GBIO009-1: Bioinformatics 2013

This is a graduate level course where students are exposed to essential bioinformatics concepts including a)accessing public databases both manually and programatically; b) sequence alignments analysis; c)working with Bioconductor and its libraries on genomic and transcriptomic data; d)programming in R; e)phylogenetic trees/clustring of biological data

This site will provide practical component of the course. In addition, all the anouncements will be posted both on the "main THEORY course website" and on this page

Final course marks

The final marks are posted here. Please use your submission site login to access the protected page

Course schedule / outline

Please consult current course schedule here

Intermediate Marks

Please periodically consult your course marks here. The login credentials are the same as the ones used for the HW submission (s***** your_password)

Exam information

The location and time of the exam is found below and had been confirmed officially. Please note that we will be writting at building B37. More information is available from Dec 10,2013 presentation

Date23 Jan 2014 (Thursday)
LocationRoom 02, building B37
Timefrom 13:30 til 17:30 (4hrs)

FAQ from students

1. Are course notes are allowed during the exam ?

You can take to the exam all the course notes and supporting documents that were either provided by Kristel or by Kirill plus your personal written notes while studying the material

2. With respect to the articles that were suggested to be read before exam, would other articles need to be read also? The articles are really complex and take time to digest and understand

There are a total of 8 articles from which questions will be asked: 4 papers that were offered while the course was ongoing (at the first half of the course - hence with in principal enough time to have read them and to answer the provided guiding questions when "studying" the course throughout the year) plus 4 papers that were presented by teams and were made part of a homework assignment (see course notes from Dec 10th, 2013)

Assignment submission

Assignments will be submitted on-line via specially dedicated website. One needs to create a new account to be able to login and submit your assignments. In the event of passed deadlines and/or thechnical difficulties, please send your work via email to course coordinators.


Homework sign-up form

Please for each assignment, use this form to notify the course coordinators about your assignment/homework selection and group composition via on-line form



• Sept 17th: First class will start Tuesday, September 17th and it will be hands-on. We will introduce a course technicalities, start working with R, explore main bioinformatics databases. This will allow you to be better prepared for the upcoming assignments. In addition a homework will be administrated. Do not forget to bring you PCs for this 1st class.

Class location and meeting times
Tuesdays (see class schedule)
Institut Montefiore, Bâtiment B28
Room 1.21
2pm-6pm (by the latest)

• Oct 1st: Next class will be held on Oct 1st by Kristel Van Steen. Check the theory website

• Oct 8th: Next class will be mainly tought by Kristel Van Steen. At the end of the class next homework (HW1b) will be introduced together with nencessary basics. Bring your laptops, will try to install necessary R libraries.

• Oct 15th: This week will have a mix of practical and theoretical material lectured by Kirill Bessonov(TA). Will cover linear regression, popular genetic inheritance models, GWAS analysis via GenABEL that should help you with HW1b completion. We have lots of ground to cover this week.

• Oct 22nd: This week the lecture will be given by Elena Gusareva. She will intoroduce GWAI(Genome-Wide Assoctiation Interaction) protocol and epistasis concepts. In addition she will also introduce on how to give a biological meaning to the mined results

• Nov 5th: This week the lecture will be given by Kristel Van Steen on the topic of DNA sequence analysis and alignment of sequences. This is a classical topic in bioinformatics and subsequent HW2 is based on the topic too. During the week of Nov 12, will have also a practical lecture on sequence alignmemnt algorithms. Finally, for this week slides please look at Kristel Van Steen's webiste

• Nov 12th: This week we will have a practical class tought by me on sequences alignmnet which is a classical topic in Bioinformatics. We will take apart global and local alignment of DNA and protein sequences. In additon HW2 will be explained and HW1 will be commented

• Nov 19th: This week you will be lectured by professor Ingrid Arijs from KU Leuven on the topic of microarray/expression data analysis. Important: please bring your laptops with R installed to this class as you will be required to execute and try some R code during the lecture to enhance material understanding. She kindly agreed to give a guest lecture this year too! Towards the end of the class I will introduce HW3 that concerns clustering and microarray analysis.

• Nov 26th: This week you will be lectured by professors Ronald Westra and Steven Kelk from Maastricht University (Holland) on the topic of phylogenetic trees and evolution of genomes. After his lecture I will follow on the topic and give a lecture on construction of phylogenetic trees in R

• December 02: This week we had covered clustering and data reduction techniques. The next week you will present the litrature style homework and give in-class presentations. I request each group to send me the title of the selected paper for presentation so that I could notify other students via this section of the website. Good luck with preparation work. I know that you have lots on your plate, but all tasks are doable and you will go through this challenge with flying colors!

• December 10th:Uff, the time really went by really fast as usual. This week we are having last lecture. I guess it will bring mixed feelings of joy and sadness? This week we have very important lecture where oral presentations of scientific papers will be held. Each presentation will be about 20 minutes long. After collecting information from you, I found that we had 4 papers that will be presented and 6 groups. This means that ironically some of groups selected the same paper. We have 3 groups presenting on the same paper! This is OK, we will have different prespectives, but I will try to avoid this scenerio for the next year.The papers to read before Tue class by ALL students are as follows: 1)Pompanon et al (2005) Genotyping errors: causes, consequences and solutions; 2)Hurd PJ Advantages of next-generation sequencing versus the microarray in epigenetic research; 3)Do R (2012), Exome sequencing and complex disease: practical aspects of rare variant association studies (the most selected paper!); 4)Day-Williams AG (2011) The effect of next-generation sequencing technology on complex trait research . Also Kristel Van Steen will give you details with respect to the final exam. The student presentaitons will be posted online for other students to learn. The presented material might be included in final examination. In addition, I will provide your marks for H1a and HW1b

• December 20th: The marks and corrected HW1 and HW2 in pdf format will posted online via the submission password-protected website sometime before Jan 01, 2014

• Jan 13th: The preliminary marks and marked HW3 is posted online under marks section of this page. Best of luck with exam preparation!

Course material

September 17, 2013 - the 1st class . Class starts at 2pm

ppt Introductory lecture: course details, R-language, databases

ppt HW1a: exploring bioinformatics databases (HW type 3)

October 1st, 2013

Please check the theory website containing Chapter 1 and 2 lecture slides

October 8th, 2013

pptHW1b practical lecture notes

pptHW1b - type 1: GWAS literature review assignment

pptHW1b - type 2: GWAS on Asthma (ACRN cohort)

pptHW1b - type 3: GWAS Q&A into to GenABEL

October 15th, 2013

pptClass notes on practical apsects of GWAS and GenABEL tutorial

October 22nd, 2013

pptClass notes on epistasis and GWAI analysis

November 5th, 2013

The lecture material will be posted on Kristel Van Steen's website

November 12th, 2013

pptSequences alignment practical: lecture notes

pptHW2 - type 1: Biological sequences - literature review assignment

pptHW2 - type 2: implementation of NW global sequence algorithm

pptHW2 - type 3: Sequences alignment graphically and using R

November 19th, 2013

pptAnalysis of microarray data: lecture notes

pptHW3 - type 1: Clustering and Phylogeny - literature review assignment

pptHW3 - type 2: analysis of microarray data

pptHW3 - type 3: Phylogenetic trees and data clustering methods

November 26th, 2013

pptPhylogenetic analysis by Ronald Westra: lecture notes

pptPhylogenetic networks by Steven Kelk: lecture notes

pptPhylogenetic tree construction based on sequence alignments in R: lecture notes

December 02, 2013

pptData Clustering lecture notes

December 10, 2013

pptExam information click here

Six students presentations on selected papers from HW1 and HW2

  1. ppt Exome sequencing : Practical aspects by MOTTART Xavier THOMAS Julien
  2. ppt Exome sequencing and complex disease by Jacquemin Jonathan & de Bournonville Sébastien
  3. ppt The effect of Next-Generation Sequencing technology on complex trait research by Ladang Auxane, Mombaerts Laurent, Uyttendaele Vincent
  4. ppt Next-generation sequencing vs. Microarray in epigenetic by Bosch Vincent, Klecker Sophie, Straat Julien
  5. ppt Genotyping errors. Causes, Consequences and Solutions by François Ancien, Sascha Kretzschmann,Olivier Suplis
  6. ppt Exome sequencing and complex disease by Alice Bouchoms, Amaury Vanvinckenroye, M. Legrand