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GBIO009-1: Bioinformatics 2012

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 analysis; c)working with Bioconductor and its libraries and many other topics

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

Exam information

The exam will be held on Mon, Jan 21, 2013 at 8.30am. Location: Building B28, room 1.21. The exam will be given both in English and French. Remember that the questions asked will be of the general nature to see if you understand the key concepts from each of the main topic sections. The exam will be open book. All material posted on the theory website serves as a potential resource for QCM(multiple choice) or open essay questions.

Final course marks

Feb 18, 2013: Please find below the link to access your final course marks. You would need to enter the password that was e-mailed to you. If you did not received the password, please contact me.



•  Oct 16, 2012: The assignment style 1 (literature review) has been just posted. The corrected lecture slides had been re-posted. Thank you for spotting mistakes!

•  Oct 23, 2012: The class this week will start at 2pm and not at 4pm

•  Oct 30, 2012: The class this week will also start at 2pm . Fist half of the class will be devoted to student presentations. Please prepare a 15 minutes presentation per group and make sure everyone can present a part. Papers that will be presented are "Genome data mining for everyone" (Lee GW 2008) and "Sequencing technologies — the next generation" (Michael L. Metzker 2010). Please note that HW2 is due the Oct 30th!

•  Nov 13, 2012: The class will start at 14:00 and end approximately at 16:00. The class will be about practical aspects of the Genome Wide Analysis Studies. We will cover GenABEL library and introduce the HW#3 assignments

•  Nov 20, 2012: The class will start at 15:00.This week will start with HW 1 and 2 review session followed by lecture on Microarray Analysis. HW 1 and 2 will be given in class too. Overall we are pleased with the results :)

•  Nov 27, 2012: Ingrid Arijs's presentation slides are posted. The data and assignment 4 will be posted soon also

•  Dec 1, 2012: The Dec 4th class will start at 14:00 . Elena Gusareva, a GWAIs post-doc expert from Dr.Dr. Kristel van Steen's lab, will give you hands-on overview of GWAS. The lecture slides are posted below.

•  Dec 9, 2012: The Dec 11th class will start at 15:00 and end around 17:00. Professor Ronald Westa from Maastricht University, Department of Knowledge Engineering, will give lecture on topic of "Phylogenetic sequence analysis". Ronald's research group has wide research interests including gene-protein networks analysis, imaging and singal analysis, etc. The lecture slides are not available at the moment, but I will post them after the lecture.

•  Dec 10, 2012: I had just updated the website and had added the supporting material for the Microarray Analysis lecture presented by Ingrid on Nov 20th. I had also posted the HW4 assignments that are due Jan 15th, 2013.

•  Dec 12, 2012: I had just added presentation slides from Steven Kelk that had given talk yesterday. The next week class (Tue, Dec 18th) will start at 14:00. The two groups will present their HW3 papers followed by a lecture on the topic of "Integrative Analysis of Omics Data" presented by Professor Kristel van Steen.

•  Dec 17, 2012: The Dec 18th class will start at 14:00.The topic of the class will be "Applications of Data Integration" presented by Professor Kristel van Steen followed by presentations of HW3 (literature style) homeworks

•  Dec 21, 2012: Happy Holidays everyone! I had just uploaded student presentations of HW3 and posted exam information

Course Materials

October 9, 2012

pdf Introduction to R

ppt Introduction to GenomeGraphs and Bioconductor

pdf HW1: Style 2 (Computer): Implementaiton of ORF finder

pdf HW1: Style 3 (Q&A): Bioconductor and GenomeGraphs library

October 16, 2012

ppt Lecture slides - 19 Oct 2012

pdf HW2: Style 1 (Literature review) assignment

doc HW2: Style 2 (Computer style) Assignment - Needleman Wunsch algorithm

doc HW2: Style 3 (Q&A)Assignment - Pairwise Alignments

October 23, 2012

IMPORTANT! Classes start from 2pm this week! You will have a classical lecture this week conducted by Dr.Dr. Kristel van Steen.

pdf Lecture notes on GWAS

pdf A tutorial on statistical methods for population association studies

October 30, 2012

pdf Lecture notes on GWAS (the same ones from the previous week)

November 13, 2012 (from 14:00 til 16:00)

pdf Class notes on hands on GWA and use of GenABEL R-library

pdf HW3: Style 1 (Literature review) assignment

pdf HW3: Style 2 (Computer style): GWAS on Asthma

pdf HW3: Style 3 (Q&A): Introduction to GenABEL functionalities and interpretation of GWAS results

November 20, 2012 (from 15:00 til 18:00)

This week we will finally give you your HW 1 and 2 marks. Me and Marie will give you small presentations describing correct answers of Homework 1 and 2 in addition to the major errors we had spotted. The homework review session will be from 3pm til 4pm. After the review session, a lecture on Microarray Analysis will be given from 4pm til 6pm by professor Ingrid Arijs from Univeristy of Leuven

ppt Homework 1 and 2 review

pdf HW1 - Computer Assignment review. ORF Finder review slides


December 4th, 2012 (from 14:00 til 16:00)

ppt How to catch epistasis: theory and practice

December 11th, 2012 (from 15:00 til 17:00)

This week you will hear a lecture from Professor Ronald Westa from Maastricht University on the topic of "Phylogenetic sequence analysis". Presentation slides will be posted later

Also please note the final assignment (i.e. HW4) being posted below. There are total of 2 types of assignemtns to choose from that include literature and Q&A syles. Do not panic as the due date is Jan 15th, 2013, so you will have whole holiday to think about it! I think it is a sweet deal!

ppt Phlogenetic Analysis of sequences by Ronald Westa

ppt An introduction to phylogenetic networks by Steven Kelk

pdf HW4: Literature style

pdf HW4: Q&A style

December 18th, 2012 (from 14:00 til 17:00)

The HW3 literature style paper presentations will be presented by two groups on paper1 and paper4 followed by class lecture given by Professor Kristel van Steen

pdf The Future of IntegrOmics presentation slides by KVS