I am a recent Ph.D. graduate in Computer Science from UC Santa Cruz. For the six years that I have been at UCSC I have been squarely focused on computational biology. For the last two years I have been working on my PhD thesis, which is concerned with the development of protein structure score functions. My advisor was Kevin Karplus. A postscript version of my curriculum vita is available.

In the four years prior to my thesis work, I was involved in a number of different research projects. I began by working with Richard Hughey on our hidden Markov model (HMM) Sequence Alignment and Modeling suite (SAM) by implementing scoring with null models. I spent some time investigating HMM construction with genetic algorithms, but this was more dabbling in genetic algorithms than an attempt to improve SAM. Later I parallelized SAM using the MPI (Message Passing Interface) standard, providing a marked speedup for model building and database scoring in a multicomputer setting. At about this time our research group became involved in CASP2, where we were recognized as one of the top groups in the fold recognition category. Following that hectic time period I applied HMM technology to the analysis of the just-sequenced genome of Methanoccocus jannaschii (MJ). In particular, I sought to find whether the genome contained the genes for phosphofructokinase and fructose bisphosphatase, which are the only two genes in the glycolysis and gluconeogenesis pathways which still have not been located. I have what I believe to be strong circumstantial evidence that they exist as a fused gene in MJ, but am still trying to find somebody to perform experimental validation. If you are interested, let me know! In concert with this directed search I spent a number of months with David Haussler attempting a complete genome analysis of MJ, in the end not publishing results for lack of a benchmark on which base my annotation claims. After this effort, I began working with Kevin Karplus on two fronts. The first was development of a protein secondary structure predictor using artificial neural networks. This was later shown to be one of the two best predictors at CASP3. The other research direction was development of an HMM-based protein sequence remote homology detection method. This effort resulted in SAM-T98, which has been shown to outperform all other methods for remote homolog detection. We used SAM-T98 (and subsequently SAM-T99 and SAM-T2K) in CASP3 (and CASP4) with success.

As a physics undergraduate at the University of Colorado at Boulder I worked in two physics labs. The first was with Scott Robertson, where we spent two years developing a charge-exchange pumped UV laser. By the time I left we were successfully guiding hydrogen plasma using multipole magnets, but absorption issues were preventing us from getting spontaneous emission. I also worked in Gordon Dunn's lab building an ion beam line for his Penning trap.

In what seems like another life I used to do quite a bit of rock and big wall climbing. The weekend missions to Yosemite got to be a bit tiring. Surfing with my friend Chuck has certainly helped to fill the void. I ride my bike quite a bit, but only in commuter mode. I much prefer riding to driving. I know how to fly an airplane, but since it's been a long time since I flew I can't really call myself a pilot. I enjoy travelling and visiting other places. After graduating from Boulder I spent ten months backpacking through the Cook Islands, New Zealand, Australia, Malaysia, Thailand, Cambodia, Nepal, Russia, Denmark, Sweden, England, Scotland, Poland, Hungary, Czech and Slovakia. I've also visited Mexico, Germany, Switzerland, France, Greece, Guatemala and Indonesia on short trips.