DAVID ORENDORFF

Position: Graduate Student.
Email: david (dot) orendorff (at) uci (dot) edu.
Office: Bren Hall 4069
Address: Department of Computer Science, University of California, Irvine CA 92697.

I am a PhD candidate advised by Eric Mjolsness at the University of California, Irvine. In June 2008 I recieved my M.S. in computer science from UC Irvine. Previously I attended the University of Washington from 2002-2006 and majored in computer science and math with biological focus. There I worked on Computational Biology problems with Howard Chizeck during '04 and with Martin Tompa in '06. I've worked at the Institute for Systems Biology, Cogent Research Laboratories and UrbanSim. I served on the board of the UW Chess Club as well as participated in UCF, UW symphonic band (F-horn) and Unleashed A capella.

Outside Interests: Piano, outdoors, badminton, literature, cinema, photography. And for the masochist, here is my blog.

Teaching

Concepts in Programming Languages I. TA. Summer 2008.
Data Structures and Algorithms (CS III). Section 1 TA. Spring 2007.

Research/Projects

analysis of orthologous DNA in mammals using comparative genomics.
urban simulation (of Seattle specifically) using an agent based engine.
expanding Gillespie's Stochastic Simulation to efficiently simulate less restricted processes.
oligonucleotide synthesis using inkjet printers.

Current
Improving chemical master equation MCMC algorithms by using rejection sampling.

Programming Competitions

I enjoy participating in programming competitions during my free time. Team AllYourBayes with Drew Frank, Todd Johnson, Julien Neel and myself recently placed 3rd for task one in the 2008 UCSD data mining contest. Additionally, I enjoy the problems at Topcoder .

Papers/Publications

Eric Mjolsness, David Orendorff, Philippe Chatelain, and Petros Koumoutsakos. An Exact Accelerated Stochastic Simulation Algorithm. Journal of Chemical Physics 130, 144110 (2009). Webpage.
David Orendorff, Philippe Chatelain and Eric Mjolsness. High-accuracy R-leaping: Implementing and exploring a potentially exact method for accelerated stochastic simulation. ICSB Conference 2007. Abstract.
David Orendorff and Todd Johnson. First-Order Probabilistic Models for Predicting the Winners of Professional Basketball Games. Project paper.

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