[2023-present]
N. A. Kalogriopoulos†, R. Tei†, Y. Yan, M. Ravalin, Y. Li, and A. Y. Ting. Synthetic G protein-coupled receptors for programmable sensing and control of cell behavior. Submitted.
J. L. Yang, S. A. Yamada-Hunter, L. Labanieh, E. Sotillo, J. S. Cheah, D. S. Roberts, C. L. Mackall, C. R. Bertozzi*, and A. Y. Ting*. Directed evolution of genetically encoded LYTACs for cell-mediated delivery. Proceedings of the National Academy of Sciences 2024, 121, e2320053121. [PubMed]
W. Qin†, J. S. Cheah†, C. Xu, J. Messing, B. D. Freibaum, S. Boeynaems, J. P. Taylor, N. D. Udeshi, S. A. Carr, and A. Y. Ting. Dynamic mapping of proteome trafficking within and between living cells by TransitID. Cell 2023, 186, 3307-3324. [PubMed][PDF]
S.-Y. Lee†, J. S. Cheah†, B. Zhao, C. Xu, H. Roh, C. K. Kim, K. F. Cho, N. D. Udeshi, S. A. Carr, and A. Y. Ting. Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells. Nature Methods 2023, 20, 908-917. [PubMed][PDF]
H. Roh, B. G. Dorner, and A. Y. Ting. Cell type-specific intracellular protein delivery with inactivated botulinum toxin. Journal of the American Chemical Society 2023, 145, 18, 10220-10226. [PubMed][PDF]
†Co-first authors; *Co-corresponding authors
[2018-2022]
M. Ravalin†, H. Roh†, R. Suryawanshi, G. R. Kumar, J. Pak, M. Ott, and A. Y. Ting. A single-component luminescent biosensor for the SARS-CoV-2 spike protein. Journal of the American Chemical Society 2022, 144, 30, 13663-13672. [PubMed][PDF]
K. F. Cho, S. M. Gillespie, N. A. Kalogriopoulos, M. A. Quezada, M. Jacko, M. Monje, and A. Y. Ting. A light-gated transcriptional recorder for detecting cell-cell contacts. eLife 2022, 11, e70881. [PubMed][PDF]
E. Erdenee and A. Y. Ting. A dual-purpose real-time indicator and transcriptional integrator for calcium detection in living cells. ACS Synthetic Biology 2022, 11, 3, 1086-1095. [PubMed][PDF]
R. Coukos†, D. Yao†, M. I. Sanchez, E. T. Strand, M. E. Olive, N. D. Udeshi, J. S. Weissman, S. A. Carr, M. C. Bassik, and A. Y. Ting. An engineered transcriptional reporter of protein localization identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput CRISPRi screens. eLife 2021, 10, e69142. [PubMed][PDF]
C. K. Kim†, M. I. Sanchez†, P. Hoerbelt, L. E. Fenno, R. C. Malenka, K. Deisseroth, and A. Y. Ting. A molecular calcium integrator reveals a striatal cell type driving aversion. Cell 2020, 183, 2003-2019. [PubMed][PDF][Stanford news]
S. Han, B. S. Zhao, S. A. Myers, S. A. Carr, C. He, and A. Y. Ting. RNA-protein interaction mapping via MS2 or Cas13-based APEX targeting. Proceedings of the National Academy of Sciences 2020, 117, 22068-22079. [PubMed][PDF]
K. F. Cho, T. C. Branon, S. Rajeev, T. Svinkina, N. D. Udeshi, T. Thoudam, C. Kwak, H. W. Rhee, I. K. Lee, S. A. Carr, and A. Y. Ting. Split-TurboID enables contact-dependent proximity labeling in cells. Proceedings of the National Academy of Sciences 2020, 117, 12143-12154. [PubMed][PDF]
J. Li†, S. Han†, H. Li, N. D. Udeshi, T. Svinkina, D. R. Mani, C. Xu, R. Guajardo, Q. Xie, T. Li, D. J. Luginbuhl, B. Wu, C. N. McLaughlin, A. Xie, P. Kaewsapsak, S. R. Quake, A. Y. Ting*, and L. Luo*. Cell-surface proteomic profiling in the fly brain uncovers new wiring regulators. Cell 2020, 180, 373-386. [PubMed][PDF][Stanford news]
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
[2014-2017]
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]
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]
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 APEX2. Nature 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
[2009-2013]
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 receptor. Molecular 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
[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 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]
[Reviews]
W. Qin†, K. F. Cho†, P. E. Cavanagh†, and A. Y. Ting. Deciphering molecular interactions by proximity labeling. Nature Methods 2021, 18, 133-143. [PubMed][PDF]
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