Computational Biology, part II (MSIAM & ENSIMAG)


This is the second part of the computational biology class (MSIAM & ENSIMAG).

Principles and design of this class

Lecture material and assigned readings

Lecture 1 : 2023-11-14

Lecture 2 : 2023-11-21

Lecture 3 : 2023-11-28

Lecture 4 : 2023-12-05

Lecture 5 : 2023-12-12

Lecture 6 : 2023-12-19

To go further

Here is the list of articles that were proposed for the article presentation, but were not picked. This is my personnal selection of important (and readable) articles in quantitative microbial evolution, specially intended to persons with a mathematical and computational background and an interest for evolutionary biology.


You will be assessed based on your work (alone or in a team of two students) on one of the following tasks, following the poll that you answered before the second class.

Beyond this choice of project or article for the assessment, you are all encouraged to read the proposed articles and work on the data challenge and the research project. But you will only be evaluated on one of these works.

General rules:

Mutagenesis data challenge

Download the instructions and dataset here for this data challenge. Keywords: mutagenesis; stochastic simulations; data analysis; parameter inference.

Strict deadline: 2024-01-07. Bonus points for early submission : +1/20 if submitted before 2023-12-22.

Evolutionary dynamics research project

You will design and implement an individual-based simulated model to study the adaptation of bacterial populations. Example questions one could study include:

You will have to choose a representation of genotypes and phenotypes suited for the specific question you want to study. To be interesting, your model should probably exhibit some degree of epistasis.

This project requires frequent interactions with the lecturer to define a specific research question and validate your research methodology.

Strict deadline: 2024-01-14. Bonus points for early submission : +1/20 if submitted before 2024-01-07.

Critical analysis and presentation of a research article

You will choose an article among the list below (on a first come first served basis) and present it in front of the class (max 15 min presentation + 5 min questions). Your presentation should include a broad overview of the topic, explain the impact of the ideas and the connection with the class, and make the main ideas understandable by a non-specialist audience. The target audience is the other students of the class (math and cs students), not the lecturer.

In addition to your presentation, you will write a ~1000 words synthesis presenting these points (once again you are not only expected to explain the content of the article, but also to present the broader scientific context and the specific connections with the content of the lectures).

There is no flexibility in the choice of date for the presentations as they have to be synchronised with the advancement of the lectures. You will email me your written synthesis and the slides for your presentation (both as pdf files) 24h before your presentation at the latest.

Beware that presenting a research article is not an easy task, and the article presentation should not be considered as an easy alternative to the data challenge or research project. A substantial reading (and writing) work is expected. It is likely that you will have to read further than the original article to be able to fully understand it and its scientific context.

FYI, the eval grid I use for the presentations is available here.

Contact the teacher

antoine DOT frenoy AT