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Computational
Molecular Biology, aka Algorithms for Computational Biology
Home
* Syllabus * Course Information
* Lecturers,TAs, office
hours * Collaboration
Policy * Programming Help
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Monday, Wednesday: 2:30-4 PM, Earth
and Planetary Sciences, Room 203, Danforth Campus
Friday, 2:30-4 PM, fifth floor
classroom, room 5206, 4444 Forest Park Boulevard building (the Genome Center)
All meetings may include some lecture style presentation and/or in-class
collaborative learning.
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Date |
Teacher |
Topics |
Module Guides |
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Aug 27 |
Brent/Lu |
Molecular biology 1 |
Intro to UNIX/C |
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Aug 29 |
Brent/Lu |
Molecular biology 2 |
Intro to UNIX/C |
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Sep 1 |
Labor Day: No class |
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Sep 3 |
Brent/Lu |
Molecular biology 3:
Sequencing |
Intro to UNIX/C |
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Sep 5 |
Brent |
Probability 1:
Definitions, finite sample spaces, permutations, combinations |
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Sep 8 |
Brent |
Probability 2: Conditional
probability, independence, random variables, expectation |
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Sep 10 |
Brent |
Probability 3: Algebra of
conditional probabilities |
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Sep 12 |
Brent |
Probability 4: Bayes
estimators, max likelihood, expectation maximization |
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Sep 15 |
TA |
Probability 5: Workshoping
the EM assignment |
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Sep 17 |
Brent |
Probability 6: Review and
remaining exercises |
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Sep 19 |
No class |
No class (Genetics
retreat) |
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Sep 22 |
Brent |
HMMs: Example, definition,
factoring, decoding problem, Viterbi mechanics |
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Sep 24 |
Brent |
HMMs: Correctness of the
Viterbi algorithm |
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Sep 26 |
Brent |
HMMs: Workshoping Viterbi
decoding Assignment |
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Sep 29 |
Brent |
HMMs: Forward algorithm,
posterior decoding |
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Oct 1 |
Brent |
HMMs: Parameter estimation
by ML and EM |
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Oct 3 |
Brent |
Gene structure prediction |
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Oct 6 |
Brent |
Tree HMMs and phylogenetic
gene prediction |
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Oct 8 |
Lu |
Pair HMMs |
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Oct 10 |
Lu |
Pair HMMs |
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Oct 13 |
Buhler |
Alignment |
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Oct 15 |
Buhler |
Alignment |
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Oct 17 |
Buhler/TA |
Paper discussion: space
efficient DP algorithms |
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Oct 20 |
Buhler |
Alignment |
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Oct 22 |
Buhler |
Alignment |
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Oct 24 |
Buhler/TA |
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Oct 27 |
Stormo |
Multiple sequence
alignment & profile HMMs |
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Oct 29 |
Stormo |
Multiple sequence alignment
& profile HMMs |
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Oct 31 |
Stormo/TA |
(Extra Credit for coming
to Recitation in a Costume) |
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Nov 3 |
Stormo |
Regulatory motif
identification |
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Nov 5 |
Stormo |
Regulatory motif identification |
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Nov 7 |
Stormo/TA |
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Nov 10 |
Brent |
Population genetics |
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Nov 12 |
Brent |
Population genetics |
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Nov 14 |
Brent/TA |
Population genetics |
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Nov 17 |
Brent |
Population genetics |
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Nov 19 |
Brent |
Dynamics of biological
networks |
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Nov 21 |
Brent |
Dynamics of biological
networks |
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Nov 24 |
Brent |
Dynamics of biological
networks |
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Nov 26 |
Thanksgiving holiday |
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Nov 28 |
Thanksgiving holiday |
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Dec 1 |
Brent |
Dynamics of biological
networks |
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Dec 3 |
Brent |
Inference of biological
networks |
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Dec 5 |
Stormo |
RNA secondary structure
analysis |
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Dec 8 |
Stormo |
RNA secondary structure
analysis |
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Dec 10 |
Stormo |
RNA secondary structure
analysis |
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