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Lihua Zhu PhD

TitleProfessor
InstitutionUniversity of Massachusetts Medical School
DepartmentMolecular, Cell and Cancer Biology
AddressUniversity of Massachusetts Medical School
364 Plantation Street, LRB-606
Worcester MA 01605
Phone508-856-5256
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentMolecular, Cell and Cancer Biology

    InstitutionUMMS - School of Medicine
    DepartmentProgram in Molecular Medicine

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionUMMS - Programs, Centers and Institutes
    DepartmentBioinformatics and Integrative Biology


    Collapse Biography 
    Collapse education and training
    China Agricultural University, Haidian, , ChinaBSAnimal Nutrition
    China Agricultural University, Haidian, , ChinaMSAnimal Nutrition
    Depaul University, Chicago, IL, United StatesM SComputer Science
    University of Wisconsin, Madison, Madison, WI, United StatesPHDNutritional Sciences

    Collapse Overview 
    Collapse overview

    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. She joined the Bioinformatics Core of the Robert H. Lurie Comprehensive Cancer Center (RHLCCC) of Northwestern University in 2001, where she was the Director of Bioinformatics Consulting Core from 2003 to 2005 and the Director of Clinical Informatics Group from 2005 to 2007. She joined the University of Massachusetts Medical School (UMMS) as the head of Bioinformatics core of Program in Gene Function and Expression (PGFE) in 2007.  Dr. Zhu is currently a professor and the head of Bioinformatics Core in the Department of Molecular, Cell and Cancer Biology (MCCB) of UMMS.


    Computational Biology and Bioinformatics


    Photo: Julie Zhu, Ph.D.


    We are interested in the understanding of gene regulation and cancer etiology, biomarker discovery, and development and application of genome editing technology by mining and integrating various high-throughput datasets such as ChIP-seq, RNA-seq, ATAC-seq, miRNA-seq, Hi-C, shRNA-seq, PAS-seq, NAD-seq and GUIDE-seq. Our expertise is algorithm and computational tool development. My group is an active contributor to the open-source open-development Bioconductor project. We have developed a dozen packages with various utilities, ranging from machine learning, peak calling, motif identification and alignment, quality assessment of ATACseq data, annotation, data integration, visualization, gRNA design and genome-wide offtargets identification in CRISPR genome editing studies.




    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Peng M, Cong K, Panzarino NJ, Nayak S, Calvo J, Deng B, Zhu LJ, Morocz M, Hegedus L, Haracska L, Cantor SB. Opposing Roles of FANCJ and HLTF Protect Forks and Restrain Replication during Stress. Cell Rep. 2018 Sep 18; 24(12):3251-3261. PMID: 30232006.
      View in: PubMed
    2. Przanowski P, Wasko U, Zheng Z, Yu J, Sherman R, Zhu LJ, McConnell MJ, Tushir-Singh J, Green MR, Bhatnagar S. Pharmacological reactivation of inactive X-linked Mecp2 in cerebral cortical neurons of living mice. Proc Natl Acad Sci U S A. 2018 Jul 16. PMID: 30012595.
      View in: PubMed
    3. Pulikkan JA, Hegde M, Ahmad HM, Belaghzal H, Illendula A, Yu J, O'Hagan K, Ou J, Muller-Tidow C, Wolfe SA, Zhu LJ, Dekker J, Bushweller JH, Castilla LH. CBFß-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell. 2018 Jun 28; 174(1):172-186.e21. PMID: 29958106.
      View in: PubMed
    4. Samanta S, Guru S, Elaimy AL, Amante JJ, Ou J, Yu J, Zhu LJ, Mercurio AM. IMP3 Stabilization of WNT5B mRNA Facilitates TAZ Activation in Breast Cancer. Cell Rep. 2018 May 29; 23(9):2559-2567. PMID: 29847788.
      View in: PubMed
    5. Gao XD, Tu LC, Mir A, Rodriguez T, Ding Y, Leszyk J, Dekker J, Shaffer SA, Zhu LJ, Wolfe SA, Sontheimer EJ. C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. Nat Methods. 2018 May 07. PMID: 29735996.
      View in: PubMed
    6. Elaimy AL, Guru S, Chang C, Ou J, Amante JJ, Zhu LJ, Goel HL, Mercurio AM. VEGF-neuropilin-2 signaling promotes stem-like traits in breast cancer cells by TAZ-mediated repression of the Rac GAP ß2-chimaerin. Sci Signal. 2018 May 01; 11(528). PMID: 29717062.
      View in: PubMed
    7. Himeda CL, Jones TI, Virbasius CM, Zhu LJ, Green MR, Jones PL. Identification of Epigenetic Regulators of DUX4-fl for Targeted Therapy of Facioscapulohumeral Muscular Dystrophy. Mol Ther. 2018 Apr 26. PMID: 29759937.
      View in: PubMed
    8. Zhu S, Ward BM, Yu J, Matthew-Onabanjo AN, Janusis J, Hsieh CC, Tomaszewicz K, Hutchinson L, Zhu LJ, Kandil D, Shaw LM. IRS2 mutations linked to invasion in pleomorphic invasive lobular carcinoma. JCI Insight. 2018 Apr 19; 3(8). PMID: 29669935.
      View in: PubMed
    9. Chen Q, Huang L, Pan D, Zhu LJ, Wang YX. Cbx4 Sumoylates Prdm16 to Regulate Adipose Tissue Thermogenesis. Cell Rep. 2018 Mar 13; 22(11):2860-2872. PMID: 29539416.
      View in: PubMed
    10. Ou J, Liu H, Yu J, Kelliher MA, Castilla LH, Lawson ND, Zhu LJ. ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data. BMC Genomics. 2018 03 01; 19(1):169. PMID: 29490630.
      View in: PubMed
    11. Yin H, Song CQ, Suresh S, Kwan SY, Wu Q, Walsh S, Ding J, Bogorad RL, Zhu LJ, Wolfe SA, Koteliansky V, Xue W, Langer R, Anderson DG. Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. Nat Chem Biol. 2018 Mar; 14(3):311-316. PMID: 29377001.
      View in: PubMed
    12. Ou J, Wolfe SA, Brodsky MH, Zhu LJ. motifStack for the analysis of transcription factor binding site evolution. Nat Methods. 2018 Jan 03; 15(1):8-9. PMID: 29298290.
      View in: PubMed
    13. Wang F, McCannell KN, Boškovic A, Zhu X, Shin J, Yu J, Gallant J, Byron M, Lawrence JB, Zhu LJ, Jones SN, Rando OJ, Fazzio TG, Bach I. Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs. Cell Rep. 2017 Dec 26; 21(13):3691-3699. PMID: 29281819.
      View in: PubMed
    14. Janostiak R, Rauniyar N, Lam TT, Ou J, Zhu LJ, Green MR, Wajapeyee N. MELK Promotes Melanoma Growth by Stimulating the NF-?B Pathway. Cell Rep. 2017 Dec 05; 21(10):2829-2841. PMID: 29212029.
      View in: PubMed
    15. Yin H, Song CQ, Suresh S, Wu Q, Walsh S, Rhym LH, Mintzer E, Bolukbasi MF, Zhu LJ, Kauffman K, Mou H, Oberholzer A, Ding J, Kwan SY, Bogorad RL, Zatsepin T, Koteliansky V, Wolfe SA, Xue W, Langer R, Anderson DG. Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing. Nat Biotechnol. 2017 Nov 13. PMID: 29131148.
      View in: PubMed
    16. Ma L, Boucher JI, Paulsen J, Matuszewski S, Eide CA, Ou J, Eickelberg G, Press RD, Zhu LJ, Druker BJ, Branford S, Wolfe SA, Jensen JD, Schiffer CA, Green MR, Bolon DN. CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy. Proc Natl Acad Sci U S A. 2017 Oct 31; 114(44):11751-11756. PMID: 29078326.
      View in: PubMed
    17. Cotton JL, Li Q, Ma L, Park JS, Wang J, Ou J, Zhu LJ, Ip YT, Johnson RL, Mao J. YAP/TAZ and Hedgehog Coordinate Growth and Patterning in Gastrointestinal Mesenchyme. Dev Cell. 2017 Oct 09; 43(1):35-47.e4. PMID: 28943241.
      View in: PubMed
    18. Choi A, Illendula A, Pulikkan JA, Roderick JE, Tesell J, Yu J, Hermance N, Zhu LJ, Castilla LH, Bushweller JH, Kelliher MA. RUNX1 is required for oncogenic Myb and Myc enhancer activity in T cell acute lymphoblastic leukemia. Blood. 2017 Aug 08. PMID: 28790107.
      View in: PubMed
    19. Quillien A, Abdalla M, Yu J, Ou J, Zhu LJ, Lawson ND. Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq. Cell Rep. 2017 Jul 18; 20(3):709-720. PMID: 28723572.
      View in: PubMed
    20. Huang L, Pan D, Chen Q, Zhu LJ, Ou J, Wabitsch M, Wang YX. Transcription factor Hlx controls a systematic switch from white to brown fat through Prdm16-mediated co-activation. Nat Commun. 2017 Jul 12; 8(1):68. PMID: 28701693.
      View in: PubMed
    21. Sun X, Bizhanova A, Matheson TD, Yu J, Zhu JL, Kaufman PD. Ki-67 contributes to normal cell cycle progression and inactive X heterochromatin in p21 checkpoint-proficient human cells. Mol Cell Biol. 2017 Jun 19. PMID: 28630280.
      View in: PubMed
    22. Zhu LJ, Lawrence M, Gupta A, Pagès H, Kucukural A, Garber M, Wolfe SA. GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases. BMC Genomics. 2017 May 15; 18(1):379. PMID: 28506212.
      View in: PubMed
    23. Sano M, Driscoll DR, DeJesus-Monge WE, Quattrochi B, Appleman VA, Ou J, Zhu LJ, Yoshida N, Yamazaki S, Takayama T, Sugitani M, Nemoto N, Klimstra DS, Lewis BC. Activation of WNT/ß-Catenin Signaling Enhances Pancreatic Cancer Development and the Malignant Potential Via Up-regulation of Cyr61. Neoplasia. 2016 Dec; 18(12):785-794. PMID: 27889647.
      View in: PubMed
    24. Hainer SJ, McCannell KN, Yu J, Ee LS, Zhu LJ, Rando OJ, Fazzio TG. DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells. Elife. 2016 Nov 16; 5. PMID: 27849519.
      View in: PubMed
    25. Wang F, Shin J, Shea JM, Yu J, Boškovic A, Byron M, Zhu X, Shalek AK, Regev A, Lawrence JB, Torres EM, Zhu LJ, Rando OJ, Bach I. Regulation of X-linked gene expression during early mouse development by Rlim. Elife. 2016 Sep 19; 5. PMID: 27642011.
      View in: PubMed
    26. Shin M, Male I, Beane TJ, Villefranc JA, Kok FO, Zhu LJ, Lawson ND. Vegfc acts through ERK to induce sprouting and differentiation of trunk lymphatic progenitors. Development. 2016 Oct 15; 143(20):3785-3795. PMID: 27621059.
      View in: PubMed
    27. Shin M, Beane TJ, Quillien A, Male I, Zhu LJ, Lawson ND. Vegfa signals through ERK to promote angiogenesis, but not artery differentiation. Development. 2016 Oct 15; 143(20):3796-3805. PMID: 27578780.
      View in: PubMed
    28. Pedanou VE, Gobeil S, Tabariès S, Simone TM, Zhu LJ, Siegel PM, Green MR. The histone H3K9 demethylase KDM3A promotes anoikis by transcriptionally activating pro-apoptotic genes BNIP3 and BNIP3L. Elife. 2016 Jul 29; 5. PMID: 27472901.
      View in: PubMed
    29. Park SM, Ou J, Chamberlain L, Simone TM, Yang H, Virbasius CM, Ali AM, Zhu LJ, Mukherjee S, Raza A, Green MR. U2AF35(S34F) Promotes Transformation by Directing Aberrant ATG7 Pre-mRNA 3' End Formation. Mol Cell. 2016 May 19; 62(4):479-90. PMID: 27184077.
      View in: PubMed
    30. Ahronian LG, Zhu LJ, Chen YW, Chu HC, Klimstra DS, Lewis BC. A novel KLF6-Rho GTPase axis regulates hepatocellular carcinoma cell migration and dissemination. Oncogene. 2016 Sep 1; 35(35):4653-62. PMID: 26876204.
      View in: PubMed
    31. Yin H, Song CQ, Dorkin JR, Zhu LJ, Li Y, Wu Q, Park A, Yang J, Suresh S, Bizhanova A, Gupta A, Bolukbasi MF, Walsh S, Bogorad RL, Gao G, Weng Z, Dong Y, Koteliansky V, Wolfe SA, Langer R, Xue W, Anderson DG. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat Biotechnol. 2016 Mar; 34(3):328-33. PMID: 26829318.
      View in: PubMed
    32. Liu X, Li H, Rajurkar M, Li Q, Cotton JL, Ou J, Zhu LJ, Goel HL, Mercurio AM, Park JS, Davis RJ, Mao J. Tead and AP1 Coordinate Transcription and Motility. Cell Rep. 2016 Feb 09; 14(5):1169-80. PMID: 26832411.
      View in: PubMed
    33. Pan D, Huang L, Zhu LJ, Zou T, Ou J, Zhou W, Wang YX. Jmjd3-Mediated H3K27me3 Dynamics Orchestrate Brown Fat Development and Regulate White Fat Plasticity. Dev Cell. 2015 Dec 07; 35(5):568-83. PMID: 26625958.
      View in: PubMed
    34. Bolukbasi MF, Gupta A, Oikemus S, Derr AG, Garber M, Brodsky MH, Zhu LJ, Wolfe SA. DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Nat Methods. 2015 Dec; 12(12):1150-6. PMID: 26480473.
      View in: PubMed
    35. Misra A, Ou J, Zhu LJ, Green MR. Global analysis of CPSF2-mediated alternative splicing: Integration of global iCLIP and transcriptome profiling data. Genom Data. 2015 Dec; 6:217-21. PMID: 26697379.
      View in: PubMed
    36. Lihua Julie Zhu. Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology. Front. Biol. 2015; 10(4):289–296.
    37. Kanekura K, Ma X, Murphy JT, Zhu LJ, Diwan A, Urano F. IRE1 prevents endoplasmic reticulum membrane permeabilization and cell death under pathological conditions. Sci Signal. 2015 Jun 23; 8(382):ra62. PMID: 26106220.
      View in: PubMed
    38. Misra A, Ou J, Zhu LJ, Green MR. Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors. Mol Cell. 2015 Jun 4; 58(5):819-31. PMID: 25921069.
      View in: PubMed
    39. Kanekura K, Ou J, Hara T, Zhu LJ, Urano F. Research resource: Monitoring endoplasmic reticulum membrane integrity in ß-cells at the single-cell level. Mol Endocrinol. 2015 Mar; 29(3):473-80. PMID: 25584413.
      View in: PubMed
    40. Bansal A, Zhu LJ, Yen K, Tissenbaum HA. Uncoupling lifespan and healthspan in Caenorhabditis elegans longevity mutants. Proc Natl Acad Sci U S A. 2015 Jan 20; 112(3):E277-86. PMID: 25561524.
      View in: PubMed
    41. Chen PB, Zhu LJ, Hainer SJ, McCannell KN, Fazzio TG. Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo. BMC Genomics. 2014 Dec 15; 15:1104. PMID: 25494698.
      View in: PubMed
    42. Bhatnagar S, Gazin C, Chamberlain L, Ou J, Zhu X, Tushir JS, Virbasius CM, Lin L, Zhu LJ, Wajapeyee N, Green MR. TRIM37 is a new histone H2A ubiquitin ligase and breast cancer oncoprotein. Nature. 2014 Dec 4; 516(7529):116-20. PMID: 25470042.
      View in: PubMed
    43. Zhu LJ, Holmes BR, Aronin N, Brodsky MH. CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. PLoS One. 2014; 9(9):e108424. PMID: 25247697.
      View in: PubMed
    44. Ma L, Shan Y, Bai R, Xue L, Eide CA, Ou J, Zhu LJ, Hutchinson L, Cerny J, Khoury HJ, Sheng Z, Druker BJ, Li S, Green MR. A therapeutically targetable mechanism of BCR-ABL-independent imatinib resistance in chronic myeloid leukemia. Sci Transl Med. 2014 Sep 3; 6(252):252ra121. PMID: 25186176.
      View in: PubMed
    45. Pan D, Mao C, Quattrochi B, Friedline RH, Zhu LJ, Jung DY, Kim JK, Lewis B, Wang YX. MicroRNA-378 controls classical brown fat expansion to counteract obesity. Nat Commun. 2014 Aug 22; 5:4725. PMID: 25145289.
      View in: PubMed
    46. Bhatnagar S, Zhu X, Ou J, Lin L, Chamberlain L, Zhu LJ, Wajapeyee N, Green MR. Genetic and pharmacological reactivation of the mammalian inactive X chromosome. Proc Natl Acad Sci U S A. 2014 Sep 2; 111(35):12591-8. PMID: 25136103.
      View in: PubMed
    47. Rahman M, Nirala NK, Singh A, Zhu LJ, Taguchi K, Bamba T, Fukusaki E, Shaw LM, Lambright DG, Acharya JK, Acharya UR. Drosophila Sirt2/mammalian SIRT3 deacetylates ATP synthase ß and regulates complex V activity. J Cell Biol. 2014 Jul 21; 206(2):289-305. PMID: 25023514.
      View in: PubMed
    48. Gupta R, Dong Y, Solomon PD, Wettersten HI, Cheng CJ, Min JN, Henson J, Dogra SK, Hwang SH, Hammock BD, Zhu LJ, Reddel RR, Saltzman WM, Weiss RH, Chang S, Green MR, Wajapeyee N. Synergistic tumor suppression by combined inhibition of telomerase and CDKN1A. Proc Natl Acad Sci U S A. 2014 Jul 29; 111(30):E3062-71. PMID: 25024194.
      View in: PubMed
    49. Lin L, Chamberlain L, Pak ML, Nagarajan A, Gupta R, Zhu LJ, Wright CM, Fong KM, Wajapeyee N, Green MR. A large-scale RNAi-based mouse tumorigenesis screen identifies new lung cancer tumor suppressors that repress FGFR signaling. Cancer Discov. 2014 Oct; 4(10):1168-81. PMID: 25015643.
      View in: PubMed
    50. Forloni M, Dogra SK, Dong Y, Conte D, Ou J, Zhu LJ, Deng A, Mahalingam M, Green MR, Wajapeyee N. miR-146a promotes the initiation and progression of melanoma by activating Notch signaling. Elife. 2014 Feb 18; 3:e01460. PMID: 24550252.
      View in: PubMed
    51. 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. PMID: 23962617.
      View in: PubMed
    52. 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. PMID: 23818862.
      View in: PubMed
    53. Huang H, Cotton JL, Wang Y, Rajurkar M, Zhu LJ, Lewis BC, Mao J. Specific requirement of Gli transcription factors in Hedgehog-mediated intestinal development. J Biol Chem. 2013 Jun 14; 288(24):17589-96. PMID: 23645682.
      View in: PubMed
    54. 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. PMID: 23540701.
      View in: PubMed
    55. 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. PMID: 23540702.
      View in: PubMed
    56. 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. PMID: 23471540.
      View in: PubMed
    57. Zhu LJ. Integrative analysis of ChIP-chip and ChIP-seq dataset. Methods Mol Biol. 2013; 1067:105-24. PMID: 23975789.
      View in: PubMed
    58. 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; 8(12):e1003151. PMID: 23284306.
      View in: PubMed
    59. 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 Nov 13; 1:e00068. PMID: 23150797.
      View in: PubMed
    60. 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. PMID: 23090999.
      View in: PubMed
    61. 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. PMID: 22883234.
      View in: PubMed
    62. 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. PMID: 22613795.
      View in: PubMed
    63. 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 Oct; 22(10):1889-98. PMID: 22539651.
      View in: PubMed
    64. 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. PMID: 22493246.
      View in: PubMed
    65. 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. PMID: 22386520.
      View in: PubMed
    66. 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. PMID: 22340502.
      View in: PubMed
    67. 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. PMID: 22308403.
      View in: PubMed
    68. 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. PMID: 22017872.
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    69. 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. PMID: 21980391.
      View in: PubMed
    70. 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. PMID: 21715304.
      View in: PubMed
    71. 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. PMID: 21589891.
      View in: PubMed
    72. 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. PMID: 21435340.
      View in: PubMed
    73. 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. PMID: 21097781.
      View in: PubMed
    74. 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; 39(1):381-92. PMID: 20843781.
      View in: PubMed
    75. 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. PMID: 20495567.
      View in: PubMed
    76. 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 May 11; 11:237. PMID: 20459804.
      View in: PubMed
    77. 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. PMID: 20080646.
      View in: PubMed
    78. 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. PMID: 20865558.
      View in: PubMed
    79. 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. PMID: 19911006.
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    80. 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 Jul 07; 10 Suppl 1:S6. PMID: 19594883.
      View in: PubMed
    81. 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. PMID: 19447876.
      View in: PubMed
    82. 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. PMID: 18500337.
      View in: PubMed
    83. 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. PMID: 17569064.
      View in: PubMed
    84. Osborne JD, Zhu LJ, Lin SM, Kibbe WA. Interpreting microarray results with gene ontology and MeSH. Methods Mol Biol. 2007; 377:223-42. PMID: 17634620.
      View in: PubMed
    85. 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. PMID: 18314582.
      View in: PubMed
    86. 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. PMID: 17146443.
      View in: PubMed
    87. Lin SM, Zhu L, Winter AQ, Sasinowski M, Kibbe WA. What is mzXML good for? Expert Rev Proteomics. 2005 Dec; 2(6):839-45. PMID: 16307524.
      View in: PubMed
    88. 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. PMID: 11889109.
      View in: PubMed
    89. Zhu LH, Strang BD, Armentano LE. Effects of triglyceride accumulation on induction of urea synthesis by glucagon and dexamethasone in monolayer cultures of bovine hepatocytes. J Anim Sci. 2000 Jun; 78(6):1659-66. PMID: 10875650.
      View in: PubMed
    90. Zhu LH, Armentano LE, Bremmer DR, Grummer RR, Bertics SJ. Plasma concentration of urea, ammonia, glutamine around calving, and the relation of hepatic triglyceride, to plasma ammonia removal and blood acid-base balance. J Dairy Sci. 2000 Apr; 83(4):734-40. PMID: 10791789.
      View in: PubMed
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