VIBS-613: Evolutionary Bioinformatics

VIBS-613 Evolutionary Bioinformatics, Spring 2018

Instructor: James Cai (

Meeting & Lab: Tue & Thr 1:30 PM - 3:30 PM, VIDI (bldg 1813) Rm 104 & 115

Office hours: Wed 10-12, VMR (bldg 1811) Rm 384

Description of Course

Principles and concepts in molecular evolution and population genetics; applications of quantitative approaches (computation, statistics, and mathematics) in analyzing large and complex biological data sets; algorithm design and scientific software development using high-level, high-performance computer languages; emerging techniques for integrative data analysis, and the assumptions, advantages and limitations of these techniques.


  1. Introduction to essential genetics, statistics, and programming techniques (1/15) [slides][whiteboard]
  2. Comparative genomics, laws of genome evolution (1/22) [slides][whiteboard]
  3. Molecular evolution, phylogeny reconstruction (1/29) [slides][whiteboard]
  4. Evolutionary change in nucleotide sequences, molecular basis of adaptation (2/5) [slides][whiteboard]
  5. Genetic drift, coalescent theory, forward-time simulation (2/12) [slides][whiteboard]
  6. Recombination, linkage disequilibrium (2/19) [slides][whiteboard]
  7. Selective sweep, hitchhiking mapping (2/26) [slides][whiteboard]
  8. Human evolution, genetic diversity, personalized medicine (3/5) [slides][whiteboard] === <Spring Break> ===
  9. Quantitative genetics: QTL, association mapping, and GWAS (3/19) [slides][whiteboard]
  10. Regulation and evolution of gene expression (3/26) [slides][whiteboard]
  11. Genetic variation and gene expression variability (4/2) [slides][whiteboard]
  12. Systems biology, analysis of biological networks (4/9) [slides][whiteboard]
  13. Next-generation sequencing applications and data analysis (4/16, guest lectured by Dr. Andrew Hillhouse)
  14. Student presentations (4/23) and final exam (4/30)


Basic knowledge of genetics and statistics.


  1. Homework Assignments (50%) [homework score sheet]
    • Consists of programming tasks or short written assignments handed out every week.
  2. Presentation (20%)
    • Towards the end of the semester, each student will give a 10-min platform presentation.
  3. Final Exam (30%), 30 multiple choice questions to be completed in 50 mins.

Class Notes and Resource Materials

Class notes are distributed in class. There is no required textbook.

Required software - Matlab:

  1. Matlab is available on computers in VIDI 115 via the VOAL.
  2. Matlab is available on computers in the Open Access Labs across the campus.
  3. (Optional) Command line-based Matlab is available on the Ada or Terra cluster. Request an HPRC account to access the clusters. A user guide page on using Matlab on the HPRC clusters (including instruction on how to install a GUI toolbox app on a desktop computer which accesses Matlab and runs scripts on the Ada or Terra cluster).
  4. (Optional) Matlab Student Version can be purchased online and installed on up to three your own computers. Please discuss with Dr. Cai before making any purchase.

Additional readings: You are responsible for additional readings that will be announced in class. There will be one reading from the primary literature each week which will be required for participation in case study discussion in class.