Parisian Master of Research in Computer Science
Master Parisien de Recherche en Informatique (MPRI)

Algorithmics and bioinformatics (26h, 3 ECTS)

Coordination: Philippe Gambette (LIGM, Univ. Paris-Est Marne-la-Vallée).

Lecturers

The lecturers are researchers in the Algorithmics for Bioinformatics group at LIGM (Univ. Gustave Eiffel at Marne-la-Vallée).

For year 2021-2022, the lecturers will be Gregory Kutcherov and Philippe Gambette.

For year 2020-2021, the lecturers were Laurent Bulteau and Mathias Weller.

Practical information

Language

Lectures will be given in English.

Location

The lectures will take place at ENS Paris-Saclay.

Motivations and main objectives

The objective of this course is to study the algorithmic approaches used in bioinformatics. The topics covered in 2020-2021 include scaffolding, reversal and transposition distances, scaffold filling and phylogenetics.

Short description

A total of 26 hours of lectures and exercise sessions, from September 21st to November 9th (to be confirmed):

  • Gregory Kucherov (stringology for bioinformatics) :
    • details to be announced
  • Philippe Gambette (algorithmics for phylogenetics) :
    • details to be announced

Evaluation / exams

The evaluation of the students will consist in a written exam (coefficient 1), as well as a coding project (optional, coefficient 1).

The written exam will be on November 9th. The exercises will be given in English, and you can write your answers in English or in French. You'll be authorized to have your lecture notes with you (but no computer, cellphone, etc.)

Students will also be in charge of coding one algorithms solving an algorithmic problem in phylogenetics, in Python. Further indications will be given here on how to send the source code.

The deadline for this programming task will be November 14th, at 23:59. The deadline may be extended only by request before the initial deadline at philippe.gambette@univ-eiffel.fr.

Questions on the coding task can be sent to philippe.gambette@univ-eiffel.fr.

Schedule

  • Gregory Kucherov (stringology for bioinformatics) :
    • 2021-09-21, 8:30-12h45
    • 2021-09-28, 8:30-12h45
    • 2021-10-05, 8:30-12h45
    • 2021-10-12, 8:30-12h45
  • Philippe Gambette (algorithmics for phylogenetics) :
    • 2021-10-19, 8:30-12h45
    • 2021-10-26, 8:30-12h45
    • 2021-11-09, 8:30-10h30: lecture, 8:45-12h45: exam

Prerequisites

  • basic algorithmics and computational complexity

Related courses

Bibliography

To be announced...

 
Universités partenaires Université Paris-Diderot
Université Paris-Saclay
ENS Cachan École polytechnique Télécom ParisTech
ENS
Établissements associés Université Pierre-et-Marie-Curie CNRS INRIA CEA