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Computational Genomics MSCBIO2070/02-710 (cross-listed as 10-810), Spring 2013

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)

 

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Date
Instructor
Lecture Topics
Slides Download
Homeworks
Lectures will be at Pitt
1/7

Bino

Introduction to molecular biology

Lecture 1
1/9

Bino

DNA sequencing 1

1/14

Bino

DNA sequencing 2 (Shot gun genome sequencing and assembly, sequencing by hybridization, BLAST analysis)
1/16

Bino

Application of computational methods for Sequence analysis and functional annotation (Fourier analysis, Neural Networks)
PS1 out
(TA in charge: AJ)
Lectures will be at CMU
1/21

Ziv

Microarrays (chip seq etc)

1/23

Ziv

Normalization, differentially expressed genes

1/28

Ziv

Differentially expressed genes

1/30

Ziv

Clustering

PS1 due, PS2 out
(TA in charge: Santosh)
2/4

Ziv

Classification

2/6

Ziv

RNA-Seq

2/11

Ziv

Time series

Lectures will be at Pitt
2/13

Bino

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

PS2 due, PS3 out
(TA in charge: Santosh)
2/18

Bino

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

2/20

Bino

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

2/25

Bino

Sequence alignment continued. Multiple sequence alignment and profile-profile alignment

2/27

Bino

Peptide sequencing (mass spec), and analysis

Lectures will be at CMU
3/4

Ziv

Motif discovery

PS3 due, PS4 out
(TA in charge: AJ)
3/4

Ziv + Bino

Midterm

Midterm covers L1-L15
3/11

(Spring Break, no class)

3/13

(Spring Break, no class)

3/18

Ziv

Regulatory network1

Project proposals due
3/20

Ziv

Regulatory network2

Lectures will be at Pitt
3/25

Bino

HMMs and their applications (CpG islands, gene prediction, Higher order markov for DNA, Duration modeling, pair HMMs for alignment)

3/27

Bino

Applications of HMM (pair and profile HMMs)

PS4 due, PS5 out
(TA in charge: AJ and Santosh)
4/1

Bino

RNAs and epigenetics (microRNA and target prediction, non-coding RNAs, histones)

4/3

Bino

RNA structure

Lectures will be at CMU
4/8

Ziv

Protein Interaction

4/10

Ziv

Sys Bio 1

PS5 due
4/15

Ziv

Sys Bio 2

4/17

Ziv + Bino

Project poster session, Location: TBD

 

Last Updated: 12/20/2012