GBIO0009-1: Topics in bioinformatics 2015-16
In this course an introduction to the bioinformatics discipline is given. We do so by introducing the students to several analysis work flows corresponding to different research questions.
The course is in part based on interactive ex-cathedra lectures and in part on interactive practical sessions. The exercise sessions allow students to become familiar with the theoretical concepts introduced during the theory classes. They prepare students to successfully carry out their homework assignments.
Exam information
The exam is open book. This written exam will count for 40% of the final mark.
Date | 04 Jan 2016 (Monday) |
Location | Room R1.123 (B28) |
Time | 08:30 am |
MARKS
Preliminary marks HW 1,2,3 are posted at the HW submission website. Please login to view.
Course schedule and location
Current course schedule (will be uploaded soon)
Start date | 15 Sept 2015 (Tuesday) |
Location | Room R.75, B28 |
Time | from 08:30 til 12:30 |
Professor | Kristel Van Steen |
Anouncements
09 Sept 2015.Bring PC to the class of Sept 22nd. We will install R on it. In this course you will extensively use R for your practical assignments
03 Nov 2015.No classes this week. Enjoy your holiday and superb weather.
26 Nov 2015.Next week we will have a guest lecture from Benoit Charloteaux on systems biology and PPI networks. The biases and problems in use of biological data in research will be presented as a case study
2 Nov 2015.The exam is fixed to January 4,2016. During the next class, we can discuss whether you prefer to have the exam on a later date. All students need to agree. Survey will be distributed.
Assignment submission
Please submit your assignments through the online system. If the deadline passed, email your assignment to the course TA.
Course material
September 15, 2015 - the 1st class . Class starts at 8.30am
Intro lecture: Administration (Kristel)
Organization of GBIO0009 Homework Assignments (Kristel)
Lecture 1: Setting the pace (Kristel)
In class paper: Dammit Jim, I’m a doctor, not a bioinformatician!
Background readings:
What is bioinformatics? An introduction and overview (Luscombe2001)
Bioinformatics and Medical Informatics: Collaborations on the Road to Genomic Medicine? (Maojo2003)
Early bioinformatics: the birth of a discipline— a personal view (Ouzounis2003)
Movie on DNA: "Programming of Life Video Lecture"
Practical lecture 1: Biological Databases (Kirill)
Note: Please bring PC to the next class and form HW groups
September 22, 2015 Class starts at 8.30am
Practical lecture 2: Intro into R language (Kirill)
*** supporting dataset from library (ISwR) (thuesen) (Kirill)
A key book reference: Applied Statistics for Bioinformatics using R (Kirill)
September 29, 2015 Class starts at 8.30am
Lecture 3: Genomewide association analysis (Kristel)
In-class reading papers:
- Anderson, Carl A., et al. "Data quality control in genetic case-control association studies." Nature protocols 5.9 (2010): 1564-1573.
- Spencer, Chris C., et al. "Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip." PLoS Genet 5.5 (2009): e1000477.
- de Bakker, Paul IW, et al. "Practical aspects of imputation-driven meta-analysis of genome-wide association studies." Human molecular genetics 17.R2 (2008): R122-R128.
Supporting doc (not exam material): 1)The Promise and Challenges of Next-Generation Genome Sequencing for Clinical Care and 2)Chapter 11: Genome-Wide Association Studies - PLoS by WS Bush
HW1 - GWAS - due Oct 27th:
Stytle 1: Literature homework titles - analytics (keeping in mind that the focus is on informatics applications in biological contexts):
- Pompanon et al (2005) Genotyping errors: causes, consequences and solutions
- On machine learning in genome-wide association studies
- On data mining in genomics
Notes: the field is rapidly evolving and hence some techniques displayed above have become more or less popular for various reasons. Putting this into context by screening the literature for more recent information will be challenging but will lead to bonus points.
Stytle 2: Programming - GWAS analysis
HW1 - type 2: Genome Wide Association Studies (GWAS) on asthma
- Pheno-file:ACRN_phenoData.phe
- Geno-file:genoeData_GenABEL.raw
Stytle 3: Q and A - GWAS
HW1 - type 3: Genome Wide Association Studies (GWAS)
October 6, 2015 Class starts at 8.30h
Note: please bring one charged PC to follow in-class GenABEL tutorial
October 13, 2015 Class starts at 8.30h (Kristel)
Lecture 5: Genomewide association interaction analysis (GWAI)
Background reading with questions(exam material):
Guiding background questions: GxG interactions questions on above readings
Supporting docs (not exam material):
- Gusareva, Elena S., and Kristel Van Steen. "Practical aspects of genome-wide association interaction analysis." Human genetics 133.11 (2014): 1343-1358.
- Bessonov, Kyrylo, Elena S. Gusareva, and Kristel Van Steen. "A cautionary note on the impact of protocol changes for genome-wide association SNP× SNP interaction studies: an example on ankylosing spondylitis." Human genetics (2015): 1-13.
Note: The second paper is an applied paper that builds on paper 1 and gives example on what a practical GWAI study entails and can lead to.
October 20, 2015 Class starts at 8.30h, as usual
Lecture 6: DNA SEQUENCE ANALYSIS and supporting R-code
Supplementary readings (exam material):
- Pabinger, Stephan, et al. "A survey of tools for variant analysis of next-generation genome sequencing data." Briefings in bioinformatics 15.2 (2014): 256-278
- Supporting Material:Additional tables
- Guiding questions(exam material)
- Pavlopoulos, Georgios A., et al. "Unraveling genomic variation from next generation sequencing data." BioData mining 6.1 (2013).
October 27, 2015 Class starts at 8.30h (Kirill)
Note: please bring a charged PC to follow in-class mini tutorials
Lecture 7: Biological sequences comparison (PowerPoint)
Lecture 7: Biological sequences comparison (PDF)
HW2: GWAS - due Nov 24th:
Style 1:Literature homework
Style 2:Implementation of the Needleman–Wunsch algorithm OR ORF detection
Style 3:Pairwise Alignments
November 10, 2015 Class starts at 8.30h (Kirill)
Lecture 8: Exploring the World of phylogenetic and biological interactions
November 17, 2015 Class starts at 9.30h (Guest lecture: Ronald Westra)
Lecture 9a:Phylogenetic Analysis
Lecture 9b:An introduction to phylogenetic networks [just for your own interest / not on exam]
November 24, 2015 Class starts at 8.30h (Kirill)
Lecture 10: Trees and networks / Data clustering (PPT version)
Lecture 10: Trees and networks / Data clustering (PDF version)
HW3: Trees and networks - due Dec 8th 2015
Style 1:Literature homework
Style 3:Phylogenetic trees / Trees / Networks OR Co-expression networks
Data: LiverFemale3600.csv
December 1, 2015 Class starts at 9.30h (Benoit Charloteaux)
Lecture 11:Systems Biology and PPI networks - a case study
December 8, 2015 Class starts at 8.30h (Kirill and Kristel)
In-class student's presentations of style 1 HWs
December 15, 2015 NO CLASS