pitt_logo

Computational Genomics MSCBIO2070/02-710 (cross-listed as 10-810), Spring 2015

Ziv Bar-Joseph (zivbj[AT]cs.cmu.edu)
Office Hours: by appointment, 8006 Gates Hillman Complex, Machine Learning Department, Carnegie-Mellon University

Chakra Chennubhotla (chakracs[AT]pitt.edu)
Office Hours: by appointment, 3064 BST-3, Department of Computational and Systems Biology, University of Pittsburgh

 

cmu logo


Date
Instructor
Lecture Topics
Slides Download
Homeworks
1/12

Ziv

Introduction to molecular biology

Lecture 1
1/14

Ziv

Introduction to computational biology

Lecture 2
1/19

No class, MLK day
1/20

Marta

Python Recitation 5-6pm
Slides
1/21

Ziv

Next generation seqeucing /RNA-Seq
Lecture 3
1/22

Silvia

R Recitation 5-6pm
Slides
1/26
Chakra

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

Lecture 4
PS1 out
1/28

Chakra

Phylogeny: Ultrametric Evolutionary Distances, Tree-Construction: UPGMA

Lecture 5
2/2
Chakra

Phylogeny: Tree-Construction: Nearest-Neighbor; Maximum Likelihood

2/4

Chakra

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

Lecture 6
2/9

Chakra

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

Lecture 7
PS1 due

2/11

Chakra

Motif discovery

Lecture 8
PS2 out
2/16

Ziv

Microarrays (chip seq etc)

Lecture 9
2/18

Ziv

Normalization, differentially expressed genes

Lecture 10
2/23

Ziv

Differentially expressed genes

Lecture 11
2/25

Chakra

Clustering

Lecture 12
PS2 due, PS3 out
3/2

Ziv

Classification

Lecture 13
3/4

Chakra

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

Lecture 14
3/9

Spring Break

3/11

Spring Break

3/16

Ziv

Time Series

PS3 due

3/18

Ziv

Regulatory networks 1

Project proposals due

3/23

Ziv

Regulatory networks 2

3/25

Ziv + Chakra

Midterm

3/30

Chakra

RNA Structure

PS4 out
4/1

Chakra

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

4/6

Chakra

Epigenetics 2

4/8

Chakra

Combining regulatory and epigenetics models

4/13

Chakra

Protein Interactions

PS4 due
4/15

No Class

4/20

Ziv

Dynamic networks

4/22

Ziv

Systems Biology 1

4/27

Ziv

Systems Biology 2

4/29

Ziv + Chakra

Poster Session

 

Last Updated: 2/24/2015