Publications

  1. Tuleta I, Venugopal H, O'Leary K, Zheng D, Frangogiannis NG. Fibroblast-Specific Loss of TGF-β Signaling Mediates Lipomatous Metaplasia in the Infarcted Heart. Circulation. 2025 Sep 19;. doi: 10.1161/CIRCULATIONAHA.125.075676. [Epub ahead of print] PubMed PMID: 40970279.
  2. Misra R, Ferrena A, Zheng D. Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values. Nat Commun. 2025 Jul 1;16(1):5763. doi: 10.1038/s41467-025-60899-8. PubMed PMID: 40595539; PubMed Central PMCID: PMC12218346.
  3. Wong EWP, Sahin M, Yang R, Lee U, Li D, Zhan YA, Misra R, Tomas F, Alomran N, Polyzos A, Lee CJ, Trieu T, Martinez-Fundichely A, Wiesner T, Rosowicz A, Cheng S, Liu C, Lallo M, Shoushtari AN, Merghoub T, Hamard PJ, Koche R, Khurana E, Apostolou E, Zheng D, Chen Y, Leslie CS, Chi P. Disruption of TAD hierarchy promotes LTR co-option in cancer. Nat Genet. 2025 Jul;57(7):1754-1765. doi: 10.1038/s41588-025-02239-6. Epub 2025 Jun 30. PubMed PMID: 40588507; PubMed Central PMCID: PMC12283374.
  4. Li J, Li Z, Yin J, Wang Y, Zheng D, Cai L, Wang GG. The sotos syndrome gene Nsd1 safeguards developmental gene enhancers poised for transcription by maintaining the precise deposition of histone methylation. J Biol Chem. 2025 May;301(5):108423. doi: 10.1016/j.jbc.2025.108423. Epub 2025 Mar 19. PubMed PMID: 40118455; PubMed Central PMCID: PMC12033923.
  5. Zhuang X, Wang Q, Joost S, Ferrena A, Humphreys DT, Li Z, Blum M, Krause K, Ding S, Landais Y, Zhan Y, Zhao Y, Chaligne R, Lee JH, Carrasco SE, Bhanot UK, Koche RP, Bott MJ, Katajisto P, Soto-Feliciano YM, Pisanic T, Thomas T, Zheng D, Wong ES, Tammela T. Ageing limits stemness and tumorigenesis by reprogramming iron homeostasis. Nature. 2025 Jan;637(8044):184-194. doi: 10.1038/s41586-024-08285-0. Epub 2024 Dec 4. PubMed PMID: 39633048.
  6. Ferrena A, Zhang X, Shrestha R, Zheng D, Liu W. Six3 and Six6 jointly control diverse target genes in multiple cell populations over developmental trajectories of mouse embryonic retinal progenitor cells. PLoS One. 2024;19(10):e0308839. doi: 10.1371/journal.pone.0308839. eCollection 2024. PubMed PMID: 39446806; PubMed Central PMCID: PMC11500937.
  7. Asmat MS, Zheng XY, Nauman M, Zheng D, Stanley P. Deletion of Mgat2 in spermatogonia blocks spermatogenesis. Front Cell Dev Biol. 2024;12:1428715. doi: 10.3389/fcell.2024.1428715. eCollection 2024. PubMed PMID: 39364139; PubMed Central PMCID: PMC11447316.
  8. Ferrena A, Zheng XY, Jackson K, Hoang B, Morrow BE, Zheng D. scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison. NAR Genom Bioinform. 2024 Sep;6(4):lqae134. doi: 10.1093/nargab/lqae134. eCollection 2024 Sep. PubMed PMID: 39345754; PubMed Central PMCID: PMC11437360.
  9. Li R, Hanna A, Huang S, Hernandez SC, Tuleta I, Kubota A, Humeres C, Chen B, Liu Y, Zheng D, Frangogiannis NG. Macrophages in the infarcted heart acquire a fibrogenic phenotype, expressing matricellular proteins, but do not undergo fibroblast conversion. J Mol Cell Cardiol. 2024 Nov;196:152-167. doi: 10.1016/j.yjmcc.2024.07.010. Epub 2024 Jul 31. PubMed PMID: 39089570; PubMed Central PMCID: PMC11534516.
  10. Muñoz Perez N, Pensabene JM, Galbo PM Jr, Sadeghipour N, Xiu J, Moziak K, Yazejian RM, Welch RL, Bell WR, Sengupta S, Aulakh S, Eberhart CG, Loeb DM, Eskandar E, Zheng D, Zang X, Martin AM. VISTA Emerges as a Promising Target against Immune Evasion Mechanisms in Medulloblastoma. Cancers (Basel). 2024 Jul 24;16(15). doi: 10.3390/cancers16152629. PubMed PMID: 39123357; PubMed Central PMCID: PMC11312086.
  11. Astorkia M, Liu Y, Pedrosa EM, Lachman HM, Zheng D. Molecular and network disruptions in neurodevelopment uncovered by single cell transcriptomics analysis of CHD8 heterozygous cerebral organoids. Heliyon. 2024 Jul 30;10(14):e34862. doi: 10.1016/j.heliyon.2024.e34862. eCollection 2024 Jul 30. PubMed PMID: 39149047; PubMed Central PMCID: PMC11325375.
  12. Yheskel M, Hatch HAM, Pedrosa E, Terry BK, Siebels AA, Zheng XY, Blok LER, Fencková M, Sidoli S, Schenck A, Zheng D, Lachman HM, Secombe J. KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons. Nucleic Acids Res. 2024 Jun 24;52(11):6201-6219. doi: 10.1093/nar/gkae261. PubMed PMID: 38597673; PubMed Central PMCID: PMC11194071.
  13. Van Arsdale A, Turker L, Chang YC, Gould J, Harmon B, Maggi EC, Meshcheryakova O, Brown MP, Luong D, Van Doorslaer K, Einstein MH, Kuo DYS, Zheng D, Haas BJ, Lenz J, Montagna C. Structure and transcription of integrated HPV DNA in vulvar carcinomas. NPJ Genom Med. 2024 Jun 19;9(1):35. doi: 10.1038/s41525-024-00418-8. PubMed PMID: 38898085; PubMed Central PMCID: PMC11187145.
  14. Jing Z, Galbo P, Ovando L, Demouth M, Welte S, Park R, Chandran K, Wu Y, MacCarthy T, Zheng D, Fooksman D. Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity. Elife. 2024 Jun 18;12. doi: 10.7554/eLife.89712. PubMed PMID: 38896451; PubMed Central PMCID: PMC11186632.
  15. Ferrena A, Zheng XY, Jackson K, Hoang B, Morrow B, Zheng D. scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison. bioRxiv. 2024 May 9;. doi: 10.1101/2024.05.06.592708. PubMed PMID: 38766089; PubMed Central PMCID: PMC11100619.
  16. Nishimura CD, Corrigan D, Zheng XY, Galbo PM Jr, Wang S, Liu Y, Wei Y, Suo L, Cui W, Mercado N, Zheng D, Zhang CC, Zang X. TOP CAR with TMIGD2 as a safe and effective costimulatory domain in CAR cells treating human solid tumors. Sci Adv. 2024 May 10;10(19):eadk1857. doi: 10.1126/sciadv.adk1857. Epub 2024 May 8. PubMed PMID: 38718110; PubMed Central PMCID: PMC11078193.
  17. O'Leary K, Zheng D. Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs. NPJ Syst Biol Appl. 2024 Apr 5;10(1):36. doi: 10.1038/s41540-024-00364-2. PubMed PMID: 38580667; PubMed Central PMCID: PMC10997786.
  18. Galbo PM Jr, Madsen AT, Liu Y, Peng M, Wei Y, Ciesielski MJ, Fenstermaker RA, Graff S, Montagna C, Segall JE, Sidoli S, Zang X, Zheng D. Functional Contribution and Clinical Implication of Cancer-Associated Fibroblasts in Glioblastoma. Clin Cancer Res. 2024 Feb 16;30(4):865-876. doi: 10.1158/1078-0432.CCR-23-0493. PubMed PMID: 38060213; PubMed Central PMCID: PMC10922678.
  19. Wang J, Ferrena A, Zhang R, Singh S, Viscarret V, Al-Harden W, Aldahamsheh O, Borjihan H, Singla A, Yaguare S, Tingling J, Zi X, Lo Y, Gorlick R, Schwartz EL, Zhao H, Yang R, Geller DS, Zheng D, Hoang BH. Targeted inhibition of SCF(SKP2) confers anti-tumor activities resulting in a survival benefit in osteosarcoma. Oncogene. 2024 Mar;43(13):962-975. doi: 10.1038/s41388-024-02942-4. Epub 2024 Feb 14. PubMed PMID: 38355807; PubMed Central PMCID: PMC10959747.
  20. Ferrena A, Wang J, Zhang R, Karadal-Ferrena B, Al-Hardan W, Singh S, Borjihan H, Schwartz EL, Zhao H, Oktay MH, Yang R, Geller DS, Hoang BH, Zheng D. SKP2 Knockout in Rb1/p53-Deficient Mouse Models of Osteosarcoma Induces Immune Infiltration and Drives a Transcriptional Program with a Favorable Prognosis. Mol Cancer Ther. 2024 Feb 1;23(2):223-234. doi: 10.1158/1535-7163.MCT-23-0173. PubMed PMID: 37871911; PubMed Central PMCID: PMC10842346.
  21. Nguyen MB, Flora P, Branch MC, Weber M, Zheng XY, Sivan U, Joost S, Annusver K, Zheng D, Kasper M, Ezhkova E. Tenascin-C expressing touch dome keratinocytes exhibit characteristics of all epidermal lineages. Sci Adv. 2024 Jan 19;10(3):eadi5791. doi: 10.1126/sciadv.adi5791. Epub 2024 Jan 19. PubMed PMID: 38241368; PubMed Central PMCID: PMC10798558.
  22. Wang H, Sica RA, Kaur G, Galbo PM Jr, Jing Z, Nishimura CD, Ren X, Tanwar A, Etemad-Gilbertson B, Will B, Zheng D, Fooksman D, Zang X. TMIGD2 is an orchestrator and therapeutic target on human acute myeloid leukemia stem cells. Nat Commun. 2024 Jan 2;15(1):11. doi: 10.1038/s41467-023-43843-6. PubMed PMID: 38167704; PubMed Central PMCID: PMC10761673.
  23. Racedo SE, Liu Y, Shi L, Zheng D, Morrow BE. Dgcr8 functions in the secondary heart field for outflow tract and right ventricle development in mammals. Dev Biol. 2024 Feb;506:72-84. doi: 10.1016/j.ydbio.2023.12.005. Epub 2023 Dec 17. PubMed PMID: 38110169; PubMed Central PMCID: PMC10793380.
  24. Li R, Chen B, Kubota A, Hanna A, Humeres C, Hernandez SC, Liu Y, Ma R, Tuleta I, Huang S, Venugopal H, Zhu F, Su K, Li J, Zhang J, Zheng D, Frangogiannis NG. Protective effects of macrophage-specific integrin α5 in myocardial infarction are associated with accentuated angiogenesis. Nat Commun. 2023 Nov 20;14(1):7555. doi: 10.1038/s41467-023-43369-x. PubMed PMID: 37985764; PubMed Central PMCID: PMC10662477.
  25. Liu Y, John P, Nishitani K, Cui J, Nishimura CD, Christin JR, Couturier N, Ren X, Wei Y, Pulanco MC, Galbo PM Jr, Zhang X, Fu W, Cui W, Bartholdy BA, Zheng D, Lauvau G, Fineberg SA, Oktay MH, Zang X, Guo W. A SOX9-B7x axis safeguards dedifferentiated tumor cells from immune surveillance to drive breast cancer progression. Dev Cell. 2023 Dec 4;58(23):2700-2717.e12. doi: 10.1016/j.devcel.2023.10.010. Epub 2023 Nov 13. PubMed PMID: 37963469; PubMed Central PMCID: PMC10842074.
  26. Astorkia M, Liu Y, Pedrosa EM, Lachman HM, Zheng D. Molecular and network disruptions in neurodevelopment uncovered by single cell transcriptomics analysis of CHD8 heterozygous cerebral organoids. bioRxiv. 2023 Sep 27;. doi: 10.1101/2023.09.27.559752. PubMed PMID: 37808768; PubMed Central PMCID: PMC10557718.
  27. Stathopoulou A, Wang P, Thellier C, Kelly RG, Zheng D, Scambler PJ. CHARGE syndrome-associated CHD7 acts at ISL1-regulated enhancers to modulate second heart field gene expression. Cardiovasc Res. 2023 Sep 5;119(11):2089-2105. doi: 10.1093/cvr/cvad059. PubMed PMID: 37052590; PubMed Central PMCID: PMC10478754.
  28. Ho YC, Geng X, O'Donnell A, Ibarrola J, Fernandez-Celis A, Varshney R, Subramani K, Azartash-Namin ZJ, Kim J, Silasi R, Wylie-Sears J, Alvandi Z, Chen L, Cha B, Chen H, Xia L, Zhou B, Lupu F, Burkhart HM, Aikawa E, Olson LE, Ahamed J, López-Andrés N, Bischoff J, Yutzey KE, Srinivasan RS. PROX1 Inhibits PDGF-B Expression to Prevent Myxomatous Degeneration of Heart Valves. Circ Res. 2023 Sep;133(6):463-480. doi: 10.1161/CIRCRESAHA.123.323027. Epub 2023 Aug 9. PubMed PMID: 37555328; PubMed Central PMCID: PMC10487359.
  29. Zhao Y, Wang Y, Shi L, McDonald-McGinn DM, Crowley TB, McGinn DE, Tran OT, Miller D, Lin JR, Zackai E, Johnston HR, Chow EWC, Vorstman JAS, Vingerhoets C, van Amelsvoort T, Gothelf D, Swillen A, Breckpot J, Vermeesch JR, Eliez S, Schneider M, van den Bree MBM, Owen MJ, Kates WR, Repetto GM, Shashi V, Schoch K, Bearden CE, Digilio MC, Unolt M, Putotto C, Marino B, Pontillo M, Armando M, Vicari S, Angkustsiri K, Campbell L, Busa T, Heine-Suñer D, Murphy KC, Murphy D, García-Miñaúr S, Fernández L, Zhang ZD, Goldmuntz E, Gur RE, Emanuel BS, Zheng D, Marshall CR, Bassett AS, Wang T, Morrow BE. Chromatin regulators in the TBX1 network confer risk for conotruncal heart defects in 22q11.2DS. NPJ Genom Med. 2023 Jul 18;8(1):17. doi: 10.1038/s41525-023-00363-y. PubMed PMID: 37463940; PubMed Central PMCID: PMC10354062.
  30. Alex L, Tuleta I, Hernandez SC, Hanna A, Venugopal H, Astorkia M, Humeres C, Kubota A, Su K, Zheng D, Frangogiannis NG. Cardiac Pericytes Acquire a Fibrogenic Phenotype and Contribute to Vascular Maturation After Myocardial Infarction. Circulation. 2023 Sep 12;148(11):882-898. doi: 10.1161/CIRCULATIONAHA.123.064155. Epub 2023 Jun 23. PubMed PMID: 37350296; PubMed Central PMCID: PMC10527624.
  31. Bera BS, Thompson TV, Sosa E, Nomaru H, Reynolds D, Dubin RA, Maqbool SB, Zheng D, Morrow BE, Greally JM, Suzuki M. An optimized approach for multiplexing single-nuclear ATAC-seq using oligonucleotide-conjugated antibodies. Epigenetics Chromatin. 2023 Apr 28;16(1):14. doi: 10.1186/s13072-023-00486-7. PubMed PMID: 37118773; PubMed Central PMCID: PMC10142415.
  32. Lü J, Zhao Q, Guo Y, Li D, Xie H, Liu C, Hu X, Liu S, Hou Z, Wei X, Zheng D, Pestell RG, Yu Z. Regulation of ERα-dependent breast cancer metastasis by a miR-29a signaling. J Exp Clin Cancer Res. 2023 Apr 20;42(1):93. doi: 10.1186/s13046-023-02665-6. PubMed PMID: 37081505; PubMed Central PMCID: PMC10116798.
  33. Lu P, Wu B, Wang Y, Russell M, Liu Y, Bernard DJ, Zheng D, Zhou B. Prerequisite endocardial-mesenchymal transition for murine cardiac trabecular angiogenesis. Dev Cell. 2023 May 8;58(9):791-805.e4. doi: 10.1016/j.devcel.2023.03.009. Epub 2023 Apr 5. PubMed PMID: 37023750; PubMed Central PMCID: PMC10656710.
  34. De Bono C, Liu Y, Ferrena A, Valentine A, Zheng D, Morrow BE. Single-cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell development. Nat Commun. 2023 Mar 21;14(1):1551. doi: 10.1038/s41467-023-37015-9. PubMed PMID: 36941249; PubMed Central PMCID: PMC10027855.
  35. Chang W, Zhao Y, Rayêe D, Xie Q, Suzuki M, Zheng D, Cvekl A. Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation. Epigenetics Chromatin. 2023 Jan 25;16(1):4. doi: 10.1186/s13072-023-00478-7. PubMed PMID: 36698218; PubMed Central PMCID: PMC9875507.
  36. Cui J, Zhang C, Lee JE, Bartholdy BA, Yang D, Liu Y, Erler P, Galbo PM Jr, Hodge DQ, Huangfu D, Zheng D, Ge K, Guo W. MLL3 loss drives metastasis by promoting a hybrid epithelial-mesenchymal transition state. Nat Cell Biol. 2023 Jan;25(1):145-158. doi: 10.1038/s41556-022-01045-0. Epub 2023 Jan 5. PubMed PMID: 36604594; PubMed Central PMCID: PMC10003829.
  37. Ren X, Peng M, Xing P, Wei Y, Galbo PM Jr, Corrigan D, Wang H, Su Y, Dong X, Sun Q, Li Y, Zhang X, Edelmann W, Zheng D, Zang X. Blockade of the immunosuppressive KIR2DL5/PVR pathway elicits potent human NK cell-mediated antitumor immunity. J Clin Invest. 2022 Nov 15;132(22). doi: 10.1172/JCI163620. PubMed PMID: 36377656; PubMed Central PMCID: PMC9663162.
  38. Piszczatowski RT, Schwenger E, Sundaravel S, Stein CM, Liu Y, Stanley P, Verma A, Zheng D, Seidel RD, Almo SC, Townley RA, Bülow HE, Steidl U. A glycan-based approach to cell characterization and isolation: Hematopoiesis as a paradigm. J Exp Med. 2022 Nov 7;219(11). doi: 10.1084/jem.20212552. Epub 2022 Sep 6. PubMed PMID: 36066492; PubMed Central PMCID: PMC9455685.
  39. Patel AJ, Warda S, Maag JLV, Misra R, Miranda-Román MA, Pachai MR, Lee CJ, Li D, Wang N, Bayshtok G, Fishinevich E, Meng Y, Wong EWP, Yan J, Giff E, Pappalardi MB, McCabe MT, Fletcher JA, Rudin CM, Chandarlapaty S, Scandura JM, Koche RP, Glass JL, Antonescu CR, Zheng D, Chen Y, Chi P. PRC2-Inactivating Mutations in Cancer Enhance Cytotoxic Response to DNMT1-Targeted Therapy via Enhanced Viral Mimicry. Cancer Discov. 2022 Sep 2;12(9):2120-2139. doi: 10.1158/2159-8290.CD-21-1671. PubMed PMID: 35789380; PubMed Central PMCID: PMC9437570.
  40. Yan J, Chen Y, Patel AJ, Warda S, Lee CJ, Nixon BG, Wong EW, Miranda-Román MA, Yang N, Wang Y, Pachai MR, Sher J, Giff E, Tang F, Khurana E, Singer S, Liu Y, Galbo PM Jr, Maag JL, Koche RP, Zheng D, Antonescu CR, Deng L, Li MO, Chen Y, Chi P. Tumor-intrinsic PRC2 inactivation drives a context-dependent immune-desert microenvironment and is sensitized by immunogenic viruses. J Clin Invest. 2022 Sep 1;132(17). doi: 10.1172/JCI153437. PubMed PMID: 35852856; PubMed Central PMCID: PMC9433107.
  41. Singh VK, Misra R, Almo SC, Steidl UG, Bülow HE, Zheng D. HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elements. Bioinformatics. 2022 Aug 10;38(16):4036-4038. doi: 10.1093/bioinformatics/btac437. PubMed PMID: 35771633; PubMed Central PMCID: PMC9364371.
  42. Lu P, Wu B, Feng X, Cheng W, Kitsis RN, Zhou B. Cardiac Myosin Heavy Chain Reporter Mice to Study Heart Development and Disease. Circ Res. 2022 Aug 5;131(4):364-366. doi: 10.1161/CIRCRESAHA.122.321461. Epub 2022 Jul 13. PubMed PMID: 35862119; PubMed Central PMCID: PMC9357176.
  43. Lu P, Wang P, Wu B, Wang Y, Liu Y, Cheng W, Feng X, Yuan X, Atteya MM, Ferro H, Sugi Y, Rydquist G, Esmaily M, Butcher JT, Chang CP, Lenz J, Zheng D, Zhou B. A SOX17-PDGFB signaling axis regulates aortic root development. Nat Commun. 2022 Jul 13;13(1):4065. doi: 10.1038/s41467-022-31815-1. PubMed PMID: 35831318; PubMed Central PMCID: PMC9279414.
  44. Trifiletti R, Lachman HM, Manusama O, Zheng D, Spalice A, Chiurazzi P, Schornagel A, Serban AM, van Wijck R, Cunningham JL, Swagemakers S, van der Spek PJ. Identification of ultra-rare genetic variants in pediatric acute onset neuropsychiatric syndrome (PANS) by exome and whole genome sequencing. Sci Rep. 2022 Jun 30;12(1):11106. doi: 10.1038/s41598-022-15279-3. PubMed PMID: 35773312; PubMed Central PMCID: PMC9246359.
  45. John P, Pulanco MC, Galbo PM Jr, Wei Y, Ohaegbulam KC, Zheng D, Zang X. The immune checkpoint B7x expands tumor-infiltrating Tregs and promotes resistance to anti-CTLA-4 therapy. Nat Commun. 2022 May 6;13(1):2506. doi: 10.1038/s41467-022-30143-8. PubMed PMID: 35523809; PubMed Central PMCID: PMC9076640.
  46. Astorkia M, Lachman HM, Zheng D. Characterization of cell-cell communication in autistic brains with single-cell transcriptomes. J Neurodev Disord. 2022 May 2;14(1):29. doi: 10.1186/s11689-022-09441-1. PubMed PMID: 35501678; PubMed Central PMCID: PMC9059394.
  47. Picarda E, Galbo PM Jr, Zong H, Rajan MR, Wallenius V, Zheng D, Börgeson E, Singh R, Pessin J, Zang X. The immune checkpoint B7-H3 (CD276) regulates adipocyte progenitor metabolism and obesity development. Sci Adv. 2022 Apr 29;8(17):eabm7012. doi: 10.1126/sciadv.abm7012. Epub 2022 Apr 27. PubMed PMID: 35476450; PubMed Central PMCID: PMC9045715.
  48. Chrysanthou S, Tang Q, Lee J, Taylor SJ, Zhao Y, Steidl U, Zheng D, Dawlaty MM. The DNA dioxygenase Tet1 regulates H3K27 modification and embryonic stem cell biology independent of its catalytic activity. Nucleic Acids Res. 2022 Apr 8;50(6):3169-3189. doi: 10.1093/nar/gkac089. PubMed PMID: 35150568; PubMed Central PMCID: PMC8989540.
  49. Wang F, Liu Y, Qiu W, Shum E, Feng M, Zhao D, Zheng D, Borczuk A, Cheng H, Halmos B. Functional Analysis of MET Exon 14 Skipping Alteration in Cancer Invasion and Metastatic Dissemination. Cancer Res. 2022 Apr 1;82(7):1365-1379. doi: 10.1158/0008-5472.CAN-21-1327. PubMed PMID: 35078819.
  50. Ma L, Tang Q, Gao X, Lee J, Lei R, Suzuki M, Zheng D, Ito K, Frenette PS, Dawlaty MM. Tet-mediated DNA demethylation regulates specification of hematopoietic stem and progenitor cells during mammalian embryogenesis. Sci Adv. 2022 Mar 4;8(9):eabm3470. doi: 10.1126/sciadv.abm3470. Epub 2022 Mar 2. PubMed PMID: 35235365; PubMed Central PMCID: PMC8890710.
  51. Ren Z, Liang H, Galbo PM Jr, Dharmaratne M, Kulkarni AS, Fard AT, Aoun ML, Martinez-Lopez N, Suyama K, Benard O, Zheng W, Liu Y, Albanese J, Zheng D, Mar JC, Singh R, Prystowsky MB, Norton L, Hazan RB. Redox signaling by glutathione peroxidase 2 links vascular modulation to metabolic plasticity of breast cancer. Proc Natl Acad Sci U S A. 2022 Feb 22;119(8). doi: 10.1073/pnas.2107266119. PubMed PMID: 35193955; PubMed Central PMCID: PMC8872779.
  52. Zhang Y, Zheng D. Pseudogene Profiling for Cancer Subtype Classification. Methods Mol Biol. 2021;2324:307-317. doi: 10.1007/978-1-0716-1503-4_19. Review. PubMed PMID: 34165723.
  53. Flora P, Li MY, Galbo PM Jr, Astorkia M, Zheng D, Ezhkova E. Polycomb repressive complex 2 in adult hair follicle stem cells is dispensable for hair regeneration. PLoS Genet. 2021 Dec;17(12):e1009948. doi: 10.1371/journal.pgen.1009948. eCollection 2021 Dec. PubMed PMID: 34905545; PubMed Central PMCID: PMC8670713.
  54. Zhao L, Zhang P, Galbo PM, Zhou X, Aryal S, Qiu S, Zhang H, Zhou Y, Li C, Zheng D, Bhatia R, Lu R. Transcription factor MEF2D is required for the maintenance of MLL-rearranged acute myeloid leukemia. Blood Adv. 2021 Nov 23;5(22):4727-4740. doi: 10.1182/bloodadvances.2021004469. PubMed PMID: 34597364; PubMed Central PMCID: PMC8759131.
  55. Nomaru H, Liu Y, De Bono C, Righelli D, Cirino A, Wang W, Song H, Racedo SE, Dantas AG, Zhang L, Cai CL, Angelini C, Christiaen L, Kelly RG, Baldini A, Zheng D, Morrow BE. Single cell multi-omic analysis identifies a Tbx1-dependent multilineage primed population in murine cardiopharyngeal mesoderm. Nat Commun. 2021 Nov 17;12(1):6645. doi: 10.1038/s41467-021-26966-6. PubMed PMID: 34789765; PubMed Central PMCID: PMC8599455.
  56. Akhmetzyanova I, Aaron T, Galbo P, Tikhonova A, Dolgalev I, Tanaka M, Aifantis I, Zheng D, Zang X, Fooksman D. Tissue-resident macrophages promote early dissemination of multiple myeloma via IL-6 and TNFα. Blood Adv. 2021 Sep 28;5(18):3592-3608. doi: 10.1182/bloodadvances.2021005327. PubMed PMID: 34550328; PubMed Central PMCID: PMC8945576.
  57. Lu P, Wang Y, Liu Y, Wang Y, Wu B, Zheng D, Harvey RP, Zhou B. Perinatal angiogenesis from pre-existing coronary vessels via DLL4-NOTCH1 signalling. Nat Cell Biol. 2021 Sep;23(9):967-977. doi: 10.1038/s41556-021-00747-1. Epub 2021 Sep 8. PubMed PMID: 34497373.
  58. Li MY, Flora P, Pu H, Bar C, Silva J, Cohen I, Galbo PM Jr, Liu H, Yu X, Jin J, Koseki H, D'Orazio JA, Zheng D, Ezhkova E. UV-induced reduction in Polycomb repression promotes epidermal pigmentation. Dev Cell. 2021 Sep 27;56(18):2547-2561.e8. doi: 10.1016/j.devcel.2021.08.006. Epub 2021 Sep 1. PubMed PMID: 34473941; PubMed Central PMCID: PMC8521440.
  59. Wei Y, Ren X, Galbo PM Jr, Moerdler S, Wang H, Sica RA, Etemad-Gilbertson B, Shi L, Zhu L, Tang X, Lin Q, Peng M, Guan F, Zheng D, Chinai JM, Zang X. KIR3DL3-HHLA2 is a human immunosuppressive pathway and a therapeutic target. Sci Immunol. 2021 Jul 9;6(61). doi: 10.1126/sciimmunol.abf9792. PubMed PMID: 34244312; PubMed Central PMCID: PMC9744578.
  60. Ahn JH, Davis ES, Daugird TA, Zhao S, Quiroga IY, Uryu H, Li J, Storey AJ, Tsai YH, Keeley DP, Mackintosh SG, Edmondson RD, Byrum SD, Cai L, Tackett AJ, Zheng D, Legant WR, Phanstiel DH, Wang GG. Phase separation drives aberrant chromatin looping and cancer development. Nature. 2021 Jul;595(7868):591-595. doi: 10.1038/s41586-021-03662-5. Epub 2021 Jun 23. PubMed PMID: 34163069; PubMed Central PMCID: PMC8647409.
  61. Xu C, Tsai YH, Galbo PM, Gong W, Storey AJ, Xu Y, Byrum SD, Xu L, Whang YE, Parker JS, Mackintosh SG, Edmondson RD, Tackett AJ, Huang J, Zheng D, Earp HS, Wang GG, Cai L. Cistrome analysis of YY1 uncovers a regulatory axis of YY1:BRD2/4-PFKP during tumorigenesis of advanced prostate cancer. Nucleic Acids Res. 2021 May 21;49(9):4971-4988. doi: 10.1093/nar/gkab252. PubMed PMID: 33849067; PubMed Central PMCID: PMC8136773.
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