Thomas E. Ferrin, Ph.D.

Professor of Pharmaceutical Chemistry
and Biopharmaceutical Sciences
Chair, Biological and Medical Informatics Graduate Program
Director, Resource for Biocomputing, Visualization, and Informatics
and the UCSF Computer Graphics Laboratory

Address:

Resource for Biocomputing, Visualization, and Informatics (RBVI)
University of California, M/S 2240
600 16th Street, Rm N472
San Francisco, CA 94158-2517

Phone: 415-476-2299
Fax: 415-502-1755
Email: tef@cgl.ucsf.edu
Call sign: N6TEF (2m and 70cm)

Education/Affiliations:

• B.Sc. University of Minnesota, Electrical Engineering and Computer Science, 1971
• Ph.D. University of California, San Francisco, Medical Information Science, 1986
• Professor, Departments of Pharmaceutical Chemistry and Biopharmaceutical Sciences, UCSF
• Chair, UCSF Biological and Medical Informatics Graduate Program
• Member, UCSF/UCB Bioengineering Graduate Program
• Member, UCSF Biophysics Graduate Program
• Member, UCSF Chemistry and Chemical Biology Graduate Program
• Member, UCSF Pharmaceutical Sciences and Pharmacogenomics Graduate Program
• Member, California Institute for Quantitative Biosciences (QB3)
• Member, UCSF Cancer Center
• Past Member, National Library of Medicine Board of Scientific Counselors

Research Activities:

My research is focused on the development of computational tools that increase our understanding of living systems through our study of sequence-structure-function relationships. Of central importance are the collection, storage, analysis, prediction and visualization of biological data at widely different scales, from atoms to supramolecular assemblies. Results include scientific advances through publication (see below), dissemination of innovative software, deposition and web-based access of primary and derived data, new standards, and educational resources. My scientific interests fall in 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 (e.g. Chimera)
• 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.

Recent Awards:

• Academic Senate University Service Award for outstanding contributions to the UCSF network.

Selected Publications:

• D. Stryke, M. Kawamoto, C.C. Huang, S.J. Johns, L.A. King, C.A. Harper, E.C. Meng, R.E. Lee, L. L'Italien, P.T. Chuang, S.G. Young, W.C. Skarnes, P.C. Babbitt, and T.E. Ferrin, "BayGenomics: A Resource for Gene-Trapped Mouse Embryonic Stem Cells," Nucleic Acids Res., 31(1):278-281, 2003.
• D. Stryke, C.C. Huang, M. Kawamoto, S.J. Johns, E.J. Carlson, J.A. DeYoung, M.K. Leabman, I. Herkowitz, K.M. Giacomini, and T.E. Ferrin, "SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project," Pacific Symposium on Biocomputing 2003, R.B Altman, A.K Dunker, L. Hunter, T.A. Jung, and T.E Klein eds., pp. 535-547, World Scientific Publishing, 2003.
• A.I. Jewett, C.C. Huang, and T.E. Ferrin, "MINRMS: An Efficient Algorithm for Determining Protein Structure Similarity Using Root-Mean Squared-Distance," Bioinformatics, 19(5):625-634, 2003.
• M.K. Leabman, C.C. Huang, J. DeYoung, E.J. Carlson, T.R. Taylor, M. De La Cruz, S.J. Johns, D. Stryke, M. Kawamoto, T.J. Urban, D.L. Kroetz, T.E. Ferrin, A.G. Clark, N. Risch, I. Herskowitz, and K.M. Giacomini, Natural Variation in Human Membrane Transporter Genes Reveals Evolutionary and Functional Constraints, Proc. Natl. Acad. Sci. U S A, 100(10):5896-901, 2003.
• U. Pieper, N. Eswar, H. Braberg, M.S. Madhusudhan, F.P. Davis, A.C. Stuart, N. Mirkovic, A. Rossi, M.A. Marti-Renom, A. Fiser, B. Webb, D. Greenblatt, C.C. Huang, T.E. Ferrin, and A. Sali, MODBASE, A Database of Annotated Comparative Protein Structure Models, and Associated Resources, Nucleic Acids Res., 32(1):D217-D222, 2004.
• E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin, UCSF Chimera - A Visualization System for Exploratory Research and Analysis, J. Comp. Chem., 25(13):1605-1612, 2004. (Reprint available on request.)
• T.E. Ferrin, C.C. Huang, D.M. Greenblatt, D. Stryke, K.M. Giacomini, and J.H. Morris, Enhancing Data Sharing in Collaborative Research Projects with DASH, Pacific Symposium on Biocomputing 2005, pp. 260-271. Edited by R.B Altman et al., World Scientific Publishing, 2005.
• T.D. Goddard, C.C. Huang, and T.E. Ferrin, Software Extensions to UCSF Chimera for Interactive Visualization of Large Molecular Assemblies, Structure, 13(3):473-482, 2005. (Reprint available on request.)
• A.S. Nord, P.J. Chang, B.R. Conklin, A. Cox, C.A. Harper, G.G. Hicks, C.C. Huang, S.J. Johns, M. Kawamoto, S. Liu, E.C. Meng, J.H. Morris, J. Rossant, P. Ruiz, W.C. Skarnes, P. Soriano, W.L. Stanford, D. Stryke, H. von Melchner, W. Wurst, K. Yamamura, S.G. Young, P.C. Babbitt, and T.E. Ferrin, The International Gene Trap Consortium Website: A portal to all publicly available gene trap cell lines in mouse, Nucleic Acids Res., 34:D642-D648, 2006.
• Y. Yoshikuni, T.E. Ferrin, and J.D. Keasling, Designed Divergent Evolution of Enzyme Function, Nature, 440(7087):1078-1082, 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.
• G.S. Couch, D.K. Hendrix, and T.E. Ferrin, Nucleic Acid Visualization with UCSF Chimera, Nucleic Acids Res., 34(4):e29, 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.
• 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 trap sequences, BMC Genomics, 7:236, 2006.
• T.D. Goddard, C.C. Huang, and T.E. Ferrin, Visualizing density maps with UCSF chimera, J. Struct. Biol., 157(1):281-287, 2007.
• J.H. Morris, C.C. Huang, P.C. Babbitt, and T.E. Ferrin, structureViz: linking Cytoscape and UCSF Chimera, Bioinformatics, 23(17):2345-2347, 2007.
• T.D. Goddard and T.E. Ferrin, Visualization Software for Molecular Assemblies, Curr Opin Struct Biol., 17(5):587-595, 2007.

PubMed search of all publications authored by T.E. Ferrin, or do the same using Google Scholar.

Recent Invited Lectures and Seminars:

• "Visualizing BayGenomics Genetraps with Genome Browsers." Presented at the NHLBI Program for Genomic Applications Annual Coordinating Committee Meeting in San Francisco, CA on April 27, 2004.
• "Multiscale Structural Visualization with UCSF Chimera." Presented at the Single Particle Reconstructions and Visualization Workshop at the Baylor College of Medicine in Houston, TX on March 18, 2005.
• "Personal Data Privacy and Information Security in Today's Digital World." Presented at UCSF's Enterprise Information Security Symposium in San Francisco, CA on October 26, 2005.
• "Visualization Tools for Complex Biological Structures." Presented at the annual BBC (BMI, Biophysics, and CCB) Joint Graduate Program Retreat at Asilomar, CA on December 4, 2005.
• "Modeling GroEL" An 'Inside the Image' interview by Apple's Nancy Eaton, February 2007.
• "Visualizing Life: A Conversation with Tom Ferrin, PhD" A 'Science Café' interview by UCSF's Jeff Miller, August 10, 2007. Also available as a podcast.

My Earlier Years:

My UNIX kernel hacking days (circa late 70's and early 80's):

The Daemon, the GNU, and the Penguin: A History of Free and Open Source
BSD and the CSRG
CSRG Members, Supporters, and Contributors
Interactive computer graphics with the UNIX time-sharing system
Modifying the PDP-11/70 mfpi  instruction hardware and the Letter reprinted from ;login: that raised a few eyebrows
Heuristics for Disk Drive Positioning in 4.3BSD
25th Anniversary UNIX Playing Cards

The early days of molecular graphics (mid-to-late 1970's):

The first interactive color display of molecules

My drag racing days (circa 1967 through early 70's):

Ky Michaelson's AA/GD dragsters
The Snow Dragster
Hydrogen Peroxide Rocket Dragsters

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