Bioinformatics Teaching 2012-2013

• When are the classes given?
• Preliminary Course Schedule
  
  (Updated December 17!!! )
  
  
• 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
• Thursdays (check availability)
• TA contact details: TBA
• EXAM: new postings on http://www.montefiore.ulg.ac.be/~kbessonov/courses.html !!!!!

• Introduction:
  • Introductary Notes
  • Organization Homeworks (updated!)
• Course notes: Chapter 1: What is bioformatics?
• In Class Discussion Paper: Workshop Paper 1: I'm not a bioinformatician...
• Supplementary document to slides: Early bioinformatics: the birth of a discipline
• Workshop papers (see HW1):
• Genome data mining for everyone
• Primer on medical genomics. Part V: Bioinformatics
• Bioinformatics software for biologists in the genomics era.
• Towards a theoretical understanding of false positives in DNA motif finding.
• 9 October Class:
• 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

• Course notes: Chapter 2: Primer on Molecular Biology
• Supplementary document to slides: The evolution of molecular markers
• Guiding questions: Click here

• Course notes: Chapter 3: Sequence analysis (updated on Oct 3 according to material effectively seen in claas. This is the correct version!!)
• Supplementary document to slides: How does DNA sequence motif discovery work?
• Preparatory reading for 23 October Class: A tutorial on statistical methods for population association studies

• Organization Homeworks (updated!) : General descriptions
• HW1 assignment: literature style
• Genome data mining for everyone
• Primer on medical genomics. Part V: Bioinformatics
• Bioinformatics software for biologists in the genomics era.
• Towards a theoretical understanding of false positives in DNA motif finding.
• HW1 assignment: computer style
• HW1 assignment: classical style

• Workshop papers (see HW2 - course "practicals" website):
• Next-generation sequencying technology and complex trait research
• Advantages of next-generation sequencing versus microarray in epigenetics
• Shaking the tree of life
• Sequencing technologies - the next generation

• Course notes: Chapter 4: Genome-wide Association Studies
• Supplementary document to slides: A tutorial on statistical methods for population association studies

• We will start with the "literature style" presentations at 2pm. Please prepare a 15 minutes presentation per group and make sure everyone can present a part.
• The solutions of the "non-literature style" HW1 and HW2 will be presented by the teaching staff on another occasion (to be communicated as soon as possible).
• Course notes: Chapter 4: Genome-wide Association Studies (same as last class)
• Supplementary document to slides 1 (see last class): A tutorial on statistical methods for population association studies
• Guiding questions Click here
• Supplementary document to slides 2: Whole-genome sequencing in personalized therapeutics

• Workshop papers (see HW3 - course "practicals" website):
• A vision for the future of genomics research
• Genotyping errors: causes, consequences and solutions
• Replicating genotype-phenotype associations together with Choice of population structure informative principal components for adjustment in a case-control study
• Rare and common variants: twenty arguments

• Course notes: Chapter 5: Microarray Analysis

• Course notes: Chapter 6: Genome-wide Association Interaction Studies

• Course notes:
• Part 1: Chapter 7: Phylogenetics A
• Part 2: Chapter 7: Phylogenetics B
• Workshop papers (see HW4 - course "practicals" website):
• Synergy between sequence and size in large-scale genomics
• pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
• Ultrafast clustering algorithms for metagenomic sequence analysis
• Post-GWAS: Phylogenetic Analysis in the Hunt for Complex Disease-Associated Loci, Pharmacogenomcs and Pharmacoproteomicsy
• Mapping Quantitative Trait Loci onto a Phylogenetic Tree

• Course notes: Chapter 8: The Future of IntegrOmics
• Supplementary document to slides 1: A systems biology view
• Supplementary document to slides 2: Data integration reviewed
• Workshop papers:
• Complementing the Genome with an Exposome
• Network Properties of Complex Human Disease Genes
• OMICS technologies: an opportunity for two-way translation
• Stay tuned for additional information about the EXAM: new postings on http://www.montefiore.ulg.ac.be/~kbessonov/courses.html !!!!!
• Student Presentations (Literature Style Homeworks)