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


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 date15 Sept 2015 (Tuesday)
LocationRoom R.75, B28
Timefrom 08:30 til 12:30
ProfessorKristel Van Steen


• 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

pdf Intro lecture: Administration (Kristel)

pdf Organization of GBIO0009 Homework Assignments (Kristel)

pdf Lecture 1: Setting the pace (Kristel)

pdf In class paper: Dammit Jim, I’m a doctor, not a bioinformatician!

Background readings:

   pdf Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing (Bao2014)

   pdf What is bioinformatics? An introduction and overview (Luscombe2001)

   pdf Bioinformatics and Medical Informatics: Collaborations on the Road to Genomic Medicine? (Maojo2003)

   pdf Early bioinformatics: the birth of a discipline— a personal view (Ouzounis2003)

video Movie on DNA: "Programming of Life Video Lecture"

pdf 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

ppt Practical lecture 2: Intro into R language (Kirill)

      *** supporting dataset from library (ISwR) (thuesen) (Kirill)

pdf A key book reference: Applied Statistics for Bioinformatics using R (Kirill)

September 29, 2015 Class starts at 8.30am

pdf Lecture 3: Genomewide association analysis (Kristel)

In-class reading papers:

  1. Anderson, Carl A., et al. "Data quality control in genetic case-control association studies." Nature protocols 5.9 (2010): 1564-1573.
  2. 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.
  3. 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):

  1. Pompanon et al (2005) Genotyping errors: causes, consequences and solutions
  2. On machine learning in genome-wide association studies
  3. 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

pdf HW1 - type 2: Genome Wide Association Studies (GWAS) on asthma

Stytle 3: Q and A - GWAS

pdf 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

pdf Lecture 4: GenABEL library

October 13, 2015 Class starts at 8.30h (Kristel)

pdf Lecture 5: Genomewide association interaction analysis (GWAI)

Background reading with questions(exam material):

  1. Cordell2009
  2. Moore2005
  3. VanSteen2011

Guiding background questions: GxG interactions questions on above readings

Supporting docs (not exam material):

  1. Gusareva, Elena S., and Kristel Van Steen. "Practical aspects of genome-wide association interaction analysis." Human genetics 133.11 (2014): 1343-1358.
  2. 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

pdf Lecture 6: DNA SEQUENCE ANALYSIS and supporting R-code

Supplementary readings (exam material):

  1. 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
  2. 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

pdf Lecture 7: Biological sequences comparison (PowerPoint)

pdf 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)

pdfLecture 8: Exploring the World of phylogenetic and biological interactions

November 17, 2015 Class starts at 9.30h (Guest lecture: Ronald Westra)

pdfLecture 9a:Phylogenetic Analysis

pdfLecture 9b:An introduction to phylogenetic networks [just for your own interest / not on exam]

November 24, 2015 Class starts at 8.30h (Kirill)

pdfLecture 10: Trees and networks / Data clustering (PPT version)

pdfLecture 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)

pdfLecture 11:Systems Biology and PPI networks - a case study

Reference: Rolland, Thomas, et al. "A proteome-scale map of the human interactome network." Cell 159.5 (2014): 1212-1226.

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