TitleAssistant Professor
InstitutionMD Anderson
DepartmentEpigenetics & Molecular Carcinogenesis
AddressPO Box 389
Smithville TX 78957-0389
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    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. Saha D, Animireddy S, Lee J, Thommen A, Murvin MM, Lu Y, Calabrese MJ, Bartholomew B. Enhancer switching in cell lineage priming is linked to eRNA, Brg1's AT-hook, and SWI/SNF recruitment. Mol Cell. 2024 Mar 29. PMID: 38593804.
    2. Figueroa M, Ma H, Alfayez M, Morales-Mantilla DE, Wang F, Lu Y, Estecio MR, King KY, Kleinerman E, Moghaddam SJ, Daver N, Andreeff M, Konopleva M, DiNardo C, Chandra J. Cigarette smoke exposure accelerates AML progression in FLT3-ITD models. Blood Adv. 2023 11 14; 7(21):6624-6629. PMID: 37486624; PMCID: PMC10628807.
      Citations:    Fields:    Translation:Humans
    3. Saha D, Hailu S, Hada A, Lee J, Luo J, Ranish JA, Lin YC, Feola K, Persinger J, Jain A, Liu B, Lu Y, Sen P, Bartholomew B. The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming. Nat Commun. 2023 08 04; 14(1):4682. PMID: 37542049; PMCID: PMC10403523.
      Citations:    Fields:    Translation:AnimalsCells
    4. Stitzlein LM, Gangadharan A, Walsh LM, Nam D, Espejo AB, Singh MM, Patel KH, Lu Y, Su X, Ezhilarasan R, Gumin J, Singh S, Sulman E, Lang FF, Chandra J. Comparison of pharmacological inhibitors of lysine-specific demethylase 1 in glioblastoma stem cells reveals inhibitor-specific efficacy profiles. Front Neurol. 2023; 14:1112207. PMID: 37082446; PMCID: PMC10111022.
    5. Hussain T, Sanchez K, Crayton J, Saha D, Jeter C, Lu Y, Abba M, Seo R, Noebels JL, Fonken L, Aldaz CM. WWOX P47T partial loss-of-function mutation induces epilepsy, progressive neuroinflammation, and cerebellar degeneration in mice phenocopying human SCAR12. Prog Neurobiol. 2023 04; 223:102425. PMID: 36828035; PMCID: PMC10835625.
      Citations: 1     Fields:    Translation:HumansAnimals
    6. Gao G, Hausmann S, Flores NM, Benitez AM, Shen J, Yang X, Person MD, Gayatri S, Cheng D, Lu Y, Liu B, Mazur PK, Bedford MT. The NFIB/CARM1 partnership is a driver in preclinical models of small cell lung cancer. Nat Commun. 2023 01 23; 14(1):363. PMID: 36690626; PMCID: PMC9870865.
      Citations: 1     Fields:    Translation:AnimalsCells
    7. Simper MS, Coletta LD, Gaddis S, Lin K, Mikulec CD, Takata T, Tomida MW, Zhang D, Tang DG, Estecio MR, Shen J, Lu Y. Commercial ChIP-Seq Library Preparation Kits Performed Differently for Different Classes of Protein Targets. J Biomol Tech. 2022 10 15; 33(3). PMID: 36910579; PMCID: PMC10001930.
      Citations:    Fields:    
    8. Darbaniyan F, Zheng H, Kanagal-Shamanna R, Lockyer P, Montalban-Bravo G, Estecio M, Lu Y, Soltysiak KA, Chien KS, Yang H, Sasaki K, Class C, Ganan-Gomez I, Do KA, Garcia-Manero G, Wei Y. Transcriptomic Signatures of Hypomethylating Agent Failure in Myelodysplastic Syndromes and Chronic Myelomonocytic Leukemia. Exp Hematol. 2022 Nov; 115:44-53. PMID: 36150563.
    9. Li H, Wang Y, Lin K, Venkadakrishnan VB, Bakht M, Shi W, Meng C, Zhang J, Tremble K, Liang X, Song JH, Feng X, Van V, Deng P, Burks JK, Aparicio A, Keyomarsi K, Chen J, Lu Y, Beltran H, Zhao D. CHD1 Promotes Sensitivity to Aurora Kinase Inhibitors by Suppressing Interaction of AURKA with Its Coactivator TPX2. Cancer Res. 2022 09 02; 82(17):3088-3101. PMID: 35771632; PMCID: PMC9444962.
      Citations:    Fields:    
    10. Wei Y, Kanagal-Shamanna R, Zheng H, Bao N, Lockyer PP, Class CA, Darbaniyan F, Lu Y, Lin K, Yang H, Montalban-Bravo G, Ganan-Gomez I, Soltysiak KA, Do KA, Colla S, Garcia-Manero G. Cooperation between KDM6B overexpression and TET2 deficiency in the pathogenesis of chronic myelomonocytic leukemia. Leukemia. 2022 08; 36(8):2097-2107. PMID: 35697791.
      Citations:    Fields:    
    11. Meng H, Gonzales NM, Jung SY, Lu Y, Putluri N, Zhu B, Dacso CC, Lonard DM, O'Malley BW. Defining the mammalian coactivation of hepatic 12-h clock and lipid metabolism. Cell Rep. 2022 03 08; 38(10):110491. PMID: 35263593; PMCID: PMC8958721.
      Citations:    Fields:    Translation:Animals
    12. Wang Z, Lu Y, Fornage M, Jiao L, Shen J, Li D, Wei P. Identification of novel susceptibility methylation loci for pancreatic cancer in a two-phase epigenome-wide association study. Epigenetics. 2022 11; 17(11):1357-1372. PMID: 35030986; PMCID: PMC9586592.
      Citations:    Fields:    
    13. Van HT, Harkins PR, Patel A, Jain AK, Lu Y, Bedford MT, Santos MA. Methyl-lysine readers PHF20 and PHF20L1 define two distinct?gene expression-regulating NSL complexes. J Biol Chem. 2022 03; 298(3):101588. PMID: 35033534; PMCID: PMC8867114.
      Citations:    Fields:    Translation:Cells
    14. Shah VV, Duncan AD, Jiang S, Stratton SA, Allton KL, Yam C, Jain A, Krause PM, Lu Y, Cai S, Tu Y, Zhou X, Zhang X, Jiang Y, Carroll CL, Kang Z, Liu B, Shen J, Gagea M, Manu SM, Huo L, Gilcrease M, Powell RT, Guo L, Stephan C, Davies PJ, Parker-Thornburg J, Lozano G, Behringer RR, Piwnica-Worms H, Chang JT, Moulder SL, Barton MC. Mammary-specific expression of Trim24 establishes a mouse model of human metaplastic breast cancer. Nat Commun. 2021 09 10; 12(1):5389. PMID: 34508101; PMCID: PMC8433435.
      Citations: 1     Fields:    Translation:HumansAnimals
    15. Kuang X, McAndrew MJ, Mustachio LM, Chen YC, Atanassov BS, Lin K, Lu Y, Shen J, Salinger A, Macatee T, Dent SYR, Koutelou E. Usp22 Overexpression Leads to Aberrant Signal Transduction of Cancer-Related Pathways but Is Not Sufficient to Drive Tumor Formation in Mice. Cancers (Basel). 2021 Aug 25; 13(17). PMID: 34503086; PMCID: PMC8428332.
    16. Yan L, Gaddis S, Coletta LD, Repass J, Powell KL, Simper MS, Chen Y, Byrom M, Zhong Y, Lin K, Liu B, Lu Y, Shen J, MacLeod MC. ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast Cancer. Int J Mol Sci. 2021 Feb 26; 22(5). PMID: 33652981; PMCID: PMC7956570.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    17. Hu X, Estecio MR, Chen R, Reuben A, Wang L, Fujimoto J, Carrot-Zhang J, McGranahan N, Ying L, Fukuoka J, Chow CW, Pham HHN, Godoy MCB, Carter BW, Behrens C, Zhang J, Antonoff MB, Sepesi B, Lu Y, Pass HI, Kadara H, Scheet P, Vaporciyan AA, Heymach JV, Wistuba II, Lee JJ, Futreal PA, Su D, Issa JJ, Zhang J. Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. Nat Commun. 2021 01 29; 12(1):687. PMID: 33514726; PMCID: PMC7846738.
      Citations: 8     Fields:    Translation:HumansCells
    18. Farria AT, Plummer JB, Salinger AP, Shen J, Lin K, Lu Y, McBride KM, Koutelou E, Dent SYR. Transcriptional Activation of MYC-Induced Genes by GCN5 Promotes B-cell Lymphomagenesis. Cancer Res. 2020 12 15; 80(24):5543-5553. PMID: 33168647; PMCID: PMC7744430.
      Citations: 7     Fields:    Translation:AnimalsCells
    19. Cortez MA, Masrorpour F, Ivan C, Zhang J, Younes AI, Lu Y, Estecio MR, Barsoumian HB, Menon H, da Silva Caetano M, Ramapriyan R, Schoenhals JE, Wang X, Skoulidis F, Wasley MD, Calin G, Hwu P, Welsh JW. Author Correction: Bone morphogenetic protein 7 promotes resistance to immunotherapy. Nat Commun. 2020 Oct 08; 11(1):5144. PMID: 33033261; PMCID: PMC7546718.
      Citations:    Fields:    
    20. Cortez MA, Masrorpour F, Ivan C, Zhang J, Younes AI, Lu Y, Estecio MR, Barsoumian HB, Menon H, Caetano MDS, Ramapriyan R, Schoenhals JE, Wang X, Skoulidis F, Wasley MD, Calin G, Hwu P, Welsh JW. Bone morphogenetic protein 7 promotes resistance to immunotherapy. Nat Commun. 2020 09 24; 11(1):4840. PMID: 32973129; PMCID: PMC7519103.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    21. Veazey KJ, Cheng D, Lin K, Villarreal OD, Gao G, Perez-Oquendo M, Van HT, Stratton SA, Green M, Xu H, Lu Y, Bedford MT, Santos MA. CARM1 inhibition reduces histone acetyltransferase activity causing synthetic lethality in CREBBP/EP300-mutated lymphomas. Leukemia. 2020 12; 34(12):3269-3285. PMID: 32576962; PMCID: PMC7688486.
      Citations: 6     Fields:    Translation:AnimalsCells
    22. Kumar J, Kaur G, Ren R, Lu Y, Lin K, Li J, Huang Y, Patel A, Barton MC, Macfarlan T, Zhang X, Cheng X. KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells. NAR Cancer. 2020 Jun; 2(2):zcaa007. PMID: 32743551; PMCID: PMC7380489.
      Citations: 2     
    23. Ikegami K, de March CA, Nagai MH, Ghosh S, Do M, Sharma R, Bruguera ES, Lu YE, Fukutani Y, Vaidehi N, Yohda M, Matsunami H. Structural instability and divergence from conserved residues underlie intracellular retention of mammalian odorant receptors. Proc Natl Acad Sci U S A. 2020 02 11; 117(6):2957-2967. PMID: 31974307; PMCID: PMC7022149.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
    24. Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X. Structural basis of specific DNA binding by the transcription factor ZBTB24. Nucleic Acids Res. 2019 09 19; 47(16):8388-8398. PMID: 31226215; PMCID: PMC6895263.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    25. Chao HP, Chen Y, Takata Y, Tomida MW, Lin K, Kirk JS, Simper MS, Mikulec CD, Rundhaug JE, Fischer SM, Chen T, Tang DG, Lu Y, Shen J. Systematic evaluation of RNA-Seq preparation protocol performance. BMC Genomics. 2019 Jul 11; 20(1):571. PMID: 31296163; PMCID: PMC6625085.
      Citations: 15     Fields:    
    26. Sinha KM, Bagheri-Yarmand R, Lahiri S, Lu Y, Zhang M, Amra S, Rizvi Y, Wan X, Navone N, Ozpolat B, Logothetis C, Gagel RF, Huard J. Oncogenic and osteolytic functions of histone demethylase NO66 in castration-resistant prostate cancer. Oncogene. 2019 06; 38(25):5038-5049. PMID: 30858546.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    27. Koutelou E, Wang L, Schibler AC, Chao HP, Kuang X, Lin K, Lu Y, Shen J, Jeter CR, Salinger A, Wilson M, Chen YC, Atanassov BS, Tang DG, Dent SYR. USP22 controls multiple signaling pathways that are essential for vasculature formation in the mouse placenta. Development. 2019 02 22; 146(4). PMID: 30718289; PMCID: PMC6398448.
      Citations: 13     Fields:    Translation:AnimalsCells
    28. Saha D, Gowher H, Zhao H, Veland N, Lu Y, Hardikar S, Gaddis S, Zeng Y, Liu B, Estecio MR, Takata Y, Lin K, Tomida MW, Shen J, Chen T. DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res. 2019 01 10; 47(1):152-167. PMID: 30321403; PMCID: PMC6326784.
      Citations: 28     Fields:    Translation:AnimalsCells
    29. Bagheri-Yarmand R, Sinha KM, Li L, Lu Y, Cote GJ, Sherman SI, Gagel RF. Combinations of Tyrosine Kinase Inhibitor and ERAD Inhibitor Promote Oxidative Stress-Induced Apoptosis through ATF4 and KLF9 in Medullary Thyroid Cancer. Mol Cancer Res. 2019 03; 17(3):751-760. PMID: 30552230; PMCID: PMC6902859.
      Citations: 7     Fields:    Translation:HumansCells
    30. Bao J, Di Lorenzo A, Lin K, Lu Y, Zhong Y, Sebastian MM, Muller WJ, Yang Y, Bedford MT. Mouse Models of Overexpression Reveal Distinct Oncogenic Roles for Different Type I Protein Arginine Methyltransferases. Cancer Res. 2019 01 01; 79(1):21-32. PMID: 30352814; PMCID: PMC6714580.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    31. Das P, Veazey KJ, Van HT, Kaushik S, Lin K, Lu Y, Ishii M, Kikuta J, Ge K, Nussenzweig A, Santos MA. Histone methylation regulator PTIP is required to maintain normal and leukemic bone marrow niches. Proc Natl Acad Sci U S A. 2018 10 23; 115(43):E10137-E10146. PMID: 30297393; PMCID: PMC6205459.
      Citations: 3     Fields:    Translation:AnimalsCells
    32. Cheng D, Vemulapalli V, Lu Y, Shen J, Aoyagi S, Fry CJ, Yang Y, Foulds CE, Stossi F, Mancini MA, O'Malley BW, Walker CL, Boyer TG, Bedford MT, Trevi?o LS. CARM1 methylates MED12 to regulate its RNA-binding ability. Life Sci Alliance. 2018 Oct; 1(5):e201800117. PMID: 30456381; PMCID: PMC6238599.
      Citations: 19     Fields:    
    33. Bao J, Perez CJ, Kim J, Zhang H, Murphy CJ, Hamidi T, Platt CD, Chou J, Deng M, Zhou MH, Huang Y, Lin K, Lu Y, Chen T, Bedford MT, Dent SY, Richburg JH, Pan HL, Geha RS, Shi Q, Benavides F, Jaubert J, Gait?n-Pe?as H, Gu?net JL, Est?vez R. Deficient LRRC8A-dependent volume-regulated anion channel activity is associated with male infertility in mice. JCI Insight. 2018 08 23; 3(16). PMID: 30135305; PMCID: PMC6141173.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    34. Bao J, Shen J, Lin K, Lu Y, Bedford MT, Rousseaux S. The arginine methyltransferase CARM1 represses p300?ACT?CREMt activity and is required for spermiogenesis. Nucleic Acids Res. 2018 05 18; 46(9):4327-4343. PMID: 29659998; PMCID: PMC5961101.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    35. Wood RD, Manandhar M, Lowery M, Boulware KS, Lin K, Lu Y. Response to "XPA is primarily cytoplasmic but is transported into the nucleus upon UV damage". DNA Repair (Amst). 2018 02; 62:30-31. PMID: 29337160.
      Citations: 2     Fields:    Translation:Cells
    36. Zhang D, Jeter C, Gong S, Tracz A, Lu Y, Shen J, Tang DG. Histone 2B-GFP Label-Retaining Prostate Luminal Cells Possess Progenitor Cell Properties and Are Intrinsically Resistant to Castration. Stem Cell Reports. 2018 01 09; 10(1):228-242. PMID: 29276153; PMCID: PMC5768933.
      Citations: 24     Fields:    Translation:AnimalsCells
    37. Wang L, Koutelou E, Hirsch C, McCarthy R, Schibler A, Lin K, Lu Y, Jeter C, Shen J, Barton MC, Dent SYR. GCN5 Regulates FGF Signaling and Activates Selective MYC Target Genes during Early Embryoid Body Differentiation. Stem Cell Reports. 2018 01 09; 10(1):287-299. PMID: 29249668; PMCID: PMC5768892.
      Citations: 16     Fields:    Translation:AnimalsCells
    38. Manandhar M, Lowery MG, Boulware KS, Lin KH, Lu Y, Wood RD. Transcriptional consequences of XPA disruption in human cell lines. DNA Repair (Amst). 2017 09; 57:76-90. PMID: 28704716; PMCID: PMC5731452.
      Citations: 7     Fields:    Translation:HumansCells
    39. Takata KI, Reh S, Yousefzadeh MJ, Zelazowski MJ, Bhetawal S, Trono D, Lowery MG, Sandoval M, Takata Y, Lu Y, Lin K, Shen J, Kusewitt DF, McBride KM, Cole F, Wood RD. Analysis of DNA polymerase ? function in meiotic recombination, immunoglobulin class-switching, and DNA damage tolerance. PLoS Genet. 2017 Jun; 13(6):e1006818. PMID: 28570559; PMCID: PMC5472330.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    40. Liu C, Liu R, Zhang D, Deng Q, Liu B, Chao HP, Rycaj K, Takata Y, Lin K, Lu Y, Zhong Y, Krolewski J, Shen J, Tang DG. MicroRNA-141 suppresses prostate cancer stem cells and metastasis by targeting a cohort of pro-metastasis genes. Nat Commun. 2017 01 23; 8:14270. PMID: 28112170; PMCID: PMC5264244.
      Citations: 96     Fields:    Translation:HumansAnimalsCells
    41. Jeter CR, Liu B, Lu Y, Chao HP, Zhang D, Liu X, Chen X, Li Q, Rycaj K, Calhoun-Davis T, Yan L, Hu Q, Wang J, Shen J, Liu S, Tang DG. NANOG reprograms prostate cancer cells to castration resistance via dynamically repressing and engaging the AR/FOXA1 signaling axis. Cell Discov. 2016; 2:16041. PMID: 27867534; PMCID: PMC5109294.
      Citations: 30     
    42. Liu C, Eng C, Shen J, Lu Y, Takata Y, Mehdizadeh A, Chang GJ, Rodriguez-Bigas MA, Li Y, Chang P, Mao Y, Hassan MM, Wang F, Li D. Serum exosomal miR-4772-3p is a predictor of tumor recurrence in stage II and III colon cancer. Oncotarget. 2016 Nov 15; 7(46):76250-76260. PMID: 27788488; PMCID: PMC5342811.
      Citations: 42     Fields:    Translation:HumansCells
    43. Zhang D, Lin K, Lu Y, Rycaj K, Zhong Y, Chao HP, Calhoun-Davis T, Shen J, Tang DG. Developing a Novel Two-Dimensional Culture System to Enrich Human Prostate Luminal Progenitors that Can Function as a Cell of Origin for Prostate Cancer. Stem Cells Transl Med. 2017 03; 6(3):748-760. PMID: 28297567; PMCID: PMC5442765.
      Citations: 14     Fields:    Translation:HumansCells
    44. Atanassov BS, Mohan RD, Lan X, Kuang X, Lu Y, Lin K, McIvor E, Li W, Zhang Y, Florens L, Byrum SD, Mackintosh SG, Calhoun-Davis T, Koutelou E, Wang L, Tang DG, Tackett AJ, Washburn MP, Workman JL, Dent SY. ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth. Mol Cell. 2016 05 19; 62(4):558-71. PMID: 27132940; PMCID: PMC4874879.
      Citations: 55     Fields:    Translation:HumansAnimalsCells
    45. Kim J, Zhao H, Dan J, Kim S, Hardikar S, Hollowell D, Lin K, Lu Y, Takata Y, Shen J, Chen T. Maternal Setdb1 Is Required for Meiotic Progression and Preimplantation Development in Mouse. PLoS Genet. 2016 Apr; 12(4):e1005970. PMID: 27070551; PMCID: PMC4829257.
      Citations: 36     Fields:    Translation:AnimalsCells
    46. Chen X, Li Q, Liu X, Liu C, Liu R, Rycaj K, Zhang D, Liu B, Jeter C, Calhoun-Davis T, Lin K, Lu Y, Chao HP, Shen J, Tang DG. Defining a Population of Stem-like Human Prostate Cancer Cells That Can Generate and Propagate Castration-Resistant Prostate Cancer. Clin Cancer Res. 2016 Sep 01; 22(17):4505-16. PMID: 27060154; PMCID: PMC5010458.
      Citations: 43     Fields:    Translation:HumansAnimalsCells
    47. Zhang D, Park D, Zhong Y, Lu Y, Rycaj K, Gong S, Chen X, Liu X, Chao HP, Whitney P, Calhoun-Davis T, Takata Y, Shen J, Iyer VR, Tang DG. Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer. Nat Commun. 2016 Feb 29; 7:10798. PMID: 26924072; PMCID: PMC4773505.
      Citations: 90     Fields:    Translation:HumansCells
    48. Kim J, Singh AK, Takata Y, Lin K, Shen J, Lu Y, Kerenyi MA, Orkin SH, Chen T. LSD1 is essential for oocyte meiotic progression by regulating CDC25B expression in mice. Nat Commun. 2015 Dec 02; 6:10116. PMID: 26626423; PMCID: PMC4686821.
      Citations: 18     Fields:    Translation:AnimalsCells
    49. Qin T, Si J, Wang X, Gharibyan V, Ahmed S, Hu X, Jin C, Lu Y, Shu J, Estecio MR, Jelinek J, Issa JJ, Raynal NJ. Epigenetic synergy between decitabine and platinum derivatives. Clin Epigenetics. 2015; 7:97. PMID: 26366234; PMCID: PMC4567801.
      Citations: 15     Fields:    
    50. Abba MC, Gong T, Lu Y, Lee J, Zhong Y, Lacunza E, Butti M, Takata Y, Gaddis S, Shen J, Estecio MR, Sahin AA, Aldaz CM. A Molecular Portrait of High-Grade Ductal Carcinoma In Situ. Cancer Res. 2015 Sep 15; 75(18):3980-90. PMID: 26249178; PMCID: PMC4768486.
      Citations: 62     Fields:    Translation:HumansCells
    51. Yamazaki J, Jelinek J, Lu Y, Cesaroni M, Madzo J, Neumann F, He R, Taby R, Vasanthakumar A, Macrae T, Ostler KR, Kantarjian HM, Liang S, Estecio MR, Godley LA, Issa JP. TET2 Mutations Affect Non-CpG Island DNA Methylation at Enhancers and Transcription Factor-Binding Sites in Chronic Myelomonocytic Leukemia. Cancer Res. 2015 Jul 15; 75(14):2833-43. PMID: 25972343; PMCID: PMC4506197.
      Citations: 42     Fields:    Translation:HumansCellsCTClinical Trials
    52. Mallampati S, Leng X, Ma H, Zeng J, Li J, Wang H, Lin K, Lu Y, Yang Y, Sun B, Gong Y, Lee JS, Konopleva M, Andreeff M, Arlinghaus RB, Cai Z, Fang B, Shen H, Han X, Hirsch-Ginsberg CF, Gao X, Paranjape AN, Mani SA, Clise-Dwyer K, Sun X. Tyrosine kinase inhibitors induce mesenchymal stem cell-mediated resistance in BCR-ABL+ acute lymphoblastic leukemia. Blood. 2015 May 07; 125(19):2968-73. PMID: 25712988; PMCID: PMC4424418.
      Citations: 13     Fields:    Translation:AnimalsCells
    53. Malouf GG, Tahara T, Fabre M, Guettier C, Yamazaki J, Long H, Lu Y, Jelinek J, Mouawad R, Khayat D, Raymond E, Issa JP, Paradis V, Raynal NJ, Brugi?res L. Methylome sequencing for fibrolamellar hepatocellular carcinoma depicts distinctive features. Epigenetics. 2015; 10(9):872-81. PMID: 26224146; PMCID: PMC4622466.
      Citations: 5     Fields:    Translation:HumansCells
    54. Raymond A, Liu B, Liang H, Wei C, Guindani M, Lu Y, Liang S, St John LS, Molldrem J, Nagarajan L. A role for BMP-induced homeobox gene MIXL1 in acute myelogenous leukemia and identification of type I BMP receptor as a potential target for therapy. Oncotarget. 2014 Dec 30; 5(24):12675-93. PMID: 25544748; PMCID: PMC4350356.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    55. Jin Q, Zhuang L, Lai B, Wang C, Li W, Dolan B, Lu Y, Wang Z, Zhao K, Peng W, Dent SY, Ge K. Gcn5 and PCAF negatively regulate interferon-? production through HAT-independent inhibition of TBK1. EMBO Rep. 2014 Nov; 15(11):1192-201. PMID: 25269644; PMCID: PMC4253493.
      Citations: 18     Fields:    Translation:HumansCells
    56. Ma H, Mallampati S, Lu Y, Sun B, Wang E, Leng X, Gong Y, Shen H, Yin CC, Jones D, Amin HM, You MJ, Zweidler-McKay P, Ma Y, Kantarjian HM, Arlinghaus RB, Glassman A, Sun X. The Sox4/Tcf7l1 axis promotes progression of BCR-ABL-positive acute lymphoblastic leukemia. Haematologica. 2014 Oct; 99(10):1591-8. PMID: 24997151; PMCID: PMC4181255.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    57. Simper MS, Rundhaug JE, Mikulec C, Bowen R, Shen J, Lu Y, Lin K, Surh I, Fischer SM. The tumor promoting activity of the EP4 receptor for prostaglandin E2 in murine skin. Mol Oncol. 2014 Dec; 8(8):1626-39. PMID: 25034079; PMCID: PMC4253556.
      Citations: 10     Fields:    Translation:Animals
    58. Jin C, Lu Y, Jelinek J, Liang S, Estecio MR, Barton MC, Issa JP. TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells. Nucleic Acids Res. 2014 Jun; 42(11):6956-71. PMID: 24875481; PMCID: PMC4066785.
      Citations: 68     Fields:    Translation:HumansCells
    59. Mallampati S, Sun B, Lu Y, Ma H, Gong Y, Wang D, Lee JS, Lin K, Sun X. Integrated genetic approaches identify the molecular mechanisms of Sox4 in early B-cell development: intricate roles for RAG1/2 and CK1e. Blood. 2014 Jun 26; 123(26):4064-76. PMID: 24786772; PMCID: PMC4073324.
      Citations: 20     Fields:    Translation:AnimalsCells
    60. Yang Y, McBride KM, Hensley S, Lu Y, Chedin F, Bedford MT. Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Mol Cell. 2014 Feb 06; 53(3):484-97. PMID: 24507716; PMCID: PMC3959860.
      Citations: 115     Fields:    Translation:HumansAnimalsCells
    61. Maegawa S, Gough SM, Watanabe-Okochi N, Lu Y, Zhang N, Castoro RJ, Estecio MR, Jelinek J, Liang S, Kitamura T, Aplan PD, Issa JP. Age-related epigenetic drift in the pathogenesis of MDS and AML. Genome Res. 2014 Apr; 24(4):580-91. PMID: 24414704; PMCID: PMC3975058.
      Citations: 46     Fields:    Translation:HumansAnimalsCells
    62. Malouf GG, Taube JH, Lu Y, Roysarkar T, Panjarian S, Estecio MR, Jelinek J, Yamazaki J, Raynal NJ, Long H, Tahara T, Tinnirello A, Ramachandran P, Zhang XY, Liang S, Mani SA, Issa JP. Architecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition. Genome Biol. 2013 Dec 24; 14(12):R144. PMID: 24367927; PMCID: PMC4053791.
      Citations: 38     Fields:    Translation:HumansCells
    63. Yamazaki J, Estecio MR, Lu Y, Long H, Malouf GG, Graber D, Huo Y, Ramagli L, Liang S, Kornblau SM, Jelinek J, Issa JP. The epigenome of AML stem and progenitor cells. Epigenetics. 2013 Jan; 8(1):92-104. PMID: 23249680; PMCID: PMC3549884.
      Citations: 21     Fields:    Translation:HumansCells
    64. Gururaj AE, Gibson L, Panchabhai S, Bai M, Manyam G, Lu Y, Latha K, Rojas ML, Hwang Y, Liang S, Bogler O. Access to the nucleus and functional association with c-Myc is required for the full oncogenic potential of ?EGFR/EGFRvIII. J Biol Chem. 2013 Feb 01; 288(5):3428-38. PMID: 23250739; PMCID: PMC3561561.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    65. Xie G, Lu Y, Sun Y, Zhang SS, Keystone EC, Gregersen PK, Plenge RM, Amos CI, Siminovitch KA. Identification of the NF-?B activating protein-like locus as a risk locus for rheumatoid arthritis. Ann Rheum Dis. 2013 Jul; 72(7):1249-54. PMID: 23223422; PMCID: PMC3686260.
      Citations: 5     Fields:    Translation:Humans
    66. Chen K, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent SY. Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res. 2013 Feb; 23(2):312-22. PMID: 23124522; PMCID: PMC3561872.
      Citations: 19     Fields:    Translation:AnimalsCells
    67. Li H, Su X, Gallegos J, Lu Y, Ji Y, Molldrem JJ, Liang S. dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes. BMC Bioinformatics. 2012 Oct 19; 13:271. PMID: 23083219; PMCID: PMC3497615.
      Citations: 6     Fields:    Translation:HumansCells
    68. Jelinek J, Liang S, Lu Y, He R, Ramagli LS, Shpall EJ, Estecio MR, Issa JP. Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique. Epigenetics. 2012 Dec 01; 7(12):1368-78. PMID: 23075513; PMCID: PMC3528692.
      Citations: 35     Fields:    Translation:HumansCells
    69. Gallegos J, Dekmezian M, Lu Y, Liang S, Issa JP, Est?cio MR. SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Mol Cancer Res. 2012 Oct; 10(10):1332-42. PMID: 22952045; PMCID: PMC3475755.
      Citations: 42     Fields:    Translation:HumansAnimalsCells
    70. Cai G, Li H, Lu Y, Huang X, Lee J, Ji Y, Liang S, M?ller P. Accuracy of RNA-Seq and its dependence on sequencing depth. BMC Bioinformatics. 2012; 13 Suppl 13:S5. PMID: 23320920; PMCID: PMC3426807.
      Citations: 11     Fields:    
    71. Ji Y, Mitra R, Quintana F, Jara A, Mueller P, Liu P, Lu Y, Liang S. BM-BC: a Bayesian method of base calling for Solexa sequence data. BMC Bioinformatics. 2012; 13 Suppl 13:S6. PMID: 23320938; PMCID: PMC3426806.
      Citations: 3     Fields:    
    72. Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JP, Godley LA, Li W, Goodell MA. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet. 2011 Dec 04; 44(1):23-31. PMID: 22138693; PMCID: PMC3637952.
      Citations: 472     Fields:    Translation:HumansAnimalsCells
    73. Jelinek J, Gharibyan V, Estecio MR, Kondo K, He R, Chung W, Lu Y, Zhang N, Liang S, Kantarjian HM, Cortes JE, Issa JP. Aberrant DNA methylation is associated with disease progression, resistance to imatinib and shortened survival in chronic myelogenous leukemia. PLoS One. 2011; 6(7):e22110. PMID: 21760961; PMCID: PMC3132778.
      Citations: 52     Fields:    Translation:HumansCells
    74. Yang Y, Lu Y, Espejo A, Wu J, Xu W, Liang S, Bedford MT. TDRD3 is an effector molecule for arginine-methylated histone marks. Mol Cell. 2010 Dec 22; 40(6):1016-23. PMID: 21172665; PMCID: PMC3090733.
      Citations: 111     Fields:    Translation:HumansCells
    75. Tonthat NK, Arold ST, Pickering BF, Van Dyke MW, Liang S, Lu Y, Beuria TK, Margolin W, Schumacher MA. Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check. EMBO J. 2011 Jan 05; 30(1):154-64. PMID: 21113127; PMCID: PMC3020112.
      Citations: 81     Fields:    Translation:Cells
    76. Hirschfield GM, Liu X, Han Y, Gorlov IP, Lu Y, Xu C, Lu Y, Chen W, Juran BD, Coltescu C, Mason AL, Milkiewicz P, Myers RP, Odin JA, Luketic VA, Speiciene D, Vincent C, Levy C, Gregersen PK, Zhang J, Heathcote EJ, Lazaridis KN, Amos CI, Siminovitch KA. Variants at IRF5-TNPO3, 17q12-21 and MMEL1 are associated with primary biliary cirrhosis. Nat Genet. 2010 Aug; 42(8):655-7. PMID: 20639879; PMCID: PMC2929126.
      Citations: 97     Fields:    Translation:Humans
    77. Liu X, Invernizzi P, Lu Y, Kosoy R, Lu Y, Bianchi I, Podda M, Xu C, Xie G, Macciardi F, Selmi C, Lupoli S, Shigeta R, Ransom M, Lleo A, Lee AT, Mason AL, Myers RP, Peltekian KM, Ghent CN, Bernuzzi F, Zuin M, Rosina F, Borghesio E, Floreani A, Lazzari R, Niro G, Andriulli A, Muratori L, Muratori P, Almasio PL, Andreone P, Margotti M, Brunetto M, Coco B, Alvaro D, Bragazzi MC, Marra F, Pisano A, Rigamonti C, Colombo M, Marzioni M, Benedetti A, Fabris L, Strazzabosco M, Portincasa P, Palmieri VO, Tiribelli C, Croce L, Bruno S, Rossi S, Vinci M, Prisco C, Mattalia A, Toniutto P, Picciotto A, Galli A, Ferrari C, Colombo S, Casella G, Morini L, Caporaso N, Colli A, Spinzi G, Montanari R, Gregersen PK, Heathcote EJ, Hirschfield GM, Siminovitch KA, Amos CI, Gershwin ME, Seldin MF. Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis. Nat Genet. 2010 Aug; 42(8):658-60. PMID: 20639880; PMCID: PMC3150510.
      Citations: 168     Fields:    Translation:Humans
    78. Gregersen PK, Amos CI, Lee AT, Lu Y, Remmers EF, Kastner DL, Seldin MF, Criswell LA, Plenge RM, Holers VM, Mikuls TR, Sokka T, Moreland LW, Bridges SL, Xie G, Begovich AB, Siminovitch KA. REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis. Nat Genet. 2009 Jul; 41(7):820-3. PMID: 19503088; PMCID: PMC2705058.
      Citations: 162     Fields:    Translation:Humans
    79. Hirschfield GM, Liu X, Xu C, Lu Y, Xie G, Lu Y, Gu X, Walker EJ, Jing K, Juran BD, Mason AL, Myers RP, Peltekian KM, Ghent CN, Coltescu C, Atkinson EJ, Heathcote EJ, Lazaridis KN, Amos CI, Siminovitch KA. Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants. N Engl J Med. 2009 Jun 11; 360(24):2544-55. PMID: 19458352; PMCID: PMC2857316.
      Citations: 233     Fields:    Translation:Humans
    80. Walker EJ, Hirschfield GM, Xu C, Lu Y, Liu X, Lu Y, Coltescu C, Wang K, Newman WG, Bykerk V, Keystone EC, Mosher D, Amos CI, Heathcote EJ, Siminovitch KA. CTLA4/ICOS gene variants and haplotypes are associated with rheumatoid arthritis and primary biliary cirrhosis in the Canadian population. Arthritis Rheum. 2009 Apr; 60(4):931-7. PMID: 19333938.
      Citations: 24     Fields:    Translation:Humans
    81. Liang S, Lu Y, Jelinek J, Estecio M, Li H, Issa JP. Analysis of epigenetic modifications by next generation sequencing. Annu Int Conf IEEE Eng Med Biol Soc. 2009; 2009:6730. PMID: 19963934.
      Citations: 2     Fields:    Translation:AnimalsCells
    82. Lu Y, Sze SH. Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Res. 2009 Feb; 37(2):463-72. PMID: 19056820; PMCID: PMC2632924.
      Citations: 8     Fields:    
    83. Lu Y, Sze SH. Multiple sequence alignment based on profile alignment of intermediate sequences. J Comput Biol. 2008 Sep; 15(7):767-77. PMID: 18662101.
      Citations: 4     Fields:    Translation:Cells
    84. Daw EW, Lu Y, Marian AJ, Shete S. Identifying modifier loci in existing genome scan data. Ann Hum Genet. 2008 Sep; 72(Pt 5):670-5. PMID: 18494837; PMCID: PMC4003897.
      Citations: 11     Fields:    Translation:Humans
    85. Daw EW, Chen SN, Czernuszewicz G, Lombardi R, Lu Y, Ma J, Roberts R, Shete S, Marian AJ. Genome-wide mapping of modifier chromosomal loci for human hypertrophic cardiomyopathy. Hum Mol Genet. 2007 Oct 15; 16(20):2463-71. PMID: 17652099; PMCID: PMC2772866.
      Citations: 41     Fields:    Translation:HumansCells
    86. Shete S, Elston RC, Lu Y. A novel approach to detect parent-of-origin effects from pedigree data with application to Beckwith-Wiedemann syndrome. Ann Hum Genet. 2007 Nov; 71(Pt 6):804-14. PMID: 17578507.
      Citations: 3     Fields:    Translation:Humans
    87. Viswanath L, Lu Y, Fox GE. Genome display tool: visualizing features in complex data sets. Source Code Biol Med. 2007 Feb 14; 2:1. PMID: 17300731; PMCID: PMC1805442.
      Citations: 3     
    88. Sze SH, Lu Y, Yang Q. A polynomial time solvable formulation of multiple sequence alignment. J Comput Biol. 2006 Mar; 13(2):309-19. PMID: 16597242.
      Citations: 4     Fields:    
    89. Daw EW, Heath SC, Lu Y. Single-nucleotide polymorphism versus microsatellite markers in a combined linkage and segregation analysis of a quantitative trait. BMC Genet. 2005 Dec 30; 6 Suppl 1:S32. PMID: 16451642; PMCID: PMC1866753.
      Citations: 12     Fields:    Translation:HumansCells
    90. Martin KA, Siefert JL, Yerrapragada S, Lu Y, McNeill TZ, Moreno PA, Weinstock GM, Widger WR, Fox GE. Cyanobacterial signature genes. Photosynth Res. 2003; 75(3):211-21. PMID: 16228602.
      Citations: 12     Fields:    
    91. Erratum. PLoS One. 10.
    92. ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth. Molecular Cell.
    93. A polynomial time solvable formulation of multiple sequence alignment. 204-216.
    94. Defining a population of stem-like human prostate cancer cells that can generate and propagate castration-resistant prostate cancer. Clinical Cancer Research. 22:4505-4516.
    95. A Bayesian graphical model for ChIP-Seq data on histone modifications. Journal of the American Statistical Association. 108:69-80.
    96. Activation of HERV-K Env protein is essential for tumorigenesis and metastasis of breast cancer cells. Oncotarget. 7:84093-84117.
    97. Genome display tool. Source Code for Biology and Medicine. 2.
    98. Epigenetic synergy between decitabine and platinum derivatives. Clinical Epigenetics. 7.
    99. Analysis of epigenetic modifications by next generation sequencing. 6730.
    100. Expanded GAA repeats impede transcription elongation through the FXN gene and induce transcriptional silencing that is restricted to the FXN locus. Human Molecular Genetics. 24:6932-6943.
    101. PHF20 Readers Link Methylation of Histone H3K4 and p53 with H4K16 Acetylation. Cell Reports. 17:1158-1170.
    102. Maternal Setdb1 Is Required for Meiotic Progression and Preimplantation Development in Mouse. PLoS Genetics. 12.
    103. Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer. Nature Communications. 7.
    104. Methylome sequencing for fibrolamellar hepatocellular carcinoma depicts distinctive features. Epigenetics. 10:872-881.
    105. Erratum. Nature Communications. 7.
    106. Serum exosomal miR-4772-3p is a predictor of tumor recurrence in stage II and III colon cancer. Oncotarget. 7:76250-76260.
    107. DMBA induced mouse mammary tumors display high incidence of activating Pik3caH1047 and loss of function Pten mutations. Oncotarget. 7:64289-64299.
    108. Histone H3K4 methylation regulates deactivation of the spindle assembly checkpoint through direct binding of Mad2. Genes and Development. 30:1187-1197.
    109. CSA-RRBS. 105-110.
    110. Cyanobacterial signature genes. Photosynthesis Research. 75:211-221.
    111. Multiple sequence alignment based on profile alignment of intermediate sequences. 283-295.
    112. DNA methylation signature reveals cell ontogeny of renal cell carcinomas. Clinical Cancer Research. 22:6236-6246.
    113. LSD1 is essential for oocyte meiotic progression by regulating CDC25B expression in mice. Nature Communications. 6.
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