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Computational Genomics MSCBIO2070/02-710 (cross-listed as 10-810), Spring 2012

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

Seyoung Kim (7721 Gates Hillman Complex, Lane Center for Computational Biology, Carnegie-Mellon University)

 

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Date
Module
Lecture Topics
Slides Download
Homeworks and Recitations
Lectures will be at Pitt (BST3 3073)
1/19
Basics of Genomics

Introduction to molecular biology

Lecture 1
1/24

DNA sequencing 1

Lecture 2
1/26
DNA sequencing 2 (Shot gun genome sequencing and assembly, sequencing by hybridization, BLAST analysis)
Lecture 3
1/31
Sequence Analysis

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

Lecture 4
PS1 out (TA: Aaron)
E. coli genome
PS1 solutions
2/2

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

Lecture 5
2/7

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

Lecture 6
2/9

Sequence alignment continued. Application of Machine learning to sequences. Fourier analysis for cyclic patterns (genes, nucleosome binding)

Lecture 7
2/14
Machine Learning Applications

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

Lecture 8
PS1 due, PS2 out(TA: Salim)
Fasta for problem 1
PS2 solutions
2/16

Applications of HMM (pair and profile HMMs, multiple sequence alignment)

Lecture 9
2/21
Genomics of RNAs

RNA structure prediction (Nussinov, and stochastic context-free grammar)

Lecture 10
2/23

RNAs and epigenetics (non-coding RNAs, histones)

Lecture 11
Lectures will be at CMU (MI 409)
2/28
Population Genetics

Genetic polymorphisms, haplotype inference, recombination

Lecture 12
PS2 due, PS3 out (TA: Aaron)
3/1

Population structure, coalescent process

Lecture 13
3/6

(Pitt Spring Break, no class)

3/8

(Pitt Spring Break, no class)

3/13

(CMU Spring Break, no class)

3/15

(CMU Spring Break, no class)

3/20
Transcriptome Analysis

Transcriptome analysis

Lecture 14
3/22

Linkage analysis, QTL mapping, GWAS

Lecture 15
Project proposal due
3/27

Mid-Term Exam (MI 409)

PS3 due, PS4 out (TA: Salim)
HW files
3/29

Normalization, differentially expressed genes

Lecture 16
4/3

Differentially expressed genes 2

Lecture 17
4/5

Clustering

Lecture 18
4/10

Classification, time-series analysis

Lecture 19
4/12
Systems Biology

Regulatory Networks

Lecture 20
4/17

Regulatory Modules

Lecture 21
PS4 due, PS5 out (TA: Aaron)
4/19

No class

4/24
DNA Sequence Analysis

Motif Discovery

Lecture 22
4/26

Poster session

PS5 and Project are due 4/28

 

Last Updated: 1/1/2012