Richard Hughey's research has focussed on two areas: high-performance VLSI computer architecture and biological sequence analysis. The Kestrel programmable sequence analysis accelerator was a single-board parallel processor designed to speed biological sequence analysis for Smith & Waterman searchin, HMMs, conformational chemistry, graph coloring, and other areas. Hughey, Dr. Anders Krogh, Professors Haussler and Karplus, and UC Santa Cruz student researchers developed developed the Sequence Analysis and Modeling (SAM) software suite. SAM is a a collection of algorithms and software used to create statistical models of RNA, DNA, and protein families with profile hidden Markov models. Dr. Hughey has been active in program development, including the UC Santa Cruz Bioinformatics and Bioengineering programs. He is presently Vice Provost and Dean of Undergraduate Education at UC Santa Cruz.
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