Welcome to Zhu lab
Home: General Info: Research: Lab Member: Protocol/Facility: Publication: Curriculum Vitae: Contact Info: JHMI Home


Publications

  Peer-reviewed original research articles (in reverse chronological order)

 

1.      Tarrant MK, Rho H-S, Xie Z, Jiang YL, Gross C, Qian J, Ichikawa Y, Zachara N, Etzkorn F, Hart GW, Jeong J-S, Blackshaw S, Zhu H, Cole PA. Multi-faceted regulation of protein kinase CK2 by phosphorylation and glycosylation revealed through semisynthesis. Nat Chem Biol 2011, accepted.

2.      Reece-Hoyes JS, Barutcu AR, McCord RP, Jeong J-S, Jiang L, MacWilliams A, Yang X, Salehi-Ashtiani K, Hill DE, Blackshaw S, Zhu H, Dekker J, Walhout AJM. Yeast one-hybrid assays for high-throughput human gene regulatory network mapping. Nat Methods 2011; Oct 30. doi: 10.1038/nmeth.1764. [Epub ahead of print].

3.      Zheng D, Wan J, Cho YG, Wang L, Chiou C-J, Pai S, Woodard C, Zhu J, Kiao G, Martinez-Maza O, Qian J, Zhu H, Hayward GS, Ambinder RF, Hayward SD. Comparison of humoral immune responses to Epstein-Barr virus and Kaposis Sarcoma-assoicated herpesvirus using a viral proteome microarray. J Infect Dis 2011; 204(11):1683-91.

4.      Li Y; Tao S-C; Bova G, Liu A, Chan D, Zhu H, Zhang H. Detection and verification of glycosylation patterns of glycoproteins from clinical specimens using lectin microarrays and lectin-based immunosorbent assays. Anal Chem 2011; 83(22):8509-16.

5.      Li R, Zhu J, Xie Z, Liao G, Liu J, Chen M-R, Hu S, Woodard C, Lin J, Taverna S, Desai P, Ambinder R, Hayward GS, Qian J, Zhu H*, Hayward SD. Conserved herpesvirus kinases regulate TIP60 to promote virus replication. Cell Host & Microbe 2011; 10(4):390-400.

6.      Rapicavoli NA, Poth EM, Zhu H, Blackshaw S. The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Neural Dev 2011; 6(1):32.

7.      Lu J-Y, Lin Y-Y, Sheu J-C, Wu J-T, Lee F-J, Chen Y, Lin M-I, Chiang F-T, Tai T-Y, Berger SL, Zhao Y, Tsai K-S, Zhu H*, Chuang L-M, and Boeke JD. Acetylation of AMPK controls intrinsic aging independently of caloric restriction. Cell 2011; 146: 969-79.

8.      Li G, Zhou X, Kong L, Wang Y, Zhang H, Zhu H, Mitchell TK, Dean RA, Xu JR. MoSfl1 is important for virulence and heat tolerance in Magnaporthe oryzae. PLoS One 2011; 6(5):e19951.

9.      Hu S, Xie Z, Blackshaw S, Qian J, Zhu H*. Characterization of protein-DNA interactions using protein microarrays. Cold Spring Harb Protoc 2011(5). doi: 0.1101/pdb.prot5614.

10.  Thao S, Chen CS, Zhu H, Escalante-Semerena JC. N-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity. PLoS One 2010; 31;5(12):e15123. PMCID: PMC3013089

11.  Yin Z, Tao SC, Cheong R, Zhu H, Levchenko A. An integrated micro-electro-fluidic and protein arraying system for parallel analysis of cell responses to controlled microenvironments. Integr Biol (Camb) 2010; 2(9):416-23. Epub 2010 Aug 10.

12.  Zhang K, Chen Y, Zhang Z, Tao S, Zhu H, Zhao Y. Unrestrictive identification of non-phosphorylation PTMs in yeast kinases by MS and PTMap. Proteomics 2010; 10(5):896-903. PMCID: PMC2892973

13.  Xie Z, Hu S, Blackshaw S, Zhu H*, Qian J. hPDI: a database of experimental human protein-DNA interactions. Bioinformatics 2009; 26(2):287-9. PMCID: PMC2804296

14.  Hu S, Xie Z, Onishi A, Yu X, Jiang L, Lin J, Rho H-S, Woodard C, Wang H, Jeong J-S, Long S, He X, Wade H, Blackshaw S, Qian J, Zhu H*. Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signalling. Cell 2009; 139:610-22. PMCID: PMC2774939

15.  Kung L, Tao, S-C, Qian J, Smith M, Snyder M, Zhu H*. Global analysis of the glycoproteome in S. cerevisiae reveals new roles for protein glycosylation. Mol Syst Biol 2009; 5:308. Epub 2009 Sep 15. PMCID: PMC2758718

16.  Song Q, Liu G, Hu S, Zhang Y, Tao Y, Han Y, Zeng H, Huang W, Li F, Chen P, Zhu J, Hu C, Zhang S, Li Y, Zhu H*, Wu L. Novel Autoimmune Hepatitis-Specific Autoantigens Identified Using Protein Microarray Technology. J Proteome Res 2010; 9(1):30-9. [Epub ahead of print]. PMCID: PMC2801765

17.  Chen CS, Sullivan S, Anderson T, Tan AC, Alex PJ, Brant S, Taylor MV, Burek L, Cuffari C, Wang H, Li R, Datta LW, Winslow R, Zhu H*, Li X. Identification of novel serological biomarkers for inflammatory bowel disease using a protein chip of whole E. coli proteome. Mol Cell Proteomics 2009; 8(8):1765-76. Epub 2009 Apr 7. PMCID: PMC2722769

18.  Zhu J, Liao G, Shan L, Zhang J, Chen M-R, Hayward GS, Hayward SD, Desai P, Zhu H*. Protein array identification of substrates of the Epstein-Barr Virus protein kinase BGLF4. J Virol 2009; 83:5219-31. Epub 2009 Feb 25. PMCID: PMC2682057

19.  Lin Y-y, Lu J-y, Zhang J, Walter W, Dang W, Wan J, Tao SC, Qian J, Zhao Y, Boeke JD, Berger SL, Zhu H*. Protein acetylation microarray reveals NuA4 controls key metabolic target regulating gluconeogenesis. Cell 2009; 136:1073C1084. PMCID: PMC2696288

20.  Brody JR, Hucl T, Costantino CL, Eshleman JR, Gallmeier E, Zhu H, van der Heijden MS, Winter JM, Wikiewicz AK, Yeo CJ, Kern SE. Limits to thymidylate synthase and TP53 genes as predictive determinants for fluoropyrimidine sensitivity and further evidence for RNA-based toxicity as a major influence. Cancer Res. 2009; 69:984-91.

21.  Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y. Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics 2009; 8:215-25. Epub 2008 Aug 23.

22.  Tao SC, Li Y, Zhou J, Qian J, Schnaar RL, Zhang Y, Goldstein IJ, Zhu H*, Schneck JP. Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers. Glycobiology 2008; 18:761-9. Epub 2008 Jul 14. PMCID: PMC2733773

23.  Chen CS, Korobkova E, Chen H, Zhu J, Jian X, Tao S-C, He H, Zhu H*. A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nat Methods 2008; 5:69-74. Epub 2007 Dec 16. PMCID: PMC2576280

24.  Liu X, Yu X, Zack DJ, Zhu H, Qian J. TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics 2008; 9:271. PMCID: PMC2438328

25.  Evans-Nguyen KM, Tao SC, Zhu H, Cotter RJ. Protein arrays on patterned porous gold substrates interrogated with mass spectrometry: detection of peptides in plasma. Anal Chem 2008; 80:1448-58. Epub 2008 Feb 7.

26.  Lu J-Y, Lin Y-Y, Tao S-C, Zhu J, Pickart CM, Qian J, Zhu H*. Functional dissection of a HECT ubiquitin E3 ligase. Mol Cell Proteomics 2008; 7:35-45. Epub 2007 Oct 19. PMCID: PMC2861892

27.  Hu S, Li Y, Liu G, Song Q, Wang L, Han Y, Zhang Y, Song Y, Yao X, Tao Y, Zeng H, Wang J, Zhu H*, Chen Z-N, Wu L. A protein chip approach for high-throughput antigen identification and characterization. Proteomics 2007; 7:2151-61.

28.  Zhu J, Gopinath K, Murali A, Yi G, Hayward SD, Zhu H*, Kao C. RNA binding proteins that inhibit RNA virus infection. Proc Natl Acad Sci U S A 2007; 104:3129-34. Epub 2007 Feb 20.

29.  Tao S-C & Zhu H*. Protein chip fabrication by capture of nascent polypeptides. Nat Biotechnol 2006; 24:1253-4.

30.  Zhu H, Hu S, Jona G, Zhu X, Kreiswirth N, Willey BM, Mazzulli T, Liu G, Song Q, Chen P, Cameron M, Tyler A, Wang J, Wen J, Chen W, Compton S, Snyder M. Severe acute respiratory syndrome diagnostics using a coronavirus protein chip. Proc Natl Acad Sci U S A 2006; 103:4011-6.

31.  Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M. Global analysis of protein phosphorylation in yeast. Nature 2005; 438:679-84.

32.  Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL. Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc Natl Acad Sci U S A 2004; 101:16594-9.

33.  Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M. Regulation of gene expression by a metabolic enzyme. Science 2004; 306:482-4.

34.  Liu G, Hu S, Hu Y, Chen P, Yin J, Wen J, Wang J, Lin L, Liu J, You B, Yin Y, Li S, Wang H, Ren Y, Ji J, Zhao X, Sun Y, Zhang X, Fang J, Wang J, Liu S, Yu J, Zhu H, Yang H. The C-terminal portion of the nucleocapsid protein demonstrates SARS-CoV antigenicity. Genomics Proteomics Bioinformatics 2003; 1:193-7.

35.  Kafadar KA, Zhu H, Snyder M, Cyert MS. Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I. Genes Dev 2003; 17:2698-708.

36.  Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M. Global analysis of protein activities using proteome chips. Science 2001; 293:2101-5.

37.  Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M. Analysis of yeast protein kinases using protein chips. Nature Genet 2000; 26: 283-9.

38.  Zhu H, Blackmon BP, Sasinowski M, Dean RA. Physical map and organization of chromosome 7 in the rice blast fungus, Magnaporthe grisea. Genome Res 1999; 9: 751-62.

39.  Zhu H & Dean RA. A novel method increases the transformation efficiency by 70-fold in the construction of a bacterial artificial chromosome (BAC) library. Nucl Acids Res 1999; 27: 910-1.

40.  Zhu H, Choi SD, Johnston AK, Wing RA, Dean RA. A large-insert (130 kbp) bacterial artificial chromosome library of the rice blast fungus Magnaporthe grisea: genome analysis, contig assembly, and gene cloning. Fungal Gen Biol 1997; 21: 337-47.

41.  Li D & Zhu H. Investigation of genomic polymorphisms and phylogenetics in pathogenic fungi. Acta Micro Sinica 1997; 37: 135-41.

42.  Zhu H, Whitehead DS, Lee Y-H, Dean RA. Genetic analysis of developmental mutants and rapid chromosome mapping of APP1, a gene required for appressorium formation in Magnaporthe grisea. Mol Plant-Microbe Interact 1996; 9: 767-74.

43.  Liu G, Liu Z, Jia J, Liu L, Tai L, Li X, Zhu H, Zhu L-H. Studies on fusants derived from intergeneric protoplast fusion of P. sapidus and L. edodes by RAPD analysis. Hereditas 1995; 17(5): 37-40.

44.  Zhu H, Zhai W, Chen M, Wang J, Lei CL, Ling ZZ, Zhu L-H. Fingerprinting field isolates using a repetitive element POR6 in Pyricularia oryzae. Acta Mycologica Sinica 1995; 14: 218-25.

45.  Zhu H, Zhang Q, Wang CL, Yang WC, Zhu L-H. RAPD fingerprints of the rice blight pathogen, Xanthomonas oryzae pv. oryzae. Chinese Journal of Biotechnology 1995; 11: 281-4.

46.  YB Xu, Shen ZT, Xu JC, Zhu H, Chen Y, Zhu L-H. Interval mapping quantitative-trait loci using molecular markers in rice (Oryza sativa L.). Science in China (Series B) 1995; 38: 971-6.

47.  DM Li, Wang DL, Li RY, Zhu H, Zhu L-H. Fingerprinting the clinical isolates of Candida albican using RAPD markers. Acta Mycologica Sinica 1995; 14: 123-9.

48.  Zhu H, Chen ML, Zhu L-H*, Jiang WR, Wang JL, Lei CL, Ling ZZ. DNA fingerprinting the pathogenicity in the rice blast fungus. Acta Agronomica Sinica 1994; 20: 257-63.

49.  Zhu H, Qu F, Zhu L-H. Isolation of genomic DNAs from fungi using benzyl chloride. Mycosystema 1994; 01: 36-42.

50.  Zhu H, Qu F, Zhu L-H. Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride. Nucl Acids Res 1993; 34: 1156-7.

51.  Zhu H & Zhu L-H. DNA fingerprinting of the field isolates of the rice blast fungus in East Asia. Mycologia 1993; 5: 56-61.

52.  Zhu H & Zhu L-H. A novel DNA purification method for fungi. Acta Mycologia 1993; 45: 354-9.

 

  Review articles

 

1.      Xie Z, Hu S, Qian J, Blackshaw S, Zhu H*. Systematic characterization of protein-DNA interactions. Cell Mol Life Sci. 2011 May; 68(10):1657-68. Epub 2011 Jan 5.

2.      Hu S, Xie Z, Qian J, Blackshaw S, Zhu H*. Functional protein microarray technology. Wiley Interdiscip Rev Syst Biol Med. 2011 May-Jun; 3(3):255-68. doi: 10.1002/wsbm.118.

3.      Lin J, Xie Z, Zhu H*, Qian J. Understanding protein phosphorylation on a systems level. Brief Funct Genomic Proteomic 2009; 9:32-42. Epub 2010 Jan 7. PMCID: PMC2813495

4.      Zhu H* & Huang J. A combined force of chemical genetics and protein microarrays. Drug Discovery Ser 2007; 8:261-274.

5.      Chen C and Zhu H*. Protein microarrays. Biotechniques 2006; Vol 40:432-9.

6.      Tao SC, Chen CS, Zhu H*. Applications of protein microarray technology. Comb Chem High Throughput Screen 2007; 10:706-18.

7.      Smith MG, Jona G, Ptacek J, Devgan G, Zhu H, Zhu X, Snyder M. Global analysis of protein function using protein microarrays. Mech Ageing Dev 2005; 126:171-5.

8.      Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. Protein analysis on a proteomic scale. Nature 2003; 422:208-15.

9.      Zhu H, Bilgin M, Snyder M. Proteomics. Ave Rev Biochem 2003; 72:783-812.

10.  Zhu H & Snyder M. 'Omic' approaches for unraveling signaling networks. Curr Opin Cell Biol 2002; 14:173-9.

11.  Zhu H & Snyder M. Protein arrays and microarrays. Curr Opin Chem Biol 2001; 5:40-5.

12.  Zhu H & Snyder M. Biochemical assays in a chip format. Curr Drug Disc 2001; 6:31-4.

 

  Book chapters, monographs

 

1. Dean RA, Gilbert RW, Liu SH, Mitchell TK, Zhu H. Signal transduction in appressorium formation. In: Fungal Molecular Biology. Ed Edward, RS, APS Academy.1996; pp. 328-47.

2. Chen C-S, Tao S-C, Zhu H*. Protein microarray technologies. In: Proteomics. Ed CD OConnor & BD Hames, Scion Publishing Ltd. 2008; pp. 183-206.

3. Mitchell TK, Dean RA, Xu J-R, Zhu H, Oh YY, Rho H-S. Protein Chips and Chromatin Immunoprecipitation C Emerging Technologies to Study Macromolecule Interactions in M. grisea. In: Advances in Genetics, Genomics and Control of Rice Blast Disease. Ed G-L Wang and B Valent, Springer Netherlands Ltd. 2009; pp. 73-82.

5. Li Y, Tao S-C, Zhu H, Schneck JP. High\throughput lectin microarray\based analysis of live cell surface glycosylation. In Current Protocols in Protein Science 12.9.1-12.9.7, February 2011.

6. Jeong JS, Rho H-S, Zhu H*. A Functional Protein Microarray Approach to Characterizing Posttranslational Modifications on Lysine Residues. In: Protein Microarray for Disease Analysis. Ed Catherine J. Wu, SpringerLink, Volume 723, 2011, DOI: 10.1007/978-1-61779-043-0.

*Corresponding author.