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Computational Molecular Biology, aka Algorithms for Computational Biology Home * Syllabus * Course Information * Readings and Resources * Lecturers, TAs, Office Hours * Homework Submission |
Monday, Wednesday, Friday: 2:45-4:15 PM, fifth floor classroom,
room 5206, 4444 Forest Park Boulevard building
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 29 |
Brent |
Intro to the course & Java |
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Aug 31 |
Chaudhari |
Organization, Java tutorial |
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Sep 3 |
No class |
Labor Day |
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Sep 5 |
Brent |
Probability 1: Nature of probability; Expectation maximization demo |
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Sep 7 |
Brent |
Probability 2: Counting problems |
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Sep 10 |
Brent |
Probability 3: Conditional probability, independence, random vars |
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Sep 12 |
Brent |
Probability 4: Bayes’ rule, manipulating probability expressions |
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Sep 14 |
Brent |
Probability 5: Likelihood, Max likelihood estimation, expectation |
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Sep 17 |
Chaudhari |
Probability 6: Workshop EM programming assignment Part 1 |
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Sep 19 |
Brent |
Probability 7: Expectation maximization |
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Sep 21 |
Chaudhari |
Probability 8: Workshop EM programming assignment Part 2 |
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Sep 24 |
Brent |
TF Binding Motifs 1: Simple EM motif finder |
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Sep 26 |
Brent |
TF Binding Motifs 2: |
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Sep 28 |
No class |
C&SB/MGG retreat |
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Oct 1 |
Chaudhari |
TF Binding Motifs 3: Workshop |
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Oct 3 |
Brent |
Network inference 1: Network mapping & expression data |
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Oct 5 |
Brent |
Network inference 2: Network mapping by regression |
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Oct 8 |
Brent |
Network inference 3: Network mapping by DE and expression |
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Oct 10 |
Chaudhari |
Network inference 4: Workshop TF network assignment |
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Oct 12 |
Brent |
Network inference: time to work on group project |
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Oct 15 |
Brent |
HMMs 1: Examples, definition, independence properties |
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Oct 17 |
Brent |
HMMs 2: Factoring, decoding problem, Viterbi |
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Oct 19 |
No Class |
Fall Break |
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Oct 22 |
Chaudhari |
HMMs 3: Workshop Viterbi programming assignment |
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Oct 24 |
Chaudhari |
HMMs 4: Forward algorithm, posterior decoding |
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Oct 26 |
Chaudhari |
HMMs 5: Parameter estimation by ML and EM |
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Oct 29 |
Brent |
Profile HMMs |
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Oct 31 |
Brent |
Profile HMMs |
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Nov 2 |
Brent |
Profile HMMs |
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Nov 5 |
Mogno |
Modeling gene regulation dynamics in MATLAB |
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Nov 7 |
Mogno |
Modeling gene regulation dynamics in MATLAB |
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Nov 9 |
Mogno |
Modeling gene regulation dynamics in MATLAB |
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Nov 12 |
Mogno |
Modeling gene regulation dynamics in MATLAB |
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Nov 14 |
Mogno |
Modeling gene regulation dynamics in MATLAB |
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Nov 16 |
Mogno |
Modeling gene regulation dynamics in MATLAB |
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Nov 19 |
Mogno |
Modeling gene regulation dynamics in MATLAB |
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Nov 21 |
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Thanksgiving holiday |
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Nov 23 |
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Thanksgiving holiday |
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Nov 26 |
Mogno |
Modeling gene regulation dynamics in MATLAB |
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Nov 28 |
Mogno |
Modeling gene regulation dynamics in MATLAB |
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Nov 30 |
Brent |
Metabolic modeling |
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Dec 3 |
Brent |
Metabolic modeling |
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Dec 5 |
Brent |
Metabolic modeling |
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Dec 7 |
Brent |
Metabolic modeling |
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