pitt_logo

Computational Genomics MSCBIO2070/02-710 (cross-listed as 10-810), Spring 2011

Ziv Bar-Joseph (8006 Gates Hillman Complex, Machine Learning Department, Carnegie-Mellon University)

Bino John (3080 BST-3, Department of Computational Biology, University of Pittsburgh)

 

cmu logo
Date
Lecture Topics
Slides Download
Homeworks and Recitations
Lectures will be at Pitt (BST3 3073)
1/10

Introduction to molecular biology

Lecture 1
1/12

DNA sequencing 1

Lecture 2
1/17
(Martin Luther King's Day, no class)
1/19
DNA sequencing 2 (Shot gun genome sequencing and assembly, sequencing by hybridization, BLAST analysis)
Lecture 3



1/24

Molecular evolution ( Molecular clock, selection tests, Evolutionary distance calculation using Jukes cantor & Kimura models)

Lecture 4
1/26 -> (1/30)

Phylogeny – Parsimony, Sankoff algorithm, Least square estimates for distances, Tree construction (UPGMA, and NJ)

Lecture 5
1/31

Scoring matrices, Pair wise Sequence alignment using DP (global, local, affine gap)

Lecture 6
2/2

Genomic features and  their analysis: Fourier analysis for cyclic patterns (genes, nucleosome binding), Review of sensitivity/specificity concepts, Homolog search BLAST

Lecture 7

2/7

HMMs and their applications (Review of HMMs:Viterbi, Forward/Backward, and Baum, application to CpG islands)

Lecture 8
2/9

Applications of HMM (gene prediction, Higher order markov for DNA, Duration modeling, pair HMMs for alignment)

Lecture 9
2/14 (GHC 4405)

Applications of HMM 2 (pair HMMs – cont’d, profile HMMs, multiple sequence alignment)

Lecture 10
2/16

RNAs: structure prediction, microRNA, ncRNA

Lecture 11


2/21

motif discovery (Motif representation, Gibbs, EM)

Lecture 12
From 2/23, lectures will be at CMU (Location: GHC 6501) [google map]
2/23

Microarrays (chip seq etc)

Lecture 13
2/28

Normalization, differentially expressed genes

Lecture 14
3/2

Differentially expressed genes

Lecture 15



3/7

(Spring Break, no class)

3/9

(Spring Break, no class)

3/14

Clustering

Lecture 16
3/16

Classification

Lecture 17
PS4 due
3/21

Classification II

Project proposals due
3/23

Mid-Term Exam (TA in charge: Selen)


3/28

Time series analysis

Lecture 18
3/30

RNA-Seq

Lecture 19
PS5 out (TA in charge: Selen)
4/4

Guest Speaker: Elodie Ghedin

4/6

Regulatory networks

Lecture 20
4/11

Regulatory Modules

Lecture 21
4/13

Protein interactions

Lecture 22
PS5 due
(Submission is extended to 4/14)
4/18

Genome variation

4/20

Project poster session, Location: TBD

5/3

Project report due at noon

 

Last Updated: 4/21/2011 1:13 PM