Thomas E. Ferrin, PhD

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Thomas E. Ferrin, PhD

Professor in Residence, Department of Pharmaceutical Chemistry; and Director, Computer Graphics Laboratory, UCSF

tef@cgl.ucsf.edu

Phone: (415) 476-2299 (voice)
Box 0446, UCSF
San Francisco, CA 94143-0446

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Cancer Center Membership

Associate Member » Cancer Genetics

Research Summary

My research lab develops cutting-edge interactive software tools and advanced web-based computational resources that provide integrated visualizations and analyses of molecular structures and related non-structural biological information. Our tools can be applied to diverse types of biomolecular data, including atomic-resolution coordinates, 3D density maps and light microscopy data, and protein and nucleic acid sequences, annotations, and networks. We focus on unmet software needs for basic and applied biomedical research using highly trained and talented staff, with excellent interdisciplinary knowledge and specialized, state-of-the-art expertise in software engineering, computer graphics visualization, and data analysis. Our primary efforts are in the interactive visualization and analysis of structures of molecules and molecular assemblies, protein sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. These areas are critical for addressing important and highly relevant biomedical problems such as identifying the molecular bases of disease, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions.

I'm also the director of the Resource for Biocomputing, Visualization, and Informatics, an NIH Biomedical Technology Research Resource.

Education

University of Minnesota, B.S., 1971
University of California San Francisco, Ph.D., 1986, Med. Info. Science


Professional Experience

  • 1970-71
    Engineering Assistant, Biophysics Group, University of Minnesota
  • 1972-76
    Development Engineer, Cardiovascular Research Institute, UCSF
  • 1976-86
    Computer Facilities Manager, Computer Graphics Laboratory, UCSF
  • 1977-87
    Lecturer, School of Pharmacy, UCSF
  • 1986-93
    Director of Computing, Computer Graphics Laboratory, UCSF
  • 1987-89
    Adjunct Associate Professor, School of Pharmacy, UCSF
  • 1989-93
    Adjunct Professor, School of Pharmacy, UCSF
  • 1993-present
    Professor In-Residence, School of Pharmacy, and Director, Computer Graphics Laboratory, UCSF

Selected Publications

  1. Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015; 4:482.
    View on PubMed
  2. Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure. 2015 Jul 7; 23(7):1156-67.
    View on PubMed
  3. Hertig S, Goddard TD, Johnson GT, Ferrin TE. MDA Generates Models of Large Multidomain Proteins. Biophysical Journal. 2015; 108(9):2097-2102.
    View on PubMed
  4. Hertig S, Goddard TD, Johnson GT, Ferrin TE. Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophys J. 2015 May 5; 108(9):2097-102.
    View on PubMed
  5. Chen JE, Huang CC, Ferrin TE. RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Bioinformatics. 2015 May 1; 31(9):1484-6.
    View on PubMed
  6. Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE. cddApp: a Cytoscape app for accessing the NCBI conserved domain database. Bioinformatics. 2015 Jan 1; 31(1):134-6.
    View on PubMed
  7. Morris JH, Kuchinsky A, Ferrin TE, Pico AR. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147.
    View on PubMed
  8. Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE. setsApp: Set operations for Cytoscape Nodes and Edges. F1000Res. 2014; 3:149.
    View on PubMed
  9. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. Enhancing UCSF Chimera through web services. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W478-84.
    View on PubMed
  10. Akiva E, Brown S, Almonacid DE, Barber AE, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC. The Structure-Function Linkage Database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D521-30.
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  11. Chen L, Hong C, Chen EC, Yee SW, Xu L, Almof EU, Wen C, Fujii K, Johns SJ, Stryke D, Ferrin TE, Simko J, Chen X, Costello JF, Giacomini KM. Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3. Pharmacogenomics J. 2013 Apr; 13(2):110-20.
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  12. Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A. Macromolecular assembly structures by comparative modeling and electron microscopy. Methods Mol Biol. 2012; 857:331-50.
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  13. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics. 2011; 12:436.
    View on PubMed
  14. Choi JH, Yee SW, Ramirez AH, Morrissey KM, Jang GH, Joski PJ, Mefford JA, Hesselson SE, Schlessinger A, Jenkins G, Castro RA, Johns SJ, Stryke D, Sali A, Ferrin TE, Witte JS, Kwok PY, Roden DM, Wilke RA, McCarty CA, Davis RL, Giacomini KM. A common 5'-UTR variant in MATE2-K is associated with poor response to metformin. Clin Pharmacol Ther. 2011 Nov; 90(5):674-84.
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  15. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol. 2012 Sep; 179(3):269-78.
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  16. Kim MJ, Skewes-Cox P, Fukushima H, Hesselson S, Yee SW, Ramsey LB, Nguyen L, Eshragh JL, Castro RA, Wen CC, Stryke D, Johns SJ, Ferrin TE, Kwok PY, Relling MV, Giacomini KM, Kroetz DL, Ahituv N. Functional characterization of liver enhancers that regulate drug-associated transporters. Clin Pharmacol Ther. 2011 Apr; 89(4):571-8.
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  17. Apeltsin L, Morris JH, Babbitt PC, Ferrin TE. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics. 2011 Feb 1; 27(3):326-33.
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  18. Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2011 Jan; 39(Database issue):D465-74.
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  19. Chen L, Pawlikowski B, Schlessinger A, More SS, Stryke D, Johns SJ, Portman MA, Chen E, Ferrin TE, Sali A, Giacomini KM. Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin. Pharmacogenet Genomics. 2010 Nov; 20(11):687-99.
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  20. Bromberg S, Chiu W, Ferrin TE. Workshop on molecular animation. Structure. 2010 Oct 13; 18(10):1261-5.
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