My Bibliography

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Lee M, Guo Q, Kim M, Choi J, Segura A, Genceroglu A, LeBlanc L, Ramirez N, Jang YJ, Jang Y, Lee BK, Marcotte EM, Kim J. Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches. Genome Res. 2024 Apr 25;34(3):484-497. doi: 10.1101/gr.277926.123. PubMed PMID: 38580401; PubMed Central PMCID: PMC11067882.

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Kim M, Jang YJ, Lee M, Guo Q, Son AJ, Kakkad NA, Roland AB, Lee BK, Kim J. The transcriptional regulatory network modulating human trophoblast stem cells to extravillous trophoblast differentiation. Nat Commun. 2024 Feb 12;15(1):1285. doi: 10.1038/s41467-024-45669-2. PubMed PMID: 38346993; PubMed Central PMCID: PMC10861538.

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Rhee C, Scadden EW, Wong LP, Schiroli G, Mazzola MC, Chea PL, Kato H, Hoyer FF, Mistry M, Lee BK, Kim J, Nahrendorf M, Mansour MK, Sykes DB, Sadreyev RI, Scadden DT. Limited plasticity of monocyte fate and function associated with epigenetic scripting at the level of progenitors. Blood. 2023 Aug 17;142(7):658-674. doi: 10.1182/blood.2023020257. PubMed PMID: 37267513; PubMed Central PMCID: PMC10447620.

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Kim M, Adu-Gyamfi EA, Kim J, Lee BK. Super-enhancer-associated transcription factors collaboratively regulate trophoblast-active gene expression programs in human trophoblast stem cells. Nucleic Acids Res. 2023 May 8;51(8):3806-3819. doi: 10.1093/nar/gkad215. PubMed PMID: 36951126; PubMed Central PMCID: PMC10164554.

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Kim M, Singh M, Lee BK, Hibbs M, Richardson K, Ellies L, Wintle L, Stuart LM, Wang JY, Voon DC, Blancafort P, Wang J, Kim J, Leedman PJ, Woo AJ. A MYC-ZNF148-ID1/3 regulatory axis modulating cancer stem cell traits in aggressive breast cancer. Oncogenesis. 2022 Oct 7;11(1):60. doi: 10.1038/s41389-022-00435-1. PubMed PMID: 36207293; PubMed Central PMCID: PMC9546828.

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Jang YJ, Kim M, Lee BK, Kim J. Induction of human trophoblast stem-like cells from primed pluripotent stem cells. Proc Natl Acad Sci U S A. 2022 May 17;119(20):e2115709119. doi: 10.1073/pnas.2115709119. Epub 2022 May 10. PubMed PMID: 35537047; PubMed Central PMCID: PMC9171790.

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LeBlanc L, Kim M, Kambhampati A, Son AJ, Ramirez N, Kim J. β-catenin links cell seeding density to global gene expression during mouse embryonic stem cell differentiation. iScience. 2022 Jan 21;25(1):103541. doi: 10.1016/j.isci.2021.103541. eCollection 2022 Jan 21. PubMed PMID: 34977504; PubMed Central PMCID: PMC8689156.

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Li J, Kumari T, Barazia A, Jha V, Jeong SY, Olson A, Kim M, Lee BK, Manickam V, Song Z, Clemens R, Razani B, Kim J, Dinauer MC, Cho J. Neutrophil DREAM promotes neutrophil recruitment in vascular inflammation. J Exp Med. 2022 Jan 3;219(1). doi: 10.1084/jem.20211083. Epub 2021 Nov 9. PubMed PMID: 34751735; PubMed Central PMCID: PMC8719643.

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Lee JY, Davis I, Youth EHH, Kim J, Churchill G, Godwin J, Korstanje R, Beck S. Misexpression of genes lacking CpG islands drives degenerative changes during aging. Sci Adv. 2021 Dec 17;7(51):eabj9111. doi: 10.1126/sciadv.abj9111. Epub 2021 Dec 15. PubMed PMID: 34910517; PubMed Central PMCID: PMC8673774.

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Choi J, Jang YJ, Dabrowska C, Iich E, Evans KV, Hall H, Janes SM, Simons BD, Koo BK, Kim J, Lee JH. Release of Notch activity coordinated by IL-1β signalling confers differentiation plasticity of airway progenitors via Fosl2 during alveolar regeneration. Nat Cell Biol. 2021 Sep;23(9):953-966. doi: 10.1038/s41556-021-00742-6. Epub 2021 Sep 2. PubMed PMID: 34475534; PubMed Central PMCID: PMC7611842.

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Lee BK, Kim J. Integrating High-Throughput Approaches and in vitro Human Trophoblast Models to Decipher Mechanisms Underlying Early Human Placenta Development. Front Cell Dev Biol. 2021;9:673065. doi: 10.3389/fcell.2021.673065. eCollection 2021. Review. PubMed PMID: 34150768; PubMed Central PMCID: PMC8206641.

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LeBlanc L, Ramirez N, Kim J. Context-dependent roles of YAP/TAZ in stem cell fates and cancer. Cell Mol Life Sci. 2021 May;78(9):4201-4219. doi: 10.1007/s00018-021-03781-2. Epub 2021 Feb 13. Review. PubMed PMID: 33582842; PubMed Central PMCID: PMC8164607.

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Golden E, Rashwan R, Woodward EA, Sgro A, Wang E, Sorolla A, Waryah C, Tie WJ, Cuyàs E, Ratajska M, Kardaś I, Kozlowski P, Johnstone EKM, See HB, Duffy C, Parry J, Lagerborg KA, Czapiewski P, Menendez JA, Gorczyński A, Wasag B, Pfleger KDG, Curtis C, Lee BK, Kim J, Cursons J, Pavlos NJ, Biernat W, Jain M, Woo AJ, Redfern A, Blancafort P. The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer. Nat Commun. 2021 Mar 26;12(1):1920. doi: 10.1038/s41467-021-22101-7. PubMed PMID: 33772001; PubMed Central PMCID: PMC7998036.

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Lee JY, Song J, LeBlanc L, Davis I, Kim J, Beck S. Conserved dual-mode gene regulation programs in higher eukaryotes. Nucleic Acids Res. 2021 Mar 18;49(5):2583-2597. doi: 10.1093/nar/gkab108. PubMed PMID: 33621342; PubMed Central PMCID: PMC7969006.

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Lee J, Henderson K, Massidda MW, Armenta-Ochoa M, Im BG, Veith A, Lee BK, Kim M, Maceda P, Yoon E, Samarneh L, Wong M, Dunn AK, Kim J, Baker AB. Mechanobiological conditioning of mesenchymal stem cells for enhanced vascular regeneration. Nat Biomed Eng. 2021 Jan;5(1):89-102. doi: 10.1038/s41551-020-00674-w. Epub 2021 Jan 22. PubMed PMID: 33483713; PubMed Central PMCID: PMC8875880.

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Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K. Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Cell Rep. 2019 Oct 29;29(5):1351-1368.e5. doi: 10.1016/j.celrep.2019.09.060. PubMed PMID: 31665645; PubMed Central PMCID: PMC6873818.

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Lee BK, Jang YJ, Kim M, LeBlanc L, Rhee C, Lee J, Beck S, Shen W, Kim J. Super-enhancer-guided mapping of regulatory networks controlling mouse trophoblast stem cells. Nat Commun. 2019 Oct 18;10(1):4749. doi: 10.1038/s41467-019-12720-6. PubMed PMID: 31628347; PubMed Central PMCID: PMC6802173.

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Seruggia D, Oti M, Tripathi P, Canver MC, LeBlanc L, Di Giammartino DC, Bullen MJ, Nefzger CM, Sun YBY, Farouni R, Polo JM, Pinello L, Apostolou E, Kim J, Orkin SH, Das PP. TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network. Mol Cell. 2019 Jun 20;74(6):1148-1163.e7. doi: 10.1016/j.molcel.2019.03.025. Epub 2019 Apr 17. PubMed PMID: 31005419; PubMed Central PMCID: PMC6671628.

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Wang E, Sorolla A, Cunningham PT, Bogdawa HM, Beck S, Golden E, Dewhurst RE, Florez L, Cruickshank MN, Hoffmann K, Hopkins RM, Kim J, Woo AJ, Watt PM, Blancafort P. Tumor penetrating peptides inhibiting MYC as a potent targeted therapeutic strategy for triple-negative breast cancers. Oncogene. 2019 Jan;38(1):140-150. doi: 10.1038/s41388-018-0421-y. Epub 2018 Aug 3. PubMed PMID: 30076412; PubMed Central PMCID: PMC6318000.

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LeBlanc L, Lee BK, Yu AC, Kim M, Kambhampati AV, Dupont SM, Seruggia D, Ryu BU, Orkin SH, Kim J. Yap1 safeguards mouse embryonic stem cells from excessive apoptosis during differentiation. Elife. 2018 Dec 18;7. doi: 10.7554/eLife.40167. PubMed PMID: 30561326; PubMed Central PMCID: PMC6307859.

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Jeon YJ, Kim T, Park D, Nuovo GJ, Rhee S, Joshi P, Lee BK, Jeong J, Suh SS, Grotzke JE, Kim SH, Song J, Sim H, Kim Y, Peng Y, Jeong Y, Garofalo M, Zanesi N, Kim J, Liang G, Nakano I, Cresswell P, Nana-Sinkam P, Cui R, Croce CM. miRNA-mediated TUSC3 deficiency enhances UPR and ERAD to promote metastatic potential of NSCLC. Nat Commun. 2018 Nov 30;9(1):5110. doi: 10.1038/s41467-018-07561-8. PubMed PMID: 30504895; PubMed Central PMCID: PMC6269493.

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Johnson TE, Lee JH, Myler LR, Zhou Y, Mosley TJ, Yang SH, Uprety N, Kim J, Paull TT. Homeodomain Proteins Directly Regulate ATM Kinase Activity. Cell Rep. 2018 Aug 7;24(6):1471-1483. doi: 10.1016/j.celrep.2018.06.089. PubMed PMID: 30089259; PubMed Central PMCID: PMC6127865.

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Kim KY, Tanaka Y, Su J, Cakir B, Xiang Y, Patterson B, Ding J, Jung YW, Kim JH, Hysolli E, Lee H, Dajani R, Kim J, Zhong M, Lee JH, Skalnik D, Lim JM, Sullivan GJ, Wang J, Park IH. Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a. Nat Commun. 2018 Jul 3;9(1):2583. doi: 10.1038/s41467-018-04818-0. PubMed PMID: 29968706; PubMed Central PMCID: PMC6030064.

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Beck S, Rhee C, Song J, Lee BK, LeBlanc L, Cannon L, Kim J. Implications of CpG islands on chromosomal architectures and modes of global gene regulation. Nucleic Acids Res. 2018 May 18;46(9):4382-4391. doi: 10.1093/nar/gky147. PubMed PMID: 29529258; PubMed Central PMCID: PMC5961348.

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Lee BK, Uprety N, Jang YJ, Tucker SK, Rhee C, LeBlanc L, Beck S, Kim J. Fosl1 overexpression directly activates trophoblast-specific gene expression programs in embryonic stem cells. Stem Cell Res. 2018 Jan;26:95-102. doi: 10.1016/j.scr.2017.12.004. Epub 2017 Dec 13. PubMed PMID: 29272857; PubMed Central PMCID: PMC5899959.

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Rhee C, Kim J, Tucker HO. Transcriptional Regulation of the First Cell Fate Decision. J Dev Biol Regen Med. 2017;1(1). Epub 2017 Oct 26. PubMed PMID: 29658952; PubMed Central PMCID: PMC5897107.

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Rhee C, Lee BK, Beck S, LeBlanc L, Tucker HO, Kim J. Mechanisms of transcription factor-mediated direct reprogramming of mouse embryonic stem cells to trophoblast stem-like cells. Nucleic Acids Res. 2017 Sep 29;45(17):10103-10114. doi: 10.1093/nar/gkx692. PubMed PMID: 28973471; PubMed Central PMCID: PMC5737334.

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Skamagki M, Correia C, Yeung P, Baslan T, Beck S, Zhang C, Ross CA, Dang L, Liu Z, Giunta S, Chang TP, Wang J, Ananthanarayanan A, Bohndorf M, Bosbach B, Adjaye J, Funabiki H, Kim J, Lowe S, Collins JJ, Lu CW, Li H, Zhao R, Kim K. ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors. Nat Cell Biol. 2017 Sep;19(9):1037-1048. doi: 10.1038/ncb3598. Epub 2017 Aug 28. PubMed PMID: 28846095; PubMed Central PMCID: PMC5843481.

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Wang L, Zhang F, Rode S, Chin KK, Ko EE, Kim J, Iyer VR, Qiao H. Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis. BMC Genomics. 2017 Jul 17;18(1):538. doi: 10.1186/s12864-017-3929-6. PubMed PMID: 28716006; PubMed Central PMCID: PMC5512946.

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Lee BK, Lee J, Shen W, Rhee C, Chung H, Kim J. Fbxl19 recruitment to CpG islands is required for Rnf20-mediated H2B mono-ubiquitination. Nucleic Acids Res. 2017 Jul 7;45(12):7151-7166. doi: 10.1093/nar/gkx310. PubMed PMID: 28453857; PubMed Central PMCID: PMC5499583.

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Rhee C, Edwards M, Dang C, Harris J, Brown M, Kim J, Tucker HO. ARID3A is required for mammalian placenta development. Dev Biol. 2017 Feb 15;422(2):83-91. doi: 10.1016/j.ydbio.2016.12.003. Epub 2016 Dec 11. PubMed PMID: 27965054; PubMed Central PMCID: PMC5540318.

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Sanchez A, De Vivo A, Uprety N, Kim J, Stevens SM Jr, Kee Y. BMI1-UBR5 axis regulates transcriptional repression at damaged chromatin. Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11243-11248. doi: 10.1073/pnas.1610735113. Epub 2016 Sep 19. PubMed PMID: 27647897; PubMed Central PMCID: PMC5056041.

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Bordiya Y, Zheng Y, Nam JC, Bonnard AC, Choi HW, Lee BK, Kim J, Klessig DF, Fei Z, Kang HG. Pathogen Infection and MORC Proteins Affect Chromatin Accessibility of Transposable Elements and Expression of Their Proximal Genes in Arabidopsis. Mol Plant Microbe Interact. 2016 Sep;29(9):674-687. doi: 10.1094/MPMI-01-16-0023-R. Epub 2016 Sep 26. PubMed PMID: 27482822.

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Chung H, Lee BK, Uprety N, Shen W, Lee J, Kim J. Yap1 is dispensable for self-renewal but required for proper differentiation of mouse embryonic stem (ES) cells. EMBO Rep. 2016 Apr;17(4):519-29. doi: 10.15252/embr.201540933. Epub 2016 Feb 25. PubMed PMID: 26917425; PubMed Central PMCID: PMC4818770.

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Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA. The Pluripotency Factor NANOG Binds to GLI Proteins and Represses Hedgehog-mediated Transcription. J Biol Chem. 2016 Mar 25;291(13):7171-82. doi: 10.1074/jbc.M116.714857. Epub 2016 Jan 21. PubMed PMID: 26797124; PubMed Central PMCID: PMC4807297.

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Kim SH, Ezhilarasan R, Phillips E, Gallego-Perez D, Sparks A, Taylor D, Ladner K, Furuta T, Sabit H, Chhipa R, Cho JH, Mohyeldin A, Beck S, Kurozumi K, Kuroiwa T, Iwata R, Asai A, Kim J, Sulman EP, Cheng SY, Lee LJ, Nakada M, Guttridge D, DasGupta B, Goidts V, Bhat KP, Nakano I. Serine/Threonine Kinase MLK4 Determines Mesenchymal Identity in Glioma Stem Cells in an NF-κB-dependent Manner. Cancer Cell. 2016 Feb 8;29(2):201-13. doi: 10.1016/j.ccell.2016.01.005. PubMed PMID: 26859459; PubMed Central PMCID: PMC4837946.

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Hoshino K, Chung H, Wu CH, Rajendran K, Huang YY, Chen P, Sokolov KV, Kim J, Zhang JXJ. An Immunofluorescence-Assisted Microfluidic Single Cell Quantitative Reverse Transcription Polymerase Chain Reaction Analysis of Tumour Cells Separated from Blood. J Circ Biomark. 2015 Jan-Dec;4:11. doi: 10.5772/61822. eCollection 2015 Jan-Dec. PubMed PMID: 28936247; PubMed Central PMCID: PMC5572989.

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Lee BK, Shen W, Lee J, Rhee C, Chung H, Kim KY, Park IH, Kim J. Tgif1 Counterbalances the Activity of Core Pluripotency Factors in Mouse Embryonic Stem Cells. Cell Rep. 2015 Oct 6;13(1):52-60. doi: 10.1016/j.celrep.2015.08.067. Epub 2015 Sep 24. PubMed PMID: 26411691.

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Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, Choe J, Jun DL, Shen X, Gregory RI, Daley GQ, Meissner A, Kellis M, Hochedlinger K, Kim J, Orkin SH. PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep. 2015 Sep 1;12(9):1456-70. doi: 10.1016/j.celrep.2015.07.053. Epub 2015 Aug 20. PubMed PMID: 26299972; PubMed Central PMCID: PMC5384103.

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Beck S, Lee BK, Kim J. Multi-layered global gene regulation in mouse embryonic stem cells. Cell Mol Life Sci. 2015 Jan;72(2):199-216. doi: 10.1007/s00018-014-1734-9. Epub 2014 Sep 17. Review. PubMed PMID: 25227241; PubMed Central PMCID: PMC4284393.

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Beck S, Lee BK, Rhee C, Song J, Woo AJ, Kim J. CpG island-mediated global gene regulatory modes in mouse embryonic stem cells. Nat Commun. 2014 Nov 18;5:5490. doi: 10.1038/ncomms6490. PubMed PMID: 25405324; PubMed Central PMCID: PMC4236720.

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Rhee C, Lee BK, Beck S, Anjum A, Cook KR, Popowski M, Tucker HO, Kim J. Arid3a is essential to execution of the first cell fate decision via direct embryonic and extraembryonic transcriptional regulation. Genes Dev. 2014 Oct 15;28(20):2219-32. doi: 10.1101/gad.247163.114. PubMed PMID: 25319825; PubMed Central PMCID: PMC4201284.

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Ki S, Park D, Selden HJ, Seita J, Chung H, Kim J, Iyer VR, Ehrlich LIR. Global transcriptional profiling reveals distinct functions of thymic stromal subsets and age-related changes during thymic involution. Cell Rep. 2014 Oct 9;9(1):402-415. doi: 10.1016/j.celrep.2014.08.070. Epub 2014 Oct 2. PubMed PMID: 25284794; PubMed Central PMCID: PMC4194175.

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Kim MY, Park J, Lee JJ, Ha DH, Kim J, Kim CG, Hwang J, Kim CG. Staufen1-mediated mRNA decay induces Requiem mRNA decay through binding of Staufen1 to the Requiem 3'UTR. Nucleic Acids Res. 2014 Jun;42(11):6999-7011. doi: 10.1093/nar/gku388. Epub 2014 May 5. PubMed PMID: 24799437; PubMed Central PMCID: PMC4066795.

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Kim J, Park RY, Chen JK, Kim J, Jeong S, Ohn T. Splicing factor SRSF3 represses the translation of programmed cell death 4 mRNA by associating with the 5'-UTR region. Cell Death Differ. 2014 Mar;21(3):481-90. doi: 10.1038/cdd.2013.171. Epub 2013 Nov 29. PubMed PMID: 24292556; PubMed Central PMCID: PMC3921596.

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Das PP, Shao Z, Beyaz S, Apostolou E, Pinello L, De Los Angeles A, O'Brien K, Atsma JM, Fujiwara Y, Nguyen M, Ljuboja D, Guo G, Woo A, Yuan GC, Onder T, Daley G, Hochedlinger K, Kim J, Orkin SH. Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Mol Cell. 2014 Jan 9;53(1):32-48. doi: 10.1016/j.molcel.2013.11.011. Epub 2013 Dec 19. PubMed PMID: 24361252; PubMed Central PMCID: PMC3919500.

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Woo AJ, Wieland K, Huang H, Akie TE, Piers T, Kim J, Cantor AB. Developmental differences in IFN signaling affect GATA1s-induced megakaryocyte hyperproliferation. J Clin Invest. 2013 Jul 1;123(8):3292-304. doi: 10.1172/JCI40609. [Epub ahead of print] PubMed PMID: 23863621; PubMed Central PMCID: PMC3726146.

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Baena E, Shao Z, Linn DE, Glass K, Hamblen MJ, Fujiwara Y, Kim J, Nguyen M, Zhang X, Godinho FJ, Bronson RT, Mucci LA, Loda M, Yuan GC, Orkin SH, Li Z. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes Dev. 2013 Mar 15;27(6):683-98. doi: 10.1101/gad.211011.112. PubMed PMID: 23512661; PubMed Central PMCID: PMC3613614.

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Lee JH, Kim J, Gludish D, Roach RR, Saunders AH, Barrios J, Woo AJ, Chen H, Conner DA, Fujiwara Y, Stripp BR, Kim CF. Surfactant protein-C chromatin-bound green fluorescence protein reporter mice reveal heterogeneity of surfactant protein C-expressing lung cells. Am J Respir Cell Mol Biol. 2013 Mar;48(3):288-98. doi: 10.1165/rcmb.2011-0403OC. Epub 2012 Nov 29. PubMed PMID: 23204392; PubMed Central PMCID: PMC3604082.

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Park KS, Cha Y, Kim CH, Ahn HJ, Kim D, Ko S, Kim KH, Chang MY, Ko JH, Noh YS, Han YM, Kim J, Song J, Kim JY, Tesar PJ, Lanza R, Lee KA, Kim KS. Transcription elongation factor Tcea3 regulates the pluripotent differentiation potential of mouse embryonic stem cells via the Lefty1-Nodal-Smad2 pathway. Stem Cells. 2013 Feb;31(2):282-92. doi: 10.1002/stem.1284. PubMed PMID: 23169579; PubMed Central PMCID: PMC3572291.