BME 483/543: Quantitative Systems Biology

  • Office hours: Friday 1-2pm (email me if you plan to meet me during office hours).
  • Syllabus: syllabus
  • Recommended reources:
  • NCBI Pubmed Research Articles.
  • [ZB] M. Zvelebil, J.O. Baum. Understanding Bioinformatics. Garland Science. (ebook)
  • Pevzner, Computational Molecular Biology: An Algorithmic Approach. MIT press.
  • A Practical Approach to Microarray Data Analysis, D.P. Berrar, W. Dubitzky, and M. Granzow, Springer Science & Business Media.

Weekly Schedule

  • Intro:
    • Dropbox setup
    • Using file sharing and versioning systems: SVN, Github
    • Working with webpages in Matlab
    • File parsing strategies in Matlab. regular expression.
  • Week 8
    • Friday 4-6pm extra session at Bossone709.
  • Week 9 no class.

Paper Signup


  • Assignments: 70%:
    • Weekly programming and analysis assignments.
    • Research article review and presentation.
      • Find and discuss papers related to the topics we cover in the course. You need to contribute 4 papers (each from a different topic) (Bmes483 students: 3 papers). At least one of your papers must be found by you. You can find the others yourself or sign up for the existing papers. Prepare a power point presentation to facilitate discussion.
    • Active Participation.
  • Final Projects: 30%

Topics and Resources

  • Not all topics may be covered in the course.
  • Project ideas
    • Method benchmarking (evaluate several methods on the same dataset(s))
    • Reproduce/improve method and results from a paper
    • Microarray Meta-analysis
    • Protein Structure mutation analysis
  • MiRNAs
  • ChipSeq
webdata/index.txt · Last modified: 2017/05/24 15:07 by Ahmet Sacan