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    Lihua Zhu PhD

    TitleResearch Associate Professor
    InstitutionUniversity of Massachusetts Medical School
    DepartmentProgram in Molecular Medicine
    AddressUniversity of Massachusetts Medical School
    364 Plantation Street, LRB-606
    Worcester MA 01605
    Phone508-856-5256
      Other Positions
      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentBioinformatics and Integrative Biology

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentProgram in Gene Function and Expression

        Overview 
        Narrative

        Academic Background

        Lihua Julie Zhu obtained her Ph.D. in Nutritional Sciences from the University of Wisconsin-Madison in 1999, and her M.S. in Computer Science from DePaul University in Chicago in 2001. Prior to joining the Program in Gene Function and Expression at UMMS, she was an Associate Director of the Bioinformatics Core at the Cancer Center of Northwestern University.

        Computational Biology and Bioinformatics

        Photo: Julie Zhu, Ph.D.

        The purpose of our group is to provide bioinformatics support to the research community in PGFE. Our areas of greatest interest include data integration and data mining of high-throughput experiments such as ChIP-seq, ChIP-chip and microarrays. Working with PGFE researchers, we aim to develop and apply computational tools to analyze and integrate various data sources. For example, we are currently engaged in projects todetect genomic regions where epigenetic events (such as methylation) occur, and to discover transcription factor binding sites/motifs, and correlate the presence of these sites/motifs with gene expression profiles, and developmental or disease stages.

        Examples of the bioinformatics support we provide to PGFE researchers include:

        • Collaborating on grant applications that require bioinformatics expertise
        • Assisting in experimental design, and providing statistical analysis and interpretation of the analysis results
        • Providing data integration and customized bioinformatics pipeline development
        • Managing and mining datasets resulting from high-throughput experiments such as ChIP-seq, ChIP-chip and microarrays
        • Developing customized database applications
        • Offering bioinformatics training workshops


        Bibliographic 
        selected publications
        List All   |   Timeline
        1. Sheppard S, Lawson ND, Zhu LJ. Accurate identification of polyadenylation sites from 3' end deep sequencing using a naive Bayes classifier. Bioinformatics. 2013 Oct 15; 29(20):2564-71.
          View in: PubMed
        2. Nirala NK, Rahman M, Walls SM, Singh A, Zhu LJ, Bamba T, Fukusaki E, Srideshikan SM, Harris GL, Ip YT, Bodmer R, Acharya UR. Survival Response to Increased Ceramide Involves Metabolic Adaptation through Novel Regulators of Glycolysis and Lipolysis. PLoS Genet. 2013 Jun; 9(6):e1003556.
          View in: PubMed
        3. Macneil LT, Watson E, Arda HE, Zhu LJ, Walhout AJ. Diet-Induced Developmental Acceleration Independent of TOR and Insulin in C. elegans. Cell. 2013 Mar 28; 153(1):240-52.
          View in: PubMed
        4. Watson E, Macneil LT, Arda HE, Zhu LJ, Walhout AJ. Integration of Metabolic and Gene Regulatory Networks Modulates the C. elegans Dietary Response. Cell. 2013 Mar 28; 153(1):253-66.
          View in: PubMed
        5. Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, Celniker SE, Sinha S, Stormo GD, Brodsky MH, Wolfe SA. Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res. 2013 Jun; 23(6):928-40.
          View in: PubMed
        6. Zhu LJ. Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset. Methods Mol Biol. 2013; 1067:105-24.
          View in: PubMed
        7. Xie L, Gazin C, Park SM, Zhu LJ, Debily MA, Kittler EL, Zapp ML, Lapointe D, Gobeil S, Virbasius CM, Green MR. A Synthetic Interaction Screen Identifies Factors Selectively Required for Proliferation and TERT Transcription in p53-Deficient Human Cancer Cells. PLoS Genet. 2012 Dec; 8(12):e1003151.
          View in: PubMed
        8. Maston GA, Zhu LJ, Chamberlain L, Lin L, Fang M, Green MR. Non-canonical TAF complexes regulate active promoters in human embryonic stem cells. elife. 2012; 1:e00068.
          View in: PubMed
        9. Wang SZ, Ou J, Zhu LJ, Green MR. Transcription factor ATF5 is required for terminal differentiation and survival of olfactory sensory neurons. Proc Natl Acad Sci U S A. 2012 Nov 6; 109(45):18589-94.
          View in: PubMed
        10. Oslowski CM, Hara T, O'Sullivan-Murphy B, Kanekura K, Lu S, Hara M, Ishigaki S, Zhu LJ, Hayashi E, Hui ST, Greiner D, Kaufman RJ, Bortell R, Urano F. Thioredoxin-Interacting Protein Mediates ER Stress-Induced ß Cell Death through Initiation of the Inflammasome. Cell Metab. 2012 Aug 8; 16(2):265-73.
          View in: PubMed
        11. Pulikkan JA, Madera D, Xue L, Bradley P, Landrette SF, Kuo YH, Abbas S, Zhu LJ, Valk P, Castilla LH. Thrombopoietin/MPL participates in initiating and maintaining RUNX1-ETO acute myeloid leukemia via PI3K/AKT signaling. Blood. 2012 Jul 26; 120(4):868-79.
          View in: PubMed
        12. Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA. Exploring the DNA-recognition potential of homeodomains. Genome Res. 2012 Apr 26.
          View in: PubMed
        13. Rajurkar M, De Jesus-Monge WE, Driscoll DR, Appleman VA, Huang H, Cotton JL, Klimstra DS, Zhu LJ, Simin K, Xu L, McMahon AP, Lewis BC, Mao J. The activity of Gli transcription factors is essential for Kras-induced pancreatic tumorigenesis. Proc Natl Acad Sci U S A. 2012 Apr 24; 109(17):E1038-47.
          View in: PubMed
        14. Matsuoka K, Hayashi S, Urano F, Zhu LJ, Okita H, Sago H, Nakazawa A. Squamous metaplasia in the cyst epithelium of type 1 congenital pulmonary airway malformation after thoracoamniotic shunt placement. Hum Pathol. 2012 Sep; 43(9):1413-7.
          View in: PubMed
        15. Nicoli S, Knyphausen CP, Zhu LJ, Lakshmanan A, Lawson ND. miR-221 Is Required for Endothelial Tip Cell Behaviors during Vascular Development. Dev Cell. 2012 Feb 14; 22(2):418-29.
          View in: PubMed
        16. Lin L, Chamberlain L, Zhu LJ, Green MR. Analysis of Gal4-directed transcription activation using Tra1 mutants selectively defective for interaction with Gal4. Proc Natl Acad Sci U S A. 2012 Feb 7; 109(6):1997-2002.
          View in: PubMed
        17. Umbarger MA, Toro E, Wright MA, Porreca GJ, Baù D, Hong SH, Fero MJ, Zhu LJ, Marti-Renom MA, McAdams HH, Shapiro L, Dekker J, Church GM. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell. 2011 Oct 21; 44(2):252-64.
          View in: PubMed
        18. Zhang Q, Chen L, Helfand BT, Jang TL, Sharma V, Kozlowski J, Kuzel TM, Zhu LJ, Yang XJ, Javonovic B, Guo Y, Lonning S, Harper J, Teicher BA, Brendler C, Yu N, Catalona WJ, Lee C. TGF-ß regulates DNA methyltransferase expression in prostate cancer, correlates with aggressive capabilities, and predicts disease recurrence. PLoS One. 2011; 6(9):e25168.
          View in: PubMed
        19. Sheng Z, Ma L, Sun JE, Zhu LJ, Green MR. BCR-ABL suppresses autophagy through ATF5-mediated regulation of mTOR transcription. Blood. 2011 Sep 8; 118(10):2840-8.
          View in: PubMed
        20. Tabuchi TM, Deplancke B, Osato N, Zhu LJ, Barrasa MI, Harrison MM, Horvitz HR, Walhout AJ, Hagstrom KA. Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex. PLoS Genet. 2011 May; 7(5):e1002074.
          View in: PubMed
        21. Aday AW, Zhu LJ, Lakshmanan A, Wang J, Lawson ND. Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites. Dev Biol. 2011 Sep 15; 357(2):450-62.
          View in: PubMed
        22. Zhu LJ, Christensen RG, Kazemian M, Hull CJ, Enuameh MS, Basciotta MD, Brasefield JA, Zhu C, Asriyan Y, Lapointe DS, Sinha S, Wolfe SA, Brodsky MH. FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res. 2011 Jan; 39(Database issue):D111-7.
          View in: PubMed
        23. Gupta A, Meng X, Zhu LJ, Lawson ND, Wolfe SA. Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res. 2011 Jan 1; 39(1):381-92.
          View in: PubMed
        24. Sheng Z, Li L, Zhu LJ, Smith TW, Demers A, Ross AH, Moser RP, Green MR. A genome-wide RNA interference screen reveals an essential CREB3L2-ATF5-MCL1 survival pathway in malignant glioma with therapeutic implications. Nat Med. 2010 Jun; 16(6):671-7.
          View in: PubMed
        25. Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS, Green MR. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics. 2010; 11:237.
          View in: PubMed
        26. Lopes da Rosa J, Boyartchuk VL, Zhu LJ, Kaufman PD. Histone acetyltransferase Rtt109 is required for Candida albicans pathogenesis. Proc Natl Acad Sci U S A. 2010 Jan 26; 107(4):1594-9.
          View in: PubMed
        27. Desai J, Flatow JM, Song J, Zhu LJ, Du P, Huang CC, Lu H, Lin SM, Kibbe WA. Visual presentation as a welcome alternative to textual presentation of gene annotation information. Adv Exp Med Biol. 2010; 680:709-15.
          View in: PubMed
        28. Ishigaki S, Fonseca SG, Oslowski CM, Jurczyk A, Shearstone JR, Zhu LJ, Permutt MA, Greiner DL, Bortell R, Urano F. AATF mediates an antiapoptotic effect of the unfolded protein response through transcriptional regulation of AKT1. Cell Death Differ. 2010 May; 17(5):774-86.
          View in: PubMed
        29. Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL. Annotating the human genome with Disease Ontology. BMC Genomics. 2009; 10 Suppl 1:S6.
          View in: PubMed
        30. Zhang Q, Helfand BT, Jang TL, Zhu LJ, Chen L, Yang XJ, Kozlowski J, Smith N, Kundu SD, Yang G, Raji AA, Javonovic B, Pins M, Lindholm P, Guo Y, Catalona WJ, Lee C. Nuclear factor-kappaB-mediated transforming growth factor-beta-induced expression of vimentin is an independent predictor of biochemical recurrence after radical prostatectomy. Clin Cancer Res. 2009 May 15; 15(10):3557-67.
          View in: PubMed
        31. Meng X, Noyes MB, Zhu LJ, Lawson ND, Wolfe SA. Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol. 2008 Jun; 26(6):695-701.
          View in: PubMed
        32. Mishra M, Paunesku T, Woloschak GE, Siddique T, Zhu LJ, Lin S, Greco K, Bigio EH. Gene expression analysis of frontotemporal lobar degeneration of the motor neuron disease type with ubiquitinated inclusions. Acta Neuropathol. 2007 Jul; 114(1):81-94.
          View in: PubMed
        33. Osborne JD, Zhu LJ, Lin SM, Kibbe WA. Interpreting microarray results with gene ontology and MeSH. Methods Mol Biol. 2007; 377:223-42.
          View in: PubMed
        34. Osborne JD, Lin S, Zhu L, Kibbe WA. Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). Methods Mol Biol. 2007; 408:153-69.
          View in: PubMed
        35. Chebotaev D, Yemelyanov A, Zhu L, Lavker RM, Budunova I. The tumor suppressor effect of the glucocorticoid receptor in skin is mediated via its effect on follicular epithelial stem cells. Oncogene. 2007 May 10; 26(21):3060-8.
          View in: PubMed
        36. Lin SM, Zhu L, Winter AQ, Sasinowski M, Kibbe WA. What is mzXML good for? Expert Rev Proteomics. 2005 Dec; 2(6):839-45.
          View in: PubMed
        37. Kapatral V, Anderson I, Ivanova N, Reznik G, Los T, Lykidis A, Bhattacharyya A, Bartman A, Gardner W, Grechkin G, Zhu L, Vasieva O, Chu L, Kogan Y, Chaga O, Goltsman E, Bernal A, Larsen N, D'Souza M, Walunas T, Pusch G, Haselkorn R, Fonstein M, Kyrpides N, Overbeek R. Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J Bacteriol. 2002 Apr; 184(7):2005-18.
          View in: PubMed
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