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You are hereUNIL > School of biology > Master of Science in Molecular Life Sciences > Sequence a genome

A unique class in Europe and the world!

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A hands-on class to learn different aspects of genomics and bioinformatics

  • Sequence, assemble and annotate a new (microbial) genome (semester 1)

  • Functional analysis of genome-wide gene expression (semester 2)

Description

When the new master program Molecular Life Sciences was launched in 2010 in the University of Lausanne, it contained a very unusual class. One made possible by the progress of technology, the concentration of competences in Lausanne, and the daring of a small team of instructors: the “Sequence a genome” class.

The principle is simple: every year the students start with a microbe, whose genome is yet unknown. The students purify the microbe's DNA, which is send to the genome center for sequencing. A few weeks later (during which the students learn the principles of assembly) the class recovers the raw genome sequence. The students then polish and assemble the raw data to (ideally) a full genome with as few contigs as possible. The sequence is then automatically raw annotated and the students divide key topics and functions to focus on. Annotations are manually curated and key genome features are identified (e.g., plasmids, genomic islands, phages).

During the second semester the students perform an experiment to study genome-wide gene expression with the same microbe under different experimental conditions. RNA is isolated, processed and again sequenced, after which it is mapped to the genome. Reads are counted and compared, in order to understand the functional response of the microbe to the imposed conditions, and improve knowledge of the functions previously annotated. Finally, all information is gathered into a manuscript, which is submitted for publication and co-authored by all students and tutors.

A unique feature of this course is the work on an actual research project, for which the results are totally unknown at the start of every year, and for which the methods are continuously evolving: the teachers and the students must stay at the forefront of the latest experimental and computational expertise. In the end, the students have produced new knowledge, and have learned to work with cutting-edge sequencing and bioinformatics technologies.
As far as the Lausanne team knows, they were the first in the world to propose such a course. The course received a collective Excellence in teaching award from the Faculty of Biology and Medicine in 2012.Stay tuned to the blog for the latest class developments and discoveries!

Publications

 

HIV-1 latent reservoir: size matters.

Hodel F., Patxot M., Snäkä T. & Ciuffi A.

Future Virology, 2016 December; 11(12): 785-794

 

 

 

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

Bertelli C., Aeby S., Chassot B., Clulow J., Hilfiker O., Rappo S., Ritzmann S., Schumacher P., Terrettaz C., Benaglio P., Falquet L., Farinelli L., Gharib W.H., Goesmann A., Harshman K., Linke B., Miyazaki R., Rivolta C., Robinson-Rechavi M., van der Meer J.R., Greub G.

Front Microbiol. 2015, Feb 19;6:101

 

 

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Miyazaki R., Bertelli C., Benaglio P., Canton J., De Coi N., Gharib W.H., Gjoksi B., Goesmann A., Greub G., Harshman K., Linke B., Mikulic J., Mueller L., Nicolas D., Robinson-Rechavi M., Rivolta C., Roggo C., Roy S., Sentchilo V., Siebenthal A.V., Falquet L., van der Meer J.R.

Environ Microbiol, 2015, 17(1):91-104
 

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© Jan Roelof Van Der Meer

 

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