CSE 891: Open Problems in Bioinformatics

Overview

CSE 891, section 002; spring 2010, Tu/Th 12:40 PM - 2:00 PM, 1300 Engineering.

One 80 minute lecture, 2 x 40 minute student presentations each week (3 credits).

Prerequisites: graduate standing in the natural sciences and/or engineering, OR permission of instructor.

An override is necessary for non-Egr graduate students; please send your PID and NetID to Dr. Brown, ctb@msu.edu.

This course will introduce biologists to computational considerations, and computational scientists to biological considerations, in the context of modern biological "grand challenges". Likely topics for 2010 will include metagenomics, non-coding RNAs, genome sequencing and assembly, and next-generation sequencing (e.g. 454, Illumina, SOLiD, and Helicos).

Additional potential topics: genome-scale alignments; RNAi/ncRNA; gene finding; whole-genome phylogenetics; protein structure; databases, data integration, and data warehousing.

The course will be graded on homework, attendance, participation, and presentation.

Please be sure to do the reading and homework even if you must miss a class.

Homework

Each week 1-3 papers will be assigned on Thursday for everyone to read, along with several questions to answer in brief by the next Tuesday. These homeworks won't be graded for correctness but rather for engagement -- did you read the paper? What were points that confused or enlightened you? What do you think of the scientific arguments made in the paper? You will be expected to discuss your answers in class.

Presentations

Each graduate student will be expected to present at least one paper, chosen by mutual agreement between the instructor and the student.

Web site and mailing list

Reading assignments and homework will be made available through the mailing list and on the Web site.

Please sign up for the class mailing list. You can send e-mail to the entire mailing list at cse891@lists.idyll.org.

The mailing list archives are available here.

The first homework and reading assignment will be sent out on Thursday, so please be sure to sign up for the mailing list by then.

Specific Focus Topics for Spring 2010

• Metagenomics
• Next-generation sequencing -- technology & analysis
• Animal/plant genomics and genome annotation
• Phylogeny
• Computational reproducibility and reliability