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Qian Zhang

Title(s)Postdoctoral Scholar, Medicine
SchoolHealth Sciences
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    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. Kim HK, Xu J, Chu K, Park H, Jang H, Li P, Valdmanis PN, Zhang QC, Kay MA. A tRNA-Derived Small RNA Regulates Ribosomal Protein S28 Protein Levels after Translation Initiation in Humans and Mice. Cell Rep. 2019 Dec 17; 29(12):3816-3824.e4. PMID: 31851915.
      View in: PubMed
    2. Li P, Shi R, Zhang QC. icSHAPE-pipe: A comprehensive toolkit for icSHAPE data analysis and evaluation. Methods. 2019 Oct 10. PMID: 31606387.
      View in: PubMed
    3. Xiong L, Xu K, Tian K, Shao Y, Tang L, Gao G, Zhang M, Jiang T, Zhang QC. SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nat Commun. 2019 10 08; 10(1):4576. PMID: 31594952.
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    4. Zhang F, Zhuang J, Esteban Fernández de Ávila B, Tang S, Zhang Q, Fang RH, Zhang L, Wang J. A Nanomotor-Based Active Delivery System for Intracellular Oxygen Transport. ACS Nano. 2019 Oct 22; 13(10):11996-12005. PMID: 31556988.
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    5. Mell LK, Shen H, Nguyen-Tân PF, Rosenthal DI, Zakeri K, Vitzthum LK, Frank SJ, Schiff PB, Trotti AM, Bonner JA, Jones CU, Yom SS, Thorstad WL, Wong SJ, Shenouda G, Ridge JA, Zhang QE, Le QT. Nomogram to Predict the Benefit of Intensive Treatment for Locoregionally Advanced Head and Neck Cancer. Clin Cancer Res. 2019 Dec 01; 25(23):7078-7088. PMID: 31420360.
      View in: PubMed
    6. Gao Y, Pei G, Li D, Li R, Shao Y, Zhang QC, Li P. Multivalent m6A motifs promote phase separation of YTHDF proteins. Cell Res. 2019 Sep; 29(9):767-769. PMID: 31388144.
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    7. Zhang Y, Chen Y, Lo C, Zhuang J, Angsantikul P, Zhang Q, Wei X, Zhou Z, Obonyo M, Fang RH, Gao W, Zhang L. Inhibition of Pathogen Adhesion by Bacterial Outer Membrane-Coated Nanoparticles. Angew Chem Int Ed Engl. 2019 Aug 12; 58(33):11404-11408. PMID: 31206942.
      View in: PubMed
    8. Wei X, Ran D, Campeau A, Xiao C, Zhou J, Dehaini D, Jiang Y, Kroll AV, Zhang Q, Gao W, Gonzalez DJ, Fang RH, Zhang L. Multiantigenic Nanotoxoids for Antivirulence Vaccination against Antibiotic-Resistant Gram-Negative Bacteria. Nano Lett. 2019 07 10; 19(7):4760-4769. PMID: 31184899.
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    9. Sun L, Fazal FM, Li P, Broughton JP, Lee B, Tang L, Huang W, Kool ET, Chang HY, Zhang QC. RNA structure maps across mammalian cellular compartments. Nat Struct Mol Biol. 2019 04; 26(4):322-330. PMID: 30886404.
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    10. Gong H, Chen F, Huang Z, Gu Y, Zhang Q, Chen Y, Zhang Y, Zhuang J, Cho YK, Fang RH, Gao W, Xu S, Zhang L. Biomembrane-Modified Field Effect Transistors for Sensitive and Quantitative Detection of Biological Toxins and Pathogens. ACS Nano. 2019 Mar 26; 13(3):3714-3722. PMID: 30831025.
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    11. Zhao J, Qian X, Yeung PY, Zhang QC, Kwok CK. Mapping In Vivo RNA Structures and Interactions. Trends Biochem Sci. 2019 06; 44(6):555-556. PMID: 30853244.
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    12. Zakeri K, Panjwani N, Carmona R, Shen H, Vitzthum LK, Zhang QE, Murphy JD, Mell LK. Generalized Competing Event Models Can Reduce Cost and Duration of Cancer Clinical Trials. JCO Clin Cancer Inform. 2018 12; 2:1-12. PMID: 30652559.
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    13. Li P, Wei Y, Mei M, Tang L, Sun L, Huang W, Zhou J, Zou C, Zhang S, Qin CF, Jiang T, Dai J, Tan X, Zhang QC. Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity. Cell Host Microbe. 2018 12 12; 24(6):875-886.e5. PMID: 30472207.
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    14. Qian X, Zhao J, Yeung PY, Zhang QC, Kwok CK. Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches. Trends Biochem Sci. 2019 01; 44(1):33-52. PMID: 30459069.
      View in: PubMed
    15. Ju Y, Gong J, Yang YT, Zhang QC. Investigation of RNA-RNA Interactions Using the RISE Database. Curr Protoc Bioinformatics. 2018 12; 64(1):e58. PMID: 30408350.
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    16. Zhang Q, Dehaini D, Zhang Y, Zhou J, Chen X, Zhang L, Fang RH, Gao W, Zhang L. Neutrophil membrane-coated nanoparticles inhibit synovial inflammation and alleviate joint damage in inflammatory arthritis. Nat Nanotechnol. 2018 12; 13(12):1182-1190. PMID: 30177807.
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    17. Liu Z, Wang J, Cheng H, Ke X, Sun L, Zhang QC, Wang HW. Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate. Cell. 2018 05 31; 173(6):1549-1550. PMID: 29856959.
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    18. Angsantikul P, Thamphiwatana S, Zhang Q, Spiekermann K, Zhuang J, Fang RH, Gao W, Obonyo M, Zhang L. Coating nanoparticles with gastric epithelial cell membrane for targeted antibiotic delivery against Helicobacter pylori infection. Adv Ther (Weinh). 2018 Jun; 1(2). PMID: 30320205.
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    19. Liu Z, Wang J, Cheng H, Ke X, Sun L, Zhang QC, Wang HW. Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate. Cell. 2018 05 17; 173(5):1191-1203.e12. PMID: 29706542.
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    20. Gong J, Shao D, Xu K, Lu Z, Lu ZJ, Yang YT, Zhang QC. RISE: a database of RNA interactome from sequencing experiments. Nucleic Acids Res. 2018 01 04; 46(D1):D194-D201. PMID: 29040625.
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    21. Lu Z, Gong J, Zhang QC. PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution. Methods Mol Biol. 2018; 1649:59-84. PMID: 29130190.
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    22. Kim HK, Fuchs G, Wang S, Wei W, Zhang Y, Park H, Roy-Chaudhuri B, Li P, Xu J, Chu K, Zhang F, Chua MS, So S, Zhang QC, Sarnow P, Kay MA. A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature. 2017 12 07; 552(7683):57-62. PMID: 29186115.
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    23. Piao M, Sun L, Zhang QC. RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing. Genomics Proteomics Bioinformatics. 2017 10; 15(5):267-278. PMID: 29031843.
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    24. Thamphiwatana S, Angsantikul P, Escajadillo T, Zhang Q, Olson J, Luk BT, Zhang S, Fang RH, Gao W, Nizet V, Zhang L. Macrophage-like nanoparticles concurrently absorbing endotoxins and proinflammatory cytokines for sepsis management. Proc Natl Acad Sci U S A. 2017 10 24; 114(43):11488-11493. PMID: 29073076.
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    25. Zhang X, Angsantikul P, Ying M, Zhuang J, Zhang Q, Wei X, Jiang Y, Zhang Y, Dehaini D, Chen M, Chen Y, Gao W, Fang RH, Zhang L. Remote Loading of Small-Molecule Therapeutics into Cholesterol-Enriched Cell-Membrane-Derived Vesicles. Angew Chem Int Ed Engl. 2017 11 06; 56(45):14075-14079. PMID: 28892588.
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    26. Gao W, Chen Y, Zhang Y, Zhang Q, Zhang L. Nanoparticle-based local antimicrobial drug delivery. Adv Drug Deliv Rev. 2018 03 01; 127:46-57. PMID: 28939377.
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    27. Yu KH, Hart SN, Goldfeder R, Zhang QC, Parker SCJ, Snyder M. HARNESSING BIG DATA FOR PRECISION MEDICINE: INFRASTRUCTURES AND APPLICATIONS. Pac Symp Biocomput. 2017; 22:635-639. PMID: 27897013.
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    28. 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):1267-1279. PMID: 27180905.
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    29. Chen W, Zhang Q, Luk BT, Fang RH, Liu Y, Gao W, Zhang L. Coating nanofiber scaffolds with beta cell membrane to promote cell proliferation and function. Nanoscale. 2016 May 21; 8(19):10364-70. PMID: 27139582.
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    30. Gao W, Zhang Y, Zhang Q, Zhang L. Nanoparticle-Hydrogel: A Hybrid Biomaterial System for Localized Drug Delivery. Ann Biomed Eng. 2016 06; 44(6):2049-61. PMID: 26951462.
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    31. 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.
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    32. 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.
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    33. 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.
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    34. Wang F, Gao W, Thamphiwatana S, Luk BT, Angsantikul P, Zhang Q, Hu CM, Fang RH, Copp JA, Pornpattananangkul D, Lu W, Zhang L. Hydrogel Retaining Toxin-Absorbing Nanosponges for Local Treatment of Methicillin-Resistant Staphylococcus aureus Infection. Adv Mater. 2015 Jun 10; 27(22):3437-43. PMID: 25931231.
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    35. 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 09; 161(2):404-16. PMID: 25843628.
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    36. 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.
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    37. Gao W, Fang RH, Thamphiwatana S, Luk BT, Li J, Angsantikul P, Zhang Q, Hu CM, Zhang L. Modulating antibacterial immunity via bacterial membrane-coated nanoparticles. Nano Lett. 2015 Feb 11; 15(2):1403-9. PMID: 25615236.
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    38. Thamphiwatana S, Gao W, Pornpattananangkul D, Zhang Q, Fu V, Li J, Li J, Obonyo M, Zhang L. Phospholipase A2-responsive antibiotic delivery via nanoparticle-stabilized liposomes for the treatment of bacterial infection. J Mater Chem B. 2014 Dec 14; 2(46):8201-8207. PMID: 25544886.
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    39. 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.
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    40. Gao W, Vecchio D, Li J, Zhu J, Zhang Q, Fu V, Li J, Thamphiwatana S, Lu D, Zhang L. Hydrogel containing nanoparticle-stabilized liposomes for topical antimicrobial delivery. ACS Nano. 2014 Mar 25; 8(3):2900-7. PMID: 24483239.
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    41. 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.
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    42. 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.
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    43. 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 08; 342(6159):750-2. PMID: 24136358.
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    44. 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.
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    45. 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.
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    46. 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.
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    47. 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.
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    48. 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.
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    49. 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.
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