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Lihua Zhu PhD

InstitutionUMass Chan Medical School
DepartmentMolecular, Cell and Cancer Biology
AddressUMass Chan Medical School
364 Plantation Street LRB-606
Worcester MA 01605
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentMolecular, Cell and Cancer Biology

    InstitutionT.H. Chan School of Medicine
    DepartmentProgram in Molecular Medicine

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionUMass Chan Programs, Centers and Institutes
    DepartmentBioinformatics and Integrative Biology

    Collapse Biography 
    Collapse education and training
    China Agricultural University, Beijing, 11, ChinaBSAnimal Nutrition
    China Agricultural University, Beijing, 11, 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 WGS, ChIP-seq, bulk and single cell RNA-seq and ATAC-seq, miRNA-seq, Hi-C, shRNA-seq, PAS-seq, NAD-seq and GUIDE-seq. Our expertise is algorithm and computational tool development. We have developed more than 20 computational tools, including a dozen Bioconductor packages. These tools encompass functionalities such as RNA-seq data analysis, scATAC-seq data analysis, gRNA design and offtarget analysis, machine learning applications, peak calling, proteomics data analysis, motif alignment, quality assessment, annotation, model selection, data integration and visualization.


    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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Singh A, Abhilasha KV, Acharya KR, Liu H, Nirala NK, Parthibane V, Kunduri G, Abimannan T, Tantalla J, Zhu LJ, Acharya JK, Acharya UR. A nutrient responsive lipase mediates gut-brain communication to regulate insulin secretion in Drosophila. Nat Commun. 2024 May 23; 15(1):4410. PMID: 38782979.
    2. Ye T, Mishra AK, Banday S, Li R, Hu K, Coleman MM, Shan Y, Chowdhury SR, Zhou L, Pak ML, Simone TM, Malonia SK, Zhu LJ, Kelliher MA, Green MR. Identification of WNK1 as a therapeutic target to suppress IgH/MYC expression in multiple myeloma. Cell Rep. 2024 May 28; 43(5):114211. PMID: 38722741.
    3. Mishra AK, Ye T, Banday S, Thakare RP, Su CT, Pham NNH, Ali A, Kulshreshtha A, Chowdhury SR, Simone TM, Hu K, Zhu LJ, Eisenhaber B, Deibler SK, Simin K, Thompson PR, Kelliher MA, Eisenhaber F, Malonia SK, Green MR. Targeting the GPI transamidase subunit GPAA1 abrogates the CD24 immune checkpoint in ovarian cancer. Cell Rep. 2024 Apr 23; 43(4):114041. PMID: 38573857.
    4. O'Connor KW, Kishimoto K, Kuzma IO, Wagner KP, Selway JS, Roderick JE, Karna KK, Gallagher KM, Hu K, Liu H, Li R, Brehm MA, Zhu LJ, Curtis DJ, Tremblay CS, Kelliher MA. The role of quiescent thymic progenitors in TAL/LMO2-induced T-ALL chemotolerance. Leukemia. 2024 May; 38(5):951-962. PMID: 38553571.
    5. Flynn MJ, Harper NW, Li R, Zhu LJ, Lee MJ, Benanti JA. Calcineurin promotes adaptation to chronic stress through two distinct mechanisms. bioRxiv. 2024 Mar 20. PMID: 38562881.
    6. Ahmad MH, Hegde M, Wong WJ, Mohammadhosseini M, Garrett L, Carrascoso A, Issac N, Ebert B, Silva JC, Pihan G, Zhu LJ, Wolfe SA, Agarwal A, Liu PP, Castilla LH. Runx1-R188Q germ line mutation induces inflammation and predisposition to hematologic malignancies in mice. Blood Adv. 2023 12 12; 7(23):7304-7318. PMID: 37756546.
      Citations:    Fields:    Translation:HumansAnimals
    7. Malvi P, Chava S, Cai G, Hu K, Zhu LJ, Edwards YJK, Green MR, Gupta R, Wajapeyee N. HOXC6 drives a therapeutically targetable pancreatic cancer growth and metastasis pathway by regulating MSK1 and PPP2R2B. Cell Rep Med. 2023 11 21; 4(11):101285. PMID: 37951219.
      Citations:    Fields:    Translation:Animals
    8. Mukhopadhyay D, Goel HL, Xiong C, Goel S, Kumar A, Li R, Zhu LJ, Clark JL, Brehm MA, Mercurio AM. The calcium channel TRPC6 promotes chemotherapy-induced persistence by regulating integrin a6 mRNA splicing. Cell Rep. 2023 11 28; 42(11):113347. PMID: 37910503.
      Citations: 1     Fields:    
    9. Doshi MB, Lee N, Tseyang T, Ponomarova O, Goel HL, Spears M, Li R, Zhu LJ, Ashwood C, Simin K, Jang C, Mercurio AM, Walhout AJM, Spinelli JB, Kim D. Disruption of sugar nucleotide clearance is a therapeutic vulnerability of cancer cells. Nature. 2023 Nov; 623(7987):625-632. PMID: 37880368.
      Citations: 1     Fields:    Translation:HumansCells
    10. Liu H, Caliz AD, Learnard H, Koupenova M, Keaney JF, Kant S, Zhu LJ, Vertii A. Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells. bioRxiv. 2023 Oct 16. PMID: 37905100.
    11. Chibaya L, Lusi CF, DeMarco KD, Kane GI, Brassil ML, Parikh CN, Murphy KC, Li J, Naylor TE, Cerrutti J, Peura J, Pitarresi JR, Zhu LJ, Fitzgerald KA, Atukorale PU, Ruscetti M. Nanoparticle delivery of innate immune agonists combines with senescence-inducing agents to mediate T cell control of pancreatic cancer. bioRxiv. 2023 Sep 18. PMID: 37790484.
    12. Liang SQ, Liu P, Ponnienselvan K, Suresh S, Chen Z, Kramme C, Chatterjee P, Zhu LJ, Sontheimer EJ, Xue W, Wolfe SA. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nat Methods. 2023 Jun; 20(6):898-907. PMID: 37156841.
      Citations: 5     Fields:    Translation:AnimalsCells
    13. Chibaya L, Murphy KC, DeMarco KD, Gopalan S, Liu H, Parikh CN, Lopez-Diaz Y, Faulkner M, Li J, Morris JP, Ho YJ, Chana SK, Simon J, Luan W, Kulick A, de Stanchina E, Simin K, Zhu LJ, Fazzio TG, Lowe SW, Ruscetti M. EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance. Nat Cancer. 2023 06; 4(6):872-892. PMID: 37142692.
      Citations: 5     Fields:    Translation:AnimalsCells
    14. Wang M, Wisniewski CA, Xiong C, Chhoy P, Goel HL, Kumar A, Zhu LJ, Li R, St Louis PA, Ferreira LM, Pakula H, Xu Z, Loda M, Jiang Z, Brehm MA, Mercurio AM. Therapeutic blocking of VEGF binding to neuropilin-2 diminishes PD-L1 expression to activate antitumor immunity in prostate cancer. Sci Transl Med. 2023 05 03; 15(694):eade5855. PMID: 37134151.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    15. Conti MM, Li R, Narv?ez Ramos MA, Zhu LJ, Fazzio TG, Benanti JA. Phosphosite Scanning reveals a complex phosphorylation code underlying CDK-dependent activation of Hcm1. Nat Commun. 2023 01 19; 14(1):310. PMID: 36658165.
      Citations: 2     Fields:    Translation:AnimalsCells
    16. Chen Q, Huang L, Pan D, Hu K, Li R, Friedline RH, Kim JK, Zhu LJ, Guertin DA, Wang YX. A brown fat-enriched adipokine Adissp controls adipose thermogenesis and glucose homeostasis. Nat Commun. 2022 Dec 10; 13(1):7633. PMID: 36496438.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    17. Lin C, Yang Q, Guo D, Xie J, Yang YS, Chaugule S, DeSouza N, Oh WT, Li R, Chen Z, John AA, Qiu Q, Zhu LJ, Greenblatt MB, Ghosh S, Li S, Gao G, Haynes C, Emerson CP, Shim JH. Impaired mitochondrial oxidative metabolism in skeletal progenitor cells leads to musculoskeletal disintegration. Nat Commun. 2022 11 11; 13(1):6869. PMID: 36369293.
      Citations: 5     Fields:    Translation:AnimalsCells
    18. Hu K, Liu H, Lawson ND, Zhu LJ. scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data. Front Cell Dev Biol. 2022; 10:981859. PMID: 36238687.
    19. Spears ME, Lee N, Hwang S, Park SJ, Carlisle AE, Li R, Doshi MB, Armando AM, Gao J, Simin K, Zhu LJ, Greer PL, Quehenberger O, Torres EM, Kim D. De novo sphingolipid biosynthesis necessitates detoxification in cancer cells. Cell Rep. 2022 09 27; 40(13):111415. PMID: 36170811.
      Citations: 2     Fields:    Translation:Cells
    20. Iyer S, Mir A, Vega-Badillo J, Roscoe BP, Ibraheim R, Zhu LJ, Lee J, Liu P, Luk K, Mintzer E, Guo D, Soares de Brito J, Emerson CP, Zamore PD, Sontheimer EJ, Wolfe SA. Efficient Homology-Directed Repair with Circular Single-Stranded DNA Donors. CRISPR J. 2022 10; 5(5):685-701. PMID: 36070530.
      Citations: 7     Fields:    Translation:HumansCells
    21. Conti MM, Ghizzoni JM, Gil-Bona A, Wang W, Costanzo M, Li R, Flynn MJ, Zhu LJ, Myers CL, Boone C, Andrews BJ, Benanti JA. Repression of essential cell cycle genes increases cellular fitness. PLoS Genet. 2022 08; 18(8):e1010349. PMID: 36037231.
      Citations: 1     Fields:    Translation:AnimalsCells
    22. Luk K, Liu P, Zeng J, Wang Y, Maitland SA, Idrizi F, Ponnienselvan K, Iyer S, Zhu LJ, Luban J, Bauer DE, Wolfe SA. Optimization of Nuclear Localization Signal Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells. GEN Biotechnol. 2022 Jun; 1(3):271-284. PMID: 38405215.
    23. Yang Q, Liu P, Anderson NS, Shpilka T, Du Y, Naresh NU, Li R, Zhu LJ, Luk K, Lavelle J, Zeinert RD, Chien P, Wolfe SA, Haynes CM. LONP-1 and ATFS-1 sustain deleterious heteroplasmy by promoting mtDNA replication in dysfunctional mitochondria. Nat Cell Biol. 2022 02; 24(2):181-193. PMID: 35165413.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    24. Liang SQ, Liu P, Smith JL, Mintzer E, Maitland S, Dong X, Yang Q, Lee J, Haynes CM, Zhu LJ, Watts JK, Sontheimer EJ, Wolfe SA, Xue W. Genome-wide detection of CRISPR editing in vivo using GUIDE-tag. Nat Commun. 2022 Jan 21; 13(1):437. PMID: 35064134.
      Citations: 13     Fields:    Translation:AnimalsCells
    25. Walker MR, Goel HL, Mukhopadhyay D, Chhoy P, Karner ER, Clark JL, Liu H, Li R, Zhu JL, Chen S, Mahal LK, Bensing BA, Mercurio AM. O-linked a2,3 sialylation defines stem cell populations in breast cancer. Sci Adv. 2022 Jan 07; 8(1):eabj9513. PMID: 34995107.
      Citations: 5     Fields:    
    26. Oikemus SR, Pfister EL, Sapp E, Chase KO, Kennington LA, Hudgens E, Miller R, Zhu LJ, Chaudhary A, Mick EO, Sena-Esteves M, Wolfe SA, DiFiglia M, Aronin N, Brodsky MH. Allele-Specific Knockdown of Mutant Huntingtin Protein via Editing at Coding Region Single Nucleotide Polymorphism Heterozygosities. Hum Gene Ther. 2022 01; 33(1-2):25-36. PMID: 34376056.
      Citations: 5     Fields:    Translation:Animals
    27. Hidalgo D, Bejder J, Pop R, Gellatly K, Hwang Y, Maxwell Scalf S, Eastman AE, Chen JJ, Zhu LJ, Heuberger JAAC, Guo S, Koury MJ, Nordsborg NB, Socolovsky M. EpoR stimulates rapid cycling and larger red cells during mouse and human erythropoiesis. Nat Commun. 2021 12 17; 12(1):7334. PMID: 34921133.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    28. Nirala NK, Li Q, Ghule PN, Chen HJ, Li R, Zhu LJ, Wang R, Rice NP, Mao J, Stein JL, Stein GS, van Wijnen AJ, Ip YT. Hinfp is a guardian of the somatic genome by repressing transposable elements. Proc Natl Acad Sci U S A. 2021 10 12; 118(41). PMID: 34620709.
      Citations: 3     Fields:    Translation:AnimalsCells
    29. Garwain O, Sun X, Iyer DR, Li R, Zhu LJ, Kaufman PD. The chromatin-binding domain of Ki-67 together with p53 protects human chromosomes from mitotic damage. Proc Natl Acad Sci U S A. 2021 08 10; 118(32). PMID: 34353903.
      Citations: 1     Fields:    Translation:HumansCells
    30. Rodr?guez TC, Dadafarin S, Pratt HE, Liu P, Amrani N, Zhu LJ. Genome-wide detection and analysis of CRISPR-Cas off-targets. Prog Mol Biol Transl Sci. 2021; 181:31-43. PMID: 34127199.
      Citations: 7     Fields:    Translation:Humans
    31. Wang F, Gervasi MG, Bo?kovic A, Sun F, Rinaldi VD, Yu J, Wallingford MC, Tourzani DA, Mager J, Zhu LJ, Rando OJ, Visconti PE, Strittmatter L, Bach I. Deficient spermiogenesis in mice lacking Rlim. Elife. 2021 02 23; 10. PMID: 33620316.
      Citations: 4     Fields:    Translation:AnimalsCells
    32. Hwang S, Cavaliere P, Li R, Zhu LJ, Dephoure N, Torres EM. Consequences of aneuploidy in human fibroblasts with trisomy 21. Proc Natl Acad Sci U S A. 2021 02 09; 118(6). PMID: 33526671.
      Citations: 24     Fields:    Translation:HumansCells
    33. Roderick JE, Gallagher KM, Murphy LC, O'Connor KW, Tang K, Zhang B, Brehm MA, Greiner DL, Yu J, Zhu LJ, Green MR, Kelliher MA. Prostaglandin E2 stimulates cAMP signaling and resensitizes human leukemia cells to glucocorticoid-induced cell death. Blood. 2021 01 28; 137(4):500-512. PMID: 33507291.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    34. Shpilka T, Du Y, Yang Q, Melber A, Uma Naresh N, Lavelle J, Kim S, Liu P, Weidberg H, Li R, Yu J, Zhu LJ, Strittmatter L, Haynes CM. UPRmt scales mitochondrial network expansion with protein synthesis via mitochondrial import in Caenorhabditis elegans. Nat Commun. 2021 01 20; 12(1):479. PMID: 33473112.
      Citations: 32     Fields:    Translation:AnimalsCells
    35. Panzarino NJ, Krais JJ, Cong K, Peng M, Mosqueda M, Nayak SU, Bond SM, Calvo JA, Doshi MB, Bere M, Ou J, Deng B, Zhu LJ, Johnson N, Cantor SB. Replication Gaps Underlie BRCA Deficiency and Therapy Response. Cancer Res. 2021 03 01; 81(5):1388-1397. PMID: 33184108.
      Citations: 59     Fields:    Translation:HumansCells
    36. Ou J, Liu H, Nirala NK, Stukalov A, Acharya U, Green MR, Zhu LJ. dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data. PLoS One. 2020; 15(11):e0242030. PMID: 33156866.
      Citations: 4     Fields:    Translation:HumansCells
    37. Hsiao WY, Jung SM, Tang Y, Haley JA, Li R, Li H, Calejman CM, Sanchez-Gurmaches J, Hung CM, Luciano AK, DeMambro V, Wellen KE, Rosen CJ, Zhu LJ, Guertin DA. The Lipid Handling Capacity of Subcutaneous Fat Is Programmed by mTORC2 during Development. Cell Rep. 2020 10 06; 33(1):108223. PMID: 33027655.
      Citations: 5     Fields:    Translation:HumansAnimals
    38. Li R, Hu K, Liu H, Green MR, Zhu LJ. OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data. Genes (Basel). 2020 10 02; 11(10). PMID: 33023248.
      Citations: 14     Fields:    Translation:HumansCells
    39. Lawson ND, Li R, Shin M, Grosse A, Yukselen O, Stone OA, Kucukural A, Zhu L. An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes. Elife. 2020 08 24; 9. PMID: 32831172.
      Citations: 27     Fields:    Translation:AnimalsCells
    40. Gallagher KM, Roderick JE, Tan SH, Tan TK, Murphy L, Yu J, Li R, O'Connor KW, Zhu J, Green MR, Sanda T, Kelliher MA. ESRRB regulates glucocorticoid gene expression in mice and patients with acute lymphoblastic leukemia. Blood Adv. 2020 07 14; 4(13):3154-3168. PMID: 32658986.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    41. Carlisle AE, Lee N, Matthew-Onabanjo AN, Spears ME, Park SJ, Youkana D, Doshi MB, Peppers A, Li R, Joseph AB, Smith M, Simin K, Zhu LJ, Greer PL, Shaw LM, Kim D. Selenium detoxification is required for cancer-cell survival. Nat Metab. 2020 07; 2(7):603-611. PMID: 32694795.
      Citations: 48     Fields:    Translation:HumansAnimalsCells
    42. Gupta R, Malvi P, Parajuli KR, Janostiak R, Bugide S, Cai G, Zhu LJ, Green MR, Wajapeyee N. KLF7 promotes pancreatic cancer growth and metastasis by up-regulating ISG expression and maintaining Golgi complex integrity. Proc Natl Acad Sci U S A. 2020 06 02; 117(22):12341-12351. PMID: 32430335.
      Citations: 30     Fields:    Translation:HumansAnimalsCells
    43. Leech CM, Flynn MJ, Arsenault HE, Ou J, Liu H, Zhu LJ, Benanti JA. The coordinate actions of calcineurin and Hog1 mediate the stress response through multiple nodes of the cell cycle network. PLoS Genet. 2020 04; 16(4):e1008600. PMID: 32343701.
      Citations: 7     Fields:    Translation:AnimalsCells
    44. Li Q, Sun Y, Jarugumilli GK, Liu S, Dang K, Cotton JL, Xiol J, Chan PY, DeRan M, Ma L, Li R, Zhu LJ, Li JH, Leiter AB, Ip YT, Camargo FD, Luo X, Johnson RL, Wu X, Mao J. Lats1/2 Sustain Intestinal Stem Cells and Wnt Activation through TEAD-Dependent and Independent Transcription. Cell Stem Cell. 2020 05 07; 26(5):675-692.e8. PMID: 32259481.
      Citations: 55     Fields:    Translation:HumansCells
    45. Bizhanova A, Yan A, Yu J, Zhu LJ, Kaufman PD. Distinct features of nucleolus-associated domains in mouse embryonic stem cells. Chromosoma. 2020 06; 129(2):121-139. PMID: 32219510.
      Citations: 13     Fields:    Translation:AnimalsCells
    46. Sissaoui S, Yu J, Yan A, Li R, Yukselen O, Kucukural A, Zhu LJ, Lawson ND. Genomic Characterization of Endothelial Enhancers Reveals a Multifunctional Role for NR2F2 in Regulation of Arteriovenous Gene Expression. Circ Res. 2020 03 27; 126(7):875-888. PMID: 32065070.
      Citations: 17     Fields:    Translation:HumansCells
    47. Li H, Li Q, Dang K, Ma S, Cotton JL, Yang S, Zhu LJ, Deng AC, Ip YT, Johnson RL, Wu X, Punzo C, Mao J. YAP/TAZ Activation Drives Uveal Melanoma Initiation and Progression. Cell Rep. 2019 12 03; 29(10):3200-3211.e4. PMID: 31801083.
      Citations: 28     Fields:    Translation:HumansAnimalsCells
    48. Brown CW, Amante JJ, Chhoy P, Elaimy AL, Liu H, Zhu LJ, Baer CE, Dixon SJ, Mercurio AM. Prominin2 Drives Ferroptosis Resistance by Stimulating Iron Export. Dev Cell. 2019 12 02; 51(5):575-586.e4. PMID: 31735663.
      Citations: 196     Fields:    Translation:HumansCells
    49. Walker MR, Amante JJ, Li J, Liu H, Zhu LJ, Feltri ML, Goel HL, Mercurio AM. Alveolar progenitor cells in the mammary gland are dependent on the ?4 integrin. Dev Biol. 2020 01 01; 457(1):13-19. PMID: 31586558.
      Citations: 2     Fields:    Translation:AnimalsCells
    50. Wu Y, Wang Y, Liu Q, Zhu LJ, Gao H, Cui M, Liu J, Zhao P, Liu J, Chen L, Wang J, Zeng W, Woodruff TK, Zeng S. Conserved microRNA mediates heating tolerance in germ cells versus surrounding somatic cells. RNA Biol. 2019 10; 16(10):1494-1503. PMID: 31276432.
      Citations: 4     Fields:    Translation:AnimalsCells
    51. Gregory KJ, Roberts AL, Conlon EM, Mayfield JA, Hagen MJ, Crisi GM, Bentley BA, Kane JJ, Makari-Judson G, Mason HS, Yu J, Zhu LJ, Simin K, Johnson JPS, Khan A, Schneider BR, Schneider SS, Jerry DJ. Gene expression signature of atypical breast hyperplasia and regulation by SFRP1. Breast Cancer Res. 2019 06 27; 21(1):76. PMID: 31248446.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    52. Elaimy AL, Amante JJ, Zhu LJ, Wang M, Walmsley CS, FitzGerald TJ, Goel HL, Mercurio AM. The VEGF receptor neuropilin 2 promotes homologous recombination by stimulating YAP/TAZ-mediated Rad51 expression. Proc Natl Acad Sci U S A. 2019 07 09; 116(28):14174-14180. PMID: 31235595.
      Citations: 22     Fields:    Translation:HumansCells
    53. Vertii A, Ou J, Yu J, Yan A, Pag?s H, Liu H, Zhu LJ, Kaufman PD. Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin. Genome Res. 2019 08; 29(8):1235-1249. PMID: 31201210.
      Citations: 47     Fields:    Translation:AnimalsCells
    54. Whitesell TR, Chrystal PW, Ryu JR, Munsie N, Grosse A, French CR, Workentine ML, Li R, Zhu LJ, Waskiewicz A, Lehmann OJ, Lawson ND, Childs SJ. foxc1 is required for embryonic head vascular smooth muscle differentiation in zebrafish. Dev Biol. 2019 09 01; 453(1):34-47. PMID: 31199900.
      Citations: 19     Fields:    Translation:AnimalsCells
    55. Ou J, Zhu LJ. trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data. Nat Methods. 2019 06; 16(6):453-454. PMID: 31133757.
      Citations: 81     Fields:    Translation:Humans
    56. Ma L, Pak ML, Ou J, Yu J, St Louis P, Shan Y, Hutchinson L, Li S, Brehm MA, Zhu LJ, Green MR. Prosurvival kinase PIM2 is a therapeutic target for eradication of chronic myeloid leukemia stem cells. Proc Natl Acad Sci U S A. 2019 05 21; 116(21):10482-10487. PMID: 31068472.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    57. Liu P, Luk K, Shin M, Idrizi F, Kwok S, Roscoe B, Mintzer E, Suresh S, Morrison K, Fraz?o JB, Bolukbasi MF, Ponnienselvan K, Luban J, Zhu LJ, Lawson ND, Wolfe SA. Enhanced Cas12a editing in mammalian cells and zebrafish. Nucleic Acids Res. 2019 May 07; 47(8):4169-4180. PMID: 30892626.
      Citations: 41     Fields:    Translation:HumansAnimalsCells
    58. Deng P, Uma Naresh N, Du Y, Lamech LT, Yu J, Zhu LJ, Pukkila-Worley R, Haynes CM. Mitochondrial UPR repression during Pseudomonas aeruginosa infection requires the bZIP protein ZIP-3. Proc Natl Acad Sci U S A. 2019 03 26; 116(13):6146-6151. PMID: 30850535.
      Citations: 28     Fields:    Translation:AnimalsCells
    59. Chun-Qing Song, Tingting Jiang, Michelle Richter, Luke H. Rhym, Luke W. Koblan, Maria Paz Zafra, Emma M. Schatoff, Jordan L. Doman, Yueying Cao, Lukas E. Dow, Lihua Julie Zhu, Daniel G Anderson, David R. Liu, Hao Yin & Wen Xue. Adenine base editing in an adult mouse model of tyrosinaemia. Nature Biomedical Engineering. 2019. View Publication.
    60. Song CQ, Jiang T, Richter M, Rhym LH, Koblan LW, Zafra MP, Schatoff EM, Doman JL, Cao Y, Dow LE, Zhu LJ, Anderson DG, Liu DR, Yin H, Xue W. Adenine base editing in an adult mouse model of tyrosinaemia. Nat Biomed Eng. 2020 01; 4(1):125-130. PMID: 31740768.
      Citations: 84     Fields:    Translation:HumansAnimalsCells
    61. Bolukbasi MF, Liu P, Luk K, Kwok SF, Gupta A, Amrani N, Sontheimer EJ, Zhu LJ, Wolfe SA. Publisher Correction: Orthogonal Cas9-Cas9 chimeras provide a versatile platform for genome editing. Nat Commun. 2018 12 10; 9(1):5294. PMID: 30531933.
      Citations:    Fields:    
    62. Amrani N, Gao XD, Liu P, Edraki A, Mir A, Ibraheim R, Gupta A, Sasaki KE, Wu T, Donohoue PD, Settle AH, Lied AM, McGovern K, Fuller CK, Cameron P, Fazzio TG, Zhu LJ, Wolfe SA, Sontheimer EJ. NmeCas9 is an intrinsically high-fidelity genome-editing platform. Genome Biol. 2018 12 05; 19(1):214. PMID: 30518407.
      Citations: 54     Fields:    Translation:HumansAnimalsCells
    63. Bolukbasi MF, Liu P, Luk K, Kwok SF, Gupta A, Amrani N, Sontheimer EJ, Zhu LJ, Wolfe SA. Orthogonal Cas9-Cas9 chimeras provide a versatile platform for genome editing. Nat Commun. 2018 11 19; 9(1):4856. PMID: 30451839.
      Citations: 19     Fields:    Translation:HumansCells
    64. 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 09 18; 24(12):3251-3261. PMID: 30232006.
      Citations: 39     Fields:    Translation:HumansCells
    65. 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 07 31; 115(31):7991-7996. PMID: 30012595.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    66. 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. CBF?-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell. 2018 06 28; 174(1):172-186.e21. PMID: 29958106.
      Citations: 35     Fields:    Translation:HumansAnimalsCells
    67. 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 05 29; 23(9):2559-2567. PMID: 29847788.
      Citations: 23     Fields:    Translation:HumansCells
    68. 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 06; 15(6):433-436. PMID: 29735996.
      Citations: 60     Fields:    Translation:HumansCells
    69. 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 ?2-chimaerin. Sci Signal. 2018 05 01; 11(528). PMID: 29717062.
      Citations: 34     Fields:    Translation:HumansAnimalsCells
    70. 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 07 05; 26(7):1797-1807. PMID: 29759937.
      Citations: 19     Fields:    Translation:HumansCells
    71. 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 04 19; 3(8). PMID: 29669935.
      Citations: 11     Fields:    Translation:Humans
    72. Chen Q, Huang L, Pan D, Zhu LJ, Wang YX. Cbx4 Sumoylates Prdm16 to Regulate Adipose Tissue Thermogenesis. Cell Rep. 2018 03 13; 22(11):2860-2872. PMID: 29539416.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    73. 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.
      Citations: 91     Fields:    Translation:Cells
    74. 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.
      Citations: 76     Fields:    Translation:HumansCells
    75. Ou J, Wolfe SA, Brodsky MH, Zhu LJ. motifStack for the analysis of transcription factor binding site evolution. Nat Methods. 2018 01 03; 15(1):8-9. PMID: 29298290.
      Citations: 31     Fields:    Translation:HumansAnimalsCells
    76. Wang F, McCannell KN, Bo?kovic 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 12 26; 21(13):3691-3699. PMID: 29281819.
      Citations: 11     Fields:    Translation:AnimalsCells
    77. 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.
      Citations: 41     Fields:    Translation:HumansCells
    78. 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 Dec; 35(12):1179-1187. PMID: 29131148.
      Citations: 183     Fields:    Translation:AnimalsCells
    79. 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 10 31; 114(44):11751-11756. PMID: 29078326.
      Citations: 32     Fields:    Translation:AnimalsCells
    80. 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 10 09; 43(1):35-47.e4. PMID: 28943241.
      Citations: 32     Fields:    Translation:AnimalsCells
    81. Sun X, Bizhanova A, Matheson TD, Yu J, Zhu LJ, Kaufman PD. Ki-67 Contributes to Normal Cell Cycle Progression and Inactive X Heterochromatin in p21 Checkpoint-Proficient Human Cells. Mol Cell Biol. 2017 Sep 01; 37(17). PMID: 28630280.
      Citations: 30     Fields:    Translation:HumansCells
    82. 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 10 12; 130(15):1722-1733. PMID: 28790107.
      Citations: 37     Fields:    Translation:HumansAnimalsCells
    83. 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 07 18; 20(3):709-720. PMID: 28723572.
      Citations: 31     Fields:    Translation:AnimalsCells
    84. 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 07 12; 8(1):68. PMID: 28701693.
      Citations: 19     Fields:    Translation:HumansAnimals
    85. Zhu LJ, Lawrence M, Gupta A, Pag?s H, Kucukural A, Garber M, Wolfe SA. GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases. BMC Genomics. 2017 05 15; 18(1):379. PMID: 28506212.
      Citations: 18     Fields:    
    86. 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/?-Catenin Signaling Enhances Pancreatic Cancer Development and the Malignant Potential Via Up-regulation of Cyr61. Neoplasia. 2016 Dec; 18(12):785-794. PMID: 27889647.
      Citations: 26     Fields:    Translation:HumansAnimalsCells
    87. 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 11 16; 5. PMID: 27849519.
      Citations: 15     Fields:    Translation:AnimalsCells
    88. Wang F, Shin J, Shea JM, Yu J, Bo?kovic 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 09 19; 5. PMID: 27642011.
      Citations: 25     Fields:    Translation:Animals
    89. 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 10 15; 143(20):3785-3795. PMID: 27621059.
      Citations: 41     Fields:    Translation:AnimalsCells
    90. 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 10 15; 143(20):3796-3805. PMID: 27578780.
      Citations: 59     Fields:    Translation:AnimalsCells
    91. Pedanou VE, Gobeil S, Tabari?s 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 07 29; 5. PMID: 27472901.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    92. 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 05 19; 62(4):479-90. PMID: 27184077.
      Citations: 83     Fields:    Translation:HumansAnimalsCells
    93. 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 09 01; 35(35):4653-62. PMID: 26876204.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    94. 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.
      Citations: 382     Fields:    Translation:HumansAnimalsCells
    95. 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):1169-1180. PMID: 26832411.
      Citations: 118     Fields:    Translation:HumansCells
    96. 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):568-583. PMID: 26625958.
      Citations: 46     Fields:    Translation:AnimalsCells
    97. 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.
      Citations: 59     Fields:    Translation:HumansCells
    98. 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.
    99. Lihua Julie Zhu. Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology. Front. Biol. 2015; 10(4):289–296. View Publication.
    100. 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.
      Citations: 26     Fields:    Translation:HumansAnimalsCells
    101. 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 04; 58(5):819-31. PMID: 25921069.
      Citations: 28     Fields:    Translation:HumansCells
    102. Kanekura K, Ou J, Hara T, Zhu LJ, Urano F. Research resource: Monitoring endoplasmic reticulum membrane integrity in ?-cells at the single-cell level. Mol Endocrinol. 2015 Mar; 29(3):473-80. PMID: 25584413.
      Citations:    Fields:    Translation:HumansAnimalsCells
    103. 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.
      Citations: 166     Fields:    Translation:Animals
    104. 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.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    105. 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 04; 516(7529):116-20. PMID: 25470042.
      Citations: 86     Fields:    Translation:HumansAnimalsCells
    106. 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.
      Citations: 88     Fields:    Translation:HumansCells
    107. 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 03; 6(252):252ra121. PMID: 25186176.
      Citations: 63     Fields:    Translation:HumansAnimalsCells
    108. 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.
      Citations: 69     Fields:    Translation:AnimalsCells
    109. 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 02; 111(35):12591-8. PMID: 25136103.
      Citations: 41     Fields:    Translation:HumansAnimalsCells
    110. 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 ? and regulates complex V activity. J Cell Biol. 2014 Jul 21; 206(2):289-305. PMID: 25023514.
      Citations: 46     Fields:    Translation:AnimalsCells
    111. 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.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    112. 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.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    113. 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.
      Citations: 56     Fields:    Translation:HumansAnimalsCells
    114. 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.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    115. 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.
      Citations: 9     Fields:    Translation:AnimalsCells
    116. 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.
      Citations: 19     Fields:    Translation:AnimalsCells
    117. 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.
      Citations: 148     Fields:    Translation:AnimalsCells
    118. Watson E, MacNeil LT, Arda HE, Zhu LJ, Walhout AJM. Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response. Cell. 2013 Mar 28; 153(1):253-66. PMID: 23540702.
      Citations: 76     Fields:    Translation:HumansAnimalsCells
    119. 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.
      Citations: 45     Fields:    Translation:AnimalsCells
    120. Zhu LJ. Integrative analysis of ChIP-chip and ChIP-seq dataset. Methods Mol Biol. 2013; 1067:105-24. PMID: 23975789.
      Citations: 48     Fields:    Translation:HumansAnimalsCells
    121. 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.
      Citations: 16     Fields:    Translation:HumansCells
    122. 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.
      Citations: 24     Fields:    Translation:HumansCells
    123. 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 06; 109(45):18589-94. PMID: 23090999.
      Citations: 34     Fields:    Translation:HumansAnimalsCells
    124. 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 ? cell death through initiation of the inflammasome. Cell Metab. 2012 Aug 08; 16(2):265-73. PMID: 22883234.
      Citations: 311     Fields:    Translation:HumansAnimalsCells
    125. 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.
      Citations: 24     Fields:    Translation:HumansAnimalsCells
    126. 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.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    127. 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.
      Citations: 62     Fields:    Translation:Animals
    128. 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.
      Citations: 1     Fields:    Translation:Humans
    129. 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.
      Citations: 84     Fields:    Translation:AnimalsCells
    130. 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 07; 109(6):1997-2002. PMID: 22308403.
      Citations: 18     Fields:    Translation:AnimalsCells
    131. Umbarger MA, Toro E, Wright MA, Porreca GJ, Ba? 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.
      Citations: 135     Fields:    Translation:Cells
    132. 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-? regulates DNA methyltransferase expression in prostate cancer, correlates with aggressive capabilities, and predicts disease recurrence. PLoS One. 2011; 6(9):e25168. PMID: 21980391.
      Citations: 42     Fields:    Translation:HumansAnimalsCells
    133. Sheng Z, Ma L, Sun JE, Zhu LJ, Green MR. BCR-ABL suppresses autophagy through ATF5-mediated regulation of mTOR transcription. Blood. 2011 Sep 08; 118(10):2840-8. PMID: 21715304.
      Citations: 59     Fields:    Translation:HumansAnimalsCells
    134. 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.
      Citations: 38     Fields:    Translation:AnimalsCells
    135. 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.
      Citations: 45     Fields:    Translation:AnimalsCells
    136. 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.
      Citations: 132     Fields:    Translation:AnimalsCells
    137. 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.
      Citations: 66     Fields:    Translation:AnimalsCells
    138. 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.
      Citations: 93     Fields:    Translation:HumansAnimalsCells
    139. Zhu LJ, Gazin C, Lawson ND, Pag?s 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.
      Citations: 528     Fields:    Translation:Cells
    140. 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.
      Citations: 70     Fields:    Translation:AnimalsCells
    141. 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.
      Citations: 4     Fields:    Translation:Humans
    142. 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.
      Citations: 37     Fields:    Translation:HumansAnimalsCells
    143. 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.
      Citations: 136     Fields:    Translation:Humans
    144. 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.
      Citations: 62     Fields:    Translation:HumansCells
    145. 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.
      Citations: 337     Fields:    Translation:AnimalsCells
    146. 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.
      Citations: 46     Fields:    Translation:HumansCells
    147. 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.
      Citations: 11     Fields:    Translation:Humans
    148. 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.
      Citations: 9     Fields:    
    149. 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.
      Citations: 18     Fields:    Translation:AnimalsCells
    150. 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.
      Citations: 15     Fields:    
    151. 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.
      Citations: 141     Fields:    Translation:Cells
    152. 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.
      Citations: 2     Fields:    Translation:AnimalsCells
    153. 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.
      Citations: 10     Fields:    Translation:Animals
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