Performed statistical analyses of data from a novel single-molecule DNA sequencer. Created model of the statistical mechanics of the action of RNA polymerase on DNA. Developed image analysis algorithms to track motion of nano-scale beads. Derived a model for the binding of RNA polymerase to promoters, based on a synthesis of published research.

Developed algorithms and software for core signal processing and primary data analysis of Ion Torrent PGM and Proton DNA sequencers. Contributed to pipeline components for base calling, read filtering, and adapter trimming, achieving major improvements in speed, accuracy and throughput. Provided data analysis and software support to biochemistry and chip teams.

Developed algorithm and software for finding all loci identical by descent over all pairs of individuals in a large set of Illumina SNP-chip genotypes. Achieved 20-fold speed increase over previous implementation. Developed algorithms and software for SNP calling at single-copy loci.

Developed theory and algorithms for analysis of ChIP-seq and SELEX data sets. Performed detailed analysis of relationship between primary sequence and nucleosome distribution in Saccharomyces and Drosophila. Developed combinatorial algorithms and code for design of in vitro binding assays. Worked closely with biochemists to develop and troubleshoot experimental protocols.

Developed algorithms and software for an open source genome assembly suite, including vector trimming, re-assembly, overlap detection, repeat resolution, alignment and consensus.

Technical Lead for development of DVD formatting engine. This engine is the primary technology asset of Sonic Solutions, and is currently licensed by Adobe and Microsoft.

Implemented linear algebra package to correct positioning errors in stage mechanism of a scanning electron microscope.

Ported proprietary image compression library from Windows to Mac OS. Library was licensed by America Online and Apple Computer.

Developed device control software for a scanning electron microscope. Extensive use of STL and RAII.

Designed and implemented real-time, dual-processor code integrating telephony, telephone speech recognition, speech synthesis and desktop sound I/O. Extensive use of interrupt-level processing, asynchronous I/O and DSP assembly language programming.

Developed multi-threaded unit tests for inter-process communication. Developed yacc-based interpreter for a test specification language. The interpreter automatically generated large tables that previously required tedious manual coding.

Designed and developed C++ template container class library.