2019: Cancer Genomics and Class Discovery [MATH891.002]

MATH 891.002, GNET / BCB 891.001

Time: February 18 – April 15, Monday 5:00-7:10pm
Location: Marsico 5004    (Except April 1 – Marsico 6004)
Instructors: Chuck Perou, Katie Hoadley, Steve Marron, Andrew Nobel, Joel Parker, and Greg Forest

The objectives of this course are to:

  • Gain an understanding of the genomic data types being collected on human tumors
  • Learn about the basics of RNA and DNA NGS sequence analysis
  • Learn about pattern discovery tools including hierarchical clustering and biclustering
  • Understand the challenges of integrating heterogeneous data types
  • Learn real world examples of complex data integration for class discovery

Course expectations:

  • Group project with hands-on analysis of genomics data
  • Final report (3 pages)

2/18/19 – Lecture 1 (Chuck Perou and Katie Hoadley)

 

2/25/19 – Lecture 2 (Andrew Nobel)

 

3/4/19 – Lecture 3 (Steve Marron)

  • Lecture
  • Reading Material:
    • Liu, Y., Hayes, D. N., Nobel, A., & Marron, J. S. (2008). Statistical significance of clustering for high-dimension, low–sample size data. Journal of the American Statistical Association, 103(483), 1281-1293.
    • Huang, H., Liu, Y., Yuan, M., & Marron, J. S. (2015). Statistical significance of clustering using soft thresholding. Journal of Computational and Graphical Statistics, 24(4), 975-993.

 

3/11/19 – No Class Spring Break

  • Goals for week
    • Plan/work on analyses to perform
    • Email instructors as needed for advice

 

3/18/19 – Lecture 4 (Joel Parker)

  • Lecture
  • Goals for week
    • 1-2 page summary of proposed analysis for each group due
    • Feedback will be returned to each group within a few days

 

3/25/19 – Lecture 5 (Katie Hoadley)

  • Lecture
  • Goals for week
    • finalize data sets and analyses to be performed with instructors

 

4/1/19 – In Class project discussions with Professors  **Room Change Marsico 6004

4/8/19 – No Class, work on project analyses

4/15/19 – In Class Student Presentations (group) and 2-3 page written Report (individual)