CS5890 (Section 001) Bioinformatics: Problems and Solutions

June 12- Aug 4, 2006

Credits: 3

Time: MW 12:10-14:20, F 12:10-1:10

Place: Old Main 117

Instructors:

Charles Yan, Computer Science

cyan@cc.usu.edu 797-2570

Bart Weimer, Center for Integrated BioSystems

bcweimer@cc.usu.edu 797-2753

Mark Miller, Biology

Mark.Miller@usu.edu 797-7609

John Stevens, Math and Statistics

John.R.Stevens@usu.edu 797-2818

Course Goals:

• Become familiar with several bioinformatic problems

o Computational analysis of human disease mutations

o Gene finding

o Gene expression analysis

o Proteomics and metabolomics

• Understand the approaches that are used to address these problems

Learning Outcome:

• Be able to identify and utilize suitable bioinformatic resources to solve the problems covered by the course

Grading:

• Project progress reports (15%)
• Poster presentation (85%)

Project:

Each of the four instructors will introduce one topic. Students registered in the class will be divided into four groups. Each group chooses one topic as their project. If two groups bid for one topic, then the group comes first will get it. Three classes are reserved for the project progress reports. During these times, each group will report to the whole class their progress. There will be a poster session on Aug 2. Each group needs to print out their poster and present it.

Course Website:

The website for this course is http://www.cs.usu.edu/~cyan/CS5890/.

Textbook: None

Cheating Policy:

Please be aware of the department cheating policy . No cheating is tolerated in this class.

Class Schedule:

Date	Topic	Instructor	Slides
June 12	Introduction to genetics/genomics	Mark Miller	PDF
June 14	Introduction to bioinformatics	Charles Yan	PDF
June 16	Syllabus	Charles Yan
June 19	Gene expression	John Stevens	Introduction, BioConductor
June 21	Proteomics and small molecules	Bart Weimer
June 23	Gene expression analysis	John Stevens	PDF
June 26	Computational analysis of human disease mutations	Mark Miller	PDF
June 28	Metabolomics	Bart Weimer
June 30	Gene finding	Charles Yan	PDF
July 3, 5, 7	Lectures	John Stevens	1&2, 3&4, 5
July 10	Project update, lecture	Mark Miller	PDF
July 12, 14	Lectures	Mark Miller	1, 2
July 17	Project update, lecture	Charles Yan	PDF
July 19, 21	Lectures in gene finding	Charles Yan	1, 2 Poster Template, Poster2, temp
July 24	University holiday
July 26	Project update, lecture	Bart Weimer
July 28	Lecture	Bart Weimer
July 31	Help session
Aug 2	Poster session

Project Groups (Last update June 29, 2006)

Project	Students	Supervisor
Gene expression analysis	Waite, Joshua Bert Hillyard, Cody F Smith, Jake R Summers, Ryan M Mckinnon, Boyd Karl Maw, Matt Wayne	John Stevens
Computational analyses of human disease mutations	Sessions, Benjamin R Adhau, Swati Anna Flake, Darl Dennis West, Christian J Huang, Kun	Mark Miller
Metabolomics	Uppula, Sujatha Shaik, Ngalakshmi Ellsworth, Carl Sheikh, Irfan Dawson, Joshua Kolla, Rajesh	Bart Weimer
Gene finding	Sabillon, Wilberto Shurtleff, Devin Shah, Jigna	Charles Yan