Publications: 2001 to current

• Waggoner A.S., Wachman E.S., Farkas D.L. Optical filtering systems for wavelength selection in light microscopy. Current Protocols in Cytometry (2001).
• Zhou P, Wang M, Du L, Fisher G, Waggoner A.S., Ly D.H. Novel binding and efficient cellular uptake of guanidine-based peptide nucleic acids. J. Am. Chem. Soc., 125:6878 (2003) .
• Ballou B, Lagerholm B.C., Ernst L.A., Bruchez, M.P., Waggoner, A.S. Noninvasive Imaging of Quantum Dots in Mice. Bioconjugate Chem., 15:79-86 (2004).
• Renikuntla B.R., Rose H.C., Eldo J, Wagggoner A.S., Armitage B.A. Improved photostability and fluorescence properties thorough polyfluorination of a cyanine dye. Organic Let., 6:909-912 (2004).
• Lagerholm C.B., Wang M, Ernst L.A., Ly D.H., Liu H, Bruchez M.P., and Waggoner A.S. Multicolor Coding of Cells with Cationic Peptide Coated Quantum Dots. Nanoletters. 4:2019-22 (2004).
• Ballou B, Ernst L.A., Waggoner A.S. Optical Imaging of Tumors in vivo. Cur. Med. Chem., 12:795-805 (2005).
• Fischer, A.J., Rockwell N.C., Yap A, Ernst L, Waggoner, A.S., Duan Y, Lei H, Lagerias J.C. Multiple roles of a conserved GAF domain tyrosine residue in cyanobacterial and plant phytochromes. Proc. Natl. Acad. Sci. In Press (2005).
• Tsien R.Y., Ernst L.A. and Waggoner A.S. Fluorophores for confocal microscopy: Photophysics and photochemistry. Pawley, J., Ed. Handbook of Confocal Microscopy. Plenum Press, NY pp. 351-365 (2006).
• Waggoner A.S. Fluorescent Labels for Proteomics and Genomics Current Opinion in Chemical Biology. 10:62-66 (2006).
• Giuliano K.A., Taylor D.L., and Waggoner A.S. Reagents to measure and manipulate cell functions. In Methods in Molecular Biology. Ed, DL Taylor. In press (2006).
• Salama, G., Choi, B.-R., Azour, G., Lavasani, M., Tumbev, V., Salzberg, B. M., Patrick, M. J., Ernst, L. A. and Waggoner, A. S. Properties of New, Long-Wavelength, Voltage-sensitive Dyes in the Heart. Journal of Membrane Biology 208(2): 125-140 (2006).
• Ballou, B, Ernst, L.A., Andreko, S, Harper, T, Fitzpatrick, J.A.J., Waggoner, A.S. and Bruchez, M.P. Sentinel Lymph Node Imaging Using Quantum Dots in Mouse Tumor Models. Bioconjugate Chemistry 18(2): 389-396. (2007).
• Benvin, A. L., Creeger, Y., Fisher, G. W., Ballou, B., Waggoner, A. S. and Armitage, B. A. Fluorescent DNA Nanotags: Supramolecular Fluorescent Labels Based on Intercalating Dye Arrays Assembled on Nanostructured DNA Templates J. Am. Chem. Soc. 129, 2025-2034 (2007).
• Chakraborty, S.K, Lanni, E, Waggoner, A.S. (2007) Improved Photostability of cyanine dye by synthetic encapsulation, Tetrahedron Lett. (communicated).
• Chakraborty, S.K., Fitzpatrick, J.A.J., Phillippi, J.A., Andreko, S, Waggoner, A.S., Bruchez, M.P. and Ballou, B. Cholera Toxin B Conjugated Quantum Dots for Live Cell Labeling. Nano Letters, 7(9), 2618-2626 (2007).
• Patrick, M.J., Ernst, L.A., Waggoner, A.S., Thai, D, and Salama, G. Enhanced Aqueous Solubility of Long Wavelength Voltage-Sensitive Dyes by Covalent Attachment of Polyethylene Glycol. Organic and Biommolecular Chemistry, 5: 3347-3353 (2007).
• Smith, J.D, Chen, A; Ernst, L.A, Waggoner, A.S and Campbell, P.G. Immobilization of Aprotinin to Fibrinogen as a Novel Method for Controlling Degradation of Fibrin Gels. Bioconjugate Chemistry 18(3): 695-701 (2007).
• Glory, E. and Murphy, R.F. Automated Subcellular Location Determination and High Throughput Microscopy. Developmental Cell 12:7-16 (2007).
• Chen, S.-C. Zhao, T. Gordon, G.J. and Murphy, R.F. Automated Image Analysis of Protein Localization in Budding Yeast. Bioinformatics 23:i66-i71 (2007).
• Zhao, T. and Murphy, R.F. Automated Learning of Generative Models for Subcellular Location: Building Blocks for Systems Biology. Cytometry 71A:78-990 (2007).
• Szent-Gyorgyi, C., Schmidt, B. A., Creeger, Y., Fisher, G. W., Zakel, K. L., Adler, S., Fitzpatrick, J. A., Woolford, C. A., Yan, Q., Vasilev, K. V., Berget, P. B., Bruchez, M. P., Jarvik, J. W., and Waggoner, A.: Fluorogen-activating single-chain antibodies for imaging cell surface proteins, Nat Biotechnol. (2007)
• Weinstein S, Pane D, Ernst L.A., Warren-Rhodes K, Dohm J.M., Hock A.N., Piatek J.L., Emani S, Lanni F, Wagner M, Fisher G.W., Minkley E, Dansey L.E., Smith T, Grin E.A., Stubbs K, Thomas G, Cockell C.S., Marinangeli L, Ori G.G., Heys S, Teza J.P., Moersch J.E., Coppin P, Chong Diaz G, Wettergreen D.S., Cabrol N.A., Waggoner A.S. Application of Pulsed-Excitation Fluorescence Imager for Daylight Detection of Sparse Life in Tests in the Atacama Desert. Journal of Geophysical Research - Biogeosciences, In press (2007).
• Qian, Y. and Murphy, R.F. Improved Recognition of Figures containing Fluorescence Microscope Images in Online Journal Articles using Graphical Models. Bioinformatics 24:569-576 (2008).
• Chen, S.-C, Gordon, G.J, and Murphy, R.F. Graphical Models for Structured Classification, with an Application to Interpreting Images of Protein Subcellular Location Patterns. J. Machine Learning Res., in press. (2008)
• Ozhalici-Unal H., Pow C.L., Marks S.A., Jesper L.D., Silva G.L., Shank N.I., Jones E.W., Burnette J.M. 3rd, Berget P.B. and Armitage B.A. A Rainbow of Fluoromodules: A Promiscuous scFv Protein Binds to and Activates a Diverse Set of Fluorogenic Cyanine Dyes. J. Am. Chem. Soc., August (2008)
• Armitage B.A. and Berget P.B. An Enlightening Structure-Function Relationship. Science, 319:1195-1196, (2008).