Bioinformatics Teaching 2010-2011

• When are the classes given?
• Complete Course Schedule
November 20 (Updated !!!)


• Where do the classes take place?
• room 1.21 (B28) at the Montefiore
• How can I pass the exam?
• All you need to know is right here
• What if I have questions?
• Consult Kristel Van Steen (kristel.vansteen@ulg.ac.be) for any questions about theory or homeworks, preferably on
• Tuesdays before/after class
• Wednesdays or Fridays (check availability)
• Consult Olivier Stern (his website) for additional information about or help with practicals. Navigate via "Practicals Bioinformatics"

• Introductary Notes
• Course notes: Chapter 1
• Downloading instructions R and Bioconductor: Follow this link
• Information on using R:
• Part 1: R manuals
• Part 2: Basic Commands !!!
• Part 3: An introduction to R
• Part 4: Advanced
• Background reading: Ouzounis et al 2003
• In class reading: Paper 1
• Questionnaire to help you digest the paper: A primer on medical genomics: Highlight on Bioinformatics
• Reading assignment for: Class 2

• Course notes: Chapter 2
• Background reading 1: The evolving concept of the gene
• Background reading 2: Visualizing human chromosomes
• Background reading 3: Bioinformatics explained: Biological databases
• Background reading 4: Storing and sifting through data: Bioinformatics Resources
• In class reading: Paper 2a
• In class reading: Paper 2b
• In class reading: Paper 2c
• Questionnaire: About markers and genotype quality


Please bring your laptop to the classroom in case you need help to have R installed

Please consult the webpage of Olivier Stern for instructions on installing specific R packages!
Please bring your laptop to the classroom for in-class try-outs (analysis of words)


• Course notes: Chapter 4
• R code to course notes: R_Chapter 4 (make sure you have installed Tinn-R)
• R_Chapter 4 Example_data_file
• Background reading 1: ShortRead
• Background reading 2: Quality assessment using ShortRead
• Background reading 3: Motifs
October 12 (Updated)
• In class reading: Paper 3: The sequence of the human genome
• Questionnaire: See class November 16

• Course notes: See class November 9
• Background reading: Phylogenomics
• Reading assignments for next class
  • 1: BLAST
  • 2: Smith-Waterman
  • 3: BLAST versus Smith-Waterman
  
  

• Course notes: Chapter 4 (continued)
• Course notes: Chapter 5

(updated class chapter notes: Oct 24, 2010)

• In class reading: Paper 4
• Questionnaire: The meaning of dynamic programming
• Reading assignments for next class
  • 1: The importance of genetic ancestry
  • 2: Towards a whole-genome perspective on human populations
  • 3: Statistical methods for population association studies
  
  

• Homework assignment from quest professor: Homework 3
• Course notes from quest professor: Phylogenetic analysis
• Course notes for this class: Chapter 6
• R code to course notes: R_Chapter 6 (make sure you have installed Tinn-R) and the SNPassoc manual
• R_Chapter 6 Example_data_file
• Background reading 1: GWAs and human disease
• Background reading 2: Perspective on GWAs
• Background reading 3: Theoretical and practical concerns
• Background reading 4: Primer on medical genomics
• In class reading: Paper 5
• Questionnaire: During class session
• Reading assignment for next class: Episasis: what's in a name...

• In class reading: Paper 3: The sequence of the human genome
• Questionnaire: Click here
• Course notes for this class: Chapter 7
• In class reading:
• Paper 6a: Multiple testing correction
• Paper 6b: A global view on epistasis
• Note on Homework 3: Prof Westra is currently checking the assignment; according to him there should be several differences detectable
• Homework assignment: Homework 4A
NEW!!!
• Simulated data - ped file: Click here
• Simulated data - phe file: Click here

• In class reading: Paper 7: Families are in or out?
• Questionnaire: Click here
• Course notes for this class: Chapter 7
• Supporting document 1: GenABEL manual
• Supporting document 2: ABEL tutorial
• Supporting document 3: probBEL manual

• Message from Prof Westra: Click here for explanations about the Phylogenetics Homework

• New due date for homework 4: January 3 When the interaction analysis takes to long, make a subselection of consecutive markers. Take a list of markers that includes at least one of the markers you "identified" via the main effects analysis. The method is more important than the results (I am aware of computer restrictions)
• Please send an electronic copy to kristel.vansteen@ulg.ac.be (including figures and your programming code)
• Example of solution code: Click here
• An example of an exam you can find here