Understanding genome structure and function using computational approaches

Our lab focuses on attempting to understand how an organism's genome specifies its behaviour/phenotype using computational approaches. This requires finding solutions to an an extremely complex set of problems involving areas of biology, chemistry, physics, mathematics, and computing science.

With that goal in mind, there are several pragmatic projects that could be undertaken depending on skills available (or desired!) by undergraduate and graduate students. Examples of some short- and longer-term projects include applying current protein structure prediction developed in our lab to special classes of proteins such as membrane proteins or proteins that require chaperones to fold; developing statistical and computational measures to ascertain when predictions (of structure and function) are more likely to be correct; developing algorithms for determining how proteins interact with each other and other substrates; analysing whole genomes for various properties and comparing sequences, structures, and/or functions within and between genomes; and maintaining databases and webpages containing data/results originating from our research.

General areas of interest include:

• protein structure
• protein function
• protein design and evolution
• protein-protein and protein-substrate interaction
• genomics and proteomics (structure and function of components within a cell)
• understanding higher level organisation (interaction and expression) of components in a cell (DNA, RNA, proteins, and small molecules) and simulating their behaviour

• algorithmic studies of astronomically large spaces
• bioinformatics/data mining
• massively parallel and distributed computing

Candidates who seek to understand fundamental mysteries in biology using computational approaches are encouraged to contact me with a brief description of why this research topic interests you and your academic background. Programming/computing experience would be extremely helpful.

I am an assistant professor in the Microbiology Department at the University of Washington and strongly committed to research-based education at all levels. More information about our group's activities can be gotten at http://compbio.washington.edu.

Ram Samudrala
Department of Microbiology
University of Washington
Seattle, WA 98195-7242
P: (206) 732-6122
F: (206) 732-6055
E: ram@compbio.washington.edu