Publications

Software

Johnson G, Autin L, Al-Alusi M, Goodsell D, Sanner M, Olson A. autoPACK. LGPL open-source, autoPACK.org, UCSF and The Scripps Research Institute, 2006–2013.

Johnson G, Autin L, Al-Alusi M, Goodsell D, Sanner M, Olson A. cellPACK. LGPL open-source, autoPACK.org, UCSF and The Scripps Research Institute, 2006–2013.

Autin L, Johnson G, Sanner M, Olson A. Ubiquitous Python API (uPy). LGPL open-source, The Scripps Research Institute, 2012.

Autin L and Johnson G, Sanner M, Olson A. Embedded Python Molecular Viewer (ePMV). LGPL open-source, The Scripps Research Institute, 2010.


Peer Reviewed Publications

Sorger J, Mindek P, Rautek P, Gröller ME, Johnson GT, Viola I. Metamorphers: Storytelling Templates For Illustrative Animated Transitions in Molecular Visualization, Proceedings of the Spring Conference on Computer Graphics 2017, pages 27-36. May 2017.
[paper] [teaser] [video]

Mindek P, Kouřil D, Sorger J, Toloudis D, Lyons B, Johnson GT, Gröller ME, Viola I. Visualization Multi-Pipeline for Communicating Biology, IEEE Transactions on Visualization and Computer Graphics, 24(1), 2017.
[
Paper] [Preview Movie] [Slides

Sorger J, Mindek P, Klein T, Johnson GT, Viola I.  Illustrative Transitions in Molecular Visualization via Forward and Inverse Abstraction Transform, In Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), pages 21-30. September 2016. 
[paper] [video]

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 DOI: 10.1038/nmeth.3204

Sali, A. et al. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure (2015).

Johnson, G.T. & Hertig, S. A guide to the visual analysis and communication of biomolecular structural data. Nat Rev Mol Cell Biol 15, 690-8 (2014). doi:10.1038/nrm3874

Johnson, G.T., Goodsell, D. S., Autin, L., Forli, S., Sanner, M.F., Olson, A.J. 3D molecular models of whole HIV-1 virions generated with cellPACK. Faraday Discussions (2014), doi:10.1039/C4FD00017J.


Hertig, S., Goddard, T.D., Johnson, G.T. & Ferrin, T.E. Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophys J 108, 2097-102 (2015).

Autin L, Johnson G, Hake J, Olson A, Sanner M, 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, doi:10.1109/MCG.2012.93

Johnson, G.T., Autin, L., Goodsell, D.S., Sanner, M.F., Olson, A.J. (2011). ePMV Embeds Molecular Modeling into Professional Animation Software Environments. Structure 19, 293-303.

Al-Amoudi, A., Castaño-Diez, D., Devos, D. P., Russell, R. B., Johnson, G.T., Frangakis, A.S. (2011). The three- dimensional molecular structure of the desmosomal plaque. PLoS Biol 5, e308.

Goodsell, D.S., and Johnson, G.T. (2007). Filling in the gaps: artistic license in education and outreach. PLoS Biol 5, e308.


Non Peer Reviewed Publications

Johnson GT, Rafelski S. Seeing beyond site– New computational approaches to understanding cells. November 2018 ASCB Newsletter. (American Society for Cell Biology), 2018.

Horwitz R, Johnson GT. Whole cell maps chart a course for 21st-century cell biology, Science, May 26, 2017. 

Mindek P, Sorger J, Kouřil D, Klein T, Johnson GT, Viola I. The Birth of a Virtual Cellsubmitted to the Pacific Vis 2017 Storytelling Contest.

Johnson, G. (2013) AMI Newsletter: Announcing the Winners of the autoPACK Visualization Challenge2012: Present HIV in Blood Plasma. (Lexington: AMI). 

Iwasa, J, Johnson, G. (2012) The Art and Science of Cell Biology (ASCB2). President’s Column, October 2012 ASCB Newsletter. (American Society for Cell Biology).

Johnson, G., de Kok-Mercado, F., Autin, L. (2012) AMI Newsletter: ePMV embedded Python Molecular Viewer. (Lexington: AMI). 

Johnson, G. (2011) AMI Newsletter: Interview with Drew Berry, 2010 MacArthur Fellow. (Lexington: AMI).

Written Interview Response: Goodsell, D. S. (2009). RCSB Protein Data Bank Newsletter 41, PDB Community Focus: Gael McGill, Ph.D., and Graham Johnson, Molecular Animators. (Piscataway: RCSB).

Johnson, G. T., Goodsell, D. S.. Molecule of the Month: Clathrin. Protein Data Bank, www.rcsb.org, (2007). 

Co-authored as Illustrator: T Pollard, W Earnshaw, J Lippincott-Schwartz. Cell Biology 2e. Elsevier, NY, 2007.

Co-authored as Illustrator: Pollard T, Earnshaw W, Lippincott-Schwartz J. Cell Biology 1e. Elsevier, NY, 2002.


Interviews, uses, mentions

http://www.nature.com/nmeth/journal/v9/n11/full/nmeth.2223.html

Subpages (1): NRMCB
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