CS 681 Projects & Literature Surveys
Anything in general the field of "bioinformatics / computational biology"
can be proposed. The projects can be proposed/submitted by groups of 2 or 3
people, as well as individually. The purpose of the project is to increase
your knowledge about bioinformatics / computational biology in general, and
see what problems can be worked on for further improvement. You can:
- Apply known algorithms / available tools to different datasets; such
as:
- Download next-generation sequence reads for an organism (E. coli, C.
elegans) and try to assemble it. Then compare your assembly with
available reference genomes for accuracy.
- Analyze the genome(s) of one or more individuals (of any organism)
to discover variants such as SNPs, small indels, structural variation.
- Analyze RNA-seq data (from different tissues); estimate coverage
and/or expression for each gene (beware of alternative splicing).
- Implement previously described algorithms in an efficient and user
friendly manner.
- Proposals for any algorithm / tool can be submitted.
- Develop your own algorithm. Obviously this cannot be for a very
complex and hard problem due to time limitations. A simple, yet useful
problem would suffice. For example:
- A simple scaffolding algorithm that uses data from multiple
sequencing platforms (e.g. short reads [Illumina] and strobe reads
[Pacific Biosciences]) to improve assembly of a single BAC clone. For
this project, raw reads as well as pre-assembled contigs can be
provided. This can be a very complicated problem, but simple solutions
may be accepted.
- Collate information about tools for a specific purpose and perform
benchmarks. Note: This project may be publishable. You can follow the
methodology of Fonseca
et al. but focus on other types of bioinformatics applications.
Sample projects
Sample literature surveys
- Current uses of GPGPUs in genomics / bioinformatics