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| BIOL0845-1 | Introduction to bioinformatics
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| Duration : | 15h Th, 20h Pr |
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| Number of credits : |
| Master in Biochemistry and Molecular and Cell Biology, Research Focus, 1st year | | Second semester | | 2 |
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| Master in Biochemistry and Molecular and Cell Biology, Teaching Focus, 1st year | | Second semester | | 2 |
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| Master en biochimie et biologie moléculaire et cellulaire, à finalité spécialisée en bio-industrie, 1st year | | Second semester | | 2 |
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| Master in Biochemistry and Molecular and Cell Biology, Professional Focus in
Industrial Biochemistry, 1st year | | Second semester | | 2 |
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| Master en biochimie et biologie moléculaire et cellulaire, à finalité spécialisée en bioinformatique et modélisation, 1st year | | Second semester | | 2 |
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| Lecturer : | Denis Baurain |
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Language(s) of instruction :
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| French language |
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Course contents :
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| Today almost all studies involving molecular biology require a lot of data analysis (i.e., bioinformatics). Bioinformaticians act both upstream and downstream of molecular biologists, for example to propose a statistically sound experimental design and to generate new hypotheses from high-throughput data, which are then tested in the laboratory.
This trend is mainly due to technological advances (e.g., robots), which produce ever more data for ever less money and labor. Consequently, many research projects are delayed due to the lack of suitable bioinformaticians for mining the data. It is thus critical that biologists turn to bioinformatics, especially to stay completely in control of their future research.
In this context, this introductory course in bioinformatics is to educate students about the potential of this hybrid discipline between biology and computer science. In particular, it aims to show that bioinformaticians can be "real" biologists, whose tool of choice is the computer instead of the pipette.
This course will enable students to become aware of the role of bioinformatics and the place of bioinformaticians in modern biology. It may also lead some people to look more closely at this domain, for example by following the specialized master that will open next year (2012-2013) for BBMC students.
Table of Contents
1. Genomic databases
2. Probabilistic sequence models
3. Prokaryotic gene finding
4. Sequence alignment
5. Heuristics for alignment (BLAST)
6. Hidden Markov Models
7. Multiple sequence alignment and profile alignment (ClustalW, HMMER)
8. Variation in DNA sequences (*)
9. Estimating genetic distance (*)
10. Evolution and natural selection (*)
11. Quantifying natural selection on DNA sequences (*)
12. On trees and evolution (*)
13. Inferring trees (*)
14. Genome evolution (*)
15. Analysis of gene expression
16. Patterns discovery in sequences
17. Bonus
(*) Topics actually covered in GENE0432-3 (see below) |
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Learning outcomes of the course :
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| At the end of this course, students will be able to clearly explain the statistical and algorithmic bases of the analytical approaches seen in class. This requires, above all, to have UNDERSTOOD the course material. In this sense, this course is probably different from some other subjects of the curriculum in biology, in which mere memorization may be enough to pass the examination. The level of detail required when explaining the material roughly matches that of the companion textbook (see below), except when the slides shown in class (which will be available on myULg) are more comprehensive than the book. Note that the biological "background" of the case studies presented in the book is considered an illustration of the methods and is thus not part of the material.
For some algorithms (specified in class), an APPLICATION using pen and paper to solve a toy example may be requested. |
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Prerequisites and co-requisites/ Recommended optional programme components :
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| For issues of organization, this year the course is artificially divided into two parts, the first under the code [BIOL0845-1] 'Introduction to bioinformatics' (this course, taught in the second term) and the second under the code [GENE0432-3] 'Genetic and biochemical aspects of evolution' (part 'Molecular aspects of evolution', delivered in the first term by the same holder). However, since it is actually a single course, the order of topics might be revised during the year for optimal teaching.
The course assumes no prerequisites in computer science, but relies on a basic knowledge of mathematics and molecular genetics. In principle, the necessary level in both subjects is reached at the end of the 3rd year of BA in biology.
The only types of data covered in this course are primary sequences (DNA and proteins) and expression data obtained from microarray technology. For the exploitation of other 'Omics' data, students can apply to the course [INFO0090-1] 'Analysis of high-throughput data (Omics) 'delivered from next year as a thematic week (2012 -2013) by the same holder. |
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Planned learning activities and teaching methods :
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| Lectures will be given in a classroom. They will last 1h30 and will consist of a blend of short ex cathedra speeches (15-20 min) and challenges to be solved in small groups of students. The subsequent sharing of group research results will allow to discuss and synthesize the concepts addressed.
There will be no laboratory practicals per se, but those of the course [GENE0208-2] 'Genomics and bioinformatics' (taught by Prof. B. Joris in 2nd year of Master BBMC) will be designed to usefully supplement the present course. |
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Mode of delivery (face-to-face ; distance-learning) :
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| This is a face-to-face course (see above). Although topics are mostly taken from the reference book cited below, attending the lectures is strongly encouraged as they are designed so as to facilitate understanding and assimilation of the course material. |
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Recommended or required readings :
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| This course is based on a reference book [N Cristianini and MW Hahn (2007) Introduction to Computational Genomics, Cambridge University Press]. Such a choice ensures a good coverage of bioinformatics topics (here defined as the analysis of genomes) while providing students with a solid yet readable reference. The purchase of this book (about 31 EUR at full price) is highly recommended. For this purpose, a bulk order will be proposed during the first class.
Moreover, at the end of each session, the slides shown during the class will be made available to students through the web portal myULg. |
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Assessment methods and criteria :
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| Written examination (June session) including two theory questions (free-form explanation of a theorical concept) and one exercise (algorithm to be applied).
The topics covered in the other half of the course will be evaluated separately in a joint examination with Profs. C. Remacle and M. Galleni (see [GENE0432-3]). |
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Organizational remarks :
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| Taking notes on a laptop or tablet is allowed. However, students are expected not to surf or chat in the classroom. |
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Contacts :
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| Prof. Denis Baurain
Institut de Botanique B22 (P70)
denis.baurain@ulg.ac.be
Assistant: Dr. Damien Sirjacobs
Institut de Botanique B22 (P70)
04/366.38.54
D.Sirjacobs@ulg.ac.be |
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