Publications


  • Naganbabu, M, Perkins, LA, Wang, Y, Kurish, J, Schmidt, BF, Bruchez, MP. Multiexcitation Fluorogenic Labeling of Surface, Intracellular, and Total Protein Pools in Living Cells. Bioconjug. Chem. 2016; 27 (6):1525-31. PubMed PMID:27159569.
  • Vasilev, KV, Gallo, E, Shank, N, Jarvik, JW. Novel Biosensor of Membrane Protein Proximity Based on Fluorogen Activated Proteins. Comb. Chem. High Throughput Screen. 2016; 19 (5):392-9. PubMed PMID:27055753.
  • Liu, W, Saunders, MJ, Bagia, C, Freeman, EC, Fan, Y, Gawalt, ES, Waggoner, AS, Meng, WS. Local retention of antibodies in vivo with an injectable film embedded with a fluorogen-activating protein. J Control Release. 2016; 230 :1-12. PubMed PMID:27038493.
  • Oyaghire, SN, Cherubim, CJ, Telmer, CA, Martinez, JA, Bruchez, MP, Armitage, BA. RNA G-Quadruplex Invasion and Translation Inhibition by Antisense γ-Peptide Nucleic Acid Oligomers. Biochemistry. 2016; 55 (13):1977-88. PubMed PMID:26959335.
  • Kormuth, KA, Woolford, JL Jr, Armitage, BA. Homologous PNA Hybridization to Noncanonical DNA G-Quadruplexes. Biochemistry. 2016; 55 (12):1749-57. PubMed PMID:26950608.
  • Dutta, S, Armitage, BA, Lyubchenko, YL. Probing of miniPEGγ-PNA-DNA Hybrid Duplex Stability with AFM Force Spectroscopy. Biochemistry. 2016; 55 (10):1523-8. PubMed PMID:26898903.
  • He, J, Wang, Y, Missinato, MA, Onuoha, E, Perkins, LA, Watkins, SC, St Croix, CM, Tsang, M, Bruchez, MP. A genetically targetable near-infrared photosensitizer. Nat. Methods. 2016; 13 (3):263-8. PubMed PMID:26808669.
  • Wu, Y, Stauffer, SR, Stanfield, RL, Tapia, PH, Ursu, O, Fisher, GW, Szent-Gyorgyi, C, Evangelisti, A, Waller, A, Strouse, JJ, Carter, MB, Bologa, C, Gouveia, K, Poslusney, M, Waggoner, AS, Lindsley, CW, Jarvik, JW, Sklar, LA. Discovery of Small-Molecule Nonfluorescent Inhibitors of Fluorogen-Fluorogen Activating Protein Binding Pair. J Biomol Screen. 2016; 21 (1):74-87. PubMed PMID:26442911.
  • Fouz, MF, Mukumoto, K, Averick, S, Molinar, O, McCartney, BM, Matyjaszewski, K, Armitage, BA, Das, SR. Bright Fluorescent Nanotags from Bottlebrush Polymers with DNA-Tipped Bristles. ACS Cent Sci. 2015; 1 (8):431-8. PubMed PMID:27163005.
  • Snyder, JC, Pack, TF, Rochelle, LK, Chakraborty, SK, Zhang, M, Eaton, AW, Bai, Y, Ernst, LA, Barak, LS, Waggoner, AS, Caron, MG. A rapid and affordable screening platform for membrane protein trafficking. BMC Biol. 2015; 13 :107. PubMed PMID:26678094.
  • Wu, Y, Stauffer, SR, Stanfield, RL, Tapia, PH, Ursu, O, Fisher, GW, Szent-Gyorgyi, C, Evangelisti, A, Waller, A, Strouse, JJ, Carter, MB, Bologa, C, Gouveia, K, Poslusney, M, Waggoner, AS, Lindsley, CW, Jarvik, JW, Sklar, LA. Discovery of Small-Molecule Nonfluorescent Inhibitors of Fluorogen-Fluorogen Activating Protein Binding Pair. J Biomol Screen. 2016; 21 (1):74-87. PubMed PMID:26442911.
  • Zhang, M, Chakraborty, SK, Sampath, P, Rojas, JJ, Hou, W, Saurabh, S, Thorne, SH, Bruchez, MP, Waggoner, AS. Fluoromodule-based reporter/probes designed for in vivo fluorescence imaging. J. Clin. Invest. 2015; 125 (10):3915-27. PubMed PMID:26348895.
  • Saurabh, S, Zhang, M, Mann, VR, Costello, AM, Bruchez, MP. Kinetically Tunable Photostability of Fluorogen-Activating Peptide-Fluorogen Complexes. Chemphyschem. 2015; 16 (14):2974-80. PubMed PMID:26310607.
  • Pratt, CP, He, J, Wang, Y, Barth, AL, Bruchez, MP. Fluorogenic Green-Inside Red-Outside (GIRO) Labeling Approach Reveals Adenylyl Cyclase-Dependent Control of BKα Surface Expression. Bioconjug. Chem. 2015; 26 (9):1963-71. PubMed PMID:26301573.
  • Canady, TD, Telmer, CA, Oyaghire, SN, Armitage, BA, Bruchez, MP. In Vitro Reversible Translation Control Using γPNA Probes. J. Am. Chem. Soc. 2015; 137 (32):10268-75. PubMed PMID:26241615.
  • Magenau, AJ, Saurabh, S, Andreko, SK, Telmer, CA, Schmidt, BF, Waggoner, AS, Bruchez, MP. Genetically targeted fluorogenic macromolecules for subcellular imaging and cellular perturbation. Biomaterials. 2015; 66 :1-8. PubMed PMID:26183934.
  • Rastede, EE, Tanha, M, Yaron, D, Watkins, SC, Waggoner, AS, Armitage, BA. Spectral fine tuning of cyanine dyes: electron donor-acceptor substituted analogues of thiazole orange. Photochem. Photobiol. Sci. 2015; 14 (9):1703-12. PubMed PMID:26171668.
  • Bruchez, MP. Dark dyes-bright complexes: fluorogenic protein labeling. Curr Opin Chem Biol. 2015; 27 :18-23. PubMed PMID:26056741.
  • Gallo, E, Snyder, AC, Jarvik, JW. Engineering tandem single-chain Fv as cell surface reporters with enhanced properties of fluorescence detection. Protein Eng. Des. Sel. 2015; 28 (10):327-37. PubMed PMID:25843939.
  • Yan, Q, Bruchez, MP. Advances in chemical labeling of proteins in living cells. Cell Tissue Res. 2015; 360 (1):179-94. PubMed PMID:25743694.
  • Pham, HH, Szent-Gyorgyi, C, Brotherton, WL, Schmidt, BF, Zanotti, KJ, Waggoner, AS, Armitage, BA. Bichromophoric dyes for wavelength shifting of dye-protein fluoromodules. Org. Biomol. Chem. 2015; 13 (12):3699-710. PubMed PMID:25679477.
  • Telmer, CA, Verma, R, Teng, H, Andreko, S, Law, L, Bruchez, MP. Rapid, specific, no-wash, far-red fluorogen activation in subcellular compartments by targeted fluorogen activating proteins. ACS Chem. Biol. 2015; 10 (5):1239-46. PubMed PMID:25650487.
  • Yan, Q, Schmidt, BF, Perkins, LA, Naganbabu, M, Saurabh, S, Andreko, SK, Bruchez, MP. Near-instant surface-selective fluorogenic protein quantification using sulfonated triarylmethane dyes and fluorogen activating proteins. Org. Biomol. Chem. 2015; 13 (7):2078-86. PubMed PMID:25520058.
  • Wang, Y, Telmer, CA, Schmidt, BF, Franke, JD, Ort, S, Arndt-Jovin, DJ, Bruchez, MP. Fluorogen activating protein-affibody probes: modular, no-wash measurement of epidermal growth factor receptors. Bioconjug. Chem. 2015; 26 (1):137-44. PubMed PMID:25490520.
  • Ganesan, V, Schmidt, B, Avula, R, Cooke, D, Maggiacomo, T, Tellin, L, Ascherman, DP, Bruchez, MP, Minden, J. Immuno-proteomics: Development of a novel reagent for separating antibodies from their target proteins. Biochim. Biophys. Acta. 2015; 1854 (6):592-600. PubMed PMID:25466873.
  • Schwartz, SL, Yan, Q, Telmer, CA, Lidke, KA, Bruchez, MP, Lidke, DS. Fluorogen-activating proteins provide tunable labeling densities for tracking FcεRI independent of IgE. ACS Chem. Biol. 2015; 10 (2):539-46. PubMed PMID:25343439.
  • Wang, Y, Telmer, CA, Schmidt, BF, Franke, JD, Ort, S, Arndt-Jovin, DJ, Bruchez, MP. Fluorogen activating protein-affibody probes: modular, no-wash measurement of epidermal growth factor receptors. Bioconjug. Chem. 2015; 26 (1):137-44. PubMed PMID:25490520.
  • Ganesan, V, Schmidt, B, Avula, R, Cooke, D, Maggiacomo, T, Tellin, L, Ascherman, DP, Bruchez, MP, Minden, J. Immuno-proteomics: Development of a novel reagent for separating antibodies from their target proteins. Biochim. Biophys. Acta. 2015; 1854 (6):592-600. PubMed PMID:25466873.
  • Saurabh, S, Beck, LE, Maji, S, Baty, CJ, Wang, Y, Yan, Q, Watkins, SC, Bruchez, MP. Multiplexed modular genetic targeting of quantum dots. ACS Nano. 2014; 8 (11):11138-46. PubMed PMID:25380615.
  • Schwartz, SL, Yan, Q, Telmer, CA, Lidke, KA, Bruchez, MP, Lidke, DS. Fluorogen-activating proteins provide tunable labeling densities for tracking FcεRI independent of IgE. ACS Chem. Biol. 2015; 10 (2):539-46. PubMed PMID:25343439.
  • Tan, X, Wang, Y, Armitage, BA, Bruchez, MP. Label-free molecular beacons for biomolecular detection. Anal. Chem. 2014; 86 (21):10864-9. PubMed PMID:25287123.
  • Tanha, M, Chakraborty, SK, Gabris, B, Waggoner, AS, Salama, G, Yaron, D. Computational and experimental characterization of a fluorescent dye for detection of potassium ion concentration. J Phys Chem A. 2014; 118 (42):9837-43. PubMed PMID:25216181.
  • Pham, HH, Murphy, CT, Sureshkumar, G, Ly, DH, Opresko, PL, Armitage, BA. Cooperative hybridization of γPNA miniprobes to a repeating sequence motif and application to telomere analysis. Org. Biomol. Chem. 2014; 12 (37):7345-7354. PubMed PMID:25115693.
  • Saunders, MJ, Block, E, Sorkin, A, Waggoner, AS, Bruchez, MP. A bifunctional converter: fluorescein quenching scFv/fluorogen activating protein for photostability and improved signal to noise in fluorescence experiments. Bioconjug. Chem. 2014; 25 (8):1556-64. PubMed PMID:25072845.
  • Murphy, CT, Gupta, A, Armitage, BA, Opresko, PL. Hybridization of G-quadruplex-forming peptide nucleic acids to guanine-rich DNA templates inhibits DNA polymerase η extension. Biochemistry. 2014; 53 (32):5315-22. PubMed PMID:25068499.
  • Cheatle Jarvela, AM, Brubaker, L, Vedenko, A, Gupta, A, Armitage, BA, Bulyk, ML, Hinman, VF. Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. Mol. Biol. Evol. 2014; 31 (10):2672-88. PubMed PMID:25016582.
  • Gallo, E, Wienbar, S, Snyder, AC, Vasilev, KV, Armitage, BA, Jarvik, JW. A single-chain-variable-fragment fluorescence biosensor activates fluorogens from dissimilar chemical families. Protein Pept. Lett. 2014; 21 (12):1289-94. PubMed PMID:24939660.
  • Tan, C, Saurabh, S, Bruchez, MP, Schwartz, R, LeDuc, P. Reply to 'Complexity of molecular crowding in cell-free enzymatic reaction networks'. Nat Nanotechnol. 2014; 9 (6):407-8. PubMed PMID:24894472.
  • Fisher, GW, Fuhrman, MH, Adler, SA, Szent-Gyorgyi, C, Waggoner, AS, Jarvik, JW. Self-Checking Cell-Based Assays for GPCR Desensitization and Resensitization. J Biomol Screen. 2014; 19 (8):1220-6. PubMed PMID:24820110.
  • Wu, Y, Tapia, PH, Jarvik, J, Waggoner, AS, Sklar, LA. Real-time detection of protein trafficking with high-throughput flow cytometry (HTFC) and fluorogen-activating protein (FAP) base biosensor. Curr Protoc Cytom. 2014; 67 :Unit 9.43. PubMed PMID:24510772.
  • Tan, X, Dey, SK, Telmer, C, Zhang, X, Armitage, BA, Bruchez, MP. Aptamers act as activators for the thrombin mediated-hydrolysis of peptide substrates. Chembiochem. 2014; 15 (2):205-8. PubMed PMID:24339381.
  • Armitage, BA. Analysis of PNA hybridization by surface plasmon resonance. Methods Mol. Biol. 2014; 1050 :159-65. PubMed PMID:24297358.
  • Armitage, BA. Formation and characterization of PNA-containing heteroquadruplexes. Methods Mol. Biol. 2014; 1050 :73-82. PubMed PMID:24297351.
  • Lan, L, Nakajima, S, Wei, L, Sun, L, Hsieh, CL, Sobol, RW, Bruchez, M, Van Houten, B, Yasui, A, Levine, AS. Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin. Nucleic Acids Res. 2014; 42 (4):2330-45. PubMed PMID:24293652.
  • Yan, Q, Schwartz, SL, Maji, S, Huang, F, Szent-Gyorgyi, C, Lidke, DS, Lidke, KA, Bruchez, MP. Localization microscopy using noncovalent fluorogen activation by genetically encoded fluorogen-activating proteins. Chemphyschem. 2014; 15 (4):687-695. PubMed PMID:24194371.
  • Tan, X, Dey, SK, Telmer, C, Zhang, X, Armitage, BA, Bruchez, MP. Aptamers act as activators for the thrombin mediated-hydrolysis of peptide substrates. Chembiochem. 2014; 15 (2):205-8. PubMed PMID:24339381.
  • Lan, L, Nakajima, S, Wei, L, Sun, L, Hsieh, CL, Sobol, RW, Bruchez, M, Van Houten, B, Yasui, A, Levine, AS. Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin. Nucleic Acids Res. 2014; 42 (4):2330-45. PubMed PMID:24293652.
  • Patrick, MJ, Janjic, JM, Teng, H, O'Hear, MR, Brown, CW, Stokum, JA, Schmidt, BF, Ahrens, ET, Waggoner, AS. Intracellular pH measurements using perfluorocarbon nanoemulsions. J. Am. Chem. Soc. 2013; 135 (49):18445-57. PubMed PMID:24266634.
  • Yan, Q, Schwartz, SL, Maji, S, Huang, F, Szent-Gyorgyi, C, Lidke, DS, Lidke, KA, Bruchez, MP. Localization microscopy using noncovalent fluorogen activation by genetically encoded fluorogen-activating proteins. Chemphyschem. 2014; 15 (4):687-695. PubMed PMID:24194371.
  • Szent-Gyorgyi, C, Stanfield, RL, Andreko, S, Dempsey, A, Ahmed, M, Capek, S, Waggoner, AS, Wilson, IA, Bruchez, MP. Malachite green mediates homodimerization of antibody VL domains to form a fluorescent ternary complex with singular symmetric interfaces. J. Mol. Biol. 2013; 425 (22):4595-613. PubMed PMID:23978698.
  • Xu, J, Chang, J, Yan, Q, Dertinger, T, Bruchez, M, Weiss, S. Labeling Cytosolic Targets in Live Cells with Blinking Probes. J Phys Chem Lett. 2013; 4 (13):2138-2146. PubMed PMID:23930154.
  • Gupta, A, Lee, LL, Roy, S, Tanious, FA, Wilson, WD, Ly, DH, Armitage, BA. Strand invasion of DNA quadruplexes by PNA: comparison of homologous and complementary hybridization. Chembiochem. 2013; 14 (12):1476-84. PubMed PMID:23868291.
  • Tan, C, Saurabh, S, Bruchez, MP, Schwartz, R, Leduc, P. Molecular crowding shapes gene expression in synthetic cellular nanosystems. Nat Nanotechnol. 2013; 8 (8):602-8. PubMed PMID:23851358.
  • Coelho, LP, Kangas, JD, Naik, AW, Osuna-Highley, E, Glory-Afshar, E, Fuhrman, M, Simha, R, Berget, PB, Jarvik, JW, Murphy, RF. Determining the subcellular location of new proteins from microscope images using local features. Bioinformatics. 2013; 29 (18):2343-9. PubMed PMID:23836142.
  • Goldman, JM, Zhang, LA, Manna, A, Armitage, BA, Ly, DH, Schneider, JW. High affinity γPNA sandwich hybridization assay for rapid detection of short nucleic acid targets with single mismatch discrimination. Biomacromolecules. 2013; 14 (7):2253-61. PubMed PMID:23777445.
  • Saunders, MJ, Liu, W, Szent-Gyorgyi, C, Wen, Y, Drennen, Z, Waggoner, AS, Meng, WS. Engineering fluorogen activating proteins into self-assembling materials. Bioconjug. Chem. 2013; 24 (5):803-10. PubMed PMID:23573960.
  • Wu, Y, Tapia, PH, Fisher, GW, Waggoner, AS, Jarvik, J, Sklar, LA. High-throughput flow cytometry compatible biosensor based on fluorogen activating protein technology. Cytometry A. 2013; 83 (2):220-6. PubMed PMID:23303704.
  • Shank, NI, Pham, HH, Waggoner, AS, Armitage, BA. Twisted cyanines: a non-planar fluorogenic dye with superior photostability and its use in a protein-based fluoromodule. J. Am. Chem. Soc. 2013; 135 (1):242-51. PubMed PMID:23252842.
  • Thomas, SM, Sahu, B, Rapireddy, S, Bahal, R, Wheeler, SE, Procopio, EM, Kim, J, Joyce, SC, Contrucci, S, Wang, Y, Chiosea, SI, Lathrop, KL, Watkins, S, Grandis, JR, Armitage, BA, Ly, DH. Antitumor effects of EGFR antisense guanidine-based peptide nucleic acids in cancer models. ACS Chem. Biol. 2013; 8 (2):345-52. PubMed PMID:23113581.
  • Ballou, B, Andreko, SK, Osuna-Highley, E, McRaven, M, Catalone, T, Bruchez, MP, Hope, TJ, Labib, ME. Nanoparticle transport from mouse vagina to adjacent lymph nodes. PLoS ONE. 2012; 7 (12):e51995. PubMed PMID:23284844.
  • Shank, NI, Pham, HH, Waggoner, AS, Armitage, BA. Twisted cyanines: a non-planar fluorogenic dye with superior photostability and its use in a protein-based fluoromodule. J. Am. Chem. Soc. 2013; 135 (1):242-51. PubMed PMID:23252842.
  • Thomas, SM, Sahu, B, Rapireddy, S, Bahal, R, Wheeler, SE, Procopio, EM, Kim, J, Joyce, SC, Contrucci, S, Wang, Y, Chiosea, SI, Lathrop, KL, Watkins, S, Grandis, JR, Armitage, BA, Ly, DH. Antitumor effects of EGFR antisense guanidine-based peptide nucleic acids in cancer models. ACS Chem. Biol. 2013; 8 (2):345-52. PubMed PMID:23113581.
  • Yushchenko, DA, Zhang, M, Yan, Q, Waggoner, AS, Bruchez, MP. Genetically targetable and color-switching fluorescent probe. Chembiochem. 2012; 13 (11):1564-8. PubMed PMID:22777954.
  • Wu, Y, Tapia, PH, Fisher, GW, Simons, PC, Strouse, JJ, Foutz, T, Waggoner, AS, Jarvik, J, Sklar, LA. Discovery of regulators of receptor internalization with high-throughput flow cytometry. Mol. Pharmacol. 2012; 82 (4):645-57. PubMed PMID:22767611.
  • Cunningham, WA, Van Bavel, JJ, Arbuckle, NL, Packer, DJ, Waggoner, AS. Rapid social perception is flexible: approach and avoidance motivational states shape P100 responses to other-race faces. Front Hum Neurosci. 2012; 6 :140. PubMed PMID:22661937.
  • Maji, S, Bruchez, MP. Inferring biological structures from super-resolution single molecule images using generative models. PLoS ONE. 2012; 7 (5):e36973. PubMed PMID:22629348.
  • Grover, A, Schmidt, BF, Salter, RD, Watkins, SC, Waggoner, AS, Bruchez, MP. Genetically encoded pH sensor for tracking surface proteins through endocytosis. Angew. Chem. Int. Ed. Engl. 2012; 51 (20):4838-42. PubMed PMID:22461279.
  • Saurabh, S, Maji, S, Bruchez, MP. Evaluation of sCMOS cameras for detection and localization of single Cy5 molecules. Opt Express. 2012; 20 (7):7338-49. PubMed PMID:22453414.
  • Shruti, S, Urban-Ciecko, J, Fitzpatrick, JA, Brenner, R, Bruchez, MP, Barth, AL. The brain-specific Beta4 subunit downregulates BK channel cell surface expression. PLoS ONE. 2012; 7 (3):e33429. PubMed PMID:22438928.
  • Holleran, JP, Glover, ML, Peters, KW, Bertrand, CA, Watkins, SC, Jarvik, JW, Frizzell, RA. Pharmacological rescue of the mutant cystic fibrosis transmembrane conductance regulator (CFTR) detected by use of a novel fluorescence platform. Mol. Med. 2012; 18 :685-96. PubMed PMID:22396015.
  • Senutovitch, N, Stanfield, RL, Bhattacharyya, S, Rule, GS, Wilson, IA, Armitage, BA, Waggoner, AS, Berget, PB. A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red. Biochemistry. 2012; 51 (12):2471-85. PubMed PMID:22390683.
  • Saunders, MJ, Szent-Gyorgyi, C, Fisher, GW, Jarvik, JW, Bruchez, MP, Waggoner, AS. Fluorogen activating proteins in flow cytometry for the study of surface molecules and receptors. Methods. 2012; 57 (3):308-17. PubMed PMID:22366230.
  • Micheva, KD, Bruchez, MP. The gain in brain: novel imaging techniques and multiplexed proteomic imaging of brain tissue ultrastructure. Curr. Opin. Neurobiol. 2012; 22 (1):94-100. PubMed PMID:21944260.
  • Oprea, TI, Bauman, JE, Bologa, CG, Buranda, T, Chigaev, A, Edwards, BS, Jarvik, JW, Gresham, HD, Haynes, MK, Hjelle, B, Hromas, R, Hudson, L, Mackenzie, DA, Muller, CY, Reed, JC, Simons, PC, Smagley, Y, Strouse, J, Surviladze, Z, Thompson, T, Ursu, O, Waller, A, Wandinger-Ness, A, Winter, SS, Wu, Y, Young, SM, Larson, RS, Willman, C, Sklar, LA. Drug Repurposing from an Academic Perspective. Drug Discov Today Ther Strateg. 2011; 8 (3-4):61-69. PubMed PMID:22368688.
  • Armitage, BA. Imaging of RNA in live cells. Curr Opin Chem Biol. 2011; 15 (6):806-12. PubMed PMID:22055496.
  • Bruchez, MP. Quantum dots find their stride in single molecule tracking. Curr Opin Chem Biol. 2011; 15 (6):775-80. PubMed PMID:22055494.
  • Micheva, KD, Bruchez, MP. The gain in brain: novel imaging techniques and multiplexed proteomic imaging of brain tissue ultrastructure. Curr. Opin. Neurobiol. 2012; 22 (1):94-100. PubMed PMID:21944260.
  • Mohammed, HS, Delos Santos, JO, Armitage, BA. Noncovalent binding and fluorogenic response of cyanine dyes to DNA homoquadruplex and PNA-DNA heteroquadruplex structures. Artif DNA PNA XNA. 2011; 2 (2):43-49. PubMed PMID:21912726.
  • Stadler, AL, Delos Santos, JO, Stensrud, ES, Dembska, A, Silva, GL, Liu, S, Shank, NI, Kunttas-Tatli, E, Sobers, CJ, Gramlich, PM, Carell, T, Peteanu, LA, McCartney, BM, Armitage, BA. Fluorescent DNA nanotags featuring covalently attached intercalating dyes: synthesis, antibody conjugation, and intracellular imaging. Bioconjug. Chem. 2011; 22 (8):1491-502. PubMed PMID:21755981.
  • Roy, S, Zanotti, KJ, Murphy, CT, Tanious, FA, Wilson, WD, Ly, DH, Armitage, BA. Kinetic discrimination in recognition of DNA quadruplex targets by guanine-rich heteroquadruplex-forming PNA probes. Chem. Commun. (Camb.). 2011; 47 (30):8524-6. PubMed PMID:21717030.
  • Sahu, B, Sacui, I, Rapireddy, S, Zanotti, KJ, Bahal, R, Armitage, BA, Ly, DH. Synthesis and characterization of conformationally preorganized, (R)-diethylene glycol-containing γ-peptide nucleic acids with superior hybridization properties and water solubility. J. Org. Chem. 2011; 76 (14):5614-27. PubMed PMID:21619025.
  • Mittal, R, Bruchez, MP. Biotin-4-fluorescein based fluorescence quenching assay for determination of biotin binding capacity of streptavidin conjugated quantum dots. Bioconjug. Chem. 2011; 22 (3):362-8. PubMed PMID:21314110.
  • Chowdhury, S, Wu, Z, Jaquins-Gerstl, A, Liu, S, Dembska, A, Armitage, BA, Jin, R, Peteanu, LA. Wavelength Dependence of the Fluorescence Quenching Efficiency of Nearby Dyes by Gold Nanoclusters and Nanoparticles: The Roles of Spectral Overlap and Particle Size. J Phys Chem C Nanomater Interfaces. 2011; 115 (41):20105-20112. PubMed PMID:22924090.
  • Zanotti, KJ, Silva, GL, Creeger, Y, Robertson, KL, Waggoner, AS, Berget, PB, Armitage, BA. Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments. Org. Biomol. Chem. 2011; 9 (4):1012-20. PubMed PMID:21180706.
  • Stadler, AL, Renikuntla, BR, Yaron, D, Fang, AS, Armitage, BA. Substituent effects on the assembly of helical cyanine dye aggregates in the minor groove of a DNA template. Langmuir. 2011; 27 (4):1472-9. PubMed PMID:21174432.
  • Cunningham, WA, Johnsen, IR, Waggoner, AS. Orbitofrontal cortex provides cross-modal valuation of self-generated stimuli. Soc Cogn Affect Neurosci. 2011; 6 (3):286-93. PubMed PMID:20453039.
  • Zanotti, KJ, Silva, GL, Creeger, Y, Robertson, KL, Waggoner, AS, Berget, PB, Armitage, BA. Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments. Org. Biomol. Chem. 2011; 9 (4):1012-20. PubMed PMID:21180706.
  • Bruchez, M. [From loss of autonomy to dysautonomia: anticholinergic drugs in geriatrics]. Rev Med Suisse. 2010; 6 (270):2146-9. PubMed PMID:21174838.
  • Stadler, AL, Renikuntla, BR, Yaron, D, Fang, AS, Armitage, BA. Substituent effects on the assembly of helical cyanine dye aggregates in the minor groove of a DNA template. Langmuir. 2011; 27 (4):1472-9. PubMed PMID:21174432.
  • Damerla, RR, Knickelbein, KE, Kepchia, D, Jackson, A, Armitage, BA, Eckert, KA, Opresko, PL. Telomeric repeat mutagenicity in human somatic cells is modulated by repeat orientation and G-quadruplex stability. DNA Repair (Amst.). 2010; 9 (11):1119-29. PubMed PMID:20800555.
  • Szent-Gyorgyi, C, Schmidt, BF, Fitzpatrick, JA, Bruchez, MP. Fluorogenic dendrons with multiple donor chromophores as bright genetically targeted and activated probes. J. Am. Chem. Soc. 2010; 132 (32):11103-9. PubMed PMID:20698676.
  • Holleran, J, Brown, D, Fuhrman, MH, Adler, SA, Fisher, GW, Jarvik, JW. Fluorogen-activating proteins as biosensors of cell-surface proteins in living cells. Cytometry A. 2010; 77 (8):776-82. PubMed PMID:20653017.
  • Fisher, GW, Adler, SA, Fuhrman, MH, Waggoner, AS, Bruchez, MP, Jarvik, JW. Detection and quantification of beta2AR internalization in living cells using FAP-based biosensor technology. J Biomol Screen. 2010; 15 (6):703-9. PubMed PMID:20488980.
  • Cunningham, WA, Johnsen, IR, Waggoner, AS. Orbitofrontal cortex provides cross-modal valuation of self-generated stimuli. Soc Cogn Affect Neurosci. 2011; 6 (3):286-93. PubMed PMID:20453039.
  • Buck, TE, Rao, A, Coelho, LP, Fuhrman, MH, Jarvik, JW, Berget, PB, Murphy, RF. Cell cycle dependence of protein subcellular location inferred from static, asynchronous images. Conf Proc IEEE Eng Med Biol Soc. 2009; 2009 :1016-9. PubMed PMID:19963740.
  • Lusvarghi, S, Murphy, CT, Roy, S, Tanious, FA, Sacui, I, Wilson, WD, Ly, DH, Armitage, BA. Loop and backbone modifications of peptide nucleic acid improve g-quadruplex binding selectivity. J. Am. Chem. Soc. 2009; 131 (51):18415-24. PubMed PMID:19947597.
  • Shank, NI, Zanotti, KJ, Lanni, F, Berget, PB, Armitage, BA. Enhanced photostability of genetically encodable fluoromodules based on fluorogenic cyanine dyes and a promiscuous protein partner. J. Am. Chem. Soc. 2009; 131 (36):12960-9. PubMed PMID:19737016.
  • Ballou, B, Ernst, LA, Andreko, S, Fitzpatrick, JA, Lagerholm, BC, Waggoner, AS, Bruchez, MP. Imaging vasculature and lymphatic flow in mice using quantum dots. Methods Mol. Biol. 2009; 574 :63-74. PubMed PMID:19685300.
  • Lusvarghi, S, Kim, JM, Creeger, Y, Armitage, BA. Refined multivalent display of bacterial spore-binding peptides. Org. Biomol. Chem. 2009; 7 (9):1815-20. PubMed PMID:19590776.
  • Mittal, R, Bruchez, MP. Calibration of Flow Cytometry for Quantitative Quantum Dot Measurements. Curr Protoc Cytom. 2009; Chapter 6 :Unit6.26. PubMed PMID:20953266.
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  • Herrera, DA, Anavian, J, Tarkin, IS, Armitage, BA, Schroder, LK, Cole, PA. Delayed operative management of fractures of the scapula. J Bone Joint Surg Br. 2009; 91 (5):619-26. PubMed PMID:19407296.
  • Ozhalici-Unal, H, Armitage, BA. Fluorescent DNA nanotags based on a self-assembled DNA tetrahedron. ACS Nano. 2009; 3 (2):425-33. PubMed PMID:19236081.
  • Fitzpatrick, JA, Yan, Q, Sieber, JJ, Dyba, M, Schwarz, U, Szent-Gyorgyi, C, Woolford, CA, Berget, PB, Waggoner, AS, Bruchez, MP. STED nanoscopy in living cells using Fluorogen Activating Proteins. Bioconjug. Chem. 2009; 20 (10):1843-1847. PubMed PMID:20976031.
  • Ediz, V, Lee, JL, Armitage, BA, Yaron, D. Molecular engineering of torsional potentials in fluorogenic dyes via electronic substituent effects. J Phys Chem A. 2008; 112 (40):9692-701. PubMed PMID:18785691.
  • Ozhalici-Unal, H, Pow, CL, Marks, SA, Jesper, LD, Silva, GL, Shank, NI, Jones, EW, Burnette, JM 3rd, Berget, PB, Armitage, BA. A rainbow of fluoromodules: a promiscuous scFv protein binds to and activates a diverse set of fluorogenic cyanine dyes. J. Am. Chem. Soc. 2008; 130 (38):12620-1. PubMed PMID:18761447.
  • Daneshvar, H, Nelms, J, Muhammad, O, Jackson, H, Tkach, J, Davros, W, Peterson, T, Vogelbaum, MA, Bruchez, MP, Toms, SA. Imaging characteristics of zinc sulfide shell, cadmium telluride core quantum dots. Nanomedicine (Lond). 2008; 3 (1):21-9. PubMed PMID:18393664.
  • Constantin, TP, Silva, GL, Robertson, KL, Hamilton, TP, Fague, K, Waggoner, AS, Armitage, BA. Synthesis of new fluorogenic cyanine dyes and incorporation into RNA fluoromodules. Org. Lett. 2008; 10 (8):1561-4. PubMed PMID:18338898.
  • Armitage, BA, Berget, PB. Chemistry. An enlightening structure-function relationship. Science. 2008; 319 (5867):1195-6. PubMed PMID:18309067.
  • Szent-Gyorgyi, C, Schmidt, BF, Schmidt, BA, Creeger, Y, Fisher, GW, Zakel, KL, Adler, S, Fitzpatrick, JA, Woolford, CA, Yan, Q, Vasilev, KV, Berget, PB, Bruchez, MP, Jarvik, JW, Waggoner, A. Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nat. Biotechnol. 2008; 26 (2):235-40. PubMed PMID:18157118.
  • Szent-Gyorgyi, C, Schmidt, BF, Schmidt, BA, Creeger, Y, Fisher, GW, Zakel, KL, Adler, S, Fitzpatrick, JA, Woolford, CA, Yan, Q, Vasilev, KV, Berget, PB, Bruchez, MP, Jarvik, JW, Waggoner, A. Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nat. Biotechnol. 2008; 26 (2):235-40. PubMed PMID:18157118.
  • Rapireddy, S, He, G, Roy, S, Armitage, BA, Ly, DH. Strand invasion of mixed-sequence B-DNA by acridine-linked, gamma-peptide nucleic acid (gamma-PNA). J. Am. Chem. Soc. 2007; 129 (50):15596-600. PubMed PMID:18027941.
  • Patrick, MJ, Ernst, LA, Waggoner, AS, Thai, D, Tai, D, Salama, G. Enhanced aqueous solubility of long wavelength voltage-sensitive dyes by covalent attachment of polyethylene glycol. Org. Biomol. Chem. 2007; 5 (20):3347-53. PubMed PMID:17912389.
  • Roy, S, Tanious, FA, Wilson, WD, Ly, DH, Armitage, BA. High-affinity homologous peptide nucleic acid probes for targeting a quadruplex-forming sequence from a MYC promoter element. Biochemistry. 2007; 46 (37):10433-43. PubMed PMID:17718513.
  • Chakraborty, SK, Fitzpatrick, JA, Phillippi, JA, Andreko, S, Waggoner, AS, Bruchez, MP, Ballou, B. Cholera toxin B conjugated quantum dots for live cell labeling. Nano Lett. 2007; 7 (9):2618-26. PubMed PMID:17663586.
  • Smith, JD, Chen, A, Ernst, LA, Waggoner, AS, Campbell, PG. Immobilization of aprotinin to fibrinogen as a novel method for controlling degradation of fibrin gels. Bioconjug. Chem. ; 18 (3):695-701. PubMed PMID:17432824.
  • Lanni, F, Pane, DA, Weinstein, SJ, Waggoner, AS. Compact flashlamp-based fluorescence imager for use under ambient-light conditions. Rev Sci Instrum. 2007; 78 (3):033702. PubMed PMID:17411186.
  • Silva, GL, Ediz, V, Yaron, D, Armitage, BA. Experimental and computational investigation of unsymmetrical cyanine dyes: understanding torsionally responsive fluorogenic dyes. J. Am. Chem. Soc. 2007; 129 (17):5710-8. PubMed PMID:17411048.
  • Armitage, BA. The rule of four. Nat. Chem. Biol. 2007; 3 (4):203-4. PubMed PMID:17372603.
  • Jackson, H, Muhammad, O, Daneshvar, H, Nelms, J, Popescu, A, Vogelbaum, MA, Bruchez, M, Toms, SA. Quantum dots are phagocytized by macrophages and colocalize with experimental gliomas. Neurosurgery. 2007; 60 (3):524-9; discussion 529-30. PubMed PMID:17327798.
  • Ballou, B, Ernst, LA, Andreko, S, Harper, T, Fitzpatrick, JA, Waggoner, AS, Bruchez, MP. Sentinel lymph node imaging using quantum dots in mouse tumor models. Bioconjug. Chem. ; 18 (2):389-96. PubMed PMID:17263568.
  • Benvin, AL, Creeger, Y, Fisher, GW, Ballou, B, Waggoner, AS, Armitage, BA. Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates. J. Am. Chem. Soc. 2007; 129 (7):2025-34. PubMed PMID:17256855.
  • Smith, JD, Melhem, ME, Magge, KT, Waggoner, AS, Campbell, PG. Improved growth factor directed vascularization into fibrin constructs through inclusion of additional extracellular molecules. Microvasc. Res. 2007; 73 (2):84-94. PubMed PMID:17223139.
  • Smith, JD, Fisher, GW, Waggoner, AS, Campbell, PG. The use of quantum dots for analysis of chick CAM vasculature. Microvasc. Res. 2007; 73 (2):75-83. PubMed PMID:17070560.
  • Giuliano, KA, Taylor, DL, Waggoner, AS. Reagents to measure and manipulate cell functions. Methods Mol. Biol. 2007; 356 :141-63. PubMed PMID:16988401.
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  • Chattopadhyay, PK, Price, DA, Harper, TF, Betts, MR, Yu, J, Gostick, E, Perfetto, SP, Goepfert, P, Koup, RA, De Rosa, SC, Bruchez, MP, Roederer, M. Quantum dot semiconductor nanocrystals for immunophenotyping by polychromatic flow cytometry. Nat. Med. 2006; 12 (8):972-7. PubMed PMID:16862156.
  • Robertson, KL, Yu, L, Armitage, BA, Lopez, AJ, Peteanu, LA. Fluorescent PNA probes as hybridization labels for biological RNA. Biochemistry. 2006; 45 (19):6066-74. PubMed PMID:16681379.
  • Marin, VL, Armitage, BA. Hybridization of complementary and homologous peptide nucleic acid oligomers to a guanine quadruplex-forming RNA. Biochemistry. 2006; 45 (6):1745-54. PubMed PMID:16460021.
  • Salama, G, Choi, BR, Azour, G, Lavasani, M, Tumbev, V, Salzberg, BM, Patrick, MJ, Ernst, LA, Waggoner, AS. Properties of new, long-wavelength, voltage-sensitive dyes in the heart. J. Membr. Biol. 2005; 208 (2):125-40. PubMed PMID:16645742.
  • Armitage, BA. Antigene leaps forward through an open door. Nat. Chem. Biol. 2005; 1 (4):185-6. PubMed PMID:16408028.
  • Hannah, KC, Gil, RR, Armitage, BA. 1H NMR and optical spectroscopic investigation of the sequence-dependent dimerization of a symmetrical cyanine dye in the DNA minor groove. Biochemistry. 2005; 44 (48):15924-9. PubMed PMID:16313195.
  • Fischer, AJ, Rockwell, NC, Jang, AY, Ernst, LA, Waggoner, AS, Duan, Y, Lei, H, Lagarias, JC. Multiple roles of a conserved GAF domain tyrosine residue in cyanobacterial and plant phytochromes. Biochemistry. 2005; 44 (46):15203-15. PubMed PMID:16285723.
  • Bruchez, MP. Turning all the lights on: quantum dots in cellular assays. Curr Opin Chem Biol. 2005; 9 (5):533-7. PubMed PMID:16125995.
  • Marin, VL, Armitage, BA. RNA guanine quadruplex invasion by complementary and homologous PNA probes. J. Am. Chem. Soc. 2005; 127 (22):8032-3. PubMed PMID:15926825.
  • Renikuntla, BR, Armitage, BA. Role reversal in a supramolecular assembly: a chiral cyanine dye controls the helicity of a peptide-nucleic acid duplex. Langmuir. 2005; 21 (12):5362-6. PubMed PMID:15924462.
  • Ballou, B, Ernst, LA, Waggoner, AS. Fluorescence imaging of tumors in vivo. Curr. Med. Chem. 2005; 12 (7):795-805. PubMed PMID:15853712.
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  • Dilek, I, Madrid, M, Singh, R, Urrea, CP, Armitage, BA. Effect of PNA backbone modifications on cyanine dye binding to PNA-DNA duplexes investigated by optical spectroscopy and molecular dynamics simulations. J. Am. Chem. Soc. 2005; 127 (10):3339-45. PubMed PMID:15755150.
  • Waggoner, AS, Wachman, ES, Farkas, DL. Optical filtering systems for wavelength selection in light microscopy. Curr Protoc Cytom. 2001; Chapter 2 :Unit 2.4. PubMed PMID:18770698.
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  • Wu, X, Bruchez, MP. Labeling cellular targets with semiconductor quantum dot conjugates. Methods Cell Biol. 2004; 75 :171-83. PubMed PMID:15603426.
  • Zeng, X, Witchel, SF, Dobrowolski, SF, Moulder, PV, Jarvik, JW, Telmer, CA. Detection and assignment of CYP21 mutations using peptide mass signature genotyping. Mol. Genet. Metab. 2004; 82 (1):38-47. PubMed PMID:15110320.
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  • Mattheakis, LC, Dias, JM, Choi, YJ, Gong, J, Bruchez, MP, Liu, J, Wang, E. Optical coding of mammalian cells using semiconductor quantum dots. Anal. Biochem. 2004; 327 (2):200-8. PubMed PMID:15051536.
  • Renikuntla, BR, Rose, HC, Eldo, J, Waggoner, AS, Armitage, BA. Improved photostability and fluorescence properties through polyfluorination of a cyanine dye. Org. Lett. 2004; 6 (6):909-12. PubMed PMID:15012062.
  • Marin, VL, Roy, S, Armitage, BA. Recent advances in the development of peptide nucleic acid as a gene-targeted drug. Expert Opin Biol Ther. 2004; 4 (3):337-48. PubMed PMID:15006728.
  • Ballou, B, Lagerholm, BC, Ernst, LA, Bruchez, MP, Waggoner, AS. Noninvasive imaging of quantum dots in mice. Bioconjug. Chem. ; 15 (1):79-86. PubMed PMID:14733586.
  • Cao, R, Gu, Z, Patterson, GD, Armitage, BA. A recoverable enzymatic microgel based on biomolecular recognition. J. Am. Chem. Soc. 2004; 126 (3):726-7. PubMed PMID:14733541.
  • Cao, R, Gu, Z, Hsu, L, Patterson, GD, Armitage, BA. Synthesis and characterization of thermoreversible biopolymer microgels based on hydrogen bonded nucleobase pairing. J. Am. Chem. Soc. 2003; 125 (34):10250-6. PubMed PMID:12926948.
  • Telmer, CA, Retchless, AC, Kinsey, AD, Conley, Y, Rigatti, B, Gorin, MB, Jarvik, JW, Retchless, AR. Detection and assignment of mutations and minihaplotypes in human DNA using peptide mass signature genotyping (PMSG): application to the human RDS/peripherin gene. Genome Res. 2003; 13 (8):1944-51. PubMed PMID:12902384.
  • Malehorn, DE, Telmer, CA, McEwen, SB, An, J, Kinsey, AD, Retchless, AC, Mason, C, Vieta, WM, Jarvik, JW. Detection of cystic fibrosis mutations by peptide mass signature genotyping. Clin. Chem. 2003; 49 (8):1318-30. PubMed PMID:12881448.
  • Telmer, CA, An, J, Malehorn, DE, Zeng, X, Gollin, SM, Ishwad, CS, Jarvik, JW. Detection and assignment of TP53 mutations in tumor DNA using peptide mass signature genotyping. Hum. Mutat. 2003; 22 (2):158-65. PubMed PMID:12872257.
  • Larson, DR, Zipfel, WR, Williams, RM, Clark, SW, Bruchez, MP, Wise, FW, Webb, WW. Water-soluble quantum dots for multiphoton fluorescence imaging in vivo. Science. 2003; 300 (5624):1434-6. PubMed PMID:12775841.
  • Datta, B, Schmitt, C, Armitage, BA. Formation of a PNA2-DNA2 hybrid quadruplex. J. Am. Chem. Soc. 2003; 125 (14):4111-8. PubMed PMID:12670232.
  • Armitage, BA. The impact of nucleic acid secondary structure on PNA hybridization. Drug Discov. Today. 2003; 8 (5):222-8. PubMed PMID:12634014.
  • Watson, A, Wu, X, Bruchez, M. Lighting up cells with quantum dots. BioTechniques. 2003; 34 (2):296-300, 302-3. PubMed PMID:12613252.
  • Wu, X, Liu, H, Liu, J, Haley, KN, Treadway, JA, Larson, JP, Ge, N, Peale, F, Bruchez, MP. Immunofluorescent labeling of cancer marker Her2 and other cellular targets with semiconductor quantum dots. Nat. Biotechnol. 2003; 21 (1):41-6. PubMed PMID:12459735.
  • Jarvik, JW, Fisher, GW, Shi, C, Hennen, L, Hauser, C, Adler, S, Berget, PB. In vivo functional proteomics: mammalian genome annotation using CD-tagging. BioTechniques. 2002; 33 (4):852-4, 856, 858-60 passim. PubMed PMID:12398194.
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  • Telmer, CA, Berget, PB, Ballou, B, Murphy, RF, Jarvik, JW. Epitope tagging genomic DNA using a CD-tagging Tn10 minitransposon. BioTechniques. 2002; 32 (2):422-4, 426, 428-30. PubMed PMID:11848418.
  • Kushon, SA, Jordan, JP, Seifert, JL, Nielsen, H, Nielsen, PE, Armitage, BA. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins. J. Am. Chem. Soc. 2001; 123 (44):10805-13. PubMed PMID:11686681.
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  • Michel, JP, Hoffmeyer, P, Klopfenstein, C, Bruchez, M, Grab, B, d'Epinay, CL. Prognosis of functional recovery 1 year after hip fracture: typical patient profiles through cluster analysis. J. Gerontol. A Biol. Sci. Med. Sci. 2000; 55 (9):M508-15. PubMed PMID:10995048.
  • Kriegstein, AR, Shungu, DC, Millar, WS, Armitage, BA, Brust, JC, Chillrud, S, Goldman, J, Lynch, T. Leukoencephalopathy and raised brain lactate from heroin vapor inhalation ("chasing the dragon"). Neurology. 1999; 53 (8):1765-73. PubMed PMID:10563626.
  • Nelson, RW, Jarvik, JW, Taillon, BE, Tubbs, KA. BIA/MS of epitope-tagged peptides directly from E. coli lysate: multiplex detection and protein identification at low-femtomole to subfemtomole levels. Anal. Chem. 1999; 71 (14):2858-65. PubMed PMID:10424172.
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  • Dunahay, TG, Adler, SA, Jarvik, JW. Transformation of microalgae using silicon carbide whiskers. Methods Mol. Biol. 1997; 62 :503-9. PubMed PMID:9108543.
  • Dow, AI, Shafer, SA, Kirkwood, JM, Mascari, RA, Waggoner, AS. Automatic multiparameter fluorescence imaging for determining lymphocyte phenotype and activation status in melanoma tissue sections. Cytometry. 1996; 25 (1):71-81. PubMed PMID:8875056.
  • Alivisatos, AP, Johnsson, KP, Peng, X, Wilson, TE, Loweth, CJ, Bruchez, MP Jr, Schultz, PG. Organization of 'nanocrystal molecules' using DNA. Nature. 1996; 382 (6592):609-11. PubMed PMID:8757130.
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  • Graham, JE, Spanier, JG, Jarvik, JW. Isolation and characterization of Pioneer1, a novel Chlamydomonas transposable element. Curr. Genet. 1995; 28 (5):429-36. PubMed PMID:8575015.
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  • Southwick, PL, Hahn, KM, Chao, J, Perry, PL, Wagman, AS, Wagner, M, Waggoner, AS. A long-wavelength biolabeling reagent based on the oxonol fluorophore. J Fluoresc. 1995; 5 (2):231-5. PubMed PMID:24226669.
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  • Seppey, M, Hessler, C, Bruchez, M, Savary, M, Pécoud, A. Facial thermography during nasal provocation tests with histamine and allergen. Allergy. 1993; 48 (5):314-8. PubMed PMID:8368457.
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