 At the end of this course, students will be able:  - to master the basic concepts of molecular biology for appropriate use of  bioinformatics tools, - to design and develop tools or methods for  database management, information extraction  and data mining, - to formulate informed decisions between the many  computational methods that are available for solving biological questions, - to carry out a collaborative project aiming at the resolution of a bioinformatics problem and  taking benefit from complementary student's education and expertise, - to use the information available in major sequence databases (Genbank, Uniprot) with a critical mind and with discernment, - to master a software environment such as R (Bioconductor).

Content

• Overview of basic concepts in molecular biology
• Search in biological databases
• Sequence comparison, pairwise and multiple sequence alignments
• Hidden Markov models
• Phylogenetic tree inference algorithms
• Gene expression analysis methods (transcriptomics)
• Biomarker selection
• Predictive modeling

Teaching methods

Due to the COVID-19 crisis, the information in this section is particularly likely to change.

Lectures and computing projects.

• The projects are made in groups of (max) 2 students to implement, possibly to adapt, concrete algorithms covered in the course lectures.
• The projects are implemented in R. An R tutorial is included at the beginning of the first project.

By default, lectures can be followed face to face in the auditorium announced in the official schedule. Depending on the actual number of registered students and the evolution of the sanitary situation, students will be able to follow the lectures as well remotely on Teams.
Practical projects are submitted on line and evaluated on the Inginious platform.

Evaluation methods

Due to the COVID-19 crisis, the information in this section is particularly likely to change.

The final grade consists of

• 25% for computing projects implemented in groups during the semester
• 75% for the final exam

The projects cannot be re-implemented for the second session. Hence, the project grade is fixed at the end of the semester.
The final exam is, by default, a written exam (on paper or, when appropriate, on a computer).
These evaluation rules are subject to possible updates due to the sanitary situation.  In particular, the relative weights between the projects and the final exam could be adapted. Such possible updates would be notified to the students by a general announcement posted on the Moodle site of this course.

Online resources

Moodle
http://moodleucl.uclouvain.be/course/view.php?id=8915

Bibliography

Recommended textbooks - Ouvrages complémentaires conseillés :
- Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids, R. Durbin et al., Cambridge University Press, 1998.
- Inferring Phylogenies, J. Felsenstein, Sinauer Associates; 2nd ed., 2003.
- Bioinformatics, Sequence and Genome Analysis, D. Mount, Cold Spring Harbord Laboratory Press, 2nd ed., 2004.
- Introduction to Computational Genomics : a case-study approach, N. Cristianini M. Hand, Cambridge University Press, 2007.

Teaching materials

• Required teaching material include all documents (lecture slides, project assignments, complements, ...) available from the Moodle website for this course.
• Les supports obligatoires sont constitués de l'ensemble des documents (transparents des cours magistraux, énoncés des travaux pratiques, compléments, ...) disponibles depuis le site Moodle du cours.

Faculty or entity

GBIO