P.C. Shannon

I’ve started work on my second rotation in Andy Ellington’s lab. It’s a bioinformatics problem, so I’ve had a crash course in Perl before I started writing any programs. But so far it’s progressing very nicely, and Andy is excited about it. I hope that before too long, I’ll be able to put the keyboard down and start doing some bench work to verify the computational work.

Previous people in the lab — mainly an undergrad who is now at Cambridge on a Marshall Scholarship — developed a database of amino acid-nucleotide interactions called “AANT”. I’ll spare you the details on how this was done, but there is a Nucleic Acids Research paper on it. Now I’m going back through the data looking for nucleotide-amino acid interactions that are at approximately the same distance and orientation as other interactions. I think ultimately Andy would like to be able to intelligently design aptamers (RNA molecules that bind other molecules) to bind proteins rather than having to screen for them, which can take months.