Time:
Instructors
|
Professor Tim Ting Chen
|
Phone: (213)740-2415 |
Email: tingchen@usc.edu
|
OH: M (except 3/8-4/23) |
|
Professor Michael Waterman |
Phone: (213)740-2408 |
Email: msw@hto.usc.edu
|
OH: ?? |
|
Professor Fengzhu Sun |
Phone: (213)740-2413 |
Email: fsun@usc.edu |
|
TA
Maghna Patel, Discussion Time: ??
(one for computer lab and one for Q&A), Classroom:
??
Course Content
This course provides
an introduction to the computational side of molecular biology, with an
emphasis on genome analysis.
Experimental biology is becoming increasingly computer intensive. In
some laboratories, such as those doing genome and other large sequencing
projects, fully half of the work is done on a computer. In others the role of the computer is subtle,
but there nonetheless. This course introduces biology students to the basics of
computational and statistical thinking within the context of biology, so that
the relevance and importance is immediately evident.
Copies of lecture
notes will be given in the class.
Grading
There are two mid-term
examinations, 20% pts each, a final examination of 40%, and homework assignments
(20%).
Schedule
|
|
BISC478 |
Computational Genome Analysis |
|
|
|
Date |
Topic |
Lecturer |
|
Wk. 1 |
|
Introduction to Genomes (Chap 1) |
Chen |
|
|
|
Words: Introduction to Probability
and Statistics (Chap 2) |
Sun |
|
|
|
|
|
|
Wk. 2 |
|
Words: Introduction to Probability
and Statistics (Chap 2) |
Sun |
|
|
|
Restriction site distributions (Chap
3) |
Sun |
|
|
|
|
|
|
Wk. 3 |
|
Physical Mapping (Chap 4) |
Chen |
|
|
|
Introduction to Algorithms (Chap 4) |
Chen |
|
|
|
|
|
|
Wk. 4 |
|
Pairwise Sequence Alignments – 1
(Chap 6) |
Chen |
|
|
|
Pairwise Sequence Alignments – 2 (Chap
6) |
Chen |
|
|
|
|
|
|
Wk. 5 |
|
PAM and BLOSUM (Chap 7) |
Chen |
|
|
|
Examination I |
Chen |
|
|
|
|
|
|
Wk. 6 |
|
FASTA and BLAST (Chap 7) |
Chen |
|
|
|
Multiple Sequence Alignments – 1
(Chap 6) |
Chen |
|
|
|
|
|
|
Wk. 7 |
|
Multiple Sequence Alignments – 2
(Chap 6) |
Chen |
|
|
|
Gene Finding – 1 (Chap 9) |
Chen |
|
|
|
|
|
|
Wk. 8 |
|
Gene Finding – 2 (Chap 9) |
Chen |
|
|
|
Genome Sequencing Techniques (Chap 8) |
MSW |
|
|
|
|
|
|
Wk. 9 |
|
Genome Sequencing Statistics (Chap 8) |
MSW |
|
|
|
Genome Sequencing Algorithms (Chap 8) |
MSW |
|
|
|
|
|
|
Wk. 10 |
|
Spring Break |
|
|
|
|
Spring Break |
|
|
|
|
|
|
|
Wk. 11 |
|
Examination II |
MSW |
|
|
|
RNA Secondary Structure |
MSW |
|
|
|
|
|
|
Wk. 12 |
|
Microarray – 1 (Chap 12) |
Sun |
|
|
|
Microarray – 2 (Chap 12) |
Sun |
|
|
|
|
|
|
Wk. 13 |
|
Clustering -1 (Chap 10) |
Sun |
|
|
|
Clustering – 2 (Chap 10) |
Sun |
|
|
|
|
|
|
Wk. 14 |
|
Phylogeny I (Chap 11) |
Sun |
|
|
|
Phylogeny II (Chap 11) |
Sun |
|
|
|
|
|
|
Wk. 15 |
|
Phylogeny III (Chap 11) |
Sun |
|
|
|
Population Variation I (Chap 13) |
Sun |
|
|
|
|
|
|
Wk. 16 |
|
Population Variation II (Chap 13) |
Sun |
|
|
|
Review and QA |
|
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Final examination (Tue, |
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