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
Date | 23 Jan 2014 (Thursday) |
Location | Room 02, building B37 |
Time | from 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
Anouncements
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.
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 et.al.(2009). Advantages of next-generation sequencing versus the microarray in epigenetic research; 3)Do R et.al. (2012), Exome sequencing and complex disease: practical aspects of rare variant association studies (the most selected paper!); 4)Day-Williams AG et.al. (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
Introductory lecture: course details, R-language, databases
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
HW1b - type 1: GWAS literature review assignment
- Choice 1: Collins et al (2003) A vision for the future of genomics research
- Choice 2: Pompanon et al (2005) Genotyping errors: causes, consequences and solutions
- Choice 3 (2 papers):
- Paper 4: Gibson (2012) Rare and common variants: twenty arguments
HW1b - type 2: GWAS on Asthma (ACRN cohort)
- Phenotype file: ACRN_phenoData.phe
- Genotype file: genoeData_GenABEL.raw
HW1b - type 3: GWAS Q&A into to GenABEL
- Phenotype file: wgDat.phe
- Genotype file: wgDat.raw
- R-fucntion to plot Venn Diagram: plot-VennDiagram.R
October 15th, 2013
Class notes on practical apsects of GWAS and GenABEL tutorial
October 22nd, 2013
Class notes on epistasis and GWAI analysis
November 5th, 2013
The lecture material will be posted on Kristel Van Steen's website
November 12th, 2013
Sequences alignment practical: lecture notes
HW2 - type 1: Biological sequences - literature review assignment
- Choice 1: Day-Williams AG et.al. (2011) The effect of next-generation sequencing technology on complex trait research
- Choice 2: Do R et.al. (2012), Exome sequencing and complex disease: practical aspects of rare variant association studies
- Choice 3: Hurd PJ et.al.(2009). Advantages of next-generation sequencing versus the microarray in epigenetic research
- Choice 4: Goldstein DB et.al.(2013) Sequencing studies in human genetics: design and interpretation (password protected - obtain password by login to the course submission site)
HW2 - type 2: implementation of NW global sequence algorithm
HW2 - type 3: Sequences alignment graphically and using R
November 19th, 2013
Analysis of microarray data: lecture notes
HW3 - type 1: Clustering and Phylogeny - literature review assignment
- Choice 1: Matsen et al. (2010) pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree, BMC Bioinformatics 11:538
- Choice 2: Li et al. (2012) Ultrafast clustering algorithms for metagenomic sequence analysis, Briefings in Bioinformatics
- Choice 3: Broman et al (2012) Mapping Quantitative Trait Loci onto a Phylogenetic Tree, Genetics 192:267
- Choice 4: KY Yeung et.al.(2001) Principal component analysis for clustering gene expression data, Bioinformatics,Sep;17(9):763-74
- Choice 5: AP Gasch (2002) Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering Genome Biol,Oct 10;3(11)
HW3 - type 2: analysis of microarray data
HW3 - type 3: Phylogenetic trees and data clustering methods
- supporting uA data on cancer (nci60): download
- HW3 - type 3 ref.4: SVANTE WOLD (1987) Principal Component Analysis (password protected)
- HW3 - type 3 ref.4:T.Ross_2000_Systematic variation in gene expression(password protected)
November 26th, 2013
Phylogenetic analysis by Ronald Westra: lecture notes
Phylogenetic networks by Steven Kelk: lecture notes
Phylogenetic tree construction based on sequence alignments in R: lecture notes
December 02, 2013
Data Clustering lecture notes
December 10, 2013
Exam information click here
Six students presentations on selected papers from HW1 and HW2
- Exome sequencing : Practical aspects by MOTTART Xavier THOMAS Julien
- Exome sequencing and complex disease by Jacquemin Jonathan & de Bournonville Sébastien
- The effect of Next-Generation Sequencing technology on complex trait research by Ladang Auxane, Mombaerts Laurent, Uyttendaele Vincent
- Next-generation sequencing vs. Microarray in epigenetic by Bosch Vincent, Klecker Sophie, Straat Julien
- Genotyping errors. Causes, Consequences and Solutions by François Ancien, Sascha Kretzschmann,Olivier Suplis
- Exome sequencing and complex disease by Alice Bouchoms, Amaury Vanvinckenroye, M. Legrand