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Xiaokun Shu, PhD

TitleAssociate Professor
InstitutionUniversity of California San Francisco
DepartmentPharmaceutical Chemistry
Address555 Mission Bay Blvd South
San Francisco CA 94158
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    Collapse Biography 
    Collapse Awards and Honors
    2012NIH Director's New Innovator Award

    Collapse Overview 
    Collapse Overview
    The Shu lab is interested in applying Principles of Physics and Chemistry to develop technologies for Biology. With the completion of human genome project, the next step in understanding biology and disease is to identify protein interactome and to characterize protein machines since protein-protein interaction networks underlie most cellular processes and protein machines carry out every major cellular process and maintain homeostasis of an organism. However, unlike the genome, protein interactome is dynamic and contains weakly associated components, which are difficult to detect. Hence, toward construction of a complete human interactome, we aim to develop new technologies for: 1) identifying weak or transient protein interactions; 2) imaging protein-protein interactions with spatiotemporal resolution. To understand mechanisms of biological processes and disease, we are also interested in developing technologies for: 3) imaging spatiotemporal dynamics of cell signaling including kinase activities in whole-animals; 4) imaging neuronal activities in brain by recording calcium and membrane potential. With these technologies, our ultimate goal is to understand molecular mechanisms of animal development and disease.


    Collapse Research 
    Collapse Research Activities and Funding
    Rational design of fluorescent kinase reporters for visualizing dynamic kinase signaling in vivo
    NIH/NIGMS R01GM127664May 4, 2018 - Mar 31, 2022
    Role: Principal Investigator
    Rational design of a genetically encoded infrared fluorescent protease reporter
    NIH/NIGMS R01GM115399Aug 1, 2015 - Jul 31, 2019
    Role: Principal Investigator
    New principle-based technologies for identifying transient protein interactions
    NIH/NIGMS DP2GM105446Sep 30, 2012 - Jun 30, 2017
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF. Designed peptides that assemble into cross-a amyloid-like structures. Nat Chem Biol. 2018 Jul 30. PMID: 30061717.
      View in: PubMed
    2. Shu X, Zheng W, Yu D, Lan Li H, Lan Q, Yang G, Cai H, Ma X, Rothman N, Gao YT, Jia W, Xiang YB, Shu X. Prospective metabolomics study identifies potential novel blood metabolites associated with pancreatic cancer risk. Int J Cancer. 2018 May 01. PMID: 29717485.
      View in: PubMed
    3. Bassig BA, Willhauck-Fleckenstein M, Shu X, Koh WP, Gao YT, Purdue MP, Xiang YB, Adams-Haduch J, Wang R, Brenner N, Waterboer T, Michel A, Ji BT, Hosgood HD, Rabkin CS, Yang G, Wong JYY, Zhang J, Hu W, Seow WJ, Chow WH, Pawlita M, Zheng W, Yuan JM, Lan Q, Rothman N. Serologic markers of viral infection and risk of non-Hodgkin lymphoma: A pooled study of three prospective cohorts in China and Singapore. Int J Cancer. 2018 Mar 25. PMID: 29574937.
      View in: PubMed
    4. Yu D, Zheng W, Johansson M, Lan Q, Park Y, White E, Matthews CE, Sawada N, Gao YT, Robien K, Sinha R, Langhammer A, Kaaks R, Giovannucci EL, Liao LM, Xiang YB, Lazovich D, Peters U, Zhang X, Bueno-de-Mesquita B, Willett WC, Tsugane S, Takata Y, Smith-Warner SA, Blot W, Shu X. Overall and Central Obesity and Risk of Lung Cancer: A Pooled Analysis. J Natl Cancer Inst. 2018 Mar 06. PMID: 29518203.
      View in: PubMed
    5. Shu X, Xiang YB, Rothman N, Yu D, Li HL, Yang G, Cai H, Ma X, Lan Q, Gao YT, Jia W, Shu X, Zheng W. Prospective study of blood metabolites associated with colorectal cancer risk. Int J Cancer. 2018 Feb 26. PMID: 29479691.
      View in: PubMed
    6. Zhang Q, Zheng YW, Coughlin SR, Shu X. A rapid fluorogenic GPCR-ß-arrestin interaction assay. Protein Sci. 2018 Apr; 27(4):874-879. PMID: 29411438.
      View in: PubMed
    7. Zhang Q, Huang H, Zhang L, 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. Mol Cell. 2018 Jan 18; 69(2):347. PMID: 29351851.
      View in: PubMed
    8. Zhang Q, Huang H, Zhang L, 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. Mol Cell. 2018 Jan 18; 69(2):334-346.e4. PMID: 29307513.
      View in: PubMed
    9. To TL, Shu X. Detecting Activity at Different Length Scales: From Subdiffraction to Whole-Animal Activity. Biochemistry. 2017 10 03; 56(39):5163-5164. PMID: 28915023.
      View in: PubMed
    10. Yang JJ, Yu D, Takata Y, Smith-Warner SA, Blot W, White E, Robien K, Park Y, Xiang YB, Sinha R, Lazovich D, Stampfer M, Tumino R, Aune D, Overvad K, Liao L, Zhang X, Gao YT, Johansson M, Willett W, Zheng W, Shu X. Dietary Fat Intake and Lung Cancer Risk: A Pooled Analysis. J Clin Oncol. 2017 Sep 10; 35(26):3055-3064. PMID: 28742456.
      View in: PubMed
    11. Jordan SJ, Na R, Johnatty SE, Wise LA, Adami HO, Brinton LA, Chen C, Cook LS, Dal Maso L, De Vivo I, Freudenheim JL, Friedenreich CM, La Vecchia C, McCann SE, Moysich KB, Lu L, Olson SH, Palmer JR, Petruzella S, Pike MC, Rebbeck TR, Ricceri F, Risch HA, Sacerdote C, Setiawan VW, Sponholtz TR, Shu X, Spurdle AB, Weiderpass E, Wentzensen N, Yang HP, Yu H, Webb PM. Breastfeeding and Endometrial Cancer Risk: An Analysis From the Epidemiology of Endometrial Cancer Consortium. Obstet Gynecol. 2017 Jun; 129(6):1059-1067. PMID: 28486362.
      View in: PubMed
    12. 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 Chem Biol. 2017 Jan 19; 24(1):110-119. PMID: 28065655.
      View in: PubMed
    13. 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 Biochem Sci. 2017 02; 42(2):111-129. PMID: 27814948.
      View in: PubMed
    14. Lawrenson K, Kar S, McCue K, Kuchenbaeker K, Michailidou K, Tyrer J, Beesley J, Ramus SJ, Li Q, Delgado MK, Lee JM, Aittomäki K, Andrulis IL, Anton-Culver H, Arndt V, Arun BK, Arver B, Bandera EV, Barile M, Barkardottir RB, Barrowdale D, Beckmann MW, Benitez J, Berchuck A, Bisogna M, Bjorge L, Blomqvist C, Blot W, Bogdanova N, Bojesen A, Bojesen SE, Bolla MK, Bonanni B, Børresen-Dale AL, Brauch H, Brennan P, Brenner H, Bruinsma F, Brunet J, Buhari SA, Burwinkel B, Butzow R, Buys SS, Cai Q, Caldes T, Campbell I, Canniotto R, Chang-Claude J, Chiquette J, Choi JY, Claes KB. Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus. Nat Commun. 2016 Sep 07; 7:12675. PMID: 27601076; PMCID: PMC5023955.
    15. Rodriguez EA, Tran GN, Gross LA, Crisp JL, Shu X, Lin JY, Tsien RY. A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein. Nat Methods. 2016 09; 13(9):763-9. PMID: 27479328; PMCID: PMC5007177 [Available on 03/01/17].
    16. 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. 2016 08 09; 55(31):4263-74. PMID: 27471775.
      View in: PubMed
    17. 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 Chem Biol. 2016 Jul 21; 23(7):875-882. PMID: 27447051.
      View in: PubMed
    18. To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X. Photoactivatable protein labeling by singlet oxygen mediated reactions. Bioorg Med Chem Lett. 2016 07 15; 26(14):3359-3363. PMID: 27220724; PMCID: PMC4903891 [Available on 07/15/17].
    19. To TL, Zhang Q, Shu X. Structure-guided design of a reversible fluorogenic reporter of protein-protein interactions. Protein Sci. 2016 Mar; 25(3):748-53. PMID: 26690964; PMCID: PMC4815423 [Available on 03/01/17].
    20. 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 Sci. 2016 Feb; 25(2):308-15. PMID: 26549191; PMCID: PMC4815332 [Available on 02/01/17].
    21. Lawrenson K, Li Q, Kar S, Seo JH, Tyrer J, Spindler TJ, Lee J, Chen Y, Karst A, Drapkin R, Aben KK, Anton-Culver H, Antonenkova N. Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer. Nat Commun. 2015 Sep 22; 6:8234. PMID: 26391404; PMCID: PMC4580986.
    22. Schumacher FR, Schmit SL, Jiao S, Edlund CK, Wang H, Zhang B, Hsu L, Huang SC, Fischer CP, Harju JF, Idos GE, Lejbkowicz F, Manion FJ, McDonnell K, McNeil CE, Melas M, Rennert HS, Shi W, Thomas DC, Van Den Berg DJ, Hutter CM, Aragaki AK, Butterbach K, Caan BJ, Carlson CS, Chanock SJ, Curtis KR, Fuchs CS, Gala M, Giovannucc EL, Giocannucci EL, Gogarten SM, Hayes RB, Henderson B, Hunter DJ, Jackson RD, Kolonel LN, Kooperberg C, Küry S, Kury S, LaCroix A, Laurie CC, Laurie CA, Lemire M, Lemire M, Levine D, Ma J, Makar KW, Qu C, Taverna D, Ulrich CM, Wu K, Kono S, West DW, Berndt SI, Bezieau S, Brenner H, Campbell PT, Chan AT, Chang-Claude J, Coetzee GA, Conti DV, Duggan D, Figueiredo JC, Fortini BK, Gallinger SJ, Gauderman WJ, Giles G, Green R, Haile R, Harrison TA, Hoffmeister M, Hopper JL, Hudson TJ, Jacobs E, Iwasaki M, Jee SH, Jenkins M, Jia WH, Joshi A, Li L, Lindor NM, Matsuo K, Moreno V, Mukherjee B, Newcomb PA, Potter JD, Raskin L, Rennert G, Rosse S, Severi G, Schoen RE, Seminara D, Shu X, Slattery ML, Tsugane S, White E, Xiang YB, Zanke BW, Zheng W, Le Marchand L, Casey G, Gruber SB, Peters U. Genome-wide association study of colorectal cancer identifies six new susceptibility loci. Nat Commun. 2015 Jul 07; 6:7138. PMID: 26151821; PMCID: PMC4967357.
    23. 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. A naturally monomeric infrared fluorescent protein for protein labeling in vivo. Nat Methods. 2015 Aug; 12(8):763-5. PMID: 26098020; PMCID: PMC4521985.
    24. To TL, Piggott BJ, Makhijani K, Yu D, Jan YN, Shu X. Rationally designed fluorogenic protease reporter visualizes spatiotemporal dynamics of apoptosis in vivo. Proc Natl Acad Sci U S A. 2015 Mar 17; 112(11):3338-43. PMID: 25733847; PMCID: PMC4371907.
    25. To TL, Fadul MJ, Shu X. Singlet oxygen triplet energy transfer-based imaging technology for mapping protein-protein proximity in intact cells. Nat Commun. 2014 Jun 06; 5:4072. PMID: 24905026; PMCID: PMC4091638.
    26. 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. Nat Commun. 2014 May 15; 5:3626. PMID: 24832154; PMCID: PMC4077998.
    27. 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. Dev Cell. 2013 Nov 25; 27(4):425-37. PMID: 24210660; PMCID: PMC3974617.
    28. Setiawan VW, Yang HP, Pike MC, McCann SE, Yu H, Xiang YB, Wolk A, Wentzensen N, Weiss NS, Webb PM, van den Brandt PA, van de Vijver K, Thompson PJ. Type I and II endometrial cancers: have they different risk factors? J Clin Oncol. 2013 Jul 10; 31(20):2607-18. PMID: 23733771.
      View in: PubMed
    29. 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. Nat Neurosci. 2012 Dec; 15(12):1742-51. PMID: 23103964; PMCID: PMC3509268.
    30. 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. A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressors. Cell. 2012 Oct 12; 151(2):304-19. PMID: 23063122; PMCID: PMC3681303.
    31. Xu J, Mo Z, Ye D, Wang M, Liu F, Jin G, Xu C, Wang X, Shao Q, Chen Z, Tao Z, Qi J, Zhou F, Wang Z, Fu Y, He D, Wei Q, Guo J, Wu D, Gao X, Yuan J, Wang G, Xu Y, Wang G, Yao H, Dong P, Jiao Y, Shen M, Yang J, Ou-Yang J, Jiang H, Zhu Y, Ren S, Zhang Z, Yin C, Gao X, Dai B, Hu Z, Yang Y, Wu Q, Chen H, Peng P, Zheng Y, Zheng X, Xiang Y, Long J, Gong J, Na R, Lin X, Yu H, Wang Z, Tao S, Feng J, Sun J, Liu W, Hsing A, Rao J, Ding Q, Wiklund F, Gronberg H, Shu X, Zheng W, Shen H, Jin L, Shi R, Lu D, Zhang X, Sun J, Zheng SL, Sun Y. Genome-wide association study in Chinese men identifies two new prostate cancer risk loci at 9q31.2 and 19q13.4. Nat Genet. 2012 Nov; 44(11):1231-5. PMID: 23023329; PMCID: PMC4116636.
    32. Setiawan VW, Pike MC, Karageorgi S, Deming SL, Anderson K, Bernstein L, Brinton LA, Cai H, Cerhan JR, Cozen W, Chen C, Doherty J, Freudenheim JL, Goodman MT, Hankinson SE, Lacey JV, Liang X, Lissowska J, Lu L, Lurie G, Mack T, Matsuno RK, McCann S, Moysich KB, Olson SH, Rastogi R, Rebbeck TR, Risch H, Robien K, Schairer C, Shu X, Spurdle AB, Strom BL, Thompson PJ, Ursin G, Webb PM, Weiss NS, Wentzensen N, Xiang YB, Yang HP, Yu H, Horn-Ross PL, De Vivo I. Age at last birth in relation to risk of endometrial cancer: pooled analysis in the epidemiology of endometrial cancer consortium. Am J Epidemiol. 2012 Aug 15; 176(4):269-78. PMID: 22831825.
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    33. 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. Proc Natl Acad Sci U S A. 2012 May 08; 109(19):7499-504. PMID: 22532663; PMCID: PMC3358873.
    34. 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 Cell Biol. 2012; 111:139-55. PMID: 22857927; PMCID: PMC3532940.
    35. 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 Biol. 2011 Apr; 9(4):e1001041. PMID: 21483721; PMCID: PMC3071375.
    36. Shu X, Nelbach L, Weinstein MM, Burgess BL, Beckstead JA, Young SG, Ryan RO, Forte TM. Intravenous injection of apolipoprotein A-V reconstituted high-density lipoprotein decreases hypertriglyceridemia in apoav-/- mice and requires glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1. Arterioscler Thromb Vasc Biol. 2010 Dec; 30(12):2504-9. PMID: 20966404.
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    37. Shu X, Nelbach L, Ryan RO, Forte TM. Apolipoprotein A-V associates with intrahepatic lipid droplets and influences triglyceride accumulation. Biochim Biophys Acta. 2010 May; 1801(5):605-8. PMID: 20153840; PMCID: PMC2839894.
    38. 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. 2009 May 08; 324(5928):804-7. PMID: 19423828; PMCID: PMC2763207.
    39. 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 Sci. 2009 Feb; 18(2):460-6. PMID: 19165727; PMCID: PMC2708057.
    40. Forte TM, Shu X, Ryan RO. The ins (cell) and outs (plasma) of apolipoprotein A-V. J Lipid Res. 2009 Apr; 50 Suppl:S150-5. PMID: 19050314; PMCID: PMC2674726.
    41. Shu X, Ryan RO, Forte TM. Intracellular lipid droplet targeting by apolipoprotein A-V requires the carboxyl-terminal segment. J Lipid Res. 2008 Aug; 49(8):1670-6. PMID: 18450648; PMCID: PMC2444012.
    42. Nelbach L, Shu X, Konrad RJ, Ryan RO, Forte TM. Effect of apolipoprotein A-V on plasma triglyceride, lipoprotein size, and composition in genetically engineered mice. J Lipid Res. 2008 Mar; 49(3):572-80. PMID: 18056685.
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    43. 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 Sci. 2007 Dec; 16(12):2703-10. PMID: 17965188; PMCID: PMC2222808.
    44. 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. 2007 Oct 30; 46(43):12005-13. PMID: 17918959; PMCID: PMC2536499.
    45. 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. 2007 Oct 30; 46(43):12014-25. PMID: 17918960; PMCID: PMC2527858.
    46. 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. 2007 Oct 30; 46(43):12026-36. PMID: 17918961.
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    47. Shu X, Chan J, Ryan RO, Forte TM. Apolipoprotein A-V association with intracellular lipid droplets. J Lipid Res. 2007 Jul; 48(7):1445-50. PMID: 17460328.
      View in: PubMed
    48. Beigneux AP, Davies BS, Gin P, Weinstein MM, Farber E, Qiao X, Peale F, Bunting S, Walzem RL, Wong JS, Blaner WS, Ding ZM, Melford K, Wongsiriroj N, Shu X, de Sauvage F, Ryan RO, Fong LG, Bensadoun A, Young SG. Glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1 plays a critical role in the lipolytic processing of chylomicrons. Cell Metab. 2007 Apr; 5(4):279-91. PMID: 17403372; PMCID: PMC1913910.
    49. Shu X, Shaner NC, Yarbrough CA, Tsien RY, Remington SJ. Novel chromophores and buried charges control color in mFruits. Biochemistry. 2006 Aug 15; 45(32):9639-47. PMID: 16893165.
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    50. 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 A resolution. Biochemistry. 2005 Apr 19; 44(15):5774-87. PMID: 15823036.
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    51. X.K.Shu, P. Jiang, J.G. Che.Surface alloying of immiscible metals induced by surface state shift. Surface Science. 2003; 545(3):199-210.