This is the home page for class SDS 348, Computational Biology and Bioinformatics. All relevant course materials will be posted here.

Syllabus: SDS348_syllabus_spring2018.pdf

Lectures

1. Jan 16, 2018 – Introduction, R Markdown

2. Jan 18, 2017 – R review

3. Jan 23, 2018 – Data visualization with ggplot2

4. Jan 25, 2018 – Data visualization with ggplot2

5. Jan 30, 2018 – Working with tidy data

6. Feb 1, 2018 – Working with tidy data

7. Feb 6, 2018 – Working with tidy data

8. Feb 8, 2018 – Rearranging data tables with tidyr

9. Feb 13, 2018 – Principal Components Analysis (PCA)

10. Feb 15, 2018 – k-means clustering

11. Feb 20, 2018 – Binary prediction/logistic regression

12. Feb 22, 2018 – Sensitivity/Specificity, ROC curves

13. Feb 27, 2018 – Training and test data sets, cross-validation

14. Mar 1, 2018 – Installing and running python, basic data structures

15. Mar 6, 2018 – Control flow in python

16. Mar 8, 2018 – Functions in python

17. Mar 20, 2018 – More on python data structures, classes

18. Mar 22, 2018 – Working with files

19. Mar 27, 2018 – Introduction to Biopython

20. Mar 29, 2018 – Working with gene features and genomes

21. Apr 3, 2018 – Running queries on Entrez

22. Apr 5, 2018 – Regular expressions

23. Apr. 10, 2018 – Using regular expressions to analyze data

24. Apr. 12, 2018 – Using regular expressions to analyze data

25. Apr. 17, 2018 – Aligning sequences

26. Apr. 19, 2018 – Global and local alignments, BLAST

27. Apr. 24, 2018 – Multiple sequence alignments and phylogenetic trees

28. Apr. 26, 2018 – Working with protein structures

29. May 1, 2018 – Protein structure and PyMOL scripting

30. May 3, 2018 – Molecular evolution of proteins

  • Slides: class30.pdf
  • Relevant papers:
    • J. Echave, S. J. Spielman, C. O. Wilke (2016). Causes of evolutionary rate variation among protein sites. Nature Rev. Genet. 17:109–121. doi: 10.1038/nrg.2015.18
    • B. R. Jack, A. G. Meyer, J. Echave, C. O. Wilke (2016). Functional sites induce long-range evolutionary constraints in enzymes. PLOS Biol 14:e1002452. doi: 10.1371/journal.pbio.1002452
    • A. H. Kachroo, J. M. Laurent, C. M. Yellman, A. G. Meyer, C. O. Wilke, E. M. Marcotte (2015). Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science 348:921–925. doi: 10.1126/science.aaa0769
    • C. D. McWhite, A. G. Meyer, C. O. Wilke (2016). Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin. Virus Evol. 2:vew026. doi: 10.1093/ve/vew026

Homeworks

All homeworks are due by 7:00pm on the day they are due. Homeworks need to be submitted as pdf files on Canvas.

Labs

1. Jan 17, 2018

2. Jan 24, 2018

3. Jan 31, 2018

4. Feb 7, 2018

5. Feb 14, 2018

6. Feb 21, 2018

7. Feb 28, 2018

8. Mar 7, 2018

9. Mar 21, 2018

10. Mar 28, 2018

11. Apr 4, 2018

12. Apr 11, 2018

13. Apr 18, 2018

14. Apr 25, 2018

15. May 2, 2018

Projects

All projects are due by 7:00pm on the day they are due. Projects need to be submitted on Canvas, both in pdf format and as source code (plus data where needed).