Potential CS4983 and CS4997 Projects

General interests include algorithms, computational biology, bioinformatics, and computing fundamentals and models. For CS4983 (Technical Report), I am also interested in investigations of new types of computing and their capabilities; what is at the edge of computing, or considered to be unconventional models of computation.

1. Bioinformatics applications of new learning algorithms
Other UNB CS researchers (such as Dr. Ghorbani) have developed some new algorithms for unsupervised learning. Investigate the performance of their application to bioinformatics data.

2. Comparison of motif and pattern finding programs for genome data
Many new pattern finding algorithms have been developed to discover new motifs and patterns in genomic data (DNA and RNA). Compare a selection of algorithms both in theory and in practice, implemented and tested on available genetic data. Include a portion of the available human genome sequence in the test data.

3. Finding RNA structural patterns
I have an ongoing project investigating methods for finding common RNA structures. I am interested in projects in this line, or in searching for types of structures in currently known structures.

4. Network comparison and feature identification
I am starting to work in graph and network comparison, particularly when applied to regulatory and metabolic networks, but also in application to collaborative graphs, matchings, and document link networks in hypertext.

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