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    Qiang Zhang, PhD

    TitlePostdoctoral Scholar
    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
    Address555 Mission Bay Blvd South
    San Francisco CA 94158
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      Collapse Overview 
      Collapse Interests
      I work in generating Biosensors of protein-protein interaction in Xiaokun Shu Lab., Molecular Biology and Cell biology.

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      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.
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      1. 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):875-82. PMID: 27447051.
        View in: PubMed
      2. Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016 May 19; 165(5):1267-79. PMID: 27180905.
        View in: PubMed
      3. Quinn JJ, Zhang QC, Georgiev P, Ilik IA, Akhtar A, Chang HY. Rapid evolutionary turnover underlies conserved lncRNA-genome interactions. Genes Dev. 2016 Jan 15; 30(2):191-207. PMID: 26773003.
        View in: PubMed
      4. Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nat Protoc. 2016 Feb; 11(2):273-90. PMID: 26766114.
        View in: PubMed
      5. 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.
        View in: PubMed
      6. Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Erratum: Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 2015 Nov 12; 527(7577):264. PMID: 26416736.
        View in: PubMed
      7. Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY. Systematic discovery of Xist RNA binding proteins. Cell. 2015 Apr 9; 161(2):404-16. PMID: 25843628; PMCID: PMC4425988 [Available on 04/09/16].
      8. Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 2015 Mar 26; 519(7544):486-90. PMID: 25799993; PMCID: PMC4376618.
      9. Nguyen-Tan PF, Zhang Q, Ang KK, Weber RS, Rosenthal DI, Soulieres D, Kim H, Silverman C, Raben A, Galloway TJ, Fortin A, Gore E, Westra WH, Chung CH, Jordan RC, Gillison ML, List M, Le QT. Randomized phase III trial to test accelerated versus standard fractionation in combination with concurrent cisplatin for head and neck carcinomas in the Radiation Therapy Oncology Group 0129 trial: long-term report of efficacy and toxicity. J Clin Oncol. 2014 Dec 1; 32(34):3858-66. PMID: 25366680; PMCID: PMC4239304 [Available on 12/01/15].
      10. Chung CH, Zhang Q, Kong CS, Harris J, Fertig EJ, Harari PM, Wang D, Redmond KP, Shenouda G, Trotti A, Raben D, Gillison ML, Jordan RC, Le QT. p16 protein expression and human papillomavirus status as prognostic biomarkers of nonoropharyngeal head and neck squamous cell carcinoma. J Clin Oncol. 2014 Dec 10; 32(35):3930-8. PMID: 25267748; PMCID: PMC4251957 [Available on 12/10/15].
      11. Harari PM, Harris J, Kies MS, Myers JN, Jordan RC, Gillison ML, Foote RL, Machtay M, Rotman M, Khuntia D, Straube W, Zhang Q, Ang K. Postoperative chemoradiotherapy and cetuximab for high-risk squamous cell carcinoma of the head and neck: Radiation Therapy Oncology Group RTOG-0234. J Clin Oncol. 2014 Aug 10; 32(23):2486-95. PMID: 25002723; PMCID: PMC4121506.
      12. Deng L, Zhang QC, Chen Z, Meng Y, Guan J, Zhou S. PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W290-5. PMID: 24852252; PMCID: PMC4086081.
      13. Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. Landscape and variation of RNA secondary structure across the human transcriptome. Nature. 2014 Jan 30; 505(7485):706-9. PMID: 24476892; PMCID: PMC3973747.
      14. Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Extensive variation in chromatin states across humans. Science. 2013 Nov 8; 342(6159):750-2. PMID: 24136358; PMCID: PMC4075767.
      15. Deng L, Guan J, Wei X, Yi Y, Zhang QC, Zhou S. Boosting prediction performance of protein-protein interaction hot spots by using structural neighborhood properties. J Comput Biol. 2013 Nov; 20(11):878-91. PMID: 24134392; PMCID: PMC3822376.
      16. Zhang QC, Petrey D, Garzón JI, Deng L, Honig B. PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res. 2013 Jan; 41(Database issue):D828-33. PMID: 23193263; PMCID: PMC3531098.
      17. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. 2012 Oct 25; 490(7421):556-60. PMID: 23023127; PMCID: PMC3482288.
      18. Eletsky A, Petrey D, Zhang QC, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Honig B, Montelione GT, Szyperski T. Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771. J Struct Funct Genomics. 2012 Mar; 13(1):1-7. PMID: 22223187; PMCID: PMC3654790.
      19. Schröder S, Cho S, Zeng L, Zhang Q, Kaehlcke K, Mak L, Lau J, Bisgrove D, Schnölzer M, Verdin E, Zhou MM, Ott M. Two-pronged binding with bromodomain-containing protein 4 liberates positive transcription elongation factor b from inactive ribonucleoprotein complexes. J Biol Chem. 2012 Jan 6; 287(2):1090-9. PMID: 22084242; PMCID: PMC3256921.
      20. Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D. MarkUs: a server to navigate sequence-structure-function space. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W357-61. PMID: 21672961; PMCID: PMC3125806.
      21. Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W283-7. PMID: 21609948; PMCID: PMC3125747.
      22. Zhang QC, Petrey D, Norel R, Honig BH. Protein interface conservation across structure space. Proc Natl Acad Sci U S A. 2010 Jun 15; 107(24):10896-901. PMID: 20534496; PMCID: PMC2890749.
      23. Colby DW, Zhang Q, Wang S, Groth D, Legname G, Riesner D, Prusiner SB. Prion detection by an amyloid seeding assay. Proc Natl Acad Sci U S A. 2007 Dec 26; 104(52):20914-9. PMID: 18096717; PMCID: PMC2409241.
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