[2014-present]

M. W. Kim, W. Wang, M. I. Sanchez, R. Coukos, M. von Zastrow, and A. Y. Ting. Time-gated detection of protein-protein interactions with transcriptional readout. bioRxiv 2017, preprint. 

P. Kaewsapsak, D. M. Shechner, W. Mallard, J. L. Rinn, and A. Y. Ting. Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA cross linking. bioRxiv 2017, preprint.

W. Wang, C. P. Wildes, T. Pattarabanjird, M. I. Sanchez, G. F. Glober, G. A. Matthews, K. M. Tye, and A. Y. Ting. A light- and calcium-gated transcription factor for imaging and manipulating activated neurons. Nature Biotechnology 2017, 35, 864-871. [PubMed] [PDF][Stanford news article][MIT news article]

J. D. Martell, T. J. Deerinck, S. S. Lam, M. H. Ellisman, and A. Y. Ting. Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. Nature Protocols 2017, 12, 1792-1816. [PubMed][PDF]

V. Hung, S. S. Lam, N. D. Udeshi, T. Svinkina, G. Guzman, V. K. Mootha, S. A. Carr, and A. Y. Ting. Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. eLife 2017, 6, e24463. [PubMed][PDF]

S. Han, N. D. Udeshi, T. J. Deerinck, T. Svinkina, M. H. Ellisman, S. A. Carr, and A. Y. Ting. Proximity biotinylation as a method for mapping proteins associated with mitochondrial DNA in living cells. Cell Chemical Biology 2017, 24, 404-414. [PubMed][PDF][Preview in Cell Chemical Biology]

B. T. Lobingier, R. Huttenhain, K. Eichel, K. B. Miller, A. Y. Ting, M. von Zastrow, and N. J. Krogan. An approach to spatiotemporally resolve protein interaction networks in living cells. Cell 2017, 169, 350-360. [PubMed][PDF]

C. Y. Chung, V. Khurana, S. Yi, N. Sahni, K. H. Loh, P. K. Auluck, V. Baru, N. D. Udeshi, Y. Freyzon, S. A. Carr, D. E. Hill, M. Vidal, A. Y. Ting, and S. Lindquist. In situ peroxidase labeling and mass-spectrometry connects alpha-synuclein directly to endocytic trafficking and mRNA metabolism in neurons. Cell Systems 2017, 4, 242-250. [PubMed][PDF]

K. H. Loh, P. S. Stawski, A. S. Draycott, N. D. Udeshi, E. K. Lehrman, D. K. Wilton, T. Svinkina, T. Deerinck, M. H. Ellisman, B. Stevens, S. A. Carr, and A. Y. Ting. Proteomic analysis of unbounded cellular compartments: synaptic clefts. Cell 2016, 166, 1295-1307. [PubMed][PDF]

J. D. Martell, M. Yamagata, T. J. Deerinck, S. Phan, C. G. Kwa, M. H. Ellisman, J. R. Sanes, and A. Y. Ting. A split horseradish peroxidase for the detection of intercellular protein-protein interactions and sensitive visualization of synapses. Nature Biotechnology 2016, 34, 774-780. [PubMed][PDF]

S. Y. Lee, M. G. Kang, J. S. Park, G. Lee, A. Y. Ting, and H. W. Rhee. APEX fingerprinting reveals the subcellular localization of proteins of interest. Cell Reports 2016, 15, 1837-1847. [PubMed][PDF]

V. Hung, N. D. Udeshi, S. S. Lam, K. H. Loh, K. J. Cox, K. Pedram, S. A. Carr, and A. Y. Ting. Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2Nature Protocols 2016, 11, 456-475. [PubMed][PDF]

C. L. Chen, Y. Hu, N. D. Udeshi, T. Y. Lau, F. Wirtz-Peitz, L. He, A. Y. Ting, S. A. Carr, and N. Perrimon. Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase. Proceedings of the National Academy of Sciences 2015, 112, 12093-12098. [PubMed][PDF]

M. S. Lee, C. R. Glassman, N. R. Deshpande, H. B. Badgandi, H. L. Parrish, C. Uttamapinant, P. S. Stawski, A. Y. Ting, and M. S. Kuhns. A Mechanical Switch Couples T Cell Receptor Triggering to the Cytoplasmic Juxtamembrane Regions of CD3ζζ. Immunity 2015, 43, 227-239. [PubMed][PDF]

S. S. Lam, J. D. Martell, K. J. Kamer, T. J. Deerinck, M. H. Ellisman, V. K. Mootha, and A. Y. Ting. Directed evolution of APEX2 for electron microscopy and proximity labeling. Nature Methods 2015, 12, 51-54. [PubMed][PDF]

D. S. Liu, L. G. Nivon, F. Richter, P. J. Goldman, T. J. Deerinck, J. Z. Yao, D. Richardson, W. S. Phipps, A. Z. Ye, M. H. Ellisman, C. L. Drennan, D. Baker, and A. Y. Ting. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Proceedings of the National Academy of Sciences 2014, 111, E4551-E4559. [PubMed][PDF]

V. Hung, P. Zou, H.-W. Rhee, N. D. Udeshi, V. Cracan, T. Svinkina, S. A. Carr, V. K. Mootha, and A. Y. Ting. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Molecular Cell 2014, 55, 332-341. [PubMed][PDF]

D. J. Dwyer, P. A. Belenky, J. H. Yang, I. C. MacDonald, J. D. Martell, N. Takahashi, C. T. Chan, M. A. Lobritz, D. Braff, E. G. Schwarz, J. D. Ye, M. Pati, M. Vercruysse, P. S. Ralifo, K. R. Allison, A. S. Khalil, A. Y. Ting, G. C. Walker, and J. J. Collins. Antibiotics induce redox-related physiological alterations as part of their lethality. Proceedings of the National Academy of Sciences 2014, 111, E2100-E2109. [PubMed][PDF]


[2009-2013]

C. Uttamapinant, M. I. Sanchez, D. S. Liu, J. Z. Yao, K. A. White, S. Grecian, S. Clark, K. R. Gee, and A. Y. Ting. Site-specific protein labeling using PRIME and chelation-assisted click chemistry. Nature Protocols 2013, 8, 1620-1634. [PubMed][PDF]

H.-W. Rhee, P. Zou, N. D. Udeshi, J. D. Martell, V. K. Mootha, S. A. Carr, and A. Y. Ting. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science 2013, 339, 1328-1331. [PubMed][PDF][Highlight in Nature Methods]

D. S. Liu, K. H. Loh, S. S. Lam, K. A. White, and A. Y. Ting. Imaging trans-cellular neurexin-neuroligin interactions by enzymatic probe ligation. PLoS One 2013, 8, e52823. [PubMed][PDF]

E. Scotti, M. Calamai, C. N. Goulbourne, L. Zhang, C. Hong, R. R. Lin, J. Choi, P. F. Pilch, L. G. Fong, P. Zou, A. Y. Ting, F. S. Pavone, S. G. Young, and P. Tontonoz. IDOL stimulates clathrin-independent endocytosis and multivesicular body-mediated lysosomal degradation of the low-density lipoprotein receptorMolecular and Cellular Biology 2013, 33, 1503-1514. [PubMed][PDF]

D. S. Liu, W. S. Phipps, K. H. Loh, M. Howarth, and A. Y. Ting. Quantum dot targeting with lipoic acid ligase and HaloTag for single-molecule imaging on living cells. ACS Nano 2012, 6, 11080-11087. [PubMed][PDF]

J. D. Martell, T. J. Deerinck, Y. Sancak, T. L. Poulos, V. K. Mootha, G. E. Sosinsky, M. H. Ellisman, and A. Y. Ting. Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy. Nature Biotechnology 2012, 30, 1143-1148. [PubMed][PDF][Highlight in Nature Methods

C. Uttamapinant, A. Tangpeerachaikul, S. Grecian, S. Clarke, U. Singh, P. Slade, K. R. Gee, and A. Y. Ting. Fast, cell-compatible click chemistry with copper-chelating azides for biomolecular labeling. Angewandte Chemie International Edition 2012, 51, 5852-5856. [PubMed][PDF][Highlight in Nature Chemical Biology]

J. D. Cohen, P. Zou, and A. Y. Ting. Site-specific protein modification using lipoic acid ligase and bis-aryl hydrazone formation. ChemBioChem 2012, 13, 888-894. [PubMed][PDF]

J. Z. Yao, C. Uttamapinant, A. Poloukhtine, J. M. Baskin, J. A. Codelli, E. M. Sletten, C. R. Bertozzi, V. V. Popik, and A. Y. Ting. Fluorophore targeting to cellular proteins via enzyme-mediated azide ligation and strain-promoted cycloaddition. Journal of the American Chemical Society 2012, 134, 3720-3728. [PubMed][PDF]

D. S. Liu, A. Tangpeerachaikul, R. Selvaraj, M. T. Taylor, J. M. Fox, and A. Y. Ting. Diels-Alder cycloaddition for fluorophore targeting to specific proteins inside living cells. Journal of the American Chemical Society 2012, 134, 792-795. [PubMed][PDF]

S. A. Slavoff, D. S. Liu, J. D. Cohen, and A. Y. Ting. Imaging protein-protein interactions inside living cells via interaction-dependent fluorophore ligation. Journal of the American Chemical Society 2011, 133, 19769-19776. [PubMed][PDF]

J. D. Cohen, S. Thompson, and A. Y. Ting. Structure-guided engineering of a Pacific Blue fluorophore ligase for specific protein imaging in living cells. Biochemistry 2011, 50, 8221-8225. [PubMed][PDF]

P. Zou and A. Y. Ting. Imaging LDL receptor oligomerization during endocytosis using a co-internalization assay. ACS Chemical Biology 2011, 6, 308-313. [PubMed][PDF]

X. Jin, C. Uttamapinant, and A. Y. Ting. Synthesis of 7-aminocoumarin via Buchwald-Hartwig cross coupling for specific protein labeling in living cells. ChemBioChem 2011, 12, 65-70. [PubMed][PDF]

C. Uttamapinant, K. A. White, H. Baruah, S. Thompson, M. Fernández-Suárez, S. Puthenveetil, and A. Y. Ting. A fluorophore ligase for site-specific protein labeling inside living cells. Proceedings of the National Academy of Sciences 2010, 107, 10914-10919. [PubMed][PDF]

P. M. Allen, W. Liu, V. P. Chauhan, J. Lee, A. Y. Ting, D. Fukumura, R. K. Jain, and M. G. Bawendi. InAs(ZnCdS) quantum dots optimized for biological imaging in the near-infrared. Journal of the American Chemical Society 2010, 132, 470-471. [PubMed][PDF]

W. Liu, A. B. Greytak, J. Lee, C. R. Wong, J. Park, L. F. Marshall, W. Jiang, P. N. Curtin, A. Y. Ting, D. G. Nocera, D. Fukumura, R. K. Jain, and M. G. Bawendi. Compact biocompatible quantum dots via RAFT-mediated synthesis of imidazole-based random copolymer ligand. Journal of the American Chemical Society 2010, 132, 472-483. [PubMed][PDF]

P. W. Jane, S. H. Wimmer-Kleikamp, A. S. Frangakis, K. Treble, B. Griesshaber, O. Sabet, M. Grabenbauer M, A. Y. Ting, P. Saftig, P. I. Bastiaens, and M. Lackmann. Cytoplasmic relaxation of active Eph controls ephrin shedding by ADAM10. PLoS Biology 2009, 10, e1000215. [PubMed][PDF]

S. Puthenveetil, D. S. Liu, K. A. White, S. Thompson, and A. Y. Ting. Yeast display evolution of a kinetically-efficient 13-amino acid substrate for lipoic acid ligase. Journal of the American Chemical Society 2009, 131, 16430-16438. [PubMed][PDF]

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[2004-2008]

H. Baruah, S. Puthenveetil, Y.-A. Choi, S. Shah, and A. Y. Ting. An engineered aryl azide ligase for site-specific mapping of protein-protein interactions through photocrosslinking. Angewandte Chemie International Edition 2008, 47, 7018-7021. [PubMed][PDF]

M. Fernández-Suárez, T. S. Chen, and A. Y. Ting. Protein-protein interaction detection in vitro and in cells by proximity biotinylation. Journal of the American Chemical Society 2008, 130, 9251-9253. [PubMed][PDF]

M. Howarth, W. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting. Monovalent, reduced-size quantum dots for imaging receptors on living cells. Nature Methods 2008, 5, 397-399. [PubMed][PDF]

M. Howarth and A. Y. Ting. Imaging proteins in live mammalian cells with biotin ligase and monovalent streptavidin. Nature Protocols 2008, 3, 534-545. [PubMed][PDF]

W. Liu, M. Howarth, A. B. Greytak, Y. Zheng, D. G. Nocera, A. Y. Ting, and M. G. Bawendi. Compact biocompatible quantum dots functionalized for cellular imaging. Journal of the American Chemical Society 2008, 130, 1274-1284. [PubMed][PDF]

M. D. Stachler, I. Chen, A. Y. Ting, and J. S. Bartlett. Site-specific modification of AAV vector particles with biophysical probes and targeting ligands using biotin ligase. Molecular Therapy 2008, 8, 1467-1473. [PubMed][PDF]

S. A. Slavoff, I. Chen, Y.-A. Choi, and A. Y. Ting. Expanding the substrate tolerance of biotin ligase through exploration of enzymes from diverse species. Journal of the American Chemical Society 2008, 130, 1160-1162. [PubMed][PDF]

M. Fernández-Suárez, H. Baruah, L. Martiez-Hernádez, K. T. Xie, J. M. Baskin, C. R. Bertozzi, and A. Y. Ting. Redirecting lipoic acid ligase for cell surface protein labeling with small-molecule probes. Nature Biotechnology 2007, 25, 1483-1487. [PubMed][PDF]

I. Chen, Y.-A. Choi, and A. Y. Ting. Phage display evolution of a peptide substrate for yeast biotin ligase and application to two-color quantum dot labeling of cell surface proteins. Journal of the American Chemical Society 2007, 129, 6619-6625. [PubMed][PDF]

E. McNeill, I. Chen, and A. Y. Ting. Synthesis of a ketone analog of biotin via the intramolecular Pauson-Khand reaction. Organic Letters 2006, 8, 4593-4595. [PubMed][PDF]

C.-W. Lin and A. Y. Ting. Transglutaminase-catalyzed site-specific conjugation of small-molecule probes to proteins in vitro and on the surface of living cells. Journal of the American Chemical Society 2006, 128, 4542-4543. [PubMed][PDF]

M. Howarth, D. J.-F. Chinnapen, K. Gerrow, P. C. Dorrestein, M. R. Grandy, N. L. Kelleher, A. El-Husseini, and A. Y. Ting. A monovalent streptavidin with a single femtomolar biotin binding siteNature Methods 2006, 3, 267-273. [PubMed][PDF]      

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting. Targeting quantum dots to surface proteins in living cells with biotin ligase. Proceedings of the National Academy of Sciences 2005, 102, 7583-7588. [PubMed][PDF

I. Chen, M. Howarth, W. Lin, and A. Y. Ting. Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase. Nature Methods 2005, 2, 99-104. [PubMed][PDF]

C.-W. Lin and A. Y. Ting. A genetically encoded fluorescent reporter of histone phosphorylation in living cells. Angewandte Chemie International Edition 2004, 43, 2940-2943. [PubMed][PDF]

C.-W. Lin, C. Y. Jao, and A. Y. Ting. Genetically encoded fluorescent reporters of histone methylation in living cells. Journal of the American Chemical Society 2004, 126, 5982-5983. [PubMed][PDF]

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[Reviews]

T. Branon, S. Han and A. Y. Ting. Beyond immunoprecipitation: exploring new interaction spaces with proximity biotinylation. Biochemistry 2017, 56, 3297-3298. [PubMed][PDF]

M. Fernández-Suárez and A. Y. Ting. Fluorescent probes for super-resolution imaging in living cells. Nature Reviews Molecular Cell Biology 2008, 9, 929-943. [PubMed][PDF]

K. Deisseroth, G. Feng, A. K. Majewska, G. Miesenbock, A. Y. Ting and M. J. Schnitzer. Next-generation optical technologies for illuminating genetically targeted brain circuits. Journal of Neuroscience 2006, 26, 10380-10386. [PubMed][PDF]

M. Howarth and A. Y. Ting. Giving cells a new sugar-coating. Nature Chemical Biology 2006, 2, 127-128. [PubMed][PDF]

I. Chen and A. Y. Ting. Site-specific labeling of proteins with small molecules in live cells. Current Opinion in Biotechnology 2005, 16, 35-40. [PubMed][PDF]

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