CS6890 (Section 001) Topics in Bioinformatics

Time: MWF 9:30 AM to 10:20 AM

Place: Family and Life 115

Instructor: Charles Yan (Charles.Yan@usu.edu)

Syllabus

Lecture Notes

1. Protein function prediction

1.1 Introduction to proteins and protein function (Slides)

1.2 Similar sequence similar function paradigm (Slides)

1.3 Single motif approach (Slides)

1.4 Multiple motif approach (Slides)

1.5 Paper discussion (Gibbs Motif Sampler), extra reading (1,2)

1.6 Paper discussion (MEME), extra reading (MetaMEME, ParaMEME)

1.7 Markov chains (Slides)

1.8 Paper discussion (1, 2)

1.9 Hidden Markov Models

1.10 Paper discussion: The identification of trans-membrane helix (1,2)

1.11 Paper discussion: Application of HMMs to structural data (1,2), extra reading (1,2)

1.12 Classifiers (Decision Trees, SVM, NN)

1.13 Paper discussion (1,2)

2. Gene finding I (Slides), II (slides), and III (slides)

2.1 Paper discussion (GeneMark, GeneMark_hmm, Heuristic_approach,GeneMarkS

, GeneMark_ES, GeneMark_server)

2.2 Paper discussion (GENSCAN, GenomeScan)

2.3 Paper discussion (Glimmer1.0, Glimmer 2.0, GlimmerHmm)

3. Protein structure prediction (Slides)
4. Final project demo (Schedule)

Homework

Assignment 1	Assignment 2	Assignment 3	Papers for final presentations Final presentation Schedule
Assignment 4(htm) (pdf format)

Office Hours

Monday 8:30 am-9:20 am; Tuesday 10 am-11 am; Friday 3 pm-4 pm

Grader

Uppula Sujatha (sujatha@cc.usu.edu)