Thomas E. Ferrin

Research Interests

My research involves the development of computational tools that will increase our understanding of living systems through our study of sequence-structure-function relationships. Of central importance is the collection, storage, analysis, prediction and visualization of biological data at widely different scales from atoms to supramolecular assemblies. The results of these endeavors include scientific advances through publication, innovative software, primary and derived data, new standards, and educational resources.

Research Summary

My research focus is on three key areas:

Sequence Analysis and Bioinformatics:
The characterization and interpretation of genomic data, including knowledge discovery and transfer in nucleic acid and protein sequence analysis

Pharmacogenomics - correlating variations in clinical response to drug therapy with genetic differences in individuals

Data mining - identifying gene and regulatory motifs, protein family/superfamily relationships, and gene expression patterns

Structural Informatics:
The development, application, and dissemination of analysis methodologies and tools in computational structural biology, including the development of suitable algorithms for the study and comparison of both low- and high-resolution structural models

Molecular visualization for structural analysis

Integration of sequence and tertiary macromolecular structural information

Functional Informatics:
Analyses of how protein structures deliver function, including the identification and characterization of protein superfamilies

The development of structurally contextual definitions of protein function

Application of systems biology principles for framing research hypotheses and results, including the network visualization of functional inferences and navigation between high-level context (e.g., pathways) and low-level detail (e.g., reaction mechanisms)

We encourage collaborative interdisciplinary research projects with scientists at UCSF, other academic institutions, and industry. Research is conducted by a diverse group whose backgrounds range from computer science to bioinformatics to structural biology and molecular biology.

Selected Publications

Y. Yoshikuni, T.E. Ferrin, and J.D. Keasling, Designed Divergent Evolution of Enzyme Function. Nature, 449(7087):1078-82, 2006.

S.C.-H. Pegg, S. Brown, S. Ojha, J. Seffernick, E.C. Meng, J.H. Morris, P.J. Chang, C.C. Huang, T. E. Ferrin, and P. C. Babbitt. Leveraging Enzyme Structure-Function Relationships for Functional Inference and Experimental Design: The Structure-Function Linkage Database. Biochemistry, 45(8):2545-2555, 2006. 

C.A. Harper, C.C. Huang, D. Stryke, M. Kawamoto, T.E. Ferrin, and P.C. Babbitt. Comparison of Methods for Genomic Localization of Gene Tag Sequences. BMC Genomics, 7:236, 2006.

E.C. Meng, E.F. Pettersen, G.S. Couch, C.C. Huang, and T.E. Ferrin. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics, 7:339, 2006. 

T.D. Goddard, C.C. Huang, and T.E. Ferrin. Visualizing density maps with UCSF Chimera. J. Struct. Bio., 157(1):281-287, 2007.