Fall 2013 HONS 380

Course Materials
Get your course materials here

Facebook Group
Facebook Group

Teams
Clay Turner and Millie Thomas - 2012.Yandell

Matt Paul and Allyson Hill - Blast.pdf

Katie Kirchoff and Emily Strelka - Kharti, Sirota

Jack Meagher and Chelsea Snipes - Sense from sequence reads

Taylor Hammock, Tori McCaffrey, Barrett Hawkins - Survey of sequence alignment

Week 1

 * Tuesday
 * Introduction to the course, biology, algorithms, and bioinformatics (historical and overview)
 * Introduction to biology and bioinformatics (Naylor)
 * Molecular Biology Primer


 * Thursday
 * Select partners based on expertise
 * Select review papers
 * Discuss stand-up meeting procedures
 * Begin first lab assignment on Python programming
 * Assign first homework on Python programming

Week 2

 * Tuesday
 * Global Sequence Alignment (Naylor)
 * Algorithms and Complexity with emphasis on pairwise alignment (Anderson)


 * Thursday
 * TBD based on Tuesday's progress

Week 3

 * Needleman–Wunsch

Programming
http://rosalind.info/problems/tran/

Homework Assignments
TBA

Review papers
Individual papers are available on OAKS. Here are a list of the general topics:


 * 1) Alignment methods
 * 2) Searching
 * 3) Tree reconstruction methods
 * 4) Genome assembly
 * 5) Gene trees, species trees
 * 6) Microarrays vs RNA-seq
 * 7) Pathway networks
 * 8) Systems biology