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Computational Genomics MSCBIO2070/02-710 (cross-listed as 10-810), Spring 2014

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

 

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Date
Instructor
Lecture Topics
Slides Download
Homeworks
1/13

Ziv

Introduction to molecular biology

Lecture 1
1/15

Ziv

Introduction to probability and statistics

Lecture 2
1/20

No class, MLK day
1/22

Ziv

Next generation seqeucing /RNA-Seq
Lecture 3
PS1 out
mystery_genome.txt SOLUTIONS
(TA in charge: AJ)
1/27
Chakra

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

Lecture 4
1/29

Chakra

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

Lecture 5
1/29
AJ

Python Recitation 3-4pm PSC 103

2/3

Chakra

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

Lecture 6
2/3

Silvia

R recitation, 3-4pm PSC 103

2/5

Chakra

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

Lecture 7
PS1 due, PS2 out
mus_sapiens.fasta
(TA in charge: Kristina)
2/10

Chakra

PSSMs and Profiles

Lecture 8
2/12

Chakra

HMMs

Lecture 9
2/17

Ziv

Microarrays (chip seq etc)

Lecture 10
2/19

Ziv

Normalization, differentially expressed genes

Lecture 11
PS3 out
(TA in charge: Silvia)
2/23

PS2 due, PS2 Solutions
2/24

Ziv

Differentially expressed genes

Lecture 12
2/26

Ziv

Clustering

Lecture 13
3/3

Ziv

Classification

Lecture 14
3/5

Ziv

Time Series

Lecture 15
PS3 due, PS3 Solution
PS4 out
(TA in charge: Silvia)
3/10

(Spring Break, no class)

3/12

(Spring Break, no class)

3/17

Chakra

Applications of HMMs

Lecture 16
3/19

Chakra

Motif Discovery

Lecture 17
PS4 due, PS4 Solutions
3/24

Ziv

Regulatory Networks 1

Lecture 18
3/26

Ziv + Chakra

Midterm

Midterm
Midterm Solutions
Some Previous Midterm Questions and Partial Answers
3/31

Ziv

Regulatory Networks 2

Lecture 19
Project Proposals due, PS5 out
(TA in charge: Silvia)
4/2

Chakra

Protein Interaction

Lecture 20
4/7

Ziv

Systems Biology 1

Lecture 21
4/9

Ziv

Systems Biology 2

Lecture 22
4/14

Chakra

RNA structure

Lecture 23
PS 5 due
4/16

Chakra

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

Lecture 24
4/21

Chakra

Epigenetics 2

Lecture 25
4/23

Chakra

Combining regulatory and epigenetics models

Lecture 26
4/28

No Class

4/30

Ziv + Chakra

Project poster session, 1:30 pm GHC 4405

5/5

Final project report due. E-mail report to Ziv and Chakra by 11:59pm

 

Last Updated: 3/27/2014