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Thomas Ferrin, PhD

TitleProfessor
SchoolUCSF School of Pharmacy
DepartmentPharmaceutical Chemistry
Address600 16th St
San Francisco CA 94158
Phone415-476-2299
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    Collapse Biography 
    Collapse Education and Training
    University of California, San FranciscoPh.D.1987 Graduate Division (Biomedical Informatics)
    University of MinnesotaB.S., Electrical Engineering and Computer Science1971Institute of Technology
    Collapse Awards and Honors
    1980Recognition by UC President David S. Saxon for the accomplishments and research conducted by CGL
    1998Academic Senate University Service Award for outstanding contributions to the UCSF data network

    Collapse Overview 
    Collapse Overview
    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.


    Collapse Research 
    Collapse Research Activities and Funding
    Pharmacogenomics of Membrane Transporters
    NIH U19GM061390Apr 1, 2000 - Jun 30, 2015
    Role: Co-Investigator
    Resource for Biocomputing Visualization and Informatics
    NIH/NIGMS P41GM103311Jul 15, 1997 - May 31, 2017
    Role: Principal Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Knutson ST, Westwood BM, Leuthaeuser JB, Turner B, Nguyendac D, Shea G, Kumar K, Hayden J, Harper A, Brown SD, Morris JH, Ferrin T, 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 Jan 05. PMID: 28054422.
      View in: PubMed
    2. Leuthaeuser JB, Morris JH, Harper AF, Ferrin T, Babbitt PC, Fetrow JS. DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinformatics. 2016 Nov 11; 17(1):458. PMID: 27835946.
      View in: PubMed
    3. 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 T, 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. 2016 Feb 9. PMID: 26856248.
      View in: PubMed
    4. Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin T. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015; 4:482. PMID: 26937268.
      View in: PubMed
    5. 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 T, 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. PMID: 26095030.
      View in: PubMed
    6. Hertig S, Goddard TD, Johnson GT, Ferrin T . MDA Generates Models of Large Multidomain Proteins. Biophysical Journal. 2015; 108(9):2097-2102.
    7. Hertig S, Goddard TD, Johnson GT, Ferrin T. Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophys J. 2015 May 5; 108(9):2097-102. PMID: 25954868; PMCID: PMC4423039 [Available on 05/05/16].
    8. Chen JE, Huang CC, Ferrin T. RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Bioinformatics. 2015 May 1; 31(9):1484-6. PMID: 25540183; PMCID: PMC4410660 [Available on 05/01/16].
    9. Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin T. cddApp: a Cytoscape app for accessing the NCBI conserved domain database. Bioinformatics. 2015 Jan 1; 31(1):134-6. PMID: 25212755; PMCID: PMC4271147 [Available on 01/01/16].
    10. Morris JH, Kuchinsky A, Ferrin T, Pico AR. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147. PMID: 25285206; PMCID: PMC4176421.
    11. Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin T. setsApp: Set operations for Cytoscape Nodes and Edges. F1000Res. 2014; 3:149. PMID: 25352980; PMCID: PMC4207244.
    12. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin T. Enhancing UCSF Chimera through web services. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W478-84. PMID: 24861624; PMCID: PMC4086125.
    13. 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 T, Holliday GL, Babbitt PC. The Structure-Function Linkage Database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D521-30. PMID: 24271399; PMCID: PMC3965090.
    14. Chen L, Hong C, Chen EC, Yee SW, Xu L, Almof EU, Wen C, Fujii K, Johns SJ, Stryke D, Ferrin T, 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. PMID: 22231567; PMCID: PMC3396779.
    15. Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin T, Sali A. Macromolecular assembly structures by comparative modeling and electron microscopy. Methods Mol Biol. 2012; 857:331-50. PMID: 22323229.
      View in: PubMed
    16. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin T. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics. 2011; 12:436. PMID: 22070249; PMCID: PMC3262844.
    17. 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 T, 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. PMID: 21956618; PMCID: PMC3329222.
    18. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin T. UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol. 2012 Sep; 179(3):269-78. PMID: 21963794; PMCID: PMC3410985.
    19. 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 T, 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. PMID: 21368754; PMCID: PMC3227682.
    20. Apeltsin L, Morris JH, Babbitt PC, Ferrin T. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics. 2011 Feb 1; 27(3):326-33. PMID: 21118823; PMCID: PMC3031030.
    21. 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 T, 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. PMID: 21097780; PMCID: PMC3013688.
    22. Chen L, Pawlikowski B, Schlessinger A, More SS, Stryke D, Johns SJ, Portman MA, Chen E, Ferrin T, 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. PMID: 20859243; PMCID: PMC2976715.
    23. Bromberg S, Chiu W, Ferrin T. Workshop on molecular animation. Structure. 2010 Oct 13; 18(10):1261-5. PMID: 20947014; PMCID: PMC3071847.
    24. Shima JE, Komori T, Taylor TR, Stryke D, Kawamoto M, Johns SJ, Carlson EJ, Ferrin T, 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. PMID: 20668102; PMCID: PMC2957254.
    25. Morris JH, Meng EC, Ferrin T. Computational tools for the interactive exploration of proteomic and structural data. Mol Cell Proteomics. 2010 Aug; 9(8):1703-15. PMID: 20525940; PMCID: PMC2938059.
    26. Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin T, Giacomini KM, Sali A. Comparison of human solute carriers. Protein Sci. 2010 Mar; 19(3):412-28. PMID: 20052679; PMCID: PMC2866268.
    27. 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 T, 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. PMID: 19745787; PMCID: PMC2976711.
    28. 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 T, 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; 4(9):e6942. PMID: 19742321; PMCID: PMC2735003.
    29. Atkinson HJ, Morris JH, Ferrin T, Babbitt PC. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One. 2009; 4(2):e4345. PMID: 19190775; PMCID: PMC2631154.
    30. Chen Y, Teranishi K, Li S, Yee SW, Hesselson S, Stryke D, Johns SJ, Ferrin T, 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. PMID: 19172157; PMCID: PMC2949062.
    31. Tahara H, Yee SW, Urban TJ, Hesselson S, Castro RA, Kawamoto M, Stryke D, Johns SJ, Ferrin T, 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. PMID: 19141711; PMCID: PMC2670604.
    32. Yee SW, Shima JE, Hesselson S, Nguyen L, De Val S, Lafond RJ, Kawamoto M, Johns SJ, Stryke D, Kwok PY, Ferrin T, 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. PMID: 19098160; PMCID: PMC2682268.
    33. Abla N, Chinn LW, Nakamura T, Liu L, Huang CC, Johns SJ, Kawamoto M, Stryke D, Taylor TR, Ferrin T, 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. PMID: 18364470; PMCID: PMC2612728.
    34. Urban TJ, Yang C, Lagpacan LL, Brown C, Castro RA, Taylor TR, Huang CC, Stryke D, Johns SJ, Kawamoto M, Carlson EJ, Ferrin T, 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. PMID: 17700366.
      View in: PubMed
    35. Goddard TD, Ferrin T. Visualization software for molecular assemblies. Curr Opin Struct Biol. 2007 Oct; 17(5):587-95. PMID: 17728125; PMCID: PMC2174518.
    36. Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin T, 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; 2(7):e617. PMID: 17637833; PMCID: PMC1910612.
    37. Morris JH, Huang CC, Babbitt PC, Ferrin T. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 1; 23(17):2345-7. PMID: 17623706.
      View in: PubMed
    38. Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin T, Babbitt PC. Comparison of methods for genomic localization of gene trap sequences. BMC Genomics. 2006; 7:236. PMID: 16982004; PMCID: PMC1617135.
    39. Urban TJ, Gallagher RC, Brown C, Castro RA, Lagpacan LL, Brett CM, Taylor TR, Carlson EJ, Ferrin T, 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. PMID: 16931768.
      View in: PubMed
    40. Goddard TD, Huang CC, Ferrin T. Visualizing density maps with UCSF Chimera. J Struct Biol. 2007 Jan; 157(1):281-7. PMID: 16963278.
      View in: PubMed
    41. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin T. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics. 2006; 7:339. PMID: 16836757; PMCID: PMC1570152.
    42. Badagnani I, Castro RA, Taylor TR, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin T, 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. PMID: 16702441.
      View in: PubMed
    43. 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 T, 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. PMID: 16507879.
      View in: PubMed
    44. 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 T, 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. PMID: 16507878.
      View in: PubMed
    45. Nguyen TD, Gow JM, Chinn LW, Kelly L, Jeong H, Huang CC, Stryke D, Kawamoto M, Johns SJ, Carlson E, Taylor T, Ferrin T, 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. PMID: 16507877.
      View in: PubMed
    46. Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin T, 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. PMID: 16489747.
      View in: PubMed
    47. Yoshikuni Y, Ferrin T, Keasling JD. Designed divergent evolution of enzyme function. Nature. 2006 Apr 20; 440(7087):1078-82. PMID: 16495946.
      View in: PubMed
    48. Couch GS, Hendrix DK, Ferrin T. Nucleic acid visualization with UCSF Chimera. Nucleic Acids Res. 2006; 34(4):e29. PMID: 16478715; PMCID: PMC1368656.
    49. Yoshikuni Y, Martin VJ, Ferrin T, Keasling JD. Engineering cotton (+)-delta-cadinene synthase to an altered function: germacrene D-4-ol synthase. Chem Biol. 2006 Jan; 13(1):91-8. PMID: 16426975.
      View in: PubMed
    50. 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 T. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D642-8. PMID: 16381950; PMCID: PMC1347459.
    51. 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 T, 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. PMID: 16291576.
      View in: PubMed
    52. Owen RP, Lagpacan LL, Taylor TR, De La Cruz M, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin T, 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. PMID: 16214850.
      View in: PubMed
    53. 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 T, 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. PMID: 15864112.
      View in: PubMed
    54. Goddard TD, Huang CC, Ferrin T. Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure. 2005 Mar; 13(3):473-82. PMID: 15766548.
      View in: PubMed
    55. Owen RP, Gray JH, Taylor TR, Carlson EJ, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin T, Giacomini KM. Genetic analysis and functional characterization of polymorphisms in the human concentrative nucleoside transporter, CNT2. Pharmacogenet Genomics. 2005 Feb; 15(2):83-90. PMID: 15861032.
      View in: PubMed
    56. Ferrin T, 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. PMID: 15759632.
      View in: PubMed
    57. Pegg SC, Brown S, Ojha S, Huang CC, Ferrin T, Babbitt PC. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac Symp Biocomput. 2005; 358-69. PMID: 15759641.
      View in: PubMed
    58. Badagnani I, Chan W, Castro RA, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin T, 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. PMID: 15738947.
      View in: PubMed
    59. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin T. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 Oct; 25(13):1605-12. PMID: 15264254.
      View in: PubMed
    60. Shu Y, Leabman MK, Feng B, Mangravite LM, Huang CC, Stryke D, Kawamoto M, Johns SJ, DeYoung J, Carlson E, Ferrin T, 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. PMID: 15169925.
      View in: PubMed
    61. Gray JH, Mangravite LM, Owen RP, Urban TJ, Chan W, Carlson EJ, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin T, Giacomini KM. Functional and genetic diversity in the concentrative nucleoside transporter, CNT1, in human populations. Mol Pharmacol. 2004 Mar; 65(3):512-9. PMID: 14978229.
      View in: PubMed
    62. 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 T, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D217-22. PMID: 14681398; PMCID: PMC308829.
    63. Kroetz DL, Pauli-Magnus C, Hodges LM, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin T, DeYoung J, Taylor T, Carlson EJ, Herskowitz I, Giacomini KM, Clark AG. Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene. Pharmacogenetics. 2003 Aug; 13(8):481-94. PMID: 12893986.
      View in: PubMed
    64. Leabman MK, Huang CC, Stryke D, Johns SJ, Kawamoto M, Ferrin T, 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. PMID: 12869664.
      View in: PubMed
    65. Osato DH, Huang CC, Kawamoto M, Johns SJ, Stryke D, Wang J, Ferrin T, 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. PMID: 12724623.
      View in: PubMed
    66. Shu Y, Leabman MK, Feng B, Mangravite LM, Huang CC, Stryke D, Kawamoto M, Johns SJ, DeYoung J, Carlson E, Ferrin T, Herskowitz I, Giacomini KM. 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. PMID: 12719534; PMCID: PMC156299.
    67. 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 T, Clark AG, Risch N, Herskowitz I, Giacomini KM. 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. PMID: 12719533; PMCID: PMC156298.
    68. Jewett AI, Huang CC, Ferrin T. MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinformatics. 2003 Mar 22; 19(5):625-34. PMID: 12651721.
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    69. Stryke D, Huang CC, Kawamoto M, Johns SJ, Carlson EJ, Deyoung JA, Leabman MK, Herskowitz I, Giacomini KM, Ferrin T. SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project. Pac Symp Biocomput. 2003; 535-47. PMID: 12603056.
      View in: PubMed
    70. 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 T. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res. 2003 Jan 1; 31(1):278-81. PMID: 12520002; PMCID: PMC165511.
    71. Chiang RA, Meng EC, Huang CC, Ferrin T, Babbitt PC. The Structure Superposition Database. Nucleic Acids Res. 2003 Jan 1; 31(1):505-10. PMID: 12520064; PMCID: PMC165574.
    72. Leabman MK, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin T, DeYoung J, Taylor T, Clark AG, Herskowitz I, Giacomini KM. Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics. 2002 Jul; 12(5):395-405. PMID: 12142729.
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    73. Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin T, Klein TE. Integrated tools for structural and sequence alignment and analysis. Pac Symp Biocomput. 2000; 230-41. PMID: 10902172.
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    74. Huang CC, Couch GS, Pettersen EF, Ferrin T, 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. PMID: 9697195.
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    75. Kraemer ET, Ferrin T. Molecules to maps: tools for visualization and interaction in support of computational biology. Bioinformatics. 1998; 14(9):764-71. PMID: 9918946.
      View in: PubMed
    76. Couch GS, Pettersen EF, Huang CC, Ferrin T. Annotating PDB files with scene information. J Mol Graph. 1995 Jun; 13(3):153-8, 193. PMID: 7577842.
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    77. Lewis RA, Roe DC, Huang C, Ferrin T, Langridge R, Kuntz ID. Automated site-directed drug design using molecular lattices. J Mol Graph. 1992 Jun; 10(2):66-78, 106. PMID: 1637751.
      View in: PubMed
    78. Huang CC, Pettersen EF, Klein TE, Ferrin T, Langridge R. Conic: a fast renderer for space-filling molecules with shadows. J Mol Graph. 1991 Dec; 9(4):230-6, 242. PMID: 1772848.
      View in: PubMed
    79. Heimstad E, Edvardsen O, Ferrin T, Dahl SG. Molecular structure and dynamics of tricyclic antidepressant drugs. Eur Neuropsychopharmacol. 1991 May; 1(2):127-37. PMID: 1821702.
      View in: PubMed
    80. Ferrin T, 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. PMID: 1902113.
      View in: PubMed
    81. Klein TE, Huang CC, Pettersen EF, Couch GS, Ferrin T, Langridge R. A real-time malleable molecular surface. J Mol Graph. 1990 Mar; 8(1):16-24, 26. PMID: 2268622.
      View in: PubMed
    82. Bash PA, Pattabiraman N, Huang C, Ferrin T, Langridge R. Van der waals surfaces in molecular modeling: implementation with real-time computer graphics. Science. 1983 Dec 23; 222(4630):1325-7. PMID: 17773334.
      View in: PubMed
    83. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin T. A geometric approach to macromolecule-ligand interactions. J Mol Biol. 1982 Oct 25; 161(2):269-88. PMID: 7154081.
      View in: PubMed
    84. Blaney JM, Jorgensen EC, Connolly ML, Ferrin T, 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. PMID: 7108895.
      View in: PubMed
    85. Langridge R, Ferrin T, Kuntz ID, Connolly ML. Real-time color graphics in studies of molecular interactions. Science. 1981 Feb 13; 211(4483):661-6. PMID: 7455704.
      View in: PubMed
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