BCB 444X/544X
Revised Lecture Schedule Fall 2005
|
# |
Date |
Topic |
Reading |
Instructor |
|
1 |
Aug 22 M |
Course Overview What is bioinformatics? |
Mount, Ch 1 |
DD |
|
2 |
Aug 24 W |
Mount, Ch 3 |
DFB |
|
|
3 |
Aug 26 F |
Mount, Ch 3 |
DFB |
|
|
4 |
Aug 29 M |
Alignment of pairs of sequences:
Substitution matrices and parameter choice |
Mount, Ch 3 |
DFB |
|
5 |
Aug 31 W |
Statistical analysis of alignments:
Overview of statistical issues |
Mount, Ch 4 |
DFB |
|
6 |
Sep 2 F |
Statistical analysis of alignments:
Assessing significance |
Mount, Ch 4 |
DFB |
|
- |
Sep 5 M |
NO CLASS
University Holiday |
|
|
|
7 |
Sep 7 W |
Mount, Ch 4+ |
DFB |
|
|
8 |
Sep 9 F |
Mount, Ch 5 |
DFB |
|
|
9 |
Sep 12 M |
Mount, Ch 5 |
DFB |
|
|
10 |
Sep 14 W |
Multiple
sequence
alignment: Hidden Markov models, position-specific scoring |
Mount, Ch 5 |
DFB |
|
11 |
Sep 16 F |
Mount, Ch 6 |
DFB |
|
|
12 |
Sep 19 M |
Mount, Ch 6 |
DFB |
|
|
13 |
Sep 21 W |
Database searching: Scoring issues |
Mount, Ch 6 |
DFB |
|
14 |
Sep
23 F |
MIDTERM EXAM #1 |
|
MT |
|
15 |
Sep 26 M |
Mount, Ch 12 |
XW |
|
|
16 |
Sep 28 W |
Mount, Ch 12 |
XW |
|
|
17 |
Sep 30 F |
Phylogenetic prediction: Definitions and
basic concepts, overview of methods |
Mount, Ch 7+ |
DFB |
|
18 |
Oct 3 M |
Mount, Ch 7+ |
DFB |
|
|
19 |
Oct 5 W |
Mount, Ch 7+ |
DFB |
|
|
20 |
Oct 7 F |
Mount, Ch 7+ |
DFB |
|
|
21 |
Oct 10 M |
Mount, Ch 7+ |
DFB |
|
|
22 |
Oct 12 W |
Phylogenetic prediction: |
Mount, Ch 7+ |
DFB |
|
23 |
Oct 14 F |
Phylogenetic prediction: |
Mount, Ch 7+ |
DFB |
|
24 |
Oct 17 M |
DD |
||
|
25 |
Oct 19 W |
DD |
||
|
26 |
Oct 21 F |
DD |
||
|
27 |
Oct 24 M |
DD |
||
|
28 |
Oct 26 W |
DD |
||
|
29 |
Oct
28 F |
MIDTERM EXAM #2 |
|
DFB/DD/MT |
|
30 |
Oct 31 M |
DD |
||
|
31 |
Nov 2 W |
DD |
||
|
32 |
Nov 4 F |
DD |
||
|
33 |
Nov 7 M |
Protein structure classification, databases
& visualization tools |
Mount, Ch 10
plus |
DD |
|
34 |
Nov 9 W |
Protein structural prediction and modeling |
Mount, Ch 10
plus |
DD |
|
35 |
Nov 11 F |
Protein-nucleic acid interactions;
protein-ligand docking |
TBA |
DD |
|
36 |
Nov 14 M |
Genome analysis: Genome projects & comparative
genomics |
Mount, Ch 11
plus |
DD |
|
37 |
Nov 16 W |
ENCODE, SNPs, HapMaps & Medical genomics |
TBA |
DD |
|
38 |
Nov 18 F |
Experimental methods: microarrays, proteomics, metabolomics,
chemical genomics |
Mount, Ch 13
plus |
DD |
|
- |
Nov 21-25 |
NO CLASS
Thanksgiving Break |
|
|
|
39 |
Nov 28 M |
Machine learning algorithms |
TBA |
V Honavar |
|
40 |
Nov 30 W |
Microarrays & proteomics analysis; Protein
function prediction |
Mount, Ch 13
plus |
V Honavar |
|
41 |
Dec 2 F |
Modeling Networks: Pathway & interaction
databases; Genetic, regulatory & metabolic
networks |
TBA |
DD |
|
42 |
Dec
5 M |
Student Project Presentations (2 X 20') |
|
DFB/DD |
|
43 |
Dec
7 W |
Student Project Presentations (2 X 20') |
|
DFB/DD |
|
44 |
Dec
9 F |
Student Project Presentations (2 X 20') |
|
DFB/DD |
|
45 |
Dec 15
Th |
FINAL EXAM |
|
|
BCB
444X/544X
Revised Lab
Schedule
|
# |
Date (Th) |
Topic |
Reading |
Instructor |
|
1 |
Aug 25 |
Sequences & databases |
Mount, Ch 2 |
MT |
|
2 |
Sep 1 |
Sequence alignment |
Mount, Ch 3 |
MT |
|
3 |
Sep 8 |
Sequence alignment |
Mount, Ch 4 |
MT |
|
4 |
Sep 15 |
Sequence alignment |
Mount, Ch 5 |
MT |
|
5 |
Sep 22 |
Database searching |
Mount, Ch 6 |
MT |
|
6 |
Sep 29 |
PERL |
Mount, Ch 12 |
XW |
|
7 |
Oct 6 |
BLAST |
Mount, Ch 7+ |
MT |
|
8 |
Oct 13 |
Phylogenetic prediction |
Mount, Ch 7+ |
MT |
|
9 |
Oct 20 |
Gene & promoter prediction |
Mount, Ch 9 plus |
DD |
|
10 |
Oct 27 |
Extra
Office Hours for Exam 2 |
|
DFB/DD |
|
11 |
Nov 3 |
RNA structure
prediction |
Mount, Ch 8 plus |
MT |
|
12 |
Nov 10 |
Protein structure analysis
& prediction |
Mount, Ch 10 plus |
MT |
|
13 |
Nov 17 |
Comparative genomics, SNPs |
Mount, Ch 11 & 13 |
MT |
|
- |
Nov 24 |
NO LAB Thanksgiving Break |
|
|
|
14 |
Dev 1 |
Machine learning & -omics analyses |
Mount, Ch 13 plus |
MT |
|
15 |
Dec
8 |
Student Project Presentations
(4 X 20') |
|
DFB/DD |
|
- |
Dec 15 |
NO LAB Finals Week |
|
|