| 2024 |
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MYC phase separation selectively modulates the transcriptome |
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Junjiao Yang, Chan-I Chung, Jessica Koach, Hongjiang Liu, Ambuja Navalkar, Hao He, Zhimin Ma, Qian Zhao, Xiaoyu Yang, Liang He, Tanja Mittag, Yin Shen, William A. Weiss, Xiaokun Shu (2024) Nat. Struct. Mol. Biol. |
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Phase separation of YAP-MAML2 differentially regulates the transcriptome |
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Chung C-I, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X. (2024) PNAS |
| 2023 |
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A chemogenetic mini-tool for dissecting roles of protein phase separation |
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Chung C-I, Yang J, Shu X. (2023) ACS Central Sci. (Open Access) |
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Spatial and temporal organization of the genome: current state and future aims of the 4D Nucleome Project |
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Job Dekker, Frank Alber, Sarah Aufmkolk, Brian J. Beliveau, Benoit G. Bruneau, Andrew S. Belmont, Lacramioara Bintu, Alistair Boettiger, Riccardo Calandrelli, Christine M. Disteche, David M. Gilbert, Thomas Gregor, Anders S. Hansen, Bo Huang, Danwei Huangfu, Reza Kalhor, Christina S. Leslie, Wenbo Li, Yun Li, Jian Ma, William S. Noble, Peter J. Park, Jennifer E. Phillips-Cremins, Katherine S. Pollard, Susanne M. Rafelski, Bing Ren, Yijun Ruan, Yaron Shav-Tal, Yin Shen, Jay Shendure, Xiaokun Shu, Caterina Strambio-De-Castillia, Anastassiia Vertii, Huaiying Zhang, Sheng Zhong (2023) Mol Cell |
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Spatiotemporal dynamics of focal adhesion kinase |
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Research Briefing. Nature Chem Biol. (2023) |
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Polarized focal adhesion kinase activity within a focal adhesion during cell migration |
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Li X, Combs JD 3rd, Salaita K, Shu X. (2023) Nature Chem Biol. Jun 22. Online ahead of print. |
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ATM-SPARK: A GFP phase separation-based activity reporter of ATM |
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Li X, Chung CI, Yang J, Chaudhuri S, Munster PN, Shu X. (2023) Sci Adv. Mar;9(9):eade3760. |
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Fluorogenic reporter enables identification of compounds that inhibit SARS-CoV-2 |
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Yang J, Xiao Y, Lidsky PV, Wu CT, Bonser LR, Peng S, Garcia-Knight MA, Tassetto M, Chung CI, Li X, Nakayama T, Lee IT, Nayak JV, Ghias K, Hargett KL, Shoichet BK, Erle DJ, Jackson PK, Andino R, Shu X. (2023) Nat Microbiol. Jan;8(1):121-134. |
| 2022 |
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Phase separation of Myc differentially modulates the transcriptome |
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Junjiao Yang, Chan-I Chung, Jessica Koach, Hongjiang Liu, Ambuja Navalkar, Qian Zhao, Xiaoyu Yang, Liang He, Tanja Mittag, Yin Shen, William A. Weiss, Xiaokun Shu (2022) BioRxiv |
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Riboflavin-binding proteins for singlet oxygen production |
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Lafaye C, Aumonier S, Torra J, Signor L, von Stetten D, Noirclerc-Savoye M, Shu X, Ruiz-González R, Gotthard G, Royant A, Nonell S. (2022) Photochem Photobiol Sci. |
| 2020 |
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Imaging dynamic cell signaling in vivo with new classes of fluorescent reporters |
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Shu X. (2020) Current Opinion in Chemical Biology (pdf) |
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Ethacridine inhibits SARS-CoV-2 by inactivating viral particles |
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Xiaoquan Li, Peter Lidsky, Yinghong Xiao, Chien-Ting Wu, Miguel Garcia-Knight, Junjiao Yang, Tsuguhisa Nakayama, Jayakar V. Nayak, Peter K. Jackson, Raul Andino, Xiaokun Shu (2020) bioRxiv, Nov. 2 |
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Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry |
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Wen-Hao Guo, Xiaoli Qi, Xin Yu, Yang Liu, Chan-I Chung, Fang Bai, Xingcheng Lin, Dong Lu, Lingfei Wang, Jianwei Chen, Lynn Hsiao Su, Krystle J. Nomie, Feng Li, Meng C. Wang, Xiaokun Shu, José N. Onuchic, Jennifer A. Woyach, Michael L. Wang, Jin Wang (2020) Nature Communications |
| 2018 |
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Dynamic imaging of small molecule induced protein-protein interactions in living cells with a fluorophore phase transition based approach |
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Chung CI, Zhang Q, Shu X. (2018) Analytical Chemistry 90, 14287-14293 (pdf) (Constructs) |
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Designed peptides that assemble into cross-alpha amyloid-like structures |
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Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, , Shu X*, Liu L*, DeGrado WF* (2018) Nature Chem Biol 14, 870-875 (pdf) (Constructs) (*Co-corresponding author) |
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A Rapid Fluorogenic GPCR - Beta-arrestin Interaction Assay (Cover Story) |
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Zhang Q, Zheng YW, Coughlin SR, Shu X. (2018) Protein Science 27, 874-879 (pdf) (Constructs) |
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Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-based Kinase Reporter |
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Zhang Q*, Huang H*, Zhang L, Wu R, Chung C, Zhang SQ, Torra J, Schepis A, Coughlin SR, Kornberg TB, Shu X. (2018) Molecular Cell 69, 334-346 (pdf) (Constructs; Transgenic animals) (*Co-first author) |
| 2017 |
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Precision Optogenetic Tool for Selective Single- and Multiple-cell Ablation in a Live Animal Model System |
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Makhijani K*, To TL*, Ruiz-Gonzalez R, Lafaye C, Royant A, Shu X. (2017) Cell Chem Biol. 24, 110-119 (pdf) (Constructs; Transgenic animals) (*Co-first author) |
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The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins (Feature Review) |
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Rodriguez EA, Campbell RE, Lin JY, Lin MZ, Miyawaki A, Palmer AE, Shu X, Zhang J, Tsien RY. (2017) Trends Biochem Sci. 42, 111-129 (pdf) |
| 2016 |
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A Far-red Fluorescent Protein Evolved From a Cyanobacterial Phycobiliprotein |
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Rodriguez EA, Tran GN, Gross A, Crisp JL, Shu X, Lin JY, Tsien RY. (2016) Nature Methods 13, 763-769 (pdf) |
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Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations |
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Feliks M, Lafaye C, Shu X, Royant A, Field M. (2016) Biochemistry 55, 4263-74 (pdf) |
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Rational Design of a GFP-based Fluorogenic Caspase Reporter for Imaging Apoptosis in vivo |
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To TL, Schepis A, Ruiz-Gonzalez R, Zhang Q, Yu D, Dong Z, Coughlin SR, Shu X. (2016) Cell Chem Biol. 23, 875-882 (pdf) (Constructs) |
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Photoactivatable Protein Labeling by Singlet Oxygen Mediated Reactions |
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To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X. (2016) Bioorg Med Chem Lett. 26, 3359-3363 (pdf) |
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Structure-guided Design of a Reversible Fluorogenic Reporter of Protein-protein Interactions |
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To TL, Zhang Q, Shu X. (2016) Protein Science 25, 748-753 (pdf) |
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Rational Design of a Monomeric and Photostable Far-red Fluorescent Protein for Fluorescence Imaging In Vivo |
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Yu D, Dong Z, Gustafson WC, Ruiz-Gonzalez R, Signor L, Marzocca F, Borel F, Klassen MP, Makhijani K, Royant A, Jan YN, Weiss WA, Guo S, Shu X. (2016) Protein Science 25, 308-315 (available online on Nov. 9, 2015) (pdf) (Reagents: constructs; transgenic animals) |
| 2015 |
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A Naturally Monomeric Infrared Fluorescent Protein for Protein Labeling in vivo |
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Yu D, Baird MA, Allen JR, Howe ES, Klassen MP, Reade A, Makhijani K, Song Y, Liu S, Murthy Z, Zhang SQ, Weiner OD, Kornberg TB, Jan YN, Davidson MW, Shu X. (2015) Nature Methods 12, 763-5 (pdf) (Reagents: constructs; ~40 fusions; transgenic animals) |
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A Rationally Designed Infrared Fluorogenic Protease Reporter Visualizes Spatiotemporal Dynamics of Apoptosis in vivo |
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To TL, Piggott BJ, Makhijani K, Yu D, Jan YN, Shu X. (2015) PNAS 112, 3338-3343 (pdf) (Reagents: constructs; transgenic animals) |
| 2014 |
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Singlet oxygen triplet energy transfer-based imaging technology for mapping protein-protein proximity in intact cells |
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To TL, Fadul MJ, Shu X. (2014) Nature Communications 5, 4072 (pdf) |
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An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging |
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Yu D, Gustafson WC, Han C, Lafaye C, Noirclerc-Savoye M, Ge WP, Thayer DA, Huang H, Kornberg TB, Royant A, Jan LY, Jan YN, Weiss WA, Shu X. (2014) Nature Communications 5, 3626 (pdf) (Reagents) |
| 2012 |
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Photo-inducible cell ablation in Caenorhabditis elegans using the genetically encoded singlet oxygen generating protein miniSOG |
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Qi, Y., Garren, E.J., Shu, X., Tsien, R.Y., Jin, Y. (2012) PNAS 109, 7499-504 |
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Fluorescent and photo-oxidizing TimeSTAMP tags track protein fates in light and electron microscopy |
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Butko MT, Yang J, Geng Y, Kim HJ, Jeon NL, Shu X, Mackey MR, Ellisman MH, Tsien RY, Lin MZ. (2012) Nature Neurosci. 15,1742-51 |
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A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressors |
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Ou HD, Kwiatkowski W, Deerinck TJ, Noske A, Blain KY, Land HS, Soria C, Powers CJ, May AP, Shu X, Tsien RY, Fitzpatrick JA, Long JA, Ellisman MH, Choe S, O'Shea CC. (2012) Cell 151, 304-19 |
| 2009 |
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Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome |
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Shu, X.; Royant, A.; Lin, M. Z.; Aguilera, T.; Lev-Ram, V.; Steinbach, P. A.; Tsien, R. Y. (2009) Science 324, 804-807 |
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Unique Interactions between the Chromophore and Glutamate 16 Lead to Far-red Emission in a Red Fluorescent Protein (front cover article) |
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Shu, X.; Wang, L.; Colip, L.; Kallio, K.; Remington, S. J. (2009) Protein Science 18, 460-466 |
| 2007 |
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An alternative excited state proton transfer pathway in a green fluorescent protein variant S205 |
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Shu, X.; Leiderman P.; Gepshtein R. Smith N. R.; Kallio K.; Huppert, D.; Remington, S.J. (2007) Protein Science 16, 2703-2710 |
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Ultrafast Excited State Dynamics in The Green Fluorescent Protein Variant S65T/H148D. 1. Mutagenesis and Structural Studies |
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Shu, X.; Kallio, K.; Shi, X.; Abbyad, P.; Kanchanawong, P.; Childs, W.; Boxer, S.G.; Remington, S.J. (2007) Biochemistry 46, 12005-12013 |
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Ultrafast Excited State Dynamics in The Green Fluorescent Protein Variant S65T/H148D. 2. Unusual Photophysical Properties |
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Shi, X.; Abbyad, P.; Shu, X.; Kallio, K.; Kanchanawong, P.; Childs, W.; Remington, S.J.; Boxer, S.G. (2007) Biochemistry 46, 120014-12025 |
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Ultrafast Excited State Dynamics in The Green Fluorescent Protein Variant S65T/H148D. 3. Short- and Long-time Dynamics of the Excited-state Proton Transfer |
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Leiderman P.; Genosar L.; Huppert D.; Shu, X.; Remington, S.J.; Solntsev K.M.; Tolbert L. M. (2007) Biochemistry 46, 120026-12036 |
