Temple F. Smith, Ph.D.

Director, BMERC/Professor

B.S.    Purdue University
Ph.D.   University of Colorado

My research is centered on the application of various computer science and mathematical methods to the discovery of the syntactic and semantic patterns in nucleic acid and amino acid sequences. There have been particular focuses on identifying patterns associated with various evolutionary processes, protein domain structure and catalysis. These have resulted in the time calibration of HIV and Papilloma viral evolution, the development of new approaches to include large-scale genome duplication in evolutionary studies, and in the development of detailed mathematical models (Hidden Markov random fields) for the three-dimensional structure of protein domain cores.

In addition, I have been involved in developing database structures for large-scale sequencing and analysis.

Finally, there has been a major effort toward developing database structures suitable for complete genome functional analysis, including new Internet Web page interfaces.

As the Director of the Biomolecular Engineering Research Center, I work closely with many Boston area experimental molecular biologists in supportive and exploratory data analysis.

BMERC web site

Representative Publications

  1. Smith, Temple F. The art of matchmaking: sequence alignment methods and their structural implications. 1999. Structures 7 (1): R7-R12.
  2. Smith Temple F., Gaitatzes, Chrysanthe, Saxena, Kumkum and Neer, Eva J. 1999. The WD-repeat: A common architecture for diverse functions. Trend in the Biochemical Sciences 24(5): 181-185.
  3. Bienkowska, Jadwiga, Yu, Lihua, Zarakhovich, Sophia, Rogers, Robeert G. Jr. and Smith, Temple F. 2000. Protein fold recognition by total alignment probability. Proteins 40(3): 451-462.
  4. Das, Sudeshna and Smith, Temple F. 2000. Identifying nature’s Lego set. In Advances in Protein Chemistry, Vol 54, “Analysis of Amino Acid Sequences”, Peer Bork, ed: 159-183.
  5. Yu, Lihua, Gaitatzes, Chrysanthe, Neer, Eva, and Smith, Temple F. 2000. Thirty-plus functional families from a single motif. Protein Science 9: 2470-2476.

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Primary teaching affiliate
of BU School of Medicine