Tom Ferrin, PhD

Professor
Department of Pharmaceutical Chemistry
[email protected]
Phone: +1 415 476-2299
600 16th St, Rm N472E
UCSF Box 2240
San Francisco, CA 94158
United States

Links

Resource for Biocomputing, Visualization, and Informatics UCSF Profiles

Affiliations

Joint appointments

Department of Bioengineering and Therapeutic Sciences

UCSF centers, institutes, and research programs

Director, Resource for Biocomputing, Visualization, and Informatics (RBVI)
Quantitative Biosciences Institute (QBI)

External affiliations

Scientific Advisory Panel, RCSB Protein Data Bank (PDB)

What I do

My lab develops software tool for visualizing and analyzing molecular structures at scales ranging from the atomic to the supramolecular.

Departmental research area

computational biology and chemistry

My research expertise

biological and medical informatics, biocomputing, visualization, informatics, pharmaceutical chemistry, bioengineering and therapeutic sciences

Professional background

Degrees

PhD, Med. Info. Science, University of California, San Francisco, 1986
BSc, Electrical Engineering and Computer Science, University of Minnesota, 1971

Biography

My research focuses on developing cutting-edge interactive software tools and advanced web-based computational resources that provide integrated visualization and analyses of molecular structures and related non-structural biological information. Our tools are applied daily to diverse types of biomolecular data, including atomic-resolution coordinates, 3D cryo-EM and X-ray density maps, light microscopy data sets, and protein and nucleic acid sequences, annotations, and networks. Our primary research efforts are in the interactive visualization and analysis of structures of molecules and molecular assemblies, protein sequence-structure 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 new drugs, and engineering proteins with new functions. For many years we have been disseminating well-documented and robust software tools via our web site so that scientists world-wide can advance their own research programs effectively. Our current software development efforts are focused on ChimeraX, our next-generation desktop app for the interactive visualization and analysis of molecular structures and related data.

Research keywords

  • Imaging, Three-Dimensional
  • Protein Databases
  • software
  • Molecular Conformation
  • Molecular Models
  • Chlamydia trachomatis
  • Sequence Alignment
  • Protein Sequence Analysis
  • computational biology
  • computer graphics
  • Organic Cation Transport Proteins
  • proteins
  • User-Computer Interface
  • Protein Conformation
  • Molecular Sequence Annotation

Publications

Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 2021 01; 30(1):70-82.
Dean D, Ziklo N, Somboonna N, Suh JH, Ferrin T. Reply to Rockey et al., "Genomics and Chlamydial Persistence In Vivo". mBio. 2019 12 17; 10(6).
Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure. 2019 12 03; 27(12):1745-1759.
Somboonna N, Ziklo N, Ferrin TE, Hyuk Suh J, Dean D. Clinical Persistence of Chlamydia trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional a��a Tetramer of the Tryptophan Synthase Operon. mBio. 2019 07 16; 10(4).
Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE. Molecular Visualization on the Holodeck. J Mol Biol. 2018 10 19; 430(21):3982-3996.
Fritz-Laylin LK, Riel-Mehan M, Chen BC, Lord SJ, Goddard TD, Ferrin TE, Nicholson-Dykstra SM, Higgs H, Johnson GT, Betzig E, Mullins RD. Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes. Elife. 2017 09 26; 6.
Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 2018 01; 27(1):14-25.
Knutson ST, Westwood BM, Leuthaeuser JB, Turner BE, Nguyendac D, Shea G, Kumar K, Hayden JD, Harper AF, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci. 2017 04; 26(4):677-699.
Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput Biol. 2017 02; 13(2):e1005284.
Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 01 01; 2017(1).
Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 Jan 01; 2017.
Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS. DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinformatics. 2016 Nov 11; 17(1):458.
Chhibber A, French CE, Yee SW, Gamazon ER, Theusch E, Qin X, Webb A, Papp AC, Wang A, Simmons CQ, Konkashbaev A, Chaudhry AS, Mitchel K, Stryke D, Ferrin TE, Weiss ST, Kroetz DL, Sadee W, Nickerson DA, Krauss RM, George AL, Schuetz EG, Medina MW, Cox NJ, Scherer SE, Giacomini KM, Brenner SE. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. Pharmacogenomics J. 2017 03; 17(2):137-145.
Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015; 4:482.
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, Gr?newald 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, Schr?der 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 07; 23(7):1156-67.
Hertig S, Goddard TD, Johnson GT, Ferrin TE. MDA Generates Models of Large Multidomain Proteins. Biophysical Journal. 2015; 108(9):2097-2102.
Hertig S, Goddard TD, Johnson GT, Ferrin TE. Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophys J. 2015 May 05; 108(9):2097-102.
Chen JE, Huang CC, Ferrin TE. RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Bioinformatics. 2015 May 01; 31(9):1484-6.
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 01; 31(1):134-6.
Morris JH, Kuchinsky A, Ferrin TE, Pico AR. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147.
Morris JH, Lotia S, Wu A, Doncheva NT, Albrecht M, Pico AR, Ferrin TE. setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges. F1000Res. 2014; 3:149.
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.
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.
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.
Lasker K, Vel?zquez-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.
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 Nov 09; 12:436.
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.
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.
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.
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 01; 27(3):326-33.
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, Sj?lander 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.
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.
Bromberg S, Chiu W, Ferrin TE. Workshop on molecular animation. Structure. 2010 Oct 13; 18(10):1261-5.
Shima JE, Komori T, Taylor TR, Stryke D, Kawamoto M, Johns SJ, Carlson EJ, Ferrin TE, Giacomini KM. Genetic variants of human organic anion transporter 4 demonstrate altered transport of endogenous substrates. Am J Physiol Renal Physiol. 2010 Oct; 299(4):F767-75.
Morris JH, Meng EC, Ferrin TE. Computational tools for the interactive exploration of proteomic and structural data. Mol Cell Proteomics. 2010 Aug; 9(8):1703-15.
Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A. Comparison of human solute carriers. Protein Sci. 2010 Mar; 19(3):412-28.
Ha Choi J, Wah Yee S, Kim MJ, Nguyen L, Ho Lee J, Kang JO, Hesselson S, Castro RA, Stryke D, Johns SJ, Kwok PY, Ferrin TE, Goo Lee M, Black BL, Ahituv N, Giacomini KM. Identification and characterization of novel polymorphisms in the basal promoter of the human transporter, MATE1. Pharmacogenet Genomics. 2009 Oct; 19(10):770-80.
Hesselson SE, Matsson P, Shima JE, Fukushima H, Yee SW, Kobayashi Y, Gow JM, Ha C, Ma B, Poon A, Johns SJ, Stryke D, Castro RA, Tahara H, Choi JH, Chen L, Picard N, Sjödin E, Roelofs MJ, Ferrin TE, Myers R, Kroetz DL, Kwok PY, Giacomini KM. Genetic variation in the proximal promoter of ABC and SLC superfamilies: liver and kidney specific expression and promoter activity predict variation. PLoS One. 2009 Sep 09; 4(9):e6942.
Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One. 2009; 4(2):e4345.
Chen Y, Teranishi K, Li S, Yee SW, Hesselson S, Stryke D, Johns SJ, Ferrin TE, Kwok P, Giacomini KM. Genetic variants in multidrug and toxic compound extrusion-1, hMATE1, alter transport function. Pharmacogenomics J. 2009 Apr; 9(2):127-36.
Tahara H, Yee SW, Urban TJ, Hesselson S, Castro RA, Kawamoto M, Stryke D, Johns SJ, Ferrin TE, Kwok PY, Giacomini KM. Functional genetic variation in the basal promoter of the organic cation/carnitine transporters OCTN1 (SLC22A4) and OCTN2 (SLC22A5). J Pharmacol Exp Ther. 2009 Apr; 329(1):262-71.
Yee SW, Shima JE, Hesselson S, Nguyen L, De Val S, Lafond RJ, Kawamoto M, Johns SJ, Stryke D, Kwok PY, Ferrin TE, Black BL, Gurwitz D, Ahituv N, Giacomini KM. Identification and characterization of proximal promoter polymorphisms in the human concentrative nucleoside transporter 2 (SLC28A2). J Pharmacol Exp Ther. 2009 Mar; 328(3):699-707.
Abla N, Chinn LW, Nakamura T, Liu L, Huang CC, Johns SJ, Kawamoto M, Stryke D, Taylor TR, Ferrin TE, Giacomini KM, Kroetz DL. The human multidrug resistance protein 4 (MRP4, ABCC4): functional analysis of a highly polymorphic gene. J Pharmacol Exp Ther. 2008 Jun; 325(3):859-68.
Urban TJ, Yang C, Lagpacan LL, Brown C, Castro RA, Taylor TR, Huang CC, Stryke D, Johns SJ, Kawamoto M, Carlson EJ, Ferrin TE, Burchard EG, Giacomini KM. Functional effects of protein sequence polymorphisms in the organic cation/ergothioneine transporter OCTN1 (SLC22A4). Pharmacogenet Genomics. 2007 Sep; 17(9):773-82.
Goddard TD, Ferrin TE. Visualization software for molecular assemblies. Curr Opin Struct Biol. 2007 Oct; 17(5):587-95.
Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt PC, Doniger SW, Skarnes WC, Young SG, Conklin BR. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS One. 2007 Jul 18; 2(7):e617.
Morris JH, Huang CC, Babbitt PC, Ferrin TE. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 01; 23(17):2345-7.
Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC. Comparison of methods for genomic localization of gene trap sequences. BMC Genomics. 2006 Sep 18; 7:236.
Urban TJ, Gallagher RC, Brown C, Castro RA, Lagpacan LL, Brett CM, Taylor TR, Carlson EJ, Ferrin TE, Burchard EG, Packman S, Giacomini KM. Functional genetic diversity in the high-affinity carnitine transporter OCTN2 (SLC22A5). Mol Pharmacol. 2006 Nov; 70(5):1602-11.
Goddard TD, Huang CC, Ferrin TE. Visualizing density maps with UCSF Chimera. J Struct Biol. 2007 Jan; 157(1):281-7.
Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics. 2006 Jul 12; 7:339.
Badagnani I, Castro RA, Taylor TR, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin TE, Carlson EJ, Burchard EG, Giacomini KM. Interaction of methotrexate with organic-anion transporting polypeptide 1A2 and its genetic variants. J Pharmacol Exp Ther. 2006 Aug; 318(2):521-9.
Nguyen TD, Gow JM, Chinn LW, Kelly L, Jeong H, Huang CC, Stryke D, Kawamoto M, Johns SJ, Carlson E, Taylor T, Ferrin TE, Sali A, Giacomini KM, Kroetz DL. PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network. Pharmacol Rev. 2006 Mar; 58(1):1-2.
Shu Y, Urban TJ, Leabman MK, Fujita T, Erdman AR, Lagpacan LL, Brown C, Castro RA, Huang CC, Stryke D, Kawamoto M, Johns SJ, Taylor TR, Chan W, De La Cruz M, Carlson EJ, Ferrin TE, Brett CM, Burchard EG, Herskowitz I, Kroetz DL, Giacomini KM. PharmGKB submission update: V. PMT submissions of genetic variation in SLC22 family transporters. Pharmacol Rev. 2006 Mar; 58(1):3-4.
Badagnani I, Sorani M, Edwards RH, Brown C, Castro RA, Huang CC, Stryke D, Kawamoto M, Johns SJ, Carlson EJ, Taylor T, Chan W, De La Cruz M, Ferrin TE, Burchard EG, Herskowitz I, Kroetz DL, Giacomini KM. PharmGKB submission update: VI. PMT submissions of genetic variations in neurotransmitter transporters (SLC6, SLC17, and SLC18) to the PharmGKB network. Pharmacol Rev. 2006 Mar; 58(1):5-6.
Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry. 2006 Feb 28; 45(8):2545-55.
Yoshikuni Y, Ferrin TE, Keasling JD. Designed divergent evolution of enzyme function. Nature. 2006 Apr 20; 440(7087):1078-82.
Couch GS, Hendrix DK, Ferrin TE. Nucleic acid visualization with UCSF Chimera. Nucleic Acids Res. 2006 Feb 14; 34(4):e29.
Yoshikuni Y, Martin VJ, Ferrin TE, Keasling JD. Engineering cotton (+)-delta-cadinene synthase to an altered function: germacrene D-4-ol synthase. Chem Biol. 2006 Jan; 13(1):91-8.
Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC, Soriano P, Stanford WL, Stryke D, von Melchner H, Wurst W, Yamamura K, Young SG, Babbitt PC, Ferrin TE. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D642-8.
Erdman AR, Mangravite LM, Urban TJ, Lagpacan LL, Castro RA, de la Cruz M, Chan W, Huang CC, Johns SJ, Kawamoto M, Stryke D, Taylor TR, Carlson EJ, Ferrin TE, Brett CM, Burchard EG, Giacomini KM. The human organic anion transporter 3 (OAT3; SLC22A8): genetic variation and functional genomics. Am J Physiol Renal Physiol. 2006 Apr; 290(4):F905-12.
Owen RP, Lagpacan LL, Taylor TR, De La Cruz M, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM. Functional characterization and haplotype analysis of polymorphisms in the human equilibrative nucleoside transporter, ENT2. Drug Metab Dispos. 2006 Jan; 34(1):12-5.
Fujita T, Brown C, Carlson EJ, Taylor T, de la Cruz M, Johns SJ, Stryke D, Kawamoto M, Fujita K, Castro R, Chen CW, Lin ET, Brett CM, Burchard EG, Ferrin TE, Huang CC, Leabman MK, Giacomini KM. Functional analysis of polymorphisms in the organic anion transporter, SLC22A6 (OAT1). Pharmacogenet Genomics. 2005 Apr; 15(4):201-9.
Goddard TD, Huang CC, Ferrin TE. Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure. 2005 Mar; 13(3):473-82.
Owen RP, Gray JH, Taylor TR, Carlson EJ, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM. Genetic analysis and functional characterization of polymorphisms in the human concentrative nucleoside transporter, CNT2. Pharmacogenet Genomics. 2005 Feb; 15(2):83-90.
Ferrin TE, Huang CC, Greenblatt DM, Stryke D, Giacomini KM, Morris JH. Enhancing data sharing in collaborative research projects with DASH. Pac Symp Biocomput. 2005; 260-71.
Badagnani I, Chan W, Castro RA, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin TE, Carlson EJ, Burchard EG, Giacomini KM. Functional analysis of genetic variants in the human concentrative nucleoside transporter 3 (CNT3; SLC28A3). Pharmacogenomics J. 2005; 5(3):157-65.
Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac Symp Biocomput. 2005; 358-69.
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 Oct; 25(13):1605-12.
Shu Y, Leabman MK, Feng B, Mangravite LM, Huang CC, Stryke D, Kawamoto M, Johns SJ, DeYoung J, Carlson E, Ferrin TE, Herskowitz I, Giacomini KM. PharmGKB update: III. Genetic variants of SLC22A1, solute carrier family 22 (organic cation transporter), member 1. Pharmacol Rev. 2004 Jun; 56(2):161.
Gray JH, Mangravite LM, Owen RP, Urban TJ, Chan W, Carlson EJ, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM. Functional and genetic diversity in the concentrative nucleoside transporter, CNT1, in human populations. Mol Pharmacol. 2004 Mar; 65(3):512-9.
Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D217-22.
Kroetz DL, Pauli-Magnus C, Hodges LM, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, DeYoung J, Taylor T, Carlson EJ, Herskowitz I, Giacomini KM, Clark AG, Pharmacogenetics of Membrane Transporters Investigators. Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene. Pharmacogenetics. 2003 Aug; 13(8):481-94.
Leabman MK, Huang CC, Stryke D, Johns SJ, Kawamoto M, Ferrin TE, DeYoung J, Taylor TR, De La Cruz M, Herskowitz I, Giacomini KM. PharmGKB update: I. Genetic variants of the organic cation transporter 2 (OCT2, SLC22A2). Pharmacol Rev. 2003 Sep; 55(3):399.
Osato DH, Huang CC, Kawamoto M, Johns SJ, Stryke D, Wang J, Ferrin TE, Herskowitz I, Giacomini KM. Functional characterization in yeast of genetic variants in the human equilibrative nucleoside transporter, ENT1. Pharmacogenetics. 2003 May; 13(5):297-301.
Shu Y, Leabman MK, Feng B, Mangravite LM, Huang CC, Stryke D, Kawamoto M, Johns SJ, DeYoung J, Carlson E, Ferrin TE, Herskowitz I, Giacomini KM, Pharmacogenetics Of Membrane Transporters Investigators. Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1. Proc Natl Acad Sci U S A. 2003 May 13; 100(10):5902-7.
Leabman MK, Huang CC, DeYoung J, Carlson EJ, Taylor TR, de la Cruz M, Johns SJ, Stryke D, Kawamoto M, Urban TJ, Kroetz DL, Ferrin TE, Clark AG, Risch N, Herskowitz I, Giacomini KM, Pharmacogenetics Of Membrane Transporters Investigators. Natural variation in human membrane transporter genes reveals evolutionary and functional constraints. Proc Natl Acad Sci U S A. 2003 May 13; 100(10):5896-901.
Jewett AI, Huang CC, Ferrin TE. MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinformatics. 2003 Mar 22; 19(5):625-34.
Stryke D, Kawamoto M, Huang CC, Johns SJ, King LA, Harper CA, Meng EC, Lee RE, Yee A, L'Italien L, Chuang PT, Young SG, Skarnes WC, Babbitt PC, Ferrin TE. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res. 2003 Jan 01; 31(1):278-81.
Stryke D, Huang CC, Kawamoto M, Johns SJ, Carlson EJ, Deyoung JA, Leabman MK, Herskowitz I, Giacomini KM, Ferrin TE. SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project. Pac Symp Biocomput. 2003; 535-47.
Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC. The Structure Superposition Database. Nucleic Acids Res. 2003 Jan 01; 31(1):505-10.
Leabman MK, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, DeYoung J, Taylor T, Clark AG, Herskowitz I, Giacomini KM, Pharmacogenetics of Membrane Transporters Investigators. Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics. 2002 Jul; 12(5):395-405.
Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin TE, Klein TE. Integrated tools for structural and sequence alignment and analysis. Pac Symp Biocomput. 2000; 230-41.
Kraemer ET, Ferrin TE. Molecules to maps: tools for visualization and interaction in support of computational biology. Bioinformatics. 1998; 14(9):764-71.
Huang CC, Couch GS, Pettersen EF, Ferrin TE, Howard AE, Klein TE. The object technology framework: an object-oriented interface to molecular data and its application to collagen. Pac Symp Biocomput. 1998; 349-61.
Couch GS, Pettersen EF, Huang CC, Ferrin TE. Annotating PDB files with scene information. J Mol Graph. 1995 Jun; 13(3):153-8, 193.
Lewis RA, Roe DC, Huang C, Ferrin TE, Langridge R, Kuntz ID. Automated site-directed drug design using molecular lattices. J Mol Graph. 1992 Jun; 10(2):66-78, 106.
Huang CC, Pettersen EF, Klein TE, Ferrin TE, Langridge R. Conic: a fast renderer for space-filling molecules with shadows. J Mol Graph. 1991 Dec; 9(4):230-6, 242.
Heimstad E, Edvardsen O, Ferrin TE, Dahl SG. Molecular structure and dynamics of tricyclic antidepressant drugs. Eur Neuropsychopharmacol. 1991 May; 1(2):127-37.
Ferrin TE, Couch GS, Huang CC, Pettersen EF, Langridge R. An affordable approach to interactive desktop molecular modeling. J Mol Graph. 1991 Mar; 9(1):27-32, 37-8.
Klein TE, Huang CC, Pettersen EF, Couch GS, Ferrin TE, Langridge R. A real-time malleable molecular surface. J Mol Graph. 1990 Mar; 8(1):16-24, 26.
Bash PA, Pattabiraman N, Huang C, Ferrin TE, Langridge R. Van der waals surfaces in molecular modeling: implementation with real-time computer graphics. Science. 1983 Dec 23; 222(4630):1325-7.
Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol. 1982 Oct 25; 161(2):269-88.
Blaney JM, Jorgensen EC, Connolly ML, Ferrin TE, Langridge R, Oatley SJ, Burridge JM, Blake CC. Computer graphics in drug design: molecular modeling of thyroid hormone-prealbumin interactions. J Med Chem. 1982 Jul; 25(7):785-90.
Langridge R, Ferrin TE, Kuntz ID, Connolly ML. Real-time color graphics in studies of molecular interactions. Science. 1981 Feb 13; 211(4483):661-6.