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.

Date

Teacher

Topics

Module Guides

Aug 29

Brent

Intro to the course & Java

Programming Module

Aug 31

Chaudhari

Organization, Java tutorial

 

Sep 3

No class

Labor Day

 

Sep 5

Brent

Probability 1: Nature of probability; Expectation maximization demo

Probability Module

Sep 7

Brent

Probability 2: Counting problems

 

Sep 10

Brent

Probability 3: Conditional probability, independence, random vars

 

Sep 12

Brent

Probability 4: Bayes’ rule, manipulating probability expressions

 

Sep 14

Brent

Probability 5: Likelihood, Max likelihood estimation, expectation

 

Sep 17

Chaudhari

Probability 6: Workshop EM programming assignment Part 1

 

Sep 19

Brent

Probability 7: Expectation maximization

 

Sep 21

Chaudhari

Probability 8: Workshop EM programming assignment Part 2

Sep 24

Brent

TF Binding Motifs 1: Simple EM motif finder

 MotifModule

Sep 26

Brent

TF Binding Motifs 2:

 

Sep 28

No class

C&SB/MGG retreat

 

Oct 1

Chaudhari

TF Binding Motifs 3: Workshop

 

Oct 3

Brent

Network inference 1: Network mapping & expression data

TFNetworkModule

Oct 5

Brent

Network inference 2: Network mapping by regression

 

Oct 8

Brent

Network inference 3: Network mapping by DE and expression

 

Oct 10

Chaudhari

Network inference 4: Workshop TF network assignment

 

Oct 12

Brent

Network inference: time to work on group project

Oct 15

Brent

HMMs 1: Examples, definition, independence properties

 HmmModuleGuide

Oct 17

Brent

HMMs 2: Factoring, decoding problem, Viterbi

 

Oct 19

No Class

Fall Break

 

Oct 22

Chaudhari

HMMs 3: Workshop Viterbi programming assignment

 

Oct 24

Chaudhari

HMMs 4: Forward algorithm, posterior decoding

 

Oct 26

Chaudhari

HMMs 5: Parameter estimation by ML and EM

 

Oct 29

Brent

Profile HMMs

 ProfileHmms

Oct 31

Brent

Profile HMMs

 

Nov 2

Brent

Profile HMMs

 

Nov 5

Mogno

Modeling gene regulation dynamics in MATLAB

SysBioGuide

Nov 7

Mogno

Modeling gene regulation dynamics in MATLAB

 

Nov 9

Mogno

Modeling gene regulation dynamics in MATLAB

 

Nov 12

Mogno

Modeling gene regulation dynamics in MATLAB

 

Nov 14

Mogno

Modeling gene regulation dynamics in MATLAB

 

Nov 16

Mogno

Modeling gene regulation dynamics in MATLAB

 

Nov 19

Mogno

Modeling gene regulation dynamics in MATLAB

 

Nov 21

 

Thanksgiving holiday

 

Nov 23

 

Thanksgiving holiday

 

Nov 26

Mogno

Modeling gene regulation dynamics in MATLAB

 

Nov 28

Mogno

Modeling gene regulation dynamics in MATLAB

 

Nov 30

Brent

Metabolic modeling

 

Dec 3

Brent

Metabolic modeling

 

Dec 5

Brent

Metabolic modeling

 

Dec 7

Brent

Metabolic modeling