Final Lecture Schedule - Fall 2007 (updated
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Lec # |
Date |
Topic & Text Chapter
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Reading/URLs (before lecture) |
Homework |
Lecture PPTs |
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1 |
Aug
20 |
M |
What is Bioinformatics?
Part 1 |
Xiong, Chp 1 p 3-8 |
HW #1 Assigned |
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2 |
Aug
22 |
W |
What is Bioinformatics? Part 2 |
Chp 2 p 10-27 |
HW #1 Due |
(embedded URLs has not yet been fixed) |
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3 |
Aug
24 |
F |
Brief Biology Review |
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4 |
Aug
27 |
M |
Biological Databases
& Sequence Alignment |
Chp 2 p 10-27 Chp 3 p 31-41 |
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5 |
Aug
29 |
W |
Dynamic Programming (DP) |
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6 |
Aug
31 |
F |
More DP & Global
Alignment |
Chp 3 p 41-49 |
HW
#2 Assigned |
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- |
Sept
3 |
M |
NO CLASS – Labor Day
Holiday |
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7 |
Sept
5 |
W |
Still More DP & Local
Alignment |
Chp 3 p 41-49 |
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8 |
Sept
7 |
F |
Finish DP & Scoring
Matrices |
Chp 3 p 41-49 |
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9 |
Sept
10 |
M |
Database Searching &
BLAST |
Chp 4 p 51-62 |
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10 |
Sept
12 |
W |
BLAST Details & Gene
Jargon |
Chp 4 p 51-62 |
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11 |
Sept
14 |
F |
Multiple Sequence
Alignment (MSA) |
Chp 5 p 63-74 |
HW #2 Due |
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12 |
Sept
17 |
M |
Scoring MSAs; PSSMs &
PSI-BLAST |
Chp 5 p 63-74 |
HW
#2 Ans Posted |
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13 |
Sept
19 |
W |
Star Alignment Clustal |
Chp 5 p 63-74 |
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- |
Sept 21 |
F |
Midterm Exam #1 |
Lectures 2-12, HW2, Chps
1-6, Eddy "What is DP" Labs 1-4; see Study Guide #1 |
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14 |
Sept
24 |
M |
Review:
Nucleus, Chromosomes, Genes |
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HW #3 Assigned |
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15 |
Sept
26 |
W |
Review:
RNA, Proteins, Promoters, TFs |
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544 Extra HW #1
Assigned |
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16 |
Sept
28 |
F |
Profiles
& HMMs |
Chp 6 p 79-84 |
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17 |
Oct
1 |
M |
More HMMs, Protein Motifs & Domains |
Chp
7 |
544 Extra#1 Task 1 Due |
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18 |
Oct
3 |
W |
Protein Motifs & Domain Prediction |
Chp 12 |
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19 |
Oct
5 |
F |
Protein Structure: Basics, Visualization,
Classification, Comparison |
Chp
13 |
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20 |
Oct
8 |
M |
Protein Structure Classification |
Chp
14 |
·
i) HW #3 Due ii) 444 Students
"Project-instead-of-Final" 544 Extra#1 Task 1.1 Due |
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21 |
Oct
10 |
W |
Protein Secondary Structure Prediction |
Ch 15 |
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|
22 |
Oct
12 |
F |
Protein Secondary & Tertiary Structure Prediction |
Ch 15 |
544 Extra#1 Task 1.2 & 2 Due HW #4 Assigned |
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23 |
Oct
15 |
M |
Protein Tertiary Structure Prediction |
Ch 15 |
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|
24 |
Oct
17 |
W |
RNA Structure Prediction |
Ch
16 |
544 Extra #2
Assigned |
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25 |
Oct
19 |
F |
More RNA Structure &
544 Projects |
Ch
16 |
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26 |
Oct
22 |
M |
Gene Prediction |
Ch
8 |
HW #4 Due |
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27 |
Oct
24 |
W |
Promoter & Regulatory
Element Prediction |
Ch 9 |
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- |
Oct 26 |
F |
Midterm Exam #2 |
Lectures
13-26, HW3-4, Chps 6-8 & 12-16, Eddy "What's an HMM?"&
Ginalski "Practical Lessons" Labs 5-8; see Study Guide #2 HW #5 Assigned |
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28 |
Oct
29 |
M |
Promoter Prediction |
Ch
9 |
544 Extra#2 Due |
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29 |
Oct
31 |
W |
Phylogenetics Basics
Terribilini |
Ch
10 |
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30 |
Nov
2 |
F |
Phylogenetics Distance
Based Methods Terribilini |
Ch
11 |
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31 |
Nov
5 |
M |
Phylogenetics Character
Based Methods Terribilini |
Ch
11 |
HW #5 Due |
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32 |
Nov
7 |
W |
Machine
Learning Algorithms (NB, DT, SVM) Terribilini |
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33 |
Nov
9 |
F |
Genomics |
Ch
17 |
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34 |
Nov
12 |
M |
Comparative Genomics |
Ch
17 |
HW #6 Assigned |
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35 |
Nov
14 |
W |
Functional Genomics |
Chp
18 |
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|
36 |
Nov
16 |
F |
Microarrays |
Chp
18 |
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- |
Nov
19-23 |
NO CLASS - Thanksgiving
Break |
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37 |
Nov
26 |
M |
Clustering Algorithms |
Chp
18 |
HW #6 Due |
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38 |
Nov
28 |
W |
Proteomics
(2-D Gels & MS) |
Chp
19 |
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39 |
Nov
30 |
F |
Systems
Biology |
-- |
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- |
Dec 3 |
No Class |
BCB 544 Team Projects – Written Reports Due |
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- |
Dec 5 Dec 7 |
BCB 544 Team
Project Presentations Attendance Required |
HW #7 (Project Peer Evalutions 4 Total) Due |
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- |
Dec 10 |
M |
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40 pts In Lab: Practical
(Comprehensive) 20 pts In Class:
Comprehensive 40 pts In Class: New
material (since Exam 2): Lectures
27-38, HW5-6, Chps 9-11 & 17-19, Labs 9-11; see Study Guide Final |
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