Yuji Ishitsuka

Title Scientist
Department Singular Genomics, San Diego, CA
Email Yuji@nospam664d88133a379.SingularGenomics.com


Interdisciplinary postdoctoral researcher with 10+ years of academic research experience in biophysics and nanotechnology. Expert in biophysical characterization of lipid systems and membrane proteins in vitro and in living cells proven with internationally recognized 27 scientific publications (1550+ citations). Strengths in assay development, membrane physical chemistry, DNA nanostructure, surface chemistry, microscopy and high throughput data analysis. Seeking to develop the next generation of innovative tools that can transform the lives around the world.


B.S.               Chemistry (Biochemistry), Wheaton College, Wheaton, IL, 2000

M.S.               Physical chemistry, The University of Chicago, Chicago, IL, 2001

Ph.D.             Physical chemistry, The University of Chicago, Chicago, IL, 2006

Post. Doc.   Ha Group, University of Illinois at Urbana Champaign, 2006-2011

Post. Doc.   Ulrich Nienhaus group, Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany, 2011-2015

Res. Sci.      Paul R. Selvin group, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 2015-Present


  1. Lee S.H., Jin, C., Cai, E., Ge, P., Ishitsuka, Y., Teng, K.W., Thomaz, A.A., Nall, D.L., Baday, M., Jeyifous, O., Demonte, D., Dundas, C.M., Park, S., Delgado, J.Y., Green, W.N., Selvin, P.R.,Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probeseLife, 6:e27744, (2017).
  2. Teng, K. W. Ishitsuka, Y., Ren, P., Youn, Y., Deng, X., Ge, P., Lee, S.H., Belmont, A. S. and Selvin, P. R., Labeling Proteins Inside Living Cells Using External Fluorophores for Fluorescence MicroscopyeLife, 5:e20378,  (2016).
  3. Bergs, A., Ishitsuka, Y., Evangelinos, M., Nienhaus, G.U. and Takeshita, N., Dynamics of Actin Cables in Polarized Growth of the Filamentous Fungus Aspergillus nidulansFront. Microbiol., 7, 682 (2016)
  4. Hense, A., Prunsche, B., Gao, P., Ishitsuka, Y., Nienhaus, K., and Nienhaus, G. U.,Monomeric Garnet, a far-red fluorescent protein for live-cell STED imagingScientific Reports, 5, 18006 (2015)
  5. Ishitsuka, Y., Savage, N., Li, Y., Bergs A., Grün, N., Kohler, D., Donnelly, R., Nienhaus, G. U., Fischer, R. and Takeshita N., Superresolution microscopy reveals a dynamic picture of cell polarity maintenance during directional growthScience Advances,1, e1500947 (2015)
  6. Manck, R., Ishitsuka, Y., Herrero, S., Takeshita, N., Nienhaus, G.U. and Fischer R., Genetic evidence for a microtubule-capture mechanism during polarised growth of Aspergillus nidulansJ. Cell Science, 128, 3569–3582 (2015)
  7. Ishitsuka, Y.*Azadfar. N.*, Kobitski, A. Y., Nienhaus, K., Johnsson, N. and Nienhaus, G. U.,Evaluation of Genetically Encoded Chemical Tags as Orthogonal Fluorophore Labeling Tools for Single-Molecule FRET ApplicationsJ. Phys. Chem. B119, 6611-6619 (2015) *equal contributions.
  8. Saccà, B.*, Ishitsuka, Y.*, Meyer, R., Sprengel, A., Schöneweiß, E.S., Nienhaus, G.U. and Niemeyer, C.M., Reversible reconfiguration of DNA origami nanochambers monitored by single-molecule FRETAngew. Chem. Int. Ed., 54, 1-7 (2015) *equal contributions.
  9. Ishitsuka, Y., Nienhaus, K. and Nienhaus, G.U.,Photoactivatable Fluorescent Proteins for Super-Resolution MicroscopyMethods in Mol Biol., 1148, 239-260 (2014)
  10. Takeshita, N., Mania, D., Herrero de Vega, S., Ishitsuka, Y., Nienhaus, G.U., Podolski, M., Howard, J. and Fischer, R., The cell end marker TeaA and the microtubule polymerase AlpA contribute to microtubule guidance at the hyphal tip cortex of Aspergillus nidulansfor polarity maintenanceJ. Cell Science, 126, 5400–5411 (2013)
  11. Li, Y., Ishitsuka, Y., Hedde, P.N. and Nienhaus, G.U., Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization,ACS Nano,7, 5207-5214 (2013)
  12. Lai, Y., Diao, J., Liu, Y., Ishitsuka, Y., Su, Z., Schulten, K., Ha, T., Shin, Y.K., Fusion pore formation and expansion induced by Ca2+and synaptotagmin 1Proc. Natl. Acad. Sci. USA 22, 1333-13338 (2013)
  13. Klapper, Y., Vrânceanu, M., Ishitsuka, Y., Evans, D, Scheider, D., Nienhaus, G.U. and Leneweit, G. J., Surface energy of phospholipid bilayers and the correlation to their hydration.Colloid Interface Sci.15, 267-274 (2013)
  14. Diao, J., Ishitsuka, Y., Lee, H., Joo, C., Su, Z., Syed, S., Shin, Y.K., Yoon, T.Y., and Ha, T., A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins,Nature Protocol7, 921-934 (2011)
  15. Diao, J.*, Ishitsuka, Y.*and Bae, W., Single-molecule FRET study of SNARE-mediated membrane fusionBiosciences Report 31, 457-463 (2011) *Co-corresponding authors
  16. Jain, A., Liu,R., Ramani, B., Arauz, E., Ishitsuka, Y., Ragunathan, K., Chen, J., Xiang, Y.K. and Ha, T.,  Probing cellular protein complexes using single-molecule pull-downNature 473, 484-488 (2011)
  17. Ishitsuka, Y., Okumus, B., Arslan, S., Chen, K.H. and Ha, T.,Temperature-Independent Porous Nanocontainers for Single-Molecule Fluorescence StudiesAnalytical Chemistry 82, 9694-9701 (2010)
  18. Diao, J.*, Su Z.*, Ishitsuka, Y.*, Lu B., Lee, K.S., Lai, Y., Shin, Y.K. and Ha, T., A single-vesicle content mixing assay for SNARE-mediated membrane fusionNature Communications1, 54 (2010) *equal contributions
  19. Su, Z., Ishitsuka, Y., Ha, T. and Shin, Y.K., The SNARE complex from yeast is partially unstructured on the membraneStructure16, 1138-1146 (2008)
  20. Joo, C., Balci, H., Ishitsuka, Y., Buranachai, C. and Ha, T., Advances in single-molecule fluorescence methods for molecular biologyAnnual Review of Biochemistry77, 51-76 (2008)
  21. Neville, F., Ishitsuka, Y., Hodges, C.S., Konovalov, O., Waring, A.J., Lehrer, R.I., Lee, K.C. and Gidalevitz, D., Protegrin interaction with lipid monolayers: grazing incidence X-ray diffraction and X-ray reflectivity studySoft Matter4, 1665-1674 (2008)
  22. Danauskas, S.M., Ratajczak, M.K., Ishitsuka, Y., Gebhardt, J., Schultz, D., Meron, M., Lin, B. and Lee, K.C., Monitoring X-Ray Beam Damage on Lipid Films by an Integrated Brewster Angle Micrscope/X-Ray DiffractometerReview of Scientific Instruments78, 103705-103709 (2007)
  23. Lam, K.L., Ishitsuka, Y., Cheng, Y., Chien, K., Waring, A.J., Lehrer, R.I. and Lee, K.C.,Mechanism of Membrane Disruption by Antimicrobial Peptide Protegrin-1J. Phys. Chem. B110, 21282-21286 (2006)
  24. Ishitsuka, Y., Pham, D., Waring, A.J., Lehrer, R.I. and Lee, K.C., Insertion Selectivity of Antimicrobial Peptide Protegrin-1 into Lipid Monolayers: Effect of Head Group Electrostatic and Tail Group PackingBiochimica et Biophysica Acta1758, 1450-1560 (2006)
  25. Ishitsuka, Y., Arnt, L., Ratajczek, M.K., Frey, S., Majewski, J., Kjaer, K., Tew, G.N. and Lee, K.C., Amphiphilic Poly(phenyleneethynylene)s Can Mimic Antimicrobial Peptide Membrane Disordering Effect by Membrane InsertionJournal of American Chemical Society128, 13123-13129 (2006)
  26. Neville, F., Cahuzac, M., Konovalov, O., Lee, K.C., Ishitsuka, Y., Kuzmenko, I., Kale, G.M. and Gidalevitz, D., Lipid head group discrimination by antimicrobial peptide LL-37: Insight into mechanism of actionBiophys. J.90, 1275-1287 (2006)
  27. Gidalevitz, D.*, Ishitsuka, Y.*, Muresan, A.S., Konovalov, O., Waring, A.J., Lehrer, R.I., and Lee, K.C., Interaction of Antimicrobial Peptide Protegrin with BiomembranesProc. Natl. Acad. Sci. USA100, 6302-6307 (2003) *equal contributions