M. I. Sanchez and A. Y. Ting. Directed evolution improves the catalytic efficiency of TEV protease. Nature Methods 2019, accepted.

F. M. Fazal, S. Han, K. R. Parker, P. Kaewsapsak, J. Xu, A. N. Boettiger, H. Y. Chang*, and A. Y. Ting*. Atlas of subcellular RNA localization revealed by APEX‑seq. Cell 2019, 178, 473-490. [PubMed][PDF][APEX-seq protocol]

C. K. Kim, K. F. Cho, M. W. Kim, and A. Y. Ting. Luciferase-LOV BRET enables versatile and specific transcriptional readout of cellular protein-protein interactions. eLife 2019, 8, e43826. [PubMed][PDF]

Y. Han, T. C. Branon, J. D. Martell, D. Boassa, D. M. Shechner, M. H. Ellisman and A. Y. Ting. Directed evolution of split APEX peroxidase. ACS Chemical Biology 2019, 14, 619-635. [PubMed][PDF]

T. C. Branon, J. A. Bosch, A. D. Sanchez, N. D. Udeshi, T. Svinkina, S. A Carr, J. L. Feldman, N. Perrimon, and A. Y. Ting. Efficient proximity labeling in living cells and organisms with TurboID. Nature Biotechnology 2018, 36, 880-887. [PubMed][PDF][Highlight in Nature Methods]

†Co-first authors; *Co-corresponding authors


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. eLife 2017, 6, e29224. [PubMed][PDF]

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. eLife 2017, 6, e30233. [PubMed][PDF]

N. D. Udeshi, K. Pedram, T. Svinkina, S. Fereshetian, S. A. Myers, O. Aygun, K. Krug, K. Clauser, D. Ryan, T. Ast, V. K. Mootha, A. Y. Ting, and S. A. Carr. Antibodies to biotin enable large-scale detection of biotinylation sites on proteins. Nature Methods 2017, 14,1167-1170. [PubMed][PDF]

O. O. Abudayyeh, J. S. Gootenberg, P. Essletzbichler, S. Han, J. Joung, J. J. Belanto, V. Verdine, D. B. T. Cox, M. J. Kellner, A. Regev, E. S. Lander, D. F. Voytas, A. Y. Ting, and F. Zhang. RNA targeting with CRISPR-Cas13. Nature 2017, 550, 280-284. [PubMed][PDF]

S. Wu, R. R. Fagan, C. Uttamapinant, L. M. Lifshitz, K. E. Fogarty, A. Y. Ting, and H. E. Melikian. The dopamine transporter recycles via a retromer-dependent postendocytic mechanism: tracking studies using a novel fluorophore-coupling approach. Journal of Neuroscience 2017, 39, 9438-9452. [PubMed][PDF]

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]

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]

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]

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]

†Co-first authors; *Co-corresponding authors

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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]

†Co-first authors

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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 site. Nature 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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W. Wang, C. K. Kim and A. Y. Ting. Molecular tools for imaging and recording neuronal activity. Nature Chemical Biology 2019, 15, 101-110. [PubMed][PDF]

S. Han, J. Li, and A. Y. Ting. Proximity labeling: spatially resolved proteomic mapping for neurobiology. Current Opinion in Neurobiology 2018, 50, 17-23. [PubMed][PDF]

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]

†Co-first authors

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