Alfred Simkin

Biography

As animals, plants, bacteria, fungi, and other life forms face new challenges, the genes they need, and the genes needed to turn these genes on and off, have to change as well. I write simple programs (using a field of biology known as computational biology) to model and understand how genomes and gene regulation change over time. I became interested in Biology as an undergraduate at Earlham College. With only a few simple tools, some published datasets, and a couple of years of the Biology curriculum under our belts, we were able to correct several hundred mis-annotated malarial genes (which we validated using a sequencer). Later, in another undergraduate project, I ran several programs on sequenced genes known as ribosomal RNAs to discover the relatedness of Archaebacteria found in deep sea vents all over the globe. I did my PhD at the University of Massachusetts Medical School, studying the evolution of small RNAs. I taught myself some programming, and with some very simple programs and a lot of publicly available data, I've been able to reconstruct the origins of and changes that occurred in essential small RNA-related genes, which resulted in some high impact publications. Using what I learned, I created a crash course to teach my fellow graduate students to program so that they could better solve their own biological puzzles. I later completed a postdoctoral research project at Cornell University developing some of my programs further, assisting other researchers in analyzing and publishing their data, and continuing to teach graduate students how to write simple programs of their own. Currently, I'm very excited to share the magic of Biology (and computational biology) with Elon undergraduates. It's amazing how many questions we can answer with a solid foundation in Biology, published online genomes, and just a little bit of programming.

Research Interest

For me, biological research is a series of puzzles that I enjoy trying to solve, concerning the origins and mechanics of life. For anyone who’s interested in a longer, more formal description of my past research, I’ve posted a link to my PhD thesis. I also have a brief summary that expands on the research I’m undertaking with undergraduate researchers in a more formal research statement.