Salk Institute
Scientists and Research
James  Fitzpatrick

James Fitzpatrick

Director, Biophotonics Core
Senior Director, Strategic Technology Initiatives

As Director of the Biophotonics Core Facility at the Salk Institute, James Fitzpatrick's primary focus is the integration and application of optical and charged particle detection technologies to study problems of critical biological significance. He is a chemical physicist and laser spectroscopist by doctoral training. In his Ph.D. he designed and developed a novel injection seeded optical parametric oscillator (OPO) laser system for the study of nuclear hyperfine structure in the laser induced fluorescence spectra of gas phase free radical species. After completing his Ph.D. at the University of Bristol, he moved to the United States as a post-doctoral fellow at the University of Pittsburgh in Pennsylvania where he shifted his focus to study biological molecules such as peptide mimics and their micro-solvated clusters in the gas-phase using high-resolution fluorescence spectroscopy. In his second post-doc at Carnegie Mellon University, also in Pittsburgh, he spent his time studying protein-protein interactions using tools such as fluorescence microscopy and fluorescence correlation spectroscopy (FCS). After that he was hired to direct the Shared Imaging Facility as a part of the Carnegie Mellon National Technology Center for Networks and Pathways, an NIH funded Roadmap initiative whose mandate is to develop fluorescent probe and imaging informatics technologies to study networks and pathways in living cells.


  • BS in Chemistry, King's College London, U.K.
  • PhD in Optical Physics, Laser Spectroscopy and Dynamics Group, University of Bristol, U.K.
  • NSF Postdoctoral Fellow, University of Pittsburgh, PA, USA
  • PTEI Postdoctoral Fellow, Carnegie Mellon University, PA USA

Awards and Honors

  • Long-term quantum dot research featured in Chemical & Engineering News (2009)
  • Cholera-toxin-B quantum dot research featured in Nature Nanotechnology (2008)
  • FAP imaging technology featured in Nature Biotechnology (2008)
  • Institute of Physics Research Travel Award (2002)
  • ICI "Excellence in Graduate Research" prize University of Bristol (2001 and 2002)

Selected Publications

  • A.J. Calhoun, A. Tong, N. Pokala, J.A.J Fitzpatrick, T.O. Sharpee and S.H. Chalasani. 2015. Neural Mechanisms for evaluating environemtal variability in Caenorhabditis elegans. Neuron. 86, 1-14, April 22, 2015
  • M.W. Adams, A.F. Loftus, S.E. Dunn, M.S. Joens and J.A.J. Fitzpatrick. 2015. Invited Chapter on "Light-Sheet Fluorescence Microscopy". Current Protocols in Cytometry. 71:12.37.1-12.37.15.
  • H. Contreras, M.S. Joens, L.M. McMath, V.P. Le, M.V. Tullius, J.M. Kimmey, N. Bionghi, M.A. Horwitz, J.A.J. Fitzpatrick and C.W. Goulding. 2014. Characterization of a Mycobacterium tuberculosis nanocompartment and its potential cargo proteins. Journal of Biological Chemistry, May 22 pii: jbc.M114.570119.
  • M.S. Joens, C. Huynh, J.M. Kasuboski, D. Ferranti, Y.J. Sigal, F. Zeitvogel, M. Obst, C.J. Burkhardt, K.P. Curran, S.H. Chalasani, L.A. Stern, B. Goetze and J.A.J. Fitzpatrick. 2013. Helium Ion Microscopy (HIM) for the imaging of biological samples at sub-nanometer resolution. Scientific Reports, 3, 3514.
  • Y.S. Hu, Q. Zhu, K. Elkins, K. Tse, Y. Li, J.A.J. Fitzpatrick, I.M. Verma and H. Cang. 2013. Light-sheet Bayesian microscopy enables deep-cell super-resolution imaging of heterochromatin in live human embryonic stem cells. Optical Nanoscopy, 2:7.
  • Y.H. Chien, M.E. Werner, J. Stubbs, M.S. Joens, J. Li, S. Chien, J.A.J. Fitzpatrick, B.J. Mitchell and C. Kintner. 2013. Bbof1 is required to maintain cilia orientation. Development. Aug;140(16):3468-77.
  • L. Crabbe, A.J. Cesare, J.M. Kasuboski, J.A.J. Fitzpatrick, and J. Karlseder. 2012. Human telomeres are tethered to the nuclear envelope during postmitotic nuclear assembly. Cell Reports. Dec 27;2(6):1521-9.
  • H. D. Ou, W Kwiatkowski, T Deerinck, A Noske, K.Y. Blain, H Land, C Soria, C.J. Powers, X Shu, R Tsien, J.A.J. Fitzpatrick, J.A. Long, M.H. Ellisman, S Choe and C.C. O'Shea. 2012. Structure of E4-ORF3 reveals a viral supramolecular assembly that inactivates multiple tumor suppressors. Cell. Oct 12; 151(2):304-19.
  • J.M. Kasuboski, Y.J. Sigal, M.S. Joens, B.F. Lillemeier and J.A.J. Fitzpatrick. 2012. Invited Chapter on "Super-Resolution Microscopy: a comparative treatment" Current Protocols in Cytometry. Oct; Chapter 2: Unit 2.17.
  • M. Hatori, C. Vollmers, A. Zarrinpar, L. Ditacchio, E.A. Bushong, S. Gill, M. Leblanc, A. Chaix, M.S. Joens, J.A.J. Fitzpatrick, M.H. Ellisman and S. Panda. 2012. Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet. Cell Metabolism. Jun 6; 15(6):848-60.
  • S. Shruti, J. Urban-Ciecko, J.A.J. Fitzpatrick, R. Brenner, M.P. Bruches and A.L. Barth. 2012. The Brain- Specific Beta4 Subunit Downregulates BK Channel Cell Surface Expression. PLoS One. 7(3) e33429.
  • M.T. Hayashi, A.J. Cesare, J.A.J. Fitzpatrick, E. Lazzerini-Denchi and J. Karlseder. 2012. A Telomere-Dependent DNA Damage Checkpoint induced by Prolonged Mitotic Arrest. Nature Structural and Molecular Biology, 11(19) 387-94.
  • J.A.J. Fitzpatrick and B.L. Lillemeier. 2011. Fluorescence Correlation Spectroscopy: Linking Molecular Dynamics to Biological Function in vitro and in situ. Current Opinion in Structural Biology, 21(5) 650-60.
  • D.F. Egan, D.B. Shackelford, M.M. Mihaylova, S.R. Gelino, R.A. Kohnz, W Mair, D.S. Vasquez, A Joshi, D.M. Gwinn, R Taylor, J.M. Asara, J.A.J. Fitzpatrick, A Dillin, B Viollet, M Kundu, M Hansen, and R.J. Shaw. 2011. Phosphorylation of ULK1 (hATG1) by AMP-activated protein kinase connects energy sensing to mitophagy. Science, 331(6016) 456-461.
  • K. Padmanabhan, Shane E. Andrews and J.A.J. Fitzpatrick. 2010. Invited Chapter on "Mutli-Photon Imaging" Current Protocols in Cytometry, 2.9.1-2.9.12.
  • C.S. Szent-Gyorgyi, B.F. Schmidt, J.A.J. Fitzpatrick and M.P. Bruchez. 2010. Fluorogenic dendrons with multiple donor chromophores as bright genetically targeted and activated probes. Journal of the American Chemical Society, 132(32):11103-9.
  • E. Fishilevich, J.A.J. Fitzpatrick and J.S. Minden. 2010. pHMA, a pH-sensitive GFP reporter for cell engulfment, in Drosophila embryos, tissues, and cells. Developmental Dynamics, 239(2), 559-573.
  • S. Shenoy, R. Moldovan, J.A.J. Fitzpatrick, M. Deserno and M. Lösche. 2010. In-plane homogeneity and lipid dynamics in tethered bilayer lipid membranes (tBLMs). Softmatter, 6,1263-1274.
  • B. Ballou, L.A. Ernst, S. Andreko, J.A.J. Fitzpatrick, B.C. Lagerholm, A.S. Waggoner and M.P. Bruchez. 2009. Imaging vasculature and lymphatic flow in mice using quantum dots. Bioluminescence, Methods in Molecular Biology 574, P.B. Rich and C. Douillet (eds), Humana Press.
  • J.A.J. Fitzpatrick, S.K. Andreko, L.A. Ernst, A.S. Waggoner, B. Ballou and M.P. Bruchez. 2009. Long-term persistence and spectral blue shifting of quantum dots in vivo. Nano Letters, 9(7), 2736–2741. Highlighted in Chemical and Engineering News, June 2009.
  • J.A.J. Fitzpatrick, Q. Yan, J.J. Sieber, M. Dyba, C. Szent-Gyorgyi, A.S. Waggoner and M.P. Bruchez. 2009. STED nanoscopy in living cells using fluorogen activating proteins. Bioconjugate Chemistry, 20(10), 1843-1847.
  • N.L. Elliot, J.A.J. Fitzpatrick and C.M. Western. 2008. Sub-doppler spectroscopy of the A~2Σ+-X~2Π and B~2Π-X~2Π transitions of NCO. Journal of Chemical Physics, (129), 164301.
  • M.M. Witzberger, J.A.J. Fitzpatrick, J.C. Crowley and J.S. Minden. 2008. End-on Imaging: A new perspective on dorsoventral development in drosophila embryos. Developmental Dynamics, 237(11), 3252-3259, PMID: 18855896.
  • C. Szent-Gyorgyi, B.F. Schmidt, Y. Creeger, G. Fisher, K. Zakel, S. Adler, J.A.J. Fitzpatrick, C. Woolford, Q. Yan, K. Vasilev, P. Berget, M.P. Bruchez, J. Jarvik, A.S. Waggoner. 2008. Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nature Biotechnology, 26(2), 235-249, PMID: 18157118. Featured article in issue.
  • S.K. Chakraborty, J.A.J. Fitzpatrick, J.A. Phillippi, S. Andreko, M.P. Bruchez and B. Ballou. 2007. Choleratoxin B conjugated quantum dots for live cell labeling. Nano Letters, 7(9), 2618-2626, PMID: 17663586. Highlighted in Nature Nanotechnology Sept 2008.
  • B. Ballou, L.A. Ernst, S. Andreko, T. Harper, J.A.J Fitzpatrick, A.S. Waggoner and M.P. Bruchez. 2007. Sentinel lymph node imaging using quantum dots in mouse tumor models. Bioconjugate Chemistry, 18(2), 389-396, PMID: 17263568. Highly cited article in Bioconjugate Chemistry


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