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Xiaokun shu, Ph.D. - Publications

Affiliations: 
2010- Pharmaceutical Chemistry University of California, San Francisco, San Francisco, CA 
Area:
Physical Biology
Website:
https://shulab.ucsf.edu
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41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 To TL, Li X, Shu X. Spying on SARS-CoV-2 with Fluorescent Tags and Protease Reporters. Viruses. 15. PMID 37896782 DOI: 10.3390/v15102005  0.719
2019 Shu X. Imaging dynamic cell signaling in vivo with new classes of fluorescent reporters. Current Opinion in Chemical Biology. 54: 1-9. PMID 31678813 DOI: 10.1016/J.Cbpa.2019.09.004  0.418
2019 Zhang Q, Schepis A, Huang H, Yang J, Ma W, Torra J, Zhang SQ, Yang L, Wu H, Nonell S, Dong Z, Kornberg TB, Coughlin SR, Shu X. Designing a green fluorogenic protease reporter by flipping a beta strand of GFP for imaging apoptosis in animals. Journal of the American Chemical Society. PMID 30821975 DOI: 10.1021/Jacs.8B13042  0.403
2019 Torra J, Lafaye C, Signor L, Aumonier S, Flors C, Shu X, Nonell S, Gotthard G, Royant A. Tailing miniSOG: structural bases of the complex photophysics of a flavin-binding singlet oxygen photosensitizing protein. Scientific Reports. 9: 2428. PMID 30787421 DOI: 10.1038/S41598-019-38955-3  0.365
2018 Chung CI, Zhang Q, Shu X. Dynamic imaging of small molecule-induced protein-protein interactions in living cells with a fluorophore phase transition-based approach. Analytical Chemistry. PMID 30431263 DOI: 10.1021/Acs.Analchem.8B03476  0.479
2018 Zhang Q, Zheng YW, Coughlin SR, Shu X. A rapid fluorogenic GPCR - β-arrestin interaction assay. Protein Science : a Publication of the Protein Society. PMID 29411438 DOI: 10.1002/Pro.3385  0.386
2018 Zhang Q, Huang H, Lu Q, Wu R, Chung CI, Zhang SQ, Torra J, Schepis A, Coughlin SR, Kornberg TB, Shu X. Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-Based Kinase Reporter. Molecular Cell. PMID 29307513 DOI: 10.1016/J.Molcel.2017.12.008  0.365
2017 To TL, Shu X. Detecting Activity at Different Length Scales: From Subdiffraction to Whole-Animal Activity. Biochemistry. PMID 28915023 DOI: 10.1021/Acs.Biochem.7B00788  0.687
2016 Makhijani K, To TL, Ruiz-González R, Lafaye C, Royant A, Shu X. Precision Optogenetic Tool for Selective Single- and Multiple-Cell Ablation in a Live Animal Model System. Cell Chemical Biology. PMID 28065655 DOI: 10.1016/J.Chembiol.2016.12.010  0.715
2016 Rodriguez EA, Campbell RE, Lin JY, Lin MZ, Miyawaki A, Palmer AE, Shu X, Zhang J, Tsien RY. The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins. Trends in Biochemical Sciences. PMID 27814948 DOI: 10.1016/J.Tibs.2016.09.010  0.774
2016 Rodriguez EA, Tran GN, Gross LA, Crisp JL, Shu X, Lin JY, Tsien RY. A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein. Nature Methods. PMID 27479328 DOI: 10.1038/Nmeth.3935  0.796
2016 Feliks M, Lafaye C, Shu X, Royant A, Field M. Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations. Biochemistry. PMID 27471775 DOI: 10.1021/Acs.Biochem.6B00295  0.486
2016 To TL, Schepis A, Ruiz-González R, Zhang Q, Yu D, Dong Z, Coughlin SR, Shu X. Rational Design of a GFP-Based Fluorogenic Caspase Reporter for Imaging Apoptosis In Vivo. Cell Chemical Biology. 23: 875-82. PMID 27447051 DOI: 10.1016/J.Chembiol.2016.06.007  0.741
2016 To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X. Photoactivatable protein labeling by singlet oxygen mediated reactions. Bioorganic & Medicinal Chemistry Letters. PMID 27220724 DOI: 10.1016/J.Bmcl.2016.05.034  0.77
2016 Rodriguez EA, Tran GN, Gross LA, Crisp JL, Shu X, Lin JY, Tsien RY. Erratum: Corrigendum: A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein Nature Methods. 13: 890-890. DOI: 10.1038/Nmeth1016-890A  0.762
2015 To TL, Zhang Q, Shu X. Structure-guided design of a reversible fluorogenic reporter of protein-protein interactions. Protein Science : a Publication of the Protein Society. PMID 26690964 DOI: 10.1002/Pro.2866  0.8
2015 Yu D, Dong Z, Gustafson WC, Ruiz-González R, Signor L, Marzocca F, Borel F, Klassen MP, Makhijani K, Royant A, Jan YN, Weiss WA, Guo S, Shu X. Rational design of a monomeric and photostable far-red fluorescent protein for fluorescence imaging in vivo. Protein Science : a Publication of the Protein Society. PMID 26549191 DOI: 10.1002/Pro.2843  0.543
2015 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, et al. A naturally monomeric infrared fluorescent protein for protein labeling in vivo. Nature Methods. PMID 26098020 DOI: 10.1038/Nmeth.3447  0.531
2015 To TL, Piggott BJ, Makhijani K, Yu D, Jan YN, Shu X. Rationally designed fluorogenic protease reporter visualizes spatiotemporal dynamics of apoptosis in vivo. Proceedings of the National Academy of Sciences of the United States of America. 112: 3338-43. PMID 25733847 DOI: 10.1073/Pnas.1502857112  0.768
2014 To TL, Fadul MJ, Shu X. Singlet oxygen triplet energy transfer-based imaging technology for mapping protein-protein proximity in intact cells. Nature Communications. 5: 4072. PMID 24905026 DOI: 10.1038/Ncomms5072  0.775
2014 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. An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging. Nature Communications. 5: 3626. PMID 24832154 DOI: 10.1038/Ncomms4626  0.467
2013 Asensio CS, Sirkis DW, Maas JW, Egami K, To TL, Brodsky FM, Shu X, Cheng Y, Edwards RH. Self-assembly of VPS41 promotes sorting required for biogenesis of the regulated secretory pathway. Developmental Cell. 27: 425-37. PMID 24210660 DOI: 10.1016/J.Devcel.2013.10.007  0.727
2013 To T, Shu X. Singlet Oxygen Triplet Energy Transfer (STET) Based Imaging Technologies for Mapping Protein-Protein Proximity and Interactions in Intact Cells Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.2765  0.776
2012 Butko MT, Yang J, Geng Y, Kim HJ, Jeon NL, Shu X, Mackey MR, Ellisman MH, Tsien RY, Lin MZ. Fluorescent and photo-oxidizing TimeSTAMP tags track protein fates in light and electron microscopy. Nature Neuroscience. 15: 1742-51. PMID 23103964 DOI: 10.1038/Nn.3246  0.785
2012 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, et al. A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressors. Cell. 151: 304-19. PMID 23063122 DOI: 10.1016/J.Cell.2012.08.035  0.479
2012 Ellisman MH, Deerinck TJ, Shu X, Sosinsky GE. Picking faces out of a crowd: genetic labels for identification of proteins in correlated light and electron microscopy imaging. Methods in Cell Biology. 111: 139-55. PMID 22857927 DOI: 10.1016/B978-0-12-416026-2.00008-X  0.421
2012 Qi YB, Garren EJ, Shu X, Tsien RY, Jin Y. Photo-inducible cell ablation in Caenorhabditis elegans using the genetically encoded singlet oxygen generating protein miniSOG. Proceedings of the National Academy of Sciences of the United States of America. 109: 7499-504. PMID 22532663 DOI: 10.1073/Pnas.1204096109  0.547
2012 Deerinck T, Bushong E, Tsien R, Ellisman M, Shu X. Advances in Correlated Light and Electron Microscopy Imaging Probes Microscopy and Microanalysis. 18: 834-835. DOI: 10.1017/S1431927612006022  0.525
2011 Shu X, Lev-Ram V, Deerinck TJ, Qi Y, Ramko EB, Davidson MW, Jin Y, Ellisman MH, Tsien RY. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. Plos Biology. 9: e1001041. PMID 21483721 DOI: 10.1371/Journal.Pbio.1001041  0.654
2011 Shu X, Lev-Ram V, Olson ES, Aguilera TA, Jiang T, Whitney M, Crisp JL, Steinbach P, Deerinck T, Ellisman MH, Ellies LG, Nguyen QT, Tsien RY. Spiers Memorial Lecture. Breeding and building molecular spies. Faraday Discussions. 149: 9; discussion 63-77. PMID 21413170 DOI: 10.1039/C0Fd90021D  0.778
2011 Ellisman M, Shu X, Lev-Ram V, Deerinck T, Tsien R, Lamont S, Martinez J, Berlanga M, Bushong E, Martone M, Larson S. Bridging Gaps in Imaging by Applying EM Tomography and Serial Block Face SEM, Including a New Genetically Encoded Tag for Correlated Light and 3D Electron Microscopy of Intact Cells, Tissues and Organisms: Integrating the Resulting Correlated Image Data Using the Whole Brain Catalog Microscopy and Microanalysis. 17: 2-3. DOI: 10.1017/S1431927611000882  0.506
2010 Deerinck T, Bushong E, Lev-Ram V, Shu X, Tsien R, Ellisman M. Enhancing Serial Block-Face Scanning Electron Microscopy to Enable High Resolution 3-D Nanohistology of Cells and Tissues Microscopy and Microanalysis. 16: 1138-1139. DOI: 10.1017/S1431927610055170  0.489
2010 Shu X, Lev-Ram V, Gaietta GM, Deerinck TJ, Ramko EB, Davidson MW, Ellisman MH, Tsien R. Genetically Encoded Singlet Oxygen Generator (SOG) Requiring No Exogenous Cofactors Biophysical Journal. 98: 612a. DOI: 10.1016/J.Bpj.2009.12.3338  0.604
2009 Shu X, Royant A, Lin MZ, Aguilera TA, Lev-Ram V, Steinbach PA, Tsien RY. Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science (New York, N.Y.). 324: 804-7. PMID 19423828 DOI: 10.1126/Science.1168683  0.801
2009 Shu X, Wang L, Colip L, Kallio K, Remington SJ. Unique interactions between the chromophore and glutamate 16 lead to far-red emission in a red fluorescent protein. Protein Science : a Publication of the Protein Society. 18: 460-6. PMID 19165727 DOI: 10.1002/Pro.66  0.671
2007 Shu X, Leiderman P, Gepshtein R, Smith NR, Kallio K, Huppert D, Remington SJ. An alternative excited-state proton transfer pathway in green fluorescent protein variant S205V Protein Science. 16: 2703-2710. PMID 17965188 DOI: 10.1110/Ps.073112007  0.675
2007 Leiderman P, Genosar L, Huppert D, Shu X, Remington SJ, Solntsev KM, Tolbert LM. Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 3. Short- and long-time dynamics of the excited-state proton transfer Biochemistry. 46: 12026-12036. PMID 17918961 DOI: 10.1021/Bi7009053  0.656
2007 Shi X, Abbyad P, Shu X, Kallio K, Kanchanawong P, Childs W, Remington SJ, Boxer SG. Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 2. Unusual photophysical properties. Biochemistry. 46: 12014-25. PMID 17918960 DOI: 10.1021/Bi700904A  0.688
2007 Shu X, Kallio K, Shi X, Abbyad P, Kanchanawong P, Childs W, Boxer SG, Remington SJ. Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 1. Mutagenesis and structural studies. Biochemistry. 46: 12005-13. PMID 17918959 DOI: 10.1021/Bi7009037  0.655
2006 Shu X, Shaner NC, Yarbrough CA, Tsien RY, Remington SJ. Novel chromophores and buried charges control color in mFruits. Biochemistry. 45: 9639-47. PMID 16893165 DOI: 10.1021/Bi060773L  0.788
2005 Quillin ML, Anstrom DM, Shu X, O'Leary S, Kallio K, Chudakov DM, Remington SJ. Kindling fluorescent protein from Anemonia sulcata: Dark-state structure at 1.38 Å resolution Biochemistry. 44: 5774-5787. PMID 15823036 DOI: 10.1021/Bi047644U  0.783
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