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Graham Johnson, PhD

TitleAssistant Researcher
SchoolUCSF School of Pharmacy
DepartmentBioengineering
Address600 16th St
San Francisco CA 94158
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    Collapse Biography 
    Collapse awards and honors
    Los Alamos Labs, University of New Mexico2012Artist in Residence, The Art of Systems Biology & NanoScience
    VIZBI annual meeting, vizbi.org2012NVIDIA Best Poster Award
    National Science Foundation & Science Magazine20111st place video, NSF Science & Engineering Visualization Challenge
    National Science Foundation & Science Magazine20051st place image, NSF Science & Engineering Visualization Challenge
    National Science Foundation2006 - 2009NSF Predoctoral Fellowship
    ASCB Cell Dance20071st place Image
    ASCB Cell Dance20072nd place Animation
    Association of Medical Illustrators2010Award of Merit
    National Science Foundation & Science Magazine2007Runner Up Video, NSF Science & Engineering Visualization Challenge
    Association of Medical Illustrators2005Certificate of Merit Illustration
    Association of Medical Illustrators2002Award of Excellence, Cell Biology textbook
    Johns Hopkins School of Medicine1997Annette Burgess Award, Ophthalmological Illustration

    Collapse Overview 
    Collapse overview
    The Johnson Lab focuses primarily on developing algorithms to enable scientists to generate, simulate, and visualize molecular models of cells, namely a software called autoPACK/cellPACK. We continue to work with Ludovic Autin to develop ePMV in extended collaboration with Arthur Olson's lab at Scripps and on other uPy related projects. This summer we have engaged in a google summer of code project called sigViz with other UCSF and Gladstone researchers to generate cell signaling network flux simulators.

    The Johnson lab also develops outreach software that enables scientists and illustrators to interoperate the computational tools of science and art and works closely on these fronts with Tom Ferrin's Computer Graphics Lab (CGL) at UCSF as a Resource for Biocomputing, and Visualization, and Informatics (RBVI) collaborator, and with the Molecular Graphics Lab (MGL) at The Scripps Research Institute as a former National Biomedical Computational Resource (NBCR) member and current collaborator.


    Collapse Research 
    Collapse research activities and funding
    PGRN Administrative Coordination Hub, ACH (PGRN)
    NIH/NIGMS U24GM115370Jul 15, 2015 - Jun 30, 2020
    Role: Co-Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse Featured Videos

    Collapse Bibliographic 
    Collapse selected 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.
    List All   |   Timeline
    1. Bhabha G, Johnson GT, Schroeder CM, Vale RD. How Dynein Moves Along Microtubules. Trends Biochem Sci. 2016 Jan; 41(1):94-105. PMID: 26678005.
      View in: PubMed
    2. 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. PMID: 25954868; PMCID: PMC4423039 [Available on 05/05/16].
    3. Johnson GT, Autin L, Al-Alusi M, Goodsell DS, Sanner MF, Olson AJ. cellPACK: a virtual mesoscope to model and visualize structural systems biology. Nat Methods. 2015 Jan; 12(1):85-91. PMID: 25437435; PMCID: PMC4281296.
    4. Johnson GT, Goodsell DS, Autin L, Forli S, Sanner MF, Olson AJ. 3D molecular models of whole HIV-1 virions generated with cellPACK. Faraday Discuss. 2014; 169:23-44. PMID: 25253262; PMCID: PMC4569901.
    5. Johnson GT, Hertig S. A guide to the visual analysis and communication of biomolecular structural data. Nat Rev Mol Cell Biol. 2014 Oct; 15(10):690-8. PMID: 25245078.
      View in: PubMed
    6. Ludovic Autin, Graham Johnson, Johan Hake, Arthur Olson, Michel Sanner, "uPy: A Ubiquitous CG Python API with Biological-Modeling Applications," IEEE Computer Graphics and Applications, vol. 32, no. 5, pp. 50-61, Sept.-Oct., 2012 . IEEE Computer Graphics and Applications. uPy: A Ubiquitous CG Python API with Biological-Modeling Applications. 2012; 32(5):50-61.
    7. Autin L, Johnson G, Sanner M, Olson A. Ubiquitous Python API (uPy). 2012.
    8. Johnson, G. AMI Newsletter. autoPACK Visualization Challenge2012: present HIV in Blood Plasma. 2012.
    9. Graham T. Johnson. Automated modeling and visualization of the cellular mesoscale. 2011.
    10. Al-Amoudi A, CastaƱo-Diez D, Devos DP, Russell RB, Johnson GT, Frangakis AS. The three-dimensional molecular structure of the desmosomal plaque. Proc Natl Acad Sci U S A. 2011 Apr 19; 108(16):6480-5. PMID: 21464301; PMCID: PMC3081036.
    11. Johnson GT, Autin L, Goodsell DS, Sanner MF, Olson AJ. ePMV embeds molecular modeling into professional animation software environments. Structure. 2011 Mar 9; 19(3):293-303. PMID: 21397181; PMCID: PMC3101797.
    12. Johnson, G. AMI Newsletter. Interview with Drew Berry, 2010 MacArthur Fellow. 2011.
    13. Johnson, G., de Kok-Mercado, F., Autin, L. . AMI Newsletter. ePMV embedded Python Molecular Viewer. (Lexington: AMI). 2011.
    14. Johnson G, Autin L, Al-Alusi M, Goodsell D, Sanner M, Olson A. cellPACK. 2010.
    15. Autin L and Johnson G, Sanner M, Olson A. Embedded Python Molecular Viewer (ePMV). 2010.
    16. Written Interview Response: Goodsell, D. S. RCSB Protein Data Bank Newsletter. PDB Community Focus: Gael McGill, Ph.D., and Graham Johnson, Molecular Animators. 2009.
    17. Goodsell DS, Johnson GT. Filling in the gaps: artistic license in education and outreach. PLoS Biol. 2007 Dec; 5(12):e308. PMID: 18052608; PMCID: PMC2121112.
    18. T Pollard, W Earnshaw, J Lippincott-Schwartz, G Johnson (coauthor as illustrator). Cell Biology. 2007.
    19. T Pollard, W Earnshaw, G Johnson (coauthor as illustrator). Cell Biology. 2007.
    20. Johnson, G. T., Goodsell, D. S. Molecule of the Month: Clathrin. 2007.
    21. Johnson G, Autin L, Al-Alusi M, Goodsell D, Sanner M, Olson A. autoPACK. 2006.
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