Information for the student – Genetics and Genomics

Practical course based on the detection of gene products in development using confocal microscopy techniques and image analysis. The experimental work will be done in a laboratory, in a confocal microscopy facility, in cell culture chambers, and the results will be analyzed with the FIJI and Imaris programs.

Techniques learned include gene expression analysis, FRAP, collocation, and 3D image analysis.

All the preparations are done by the students and all the students learn to use a basic confocal microscope. Students prepare various types of embryos and developing tissues labeled with different fluorescent molecules. From the images generated, the analysis of bioimages allows the students to discuss the results obtained. Students work in small groups of 2 to 3 students to encourage learning and interactions.

The course concludes with an oral presentation of all the experimental work done by all groups.

This hands-on course introduces the most relevant aspects of bioinformatics analysis and interpretation of genomic sequencing experiments (e.g., ChIP-seq and RNA-seq). Students are introduced to basic genome-wide visualization tools and to regulatory sequence-level analysis applications, within an interactive work context that promotes student participation without the need for prior programming knowledge.

The course deals with concepts of Genomics to introduce some basic programming concepts and computational tools to facilitate the automation of analyses, leading to repeatability (obtaining the same results from a given software tool or protocol), reproducibility (being able to replicate the analyses from a previous work or from an already published one), and repurposability (to adapt the code or protocol to novel datasets or to solve novel problems). We will focus on the Unix command line interpreter, the "bash shell", on the "R shell", as well as on some general tools to process data files and command-line versions of sequence analysis software (such as BLAST or gene-finding tools). Examples will be provided along the course to illustrate how those tools and processes can be integrated into bioinformatics protocols reporting all the steps of a Computational Biology experiment.

This course has a practical part on pattern formation and growth. The students will use transgenic Drosophila strains to modify the expression of morphogens using the Gal4/UAS transactivator system. The results will be observed and interpreted in discussions.
These images were taken by students of the course 2020-2021.

This is a mainly practical course that introduces the state-of-the-art computational tools for inferring the demographic and evolutionary history of populations and species, and for determining the functional consequences of mutations, using genomic data. This fundamental knowledge has a vast importance and applicability in genetics and biomedical research, and in biodiversity studies.

Image: Interactive visualization of a recent global analysis (March 2022) of the evolution of  SARS-CoV-2 genomes (source: nextstrain.org), the case study implemented in the practical lessons of this course.