Lecture Schedule - Fall 2009
|
# |
Date |
Topic |
Reading |
||||
|
1 |
Aug 24 |
M |
What is Bioinformatics? |
Xiong, Ch 1 |
|||
|
2 |
Aug 26 |
W |
Biological
Databases |
Ch 2 |
|||
|
3 |
Aug 28 |
F |
Brief Biology Review What is Systems Biology? What is Synthetic Biology? |
||||
|
4 |
Aug 31 |
M |
Pairwise Sequence Alignment |
Ch 3 |
|||
|
5 |
Sept
2 |
W |
Dynamic Programming (DP) |
Ch 3 |
|||
|
6 |
Sept
4 |
F |
Scoring Matrices and Alignment Statistics |
Ch 3 |
|||
|
- |
Sept 7 |
M |
UNIVERSITY
HOLIDAY (Labor Day) |
||||
|
7 |
Sept
9 |
W |
Database Searching with BLAST |
Ch 4 |
|||
|
8 |
Sept 11 |
F |
PSI-BLAST, etc. |
Ch 4 |
|||
|
9 |
Sept 14 |
M |
Multiple Sequence Alignment (MSA) |
Ch 5 |
|||
|
10 |
Sept 16 |
W |
Scoring MSAs |
Ch 5 |
|||
|
11 |
Sept 18 |
F |
Position Specific Scoring Matrices (PSSMs) & VR Tour 1 PM |
Ch 5 |
|||
|
12 |
Sept 21 |
M |
CLUSTAL |
Ch 5 |
|||
|
13 |
Sept 23 |
W |
"Catchup" &
Review |
Chps 1-5 |
|||
|
- |
Sept
25 |
F |
Midterm Exam #1 |
Chps 1-5 |
|||
|
14 |
Sept 28 |
M |
Hidden Markov Models (HMMs) |
Ch 6 |
|||
|
15 |
Sept 30 |
W |
More
HMMs |
Ch 6 |
|||
|
16 |
Oct 2 |
F |
Protein
Families, Domains, and Motifs |
Ch 7 |
|||
|
17 |
Oct 5 |
M |
Gene Structure and Prediction |
Ch 8 |
|||
|
18 |
Oct 7 |
W |
Promoter & Regulatory Element Prediction |
Ch 9 |
|||
|
19 |
Oct 9 |
F |
Phylogenetics - Basics |
Ch 10 |
|||
|
20 |
Oct 12 |
M |
Phylogenetics - Distance-based Methods |
Ch 11 |
|||
|
21 |
Oct 14 |
W |
Phylogenetics - Character-based Methods |
Ch 11 |
|||
|
22 |
Oct 16 |
F |
Protein Motifs & Domain Prediction |
Ch 12 |
|||
|
23 |
Oct 19 |
M |
Protein Structure, Visualization, Comparison |
Ch 13 |
|||
|
24 |
Oct 21 |
W |
Protein Structure - Classification |
Ch 13 |
|||
|
25 |
Oct 23 |
F |
Protein Secondary Structure Prediction |
Ch 14 |
|||
|
26 |
Oct 26 |
M |
Protein Tertiary Structure Prediction |
Ch 15 |
|||
|
27 |
Oct 28 |
W |
"Catchup" &
Review |
Chps 6-15 |
|||
|
- |
Oct 30 |
F |
Midterm Exam
#2 (Add/drop deadline) |
Chps 6-15 |
|||
|
28 |
Nov 2 |
M |
RNA
Structure Prediction |
Ch 16 |
|||
|
29 |
Nov 4 |
W |
Predicting Macromolecular Functions &
Interactions |
TBA |
|||
|
30 |
Nov 6 |
F |
Machine
Learning Algorithms (Weka: NB, SVM) |
TBA |
|||
|
31 |
Nov 9 |
M |
Genomics, Comparative Genomics & Metagenomics |
Ch 17 |
|||
|
32 |
Nov 11 |
W |
Functional Genomics |
Ch 18 |
|||
|
33 |
Nov 13 |
F |
Microarrays |
Ch 18 |
|||
|
34 |
Nov 16 |
M |
Clustering Algorithms |
Ch 18 |
|||
|
35 |
Nov 18 |
W |
Proteomics (2-D Gels & MS) |
Ch 19 |
|||
|
36 |
Nov 20 |
F |
Regulatory and Developmental Networks |
TBA |
|||
|
37 |
Nov 23 - 27 |
NO CLASS -
Thanksgiving Break |
|||||
|
38 |
Nov 30 |
M |
Systems Biology |
Zvelevil & Baum Ch 17
pp 667-694 |
|||
|
39 |
Dec 2 |
W |
Synthetic Biology |
||||
|
40 |
Dec 4 |
F |
Topic of Students' Choice |
TBA |
|||
|
- |
Dec 7-11 |
BCB 544 Team
Project Presentations |
|||||
|
- |
Dec 17 |
Th |
FINAL EXAM 9:45 - 11:45 AM (Comprehensive;
includes lab practical exam) |
||||