Bioinformatics Teaching 2011-2012

GBIO009-1: Bioinformatics



SOME PRACTICAL ARRANGEMENTS:

• When are the classes given?
• Complete Course Schedule September 15 (Updated Nov 14!!!)


• 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 (navigate via "Practicals Bioinformatics") or Tom Cattaert (tom.cattaert@ulg.ac.be) for additional information about or help with practicals.

CLASS MATERIAL (use 7-Zip to unpack zipped files):

20 September 2011 : 4pm-6pm !!!
• 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:
• Early bioinformatics: the birth of a discipline
• Genome data mining for everyone
• Primer on medical genomics. Part V: Bioinformatics
• In Class Reading: ICR Paper 1: I'm not a bioinformatician...

4 October 2011 : 4pm-6pm !!! (practical session with Oliver Stern and Tom Cattaert)
• Course notes: Chapter 1 ; Last sections on Bioconductor and R packages
• Downloading instructions R and Bioconductor / Background information on R use: see previous class

• Course notes: Chapter 2
• In Class Reading:
• Paper 1: ICR Paper 2a: environmental epigenomics and disease susceptibility
• Paper 2: ICR Paper 2b: report of a cutting edge symposium
• Paper 3: ICR Paper 2c: epigenome-wide studies
• Guiding questions: see class discussion + a list of questions will follow
• Preparatory Reading (for future classes > Nov 15):
• Paper 1: PR Paper 2a
• Paper 2: PR Paper 2b
• Guiding questions: About markers and genotype quality

• Course notes: Chapter 3
• In Class Reading:
• Paper 1: ICR Paper 3a: Synergy between sequence and size in large scale genomics
• Paper 2: ICR Paper 3b: The sequence of the human genome
• Paper 3: ICR Paper 3c: Will epigenetics cause a revolution in evolution?
• Guiding questions:
• ICR Paper 3a: About whether size matters
• ICR Paper 3b: About the landmark sequencing paper
• Background Reading: you may find this useful as background to the homeworks / no questions will be asked from these on the exam
• Paper 1: ShortRead
• Paper 2: Quality assessment using ShortRead
• paper 3: Motifs
• An example of an exam: Click here

• Course notes:
  • Chapter 3 - continued
  • Chapter 4
• R code to course notes: R_Chapter 3 (make sure you have installed Tinn-R)
• R_Chapter 3 Example_data_file
• Background Reading
• Paper 1: Restriction site distributions
• Paper 2: A whole genome perspective
• Preparatory Reading
• Paper 1: Population association studies

• No new theory material will be presented. A lot of material was already provided during the previous two sessions. Take your time to go over it and to read the papers already provided. If you already have questions, please do not hesitate to ask them.

• Course notes: Chapter 5
• Background reading:
• Paper 1: ICR Paper 5a: Perspective on GWAs
• Paper 2: ICR Paper 5b: Theoretical and practical concerns
• Paper 3: ICR Paper 5c: Entering a world of multiple rare variants
• In class reading: IC Paper 5
• Questionnaire: IC Paper 5
• Preparatory Reading: Episasis: what's in a name...

• Course notes for this class: Chapter 6
• In class reading:
• Paper 6a: Multiple testing correction
• Paper 6b: A global view on epistasis
• Practical on epistasis and multiple testing - see website Olivier Stern

• In class reading: ICR 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

• Slides from the guest speakers:
• R Westra: Part 1
• S Kelp: Part 2