GeekLogan / bioinf529-winter2019

Bioinformatics 529 - Bioinformatics Concepts and Algorithms

Bioinformatics 529 (3 Credit Lecture)

Bioinformatics Concepts and Algorithms

Course Masters: Alan Boyle, Ph.D. ([e-mail])
Ryan Mills, Ph.D. ([e-mail])

Graduate Student Instructors: Shengcheng Dong ([e-mail]) Marcus Sherman ([e-mail])

No.	Date	Topic
1.	We 1/9/19	Introduction and Setup
2.	Mo 1/14/19	Obtaining, Compiling, and Organizing Software
3	We 1/16/19	Pattern matching in sequence
	MLK Day
4.	We 1/23/19	Consensus motifs
5.	Mo 1/28/19	Gibbs sampling
6.	We 1/30/19
7.	Mo 2/4/19	Graphical models
8.	We 2/6/19	Viterbi decoding; posterior decoding
9.	Mo 2/11/19	Estimating HMM parameters
10.	We 2/13/19	Profile HMMs and Classification
11.	Mo 2/18/19	Pairwise alignments
12.	We 2/20/19	Multiple sequence alignment
13.	Mo 2/25/19	Clustering
14.	We 2/27/19	Building phylogenetic trees
	Spring Break
15.	Mo 3/11/19	Tree searches / sorting + Recursion
16.	We 3/13/19	Short-read mapping 1: suffix tree + BWT
17.	Mo 3/18/19	Short-read mapping 2: suffix tree + BWT
18.	We 3/20/19	Count-based data 1: coverage, variant calling
19.	Mo 3/25/19	Count-based data 2: expression level, RNA
20.	We 3/27/19	Count-based data 3: eQTL, association test
21.	Mo 4/1/19	Genomics analysis on intervals & Genome Browsers
22.	We 4/3/19	De novo sequence assembly: de Bruijn graph
23.	Mo 4/8/19	Proteomic analysis: peptide library, spectrum comparison (MASCOT)
24.	We 4/10/19	Proteomic quantification
25.	Mo 4/15/19	Networks and Enrichment
26.	We 4/17/19	Protein folding
27.	Mo 4/22/19	Systems Biology