Algorithms in Computational Biology

INFO-F-438 (master bioinfo&mod)

  1. Goals

  2. Course content

  3. Staff

  4. Schedule

  5. Assignments

  6. Course book (mandatory)

  7. Slides

  8. exam projects

Course content


Jean Cardinal (Algo, ULB), telephone ???,

Tom Lenaerts (MLG and IB2, ULB and AI-lab, VUB), telephone 02 650 60 04,


Assistant : Sofia Papadimitriou (IB2 and MLG, ULB)


Prof. J.Cardinal and Prof. T. Lenaerts



The goal of this course to provide basic expertise in algorithm development to students with no background in computer science and to provide computer science students with an overview of the algorithms typically used in Computational Biology.

In addition, this knowledge will allow students to better understand the algorithmic  literature in bioinformatics and computational biology.

The course follows completely the book “An introduction to Bioinformatics Algorithms’ by Neil C. Jones and Pavel A. Pevzner.  More information related to this book can be found on :   An electronic version of the book is provided here.

During the year students will have to complete 3 assignments related to 3 topics discussed in the course. See at the end of this page for the announcements and the deadlines.  Students will be graded individually for these assignments.    

For the exam, students will need to select an article related to the area of bioinformatics and computational biology, with a focus on articles that discuss an algorithmic solution to a biological problem.  The exam consists of making a presentation discussing the article.   These projects will be made in groups of 2 students.

The score of the course will be 50% on the assignments and 50% on the exam.


Sessions :

  1. Tuesdays between 11:00 and 13:00, (starting 4/2/2020) at the ULB La Plaine campus, room ??.

List of sessions (provisional)

Course book (mandatory)


Some essential information concerning the assignments can be found here : Assignment_guidelines.pdf

The first assignment (deadline March ??, 2019) :

The second assignment (deadline April ??, 2019) :

The third assignment (deadline May ??, 2019) :

Note: Assignments are individual so we will check whether there is a overlap between your code and that of other students in the course.  Depending on the degree of overlap you either will receive a zero or a reduction in grade. Plagiarism is not acceptable !


The slides linked to this course can be found on :

Exam projects

Like in previous years the exam will consist of a presentation on an article presented and published in the WABI workshops.  The proceedings for the last two years of this workshop can be found via the following links

WABI 2019

You should be able to download an article or even the entire proceedings when you’re at the ULB or via EZ-proxy to the ULB.

To prepare for the exam (first or second session):

  1. 1)create a group of 2 students

  2. 2)select two or three article from the 2019 or 2020 proceedings

  3. 3)send this information together with the PDF of the article before ?? to with [BIOINFO-EXAM] in the subject of your email.

  4. 4)One of the papers will be assigned asap.

  5. 5)prepare a 20 minute presentation discussing the motivation, problem and the algorithmic solution.  Try to also discuss the relevance and be critical on the claims made by the authors of the paper.

  6. 6)Send this presentation no later than tbd (before 17:00) to with [BIOINFO-EXAM] in the subject of your email.

The exam is organized tbd  Groups will be assigned to slots of 30 minutes. Room ?? (Meeting room IB2)

Each student group will have 20 minutes (max 16 slides including title slide) to present their article and there will be 10 minutes for questions.

Evaluation criteria:

  1. 1.Quality of the presentation (slides, explanation, examples, clarity, language, ...)

  2. 2.Link to the course (wherever possible draw relationships with the knowledge you acquired during the course, ...)

  3. 3.Understanding of the paper (maths, formulas, functionality, proofs, biological and medical relevance, ...)

  4. 4.Originality (extensions by looking up additional papers, critical analysis of the paper, going beyond the paper content, consider improvements, ...)

Exam groups and schedule