|
|
Computational
Molecular Biology, aka Algorithms for Computational Biology
Home * Syllabus * Course
Information * Readings and Resources
* Lecturers,TAs, office hours * Homework Submission * Forum |
Monday, Wednesday, 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.
|
Date |
Teacher |
Topics |
Module Guides |
|
Aug 26 |
Brent |
Intro to the course &
Java |
|
|
Aug 28 |
Brent |
Probability 1: Java &
expectation maximization demo |
|
|
Aug 31 |
Brent |
Probability 2: Intro to probability
in biology, counting problems |
|
|
Sep 2 |
Brent |
Probability 3: Conditional
probability and independence |
|
|
Sep 4 |
Brent |
Probability 4: Random
variables, Bayes’ rule |
|
|
Sep 7 |
No class |
Labor Day |
|
|
Sep 9 |
Brent |
Probability 5:
Expectation, estimation |
|
|
Sep 11 |
Brent |
Probability 6: Expectation
maximization and its applications |
|
|
Sep 14 |
Brent |
Probability 7: Workshop EM
programming assignment |
|
|
Sep 16 |
Brent |
HMMs 1: Examples, definition
in terms of independence properties |
|
|
Sep 18 |
Brent |
HMMs 2: Factoring,
decoding problem, Viterbi mechanics |
|
|
Sep 21 |
Brent |
HMMs 3: Correctness of the
Viterbi algorithm |
|
|
Sep 23 |
Sloutsky ( |
Dynamic Programming in
general |
|
|
Sep 25 |
Sloutsky ( |
HMMs 4: Workshop Viterbi
programming assignment |
|
|
Sep 28 |
Brent |
HMMs 5: Forward algorithm,
posterior decoding |
|
|
Sep 30 |
Brent |
HMMs 6: Parameter
estimation by ML and EM |
|
|
Oct 2 |
No class |
Molecular Genetics &
Genomics program retreat |
|
|
Oct 5 |
Brent |
Gene structure prediction |
|
|
Oct 7 |
Brent |
Intro to Alignment and
Pair HMMs |
|
|
Oct 9 |
Brent |
Workshop alignment
programming assignment |
|
|
Oct 12 |
Buhler |
Alignment 1 |
|
|
Oct 14 |
Buhler (No GS) |
Alignment 2 |
|
|
Oct 16 |
No class |
Fall Break |
|
|
Oct 19 |
Buhler (No GS) |
Alignment 3 |
|
|
Oct 21 |
Stormo |
Multiple sequence
alignment |
|
|
Oct 23 |
Stormo |
Profile HMMs |
|
|
Oct 26 |
Stormo |
Motif finding |
|
|
Oct 28 |
Stormo |
Motif finding |
|
|
Oct 30 |
Stormo |
Motif finding |
|
|
Nov 2 |
Brent |
Network inference |
|
|
Nov 4 |
Brent (No GS) |
Network inference |
|
|
Nov 6 |
Brent (No GS) |
Network inference |
|
|
Nov 9 |
Kuttykrishnan |
ODE models |
|
|
Nov 11 |
Kuttykrishnan (No GS) |
ODE models |
|
|
Nov 13 |
Kuttykrishnan (No GS) |
ODE models |
|
|
Nov 16 |
Kuttykrishnan (No GS) |
ODE models |
|
|
Nov 18 |
Kuttykrishnan |
ODE models |
|
|
Nov 20 |
Kuttykrishnan |
ODE models |
|
|
Nov 23 |
Brent |
Flux/constraint models |
|
|
Nov 25 |
|
Thanksgiving holiday |
|
|
Nov 27 |
|
Thanksgiving holiday |
|
|
Nov 30 |
|
TBA (Project or population
genetics) |
|
|
Dec 2 |
No MB/GS |
TBA (Project or population
genetics) |
|
|
Dec 4 |
No MB/GS |
TBA (Project or population
genetics) |
|
|
Dec 7 |
|
Project presentations |
|
|
Dec 9 |
|
Project presentations |
|