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Computational Molecular Biology, aka Algorithms for Computational Biology

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Syllabus

Time and place

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.

Schedule

Date Teacher Topics Module Guides
Aug 28 Intro to Mathematica including software installation: bring laptops! Mathematica Module
Aug 30 More on Mathematica and Wolfram Workbench
Sep 2 No class Labor Day
Sep 4 Class overview & Expectation Maximization demo Probability Module
Sep 6 Probability 1
Sep 9 Probability 2
Sep 11 Probability 3
Sep 13 Probability 4
Sep 16 Probability 5
Sep 18 Probability 6
Sep 20 No class C&SB/MGG retreat
Sep 23 Probability 7
Sep 25 Probability 8
Sep 27 TF Binding Motifs 1 Motif Module
Sep 30 TF Binding Motifs 2
Oct 2 TF Binding Motifs 3
Oct 4 TF Binding Motifs 4
Oct 7 Regulatory Network inference 1 TF Network Module
Oct 9 Regulatory Network inference 2
Oct 11 Regulatory Network inference 3
Oct 14 Regulatory Network inference 4
Oct 16 Regulatory Network inference 5
Oct 18 No Class Fall Break
Oct 21 HMMs 1 HMM Module Guide
Oct 23 HMMs 2
Oct 25 TFN Workshop
Oct 28 TF network project presentations
Oct 30 HMMs 3
Nov 1 HMMs 4
Nov 4 HMMs 5
Nov 6 Profile HMMs 1 Profile HMMs
Nov 8 Profile HMMs 2
Nov 11 Profile HMMs 3
Nov 13 No class Class canceled
Nov 15 Modeling gene regulation dynamics 1 SysBio Guide
Nov 18 Modeling gene regulation dynamics 2
Nov 20 Modeling gene regulation dynamics 3
Nov 22 Modeling gene regulation dynamics 4
Nov 25 Modeling gene regulation dynamics 5
Nov 27 No class Thanksgiving holiday
Nov 29 No class Thanksgiving holiday
Dec 2 Modeling gene regulation dynamics 6
Dec 4 Modeling gene regulation dynamics 7
Dec 6 Modeling gene regulation dynamics 8