Computational Genomics

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)

Takis Benos (3064 BST-3, Department of Computational Biology, University of Pittsburgh)

Starting date: January 7, 2013
Class lectures: Mondays & Wednesdays from 1:30-3:00 pm
Location: Lectures by Bino and Takis @ Pitt from 1:40-3:00 on M/W (Location: BST 3073).
Lectures by Ziv @ CMU from 1:30-2:50 on M/W (Location: 237 Hamburg Hall).
Teaching Assistants:
AJ Sedgewick, ajs206[AT]pitt.edu, 3rd Floor BST3, Pitt; Office hours: by appointment.
Santosh Bhavani, sb[AT]cmu.edu, 7411 Gates Center, CMU; Office hours: by appointment.
Textbooks (suggested but not required): Durbin et al, Biological Sequence Analysis & Deonier et al, Computational Genome Analysis.
Course Summary and grading policies are listed here
Course Project page
Course Mailing List, join this !

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	Lecture 2
1/14	Bino	DNA sequencing 2 (Shot gun genome sequencing and assembly, sequencing by hybridization, BLAST analysis)	Lecture 3
1/16	Bino	Application of computational methods for Sequence analysis and functional annotation (Fourier analysis, Neural Networks)	Lecture 4	PS1 out, data (TA in charge: AJ)
		Lectures will be at CMU
1/21		MLK Holiday: No Class
1/23	Ziv	Microarrays (chip seq etc)	Lecture 5
1/28	Ziv	Normalization, differentially expressed genes	Lecture 6
1/30	Ziv	Differentially expressed genes	Lecture 7	PS1 due, PS2 out (TA in charge: Santosh)
2/4	Ziv	Clustering	Lecture 8	PS 2, data
2/6	Ziv	Classification	Lecture 9
2/11	Ziv	Time series	Lecture 10
		Lectures will be at Pitt
2/13	Bino	Molecular evolution ( Molecular clock, selection tests, Evolutionary distance calculation using Jukes cantor & Kimura models)	Lecture 11	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)	Lecture 12	PS 3, data
2/20	Bino	Scoring matrices, Pair wise Sequence alignment using DP (global, local, affine gap)	Lecture 13
2/25	Bino	Sequence alignment continued. Multiple sequence alignment and profile-profile alignment	Lecture 14
2/27	Bino	Peptide sequencing (mass spec), and analysis	Lecture 15
		Lectures will be at CMU
3/4	Ziv	Motif discovery	Lecture 16	PS3 due, PS4 out, data (TA in charge: AJ)
3/6	Ziv + Bino	Midterm	Past Midterms	Midterm covers L1-L15 Midterm Solutions
3/11		(Spring Break, no class)
3/13		(Spring Break, no class)
3/18	Ziv	Regulatory network1	Lecture 17	Project proposals due
3/20	Ziv	Regulatory network2	Lecture 18
		Lectures will be at Pitt
3/25	Takis	RNAs and epigenetics (microRNA and target prediction, non-coding RNAs, histones)	Lecture 19-20
3/27	Takis	RNA structure		PS4 due, PS5 out (TA in charge: AJ and Santosh)
4/1	Takis	HMMs and their applications (CpG islands, gene prediction, Higher order markov for DNA, Duration modeling, pair HMMs for alignment)	Lecture 21-22
4/3	Takis	Applications of HMM (pair and profile HMMs)
		Lectures will be at CMU
4/8	Ziv	Protein Interaction	Lecture 23
4/10	Ziv	Sys Bio 1	Lecture 24	PS5 due
4/15	Ziv	Sys Bio 2	Lecture 25
4/17	Ziv + Bino	Project poster session, Location: GHC 6115, Time: 2-4 pm
4/24	Ziv + Bino	Project writeup due midnight

Last Updated: 12/20/2012