Principal Investigator,Professor : Center of Microbial Genomics and Metagenomics

Prof. Zhu Baoli
Dept.:CAS Key Laboratory of Pathogenic Microbiology and Immunology
Address:NO.1 West Beichen Road, Chaoyang District, Beijing 100101, P.R.China
Telephone/fax:+86-10-64807362 (Office)
Fax:+86-10-64807358 (Office)
2006-present Working as principal investigator and Director of Microbial Genome Research Center in The Institute of Microbiology, full professor of the graduate school, Chinese Academy of Sciences. Research interests: immunogenomics, comparative genomics and metagenomics.
2001 – 2006 Working as assistant scientist in BACPAC Resource Center (CHORI, Children’s Hospital Oakland Research Institute, California) on few genome projects: The NIH funded ENCODE project; the rat genome project; human genome project, the zebrafish genome project; the chimpanzee genome project; The planaria genome project; the NIH funded BAC network project; the NSF funded BAC construction project.
Cancer Genomic Research: Study of genome amplicons and deletions in cancer patients using CGH (comparative genomic hybridization), ESP (BAC-End sequence Profiling), and DNA fingerprinting analysis of BAC clones created from cancer patients.
1999-2000 Working as Postdoctoral Fellow II in BAC-PAC resources (Roswell Park Cancer Institute, New York) on construction of a new circular Yeast Artificial Chromosome (cYAC) vector, which carries a conditional galatose promoter upstream the yeast centromere allowing the cYAC copy number amplification. Construction of cYAC library for Dictyostelium Discoideum genome using new cYAC vector. Application of the cYAC vector in order to isolate DNA sequences or genes by Transformation Associated Recombination.
1996-1998 As a postdoctoral research associate in The Babraham Institute, Cambridge, UK, working on the construction of Bacterial Artificial Chromosome (BAC) Library for Cattle Genome in order to study the Quantitative Trait Loci of milk production. Positional cloning of Polled gene in cattle by applying BAC clone contiqing, PCR, exon trapping and microsatellite marker screening from BAC clones.
1995-1996 As a visiting scholar in The Babraham Institute, Cambridge, working on the identification of a putative tumor suppressor gene for human hepatocellular carcinoma.
1993-1995 As a research scientist in Beijing Agricultural University (BAU), China, working on the construction of human genomic library (EMBL3) and the isolation of human erythropoietin gene and the insulin gene. The expression of both genes in CHO cells and other mammalian cell lines was achieved.
Isolation of bovine beta-lactoglobulin (BLG) gene's regulatory element by PCR, the DNA sequencing determination. The test expression of human growth hormone gene under the control BLG regulatory element both in cultured mouse mammary gland cells and in transgenic mice was succeeded.
Co-supervisor of the Project "Isolation and DNA sequence determination of human erythropoietin gene and its expression in mammalian cells" supported by China’s National Foundation for Natural Sciences".
1988-1992 As Ph.D. candidate in BAU, working on the construction of secretive-expression vector for the high-level expression of porcine growth hormone (pGH) gene in E.coli in order to obtain biologically active form of pGH directly from periplasmic space of E.coli.
Co-worker involving in the project “Construction of a vaccinia virus expression vector to express the pGH cDNA gene both in human h143 cells and in infected mouse.
1985-1987 As assistant research scientist in BAU, working on the construction of porcine genomic library, the characterization and the DNA sequence determination of pGH gene; Participating in the construction of variety prokaryotic expression vectors to express the pGH cDNA gene in E.coli as a part of the NATIONAL 7th FIVE-YEARS PLAN REASEARCH PROGRAMME; The expression of the Klenow Fragment gene in E.coli and its large-scale preparation and purification
Research Interests
His research is mainly focused on microbial genomics, metagenomics, genetic testing of pathogenic microbes and immunogenomics. His current research projects include human microbiome study on HBV patient, comparative genomics on BCG vaccine and Streptococcus suis, antibiotic resistance genes on different bacterial genomes and single cell genomics.
[1] Yongfei Hu#, Chengzhang Fu#, Yunpeng Huang, Yeshi Yin, Gong Cheng, Fang Lei, Na Lu, Jing Li, Elizabeth Jane Ashforth, Lixin Zhang and Baoli Zhu*. 2010. Novel lipolytic genes from microbial metagenomic library of South China Sea marine sediment. FEMS Microbiology Ecology. 72(2): 228-237
[2] Yongfei Hu#, Chengzhang Fu#, Yeshi Yin, Gong Cheng, Fang Lei, Xi Yang, Jing Li, Elizabeth Jane Ashforth, Lixin Zhang* and Baoli Zhu*. 2010. Construction and preliminary analysis of a deep-sea sediment metagenomic fosmid library from Qiongdongnan Basin, South China Sea. Marine Biotechnology. (Online)
[3] Florent E. Angly, Dana Willner, Alejandra Prieto-Davo, Robert A. Edwards, Robert Schmieder,Rebecca Vega-Thurber, Dionysios A. Antonopoulos5, Katie Barott, Matthew T. Cottrell, Christelle Desnues8, Elizabeth A. Dinsdale, Mike Furlan1, Matthew Haynes, Matthew R. Henn, Yongfei Hu, David L. Kirchman, Tracey McDole, John D. McPherson, Folker Meyer, R. Michael Miller, Egbert Mundt, Robert K. Naviaux, Beltran Rodriguez-Mueller, Rick Stevens, Linda Wegley, Lixin Zhang, Baoli Zhu, Forest Rohwer. (2010). The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes. PLOS Computational Biology. 5(12): e1000593. doi:10.1371/journal.pcbi.1000593.
[4] Yeshi Yin , Fang Lei, Liying Zhu, Sujuan Li, Zuowei Wu, Ruifen Zhang, George F. Gao, Baoli Zhu and Xin Wang. (2010). Exposure of different bacterial inocula to newborn chicken affects gut microbiota development and ileum gene expression.The ISME Journal. doi:10.1038/ismej.2009.128.
[5] Laurent Abi-Rached, Heiner Kuhl, Christian Roos, Boudewijn ten Hallers, Baoli Zhu, Lucia Carbone, Pieter J. de Jong, Alan R. Mootnick, Florian Knaust, Richard Reinhardt, Peter Parham,and Lutz Walter, 2010, A Small, Variable, and Irregular Killer Cell Ig-Like Receptor Locus Accompanies the Absence of MHC-C and MHC-G in Gibbons. The Journal of Immunology. 2010, 184, 1379 -1391.
[6] Xinxing Zhu#, Suhua Chang#, Kechi Fang, Sijia Cui, Jun Liu, Zuowei Wu, Xuping Yu, George F. Gao, Huanming Yang, Baoli Zhu*, Jing Wang* , 2009, MyBASE: a database for genome polymorphism and gene function studies of Mycobacterium. BMC Microbiology, 9(1): 40. (in press)
[7] Jun Liu, Vanessa Tran, Andrea S. Leung, David C. Alexander1and Baoli Zhu.,2009.BCG vaccines. Human Vaccines 5:2, 70-78; February 2009.
[8] Andrea S Leung, Vanessa Tran, Zuowei Wu, Xuping Yu, David C Alexander, George Fu Gao, Baoli Zhuand Jun Liu,2008. Novel genome polymorphisms in BCG vaccine strains and impact on efficacy. BMC Genomics 2008, 9:413doi:10.1186/1471-2164-9-413.
[9] Andrea S Leung , Vanessa Tran , Zuowei Wu , Xuping Yu , David C Alex , George Fu Gao , Baoli Zhu , Jun Liu. BioMed Central. Bmc Genomics,2008(on line).
[10] von Schalburg KR, Leong J, Cooper GA, Robb A, Beetz-Sargent MR, Lieph R, Holt RA, Moore R, Ewart KV, Driedzic WR, Ten Hallers BF, Zhu B, de Jong PJ, Davidson WS, Koop BF. Rainbow Smelt (Osmerus mordax) Genomic Library and EST Resources. Mar Biotechnol (NY). 2008 Apr 2. [Epub ahead of print]
[11] Suhua Chang, Jiajie Zhang, Xiaoyun Liao, Xinxing Zhu, Dahai Wang, Jiang Zhu, Tao Feng, Baoli Zhu, George F. Gao, Jian Wang, Huanming Yang, Jun Yu * and Jing Wang *. 2007. Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Research. (on line)
[12] Lyle R, Prandini P, Osoegawa K, ten Hallers B, Humphray S, Zhu B, Eyras E, Castelo R, Bird CP, Gagos S, Scott C, Cox A, Deutsch S, Ucla C, Cruts M, Dahoun S, She X, Bena F, Wang SY, Van Broeckhoven C, Eichler EE, Guigo R, Rogers J, de Jong PJ, Reymond A, Antonarakis SE. Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21. Genome Res. 2007 Nov;17(11):1690-6.
[13] Wang S, Xu P, Thorsen J, Zhu B, de Jong PJ, Waldbieser G, Kucuktas H, Liu Z. Characterization of a BAC library from channel catfish Ictalurus punctatus: indications of high levels of chromosomal reshuffling among teleost genomes. Mar Biotechnol (NY). 2007 Nov-Dec;9(6):701-11
[14] ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.
[15] Chang S, Zhang J, Liao X, Zhu X, Wang D, Zhu J, Feng T, Zhu B, Gao GF, Wang J, Yang H, Yu J, Wang J. Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Res. 2007 Jan;35 (Database issue):D376-80.
[16] Carbone L, Vessere GM, ten Hallers BF, Zhu B, Osoegawa K, Mootnick A, Kofler A, Wienberg J, Rogers J, Humphray S, Scott C, Harris RA, Milosavljevic A, de Jong PJ. A high-resolution map of synteny disruptions in gibbon and human genomes. PLoS Genet. 2006 Dec 29;2(12):e223. 2006 Nov 13.
[17] Chourrout D, Delsuc F, Chourrout P, Edvardsen RB, Rentzsch F, Renfer E, Jensen MF, Zhu B, de Jong P, Steele RE, Technau U (2006). Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements. Nature. 442(7103):684-7.
[18] Leeb T, Vogl C, Zhu B, de Jong PJ, Binns MM, Chowdhary BP, Scharfe M, Jarek M, Nordsiek G, Schrader F, Blocker H. A human-horse comparative map based on equine BAC end sequences. Genomics. 2006 Jun;87(6):772-6.
[19] Perrocheau M, Boutreux V, Chadi S, Mata X, Decaunes P, Raudsepp T, Durkin K, Incarnato D, Iannuzzi L, Lear TL, Hirota K, Hasegawa T, Zhu B, de Jong P, Cribiu EP, Chowdhary BP, Guerin G. Construction of a medium-density horse gene map Anim Genet. 2006 Apr;37(2):145-55.
[20] Thorsen J, Zhu B, Frengen E, Osoegawa K, de Jong PJ, Koop BF, Davidson WS, Hoyheim B. A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects. BMC Genomics. 2005 Apr 4;6(1):50.
[21] Ng SH, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJ, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddiqui A, Thorsen J, Wye N, Yang G, Zhu B. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics. 2005 Oct;86(4):396-404.
[22] Milosavljevic A, Harris RA, Sodergren EJ, Jackson AR, Kalafus KJ, Hodgson A, Cree A, Dai W, Csuros M, Zhu B, de Jong PJ, Weinstock GM, Gibbs RA. Pooled genomic indexing of rhesus macaque. Genome Res. 2005 Feb;15(2):292-301.
[23] ENCODE Project Consortium, The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40.
[24] Kingsley D, Baoli Zhu, Kazutoyo Osoegawa, Pieter de Jong, Jacqueline Schein, Marco Marra, Catherine Peichel, Chris Amemiya, Dolph Schluter, Sarita Balabhadra, Brian Friedlander, Yee Man Cha, Mark Dickson, Jane Grimwood, Jeremy Schmutz, Williams Talbot & Richard Myers. (2004) New Genomic Tools For Molecular Studies Of Evolutionary Changes In Threespine Sticklebacks. Behaviour 141, 1331-1344.
[25] Robledo R, Bender P, Leonard J, Zhu B, Osoegawa K, de Jong P, Xu X, Yao Z, Roe B. The immunoglobulin lambda variable light-chain region in primates has been shaped by multiple, independent, small-scale and large-scale insertion/deletion events. Genomics. 2004 Oct;84(4):678-85.
[26] Zhao S, Shetty J, Hou L, Delcher A, Zhu B, Osoegawa K, de Jong P, Nierman WC, Strausberg RL, Fraser CM. Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. Genome Res. 2004 Oct;14(10A):1851-60. Epub 2004 Sep 13.
[27] Zhu B, Osoegawa K, Shu CL, Ren T, Cao Q, Vessere GM, Lutz MM, Jensen-Seaman MI, Zhao S, de Jong PJ. BAC resources for the rat genome project. Genome Res. 2004 Apr;14(4):780-5.
[28] Krzywinski M, Wallis J, Gosele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, Albracht D, Asano J, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Davito J, Fjell C, Gaige T, Ganten D, Girn N, Guggenheimer K, Himmelbauer H, Kreitler T, Leach S, Lee D, Lehrach H, Mayo M, Mead K, Olson T, Pandoh P, Prabhu AL, Shin H, Tanzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, Zimdahl H, Marziali A, Osoegawa K, Zhao S, Siddiqui A, de Jong PJ, Warren W, Mardis E, McPherson JD, Wilson R, Hubner N, Jones S, Marra M, Schein J. Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res. 2004 Apr;14(4):766-79.
[29] Rat Genome Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521.
[30] Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 2003 Aug 14;424(6950):788-93.
[31] Gernot Glockner, …, Baoli Zhu et al (2002) Sequence and analysis of chromosome 2 of Dictyostelium Discoideum. Nature 418:79-85.
[32] Changjing Zeng, Natalay Kouprina, Baoli Zhu, Al Cairo, Maarten Hoek, George Cross, Vladimir Larionov and Pieter de Jong (2001) Large-Insert BAC/YAC Libraries for Selective Re-isolation of Genomic Regions by Homologous Recombination in Yeast. Genomics 77(1-2):27-34.
[33] Zhu B, Smith JA, Miller JR et al (1999) A 5x Genome Coverage Bovine BAC Library: Production, Characterization, and Distribution. Mammalian Genome 10(7):706-9.
[34] Siming Shou, Baoli Zhu, Shunzhang Qi (1999). Cloning of Human Insulin Genomic Gene by Enrichment Library. Chinese Journal of Biochemistry and Molecular Biology. Vol.15 #2 pp20-25.
[35] Cui Zhenzhong, Zhu Baoli, et al (1998). Cloning and Sequencing of Erythropoietin Genomic Gene. Chinese Journal of Biochemistry and Molecular Biology. Vol.14 N#6 pp684-690.
[36] Yang guoqing, Dai Yanping, Zhu Baoli, Chen Yongfu, Qi Shunzhang (1996). Cloning of 5'- regulatory Element of Bovine Beta-lactoglobulin Gene and its Utilization in generation of mammary Bioreactor; SCIENCE IN CHINA serie C-Life Sciences, 1996, Vol.39, N#6 pp662-669.
[37] Lu Danhong, Zhu Baoli, et al (1994). Expression of pGH cDNA gene in h143 cells using vaccinia virus expression vector. Chinese Biochemical Journal 11(5):504-509.
[38] Zhu Baoli et al (1993). Construction of a Secretory expression system for the overexpression of porcine growth hormone cDNA gene in E.coli. Journal of Agricultural Biotechnology, 1(1):50-56.
[39] Yang Qing, Zhu Baoli et al (1992). Cloning and partly sequencing of the porcine growth hormone gene from pituitary gland DNA. Chinese Journal of Biotechnology, 8(4):318-323