References and Links to Papers
PUBLICATIONS
At UT Austin
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73.
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 (2024) Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches. Genome Research. (Accepted)
72.
Kim M, Jang YJ, Lee M, Guo Q, Son AJ, Kakkad NA, Roland AB, Lee BK, Kim J (2024) The transcriptional regulatory network modulating human trophoblast stem cells to extravillous trophoblast differentiation. Nature Communications. (Accepted).
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71.
Rhee C, Scadden E, Wong LP, Schiroll G, Mazzola, Chea P, Kato H, Hoyer F, Mistry M, Lee BK, Kim J, Nahrendorf M, Mansour M, Sykes D, Sadreyev R, Scadden D (2023)
Limited plasticity of monocyte fate and function associated with epigenetic scripting at the level of progenitors.
Blood. 142(7):658-674. LINK
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70.
Kim M, Appiah E, Kim J*, Lee BK* (2023)
Super-enhancers-associated transcription factors collaboratively regulate trophoblast-active gene expression programs in human trophoblast stem cells.
Nucleic Acids Res. 51(8):3806-3819. LINK
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69.
Kim M, Singh M, Lee BK, Hibbs C, Richardson K, Ellies K, Wintle L, Stuart LM, Wang JY, Voon DC, Blancafort P, Wang J, Kim J, Leedman PJ, Woo AJ (2022)
A MYC-ZNF148-ID1/3 regulatory axis modulating cancer stem cell traits in aggressive breast cancer.
Oncogenesis. 11(1):60. LINK
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68.
Jang YJ, Kim M, Lee BK, Kim J (2022)
Induction of human trophoblast stem-like cells from primed pluripotent stem cells.
Proc Natl Acad Sci U S A. 119 (20) e2115709119. LINK
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67.
LeBlanc L, Kim M, Kambhampati A, Son AJ, Ramirez N, Kim J (2022)
β-catenin links cell seeding density to global gene expression programs during mouse embryonic stem cell differentiation.
iScience. 25(1):103541. LINK
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66.
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. (2022)
Neutrophil DREAM promotes neutrophil recruitment in vascular inflammation.
J Exp Med. 219(1):e20211083. LINK
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65.
Lee JY, Davis I, Youth EHH, Kim J, Churchill G, Godwin J, Korstanje R, Beck S (2021)
Misexpression of genes lacking CpG islands is a hallmark of aging. Science Advances.
Science Advances. 7(51):eabj9111. LINK
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64.
Choi J*, Jang YJ*, Dabrowska C, Iich E, Evans KV, Simons BD, Koo BK, Kim J*, Lee JH* (2021)
Release of Notch signaling coordinated by inflammation confers cross-compartment differentiation plasticity during alveolar regeneration.
Nature Cell Biology. 23(9):953-966. LINK
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63.
Lee BK*, Kim J* (2021)
Integrating high-throughput approaches and in vitro human trophoblast models to decipher mechanisms underlying early human placenta development.
Front Cell Dev Biol. 9:673065. LINK
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62.
Rashwan R, Golden E, Sgro A, Woodward EA, Sorolla A, Waryah C, Cuyas E, Ratajska M, Kardaś I, Kozlowski P, Wang E, Duffy C, Parry J, Lagerborg KA, Czapiewski P, Gorczyński A, Wasag B, Curtis C, Pavlos N, Lee BK, Kim J, Cursons J, Biernat W, Jain M, Woo AJ, Redfern A, Blancafort P (2021)
The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer.
Nature Communications. 12(1):1920. LINK
61.
Lee JY, Song J, LeBlanc L, Davis I, Kim J, Beck S (2021)
Conserved dual-mode gene regulation programs in higher eukaryotes.
Nucleic Acids Res. 49(5):2583-2597. LINK
60.
LeBlanc L*, Ramirez N, Kim J* (2021)
Context-dependent roles of YAP/TAZ in stem cell fates and cancer.
Cell Mol Life Sci. 78(9):4201-4219. LINK
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59.
Lee J, Henderson K, Massidda M, Armenta-Ochoa M, Im BG, Veith A, Lee BK, Kim M, Maceda P, Yoon E, Samarneh L, Wong M, Dunn A, Kim J, Baker A (2021)
Mechanobiological conditioning of mesenchymal stem cells for enhanced vascular regeneration.
Nature Biomedical Engineering. 5(1):89-102. LINK
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58.
Lee BK, Jang YJ, Kim MJ, LeBlanc L, Rhee C, Lee J, Beck B, Shen W, Kim J (2019)
Super-enhancer-guided mapping of regulatory networks controlling mouse trophoblast stem cells.
Nature Communications. 10(1):4749. LINK
57.
Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K (2019)
A system-wide roadmap of endogenous human ribonucleoprotein complexes.
Cell Reports. 29(5) 1351-1369. LINK
56.
Seruggia D, Oti M, Tripathi P, Canver MC, LeBlanc L, Di Giammartino D, Bullen MJ, Nefzger CM, Sun YBY, Farouni R, Polo JM, Pinello L, Apostolou E, Kim J, Orkin SH, Das PP (2019)
TAF5L and TAF6L maintain self-renewal of embryonic stem cells via the MYC regulatory network.
Mol Cell. 74, 1-16. LINK
55.
Wang E, Sorolla A, Cunningham P, Bogdawa H, Dewhurst R, Cruickshank M, Beck B, Hoffmann K, Hopkins R, Kim J, Woo A, Watt P, Blancafort P (2019)
Tumour penetrating peptides inhibiting Myc as a potent targeted therapeutic strategy for triple-negative breast cancers.
Oncogene. 38(1):140-150. LINK
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54.
LeBlanc L, Lee BK, Yu AC, Kim M, Kambhampati AV, Dupont SM, Seruggia D, Ryu BU, Orkin SH, Kim J (2018)
Yap1 safeguards mouse embryonic stem cells from excessive apoptosis during differentiation.
Elife. 7:e40167. LINK
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53.
Jeon Y, Kim T, Park D, Nuovo G, 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 Y, Zanesi N, Kim J, Liang G, Nakano I, Cresswell P, Nana-Sinkam P, Cui R, Croce C (2018).
miRNA-mediated TUSC3 deficiency enhances UPR and ERAD to promote metastatic potential of NSCLC.
Nature Communications. 9(1):5110. LINK
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52.
Johnson TE, Lee JH, Zhou Y, Mosley TJ, Yang SH, the Bio-Bricks for Molecular Machines FRI stream, Uprety N, Kim J, Paull TT (2018)
Homeodomain proteins directly regulate ATM kinase activity.
Cell Reports. 24:1471-1483. LINK
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51.
Kim KY, Tanaka Y, Su J, Cakir B, Xiang Y, Patterson B, Ding JJ, Jung YW, Kim JH, Hysolli E, Lee H, Dajani R, Kim J, Zhong M, Lee JJ, Skalnik D, Lim JM, Sullivan G, Wang J, Park IH (2018)
Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a.
Nature Communications. 9(1):2583. LINK
50.
Beck S, Rhee C, Song J, Lee BK, Leblanc L, Cannon L, Kim J (2018)
Implications of CpG islands on chromosomal architectures and modes of global gene regulation.
Nucleic Acids Res. 46(9):4382-4391. LINK
49.
Rhee C, Kim J, Tucker HO (2018)
Transcriptional regulation of the first fate decision.
J Dev Biol Regen Med. 1(1). pii: 102. LINK
48.
Lee BK*, Uprety N*, Jang YJ, Tucker S, Rhee R, LeBlanc L, Beck S, Kim J (2018)
Fosl1 overexpression directly activates trophoblast-specific gene expression programs in embryonic stem cells.
Stem Cell Research. 26(1): 95–102. LINK
47.
Skamagki M, Dogan Y, Yeung P, Ross C, Baslan T, Dang L, Wang J, Beck S, Giunta S, Liu Z, Bohndorf M, Adjaye J, Funabiki H, Kim J, Lowe S, Collins J, Li H, Lu CW, Zhao R, Kim K (2017)
ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors.
Nature Cell Biology. 19(9):1037-1048. LINK
46.
Rhee C, Lee BK, Beck S, LeBlanc L, Tucker HO, Kim J (2017)
Mechanisms of transcription factor-mediated direct reprogramming of mouse embryonic stem cells to trophoblast stem-like cells.
Nucleic Acids Res. 45(17):10103-10114. LINK
45.
Wang L, Zhang F, Rode S, Ko K, Kim J, Iyer VR, Chen J, Qiao H (2017)
Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis.
BMC Genomics. 18(1):538. LINK
44.
Lee BK, Lee J, Shen W, Rhee C, Chung H, Kim J (2017)
Fbxl19 Recruits Rnf20 to CpG Islands and Regulates H2B Mono-Ubiquitination.
Nucleic Acids Res. 45 (12):7151-7166. LINK
43.
Rhee C, Edwards M, Dang C, Harris J, Kim J, Tucker HO (2017)
Arid3a is required for mammalian placenta development.
Developmental Biology. 422(2):83-91. LINK
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42.
Sanchez A, De Vivo A, Uprety N, Kim J, Stevens SM Jr., Kee Y (2016)
The BMI1-UBR5 Axis Regulates Transcriptional Repression at Damaged Chromatin.
Proc Natl Acad Sci U S A. 113(40): 11243-11248. LINK
41.
Bordiya Y, Zheng Y, Nam J, Choi HW, Lee BK, Kim J, Klessig DF, Fei Z, Kang HG (2016)
Pathogen Infection and MORC Proteins Affect Chromatin Accessibility of Transposable Elements and Expression of Their Proximal Genes in Arabidopsis.
Mol Plant Microbe Interact. 29(9):674-687. LINK
40.
Chung H, Lee BK, Uprety N, Kim J (2016)
Yap1 is Dispensable for Self-Renewal but Required for Proper Differentiation of Mouse Embryonic Stem (ES) Cells.
EMBO Reports. 17(4):519-29. LINK
39.
Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA (2016)
The Pluripotency Factor NANOG Binds to GLI Proteins and Represses Hedgehog-mediated Transcription.
JBC. 291(13):7171-82. LINK
38.
Kim S, Ezhilarasan R, Phillips M, Gallego-Perez D, Sparks A, Taylor D, Ladner K, Furuta T, Sabit H, Chhipa R, Cho JH, Beck S, Kurozumi K, Kuroiwa T, Iwata R, Asai A, Kim J, Sulman EP, Cheng S, Lee LJ, Nakada M, Guttridge D, DasGupta B, Goidts V, Bhat KP, Nakano I (2016)
Serine/Threonine kinase MLK4 determines Mesenchymal Identity in Glioma Stem Cells in an NF-κB-dependent manner.
Cancer Cell. 29(2):201-13. LINK
37.
Hoshino K, Chung H, Wu CH, Rajendran K, Huang YY, Chen P, Sokolov KV, Kim J, Zhang X (2015)
Immunofluorescence-Assisted Microfluidic Single-Cell Quantitative Reverse Transcription Polymerase Chain Reaction Analysis for Tumour Cells Separated from Blood.
Journal of Circulating Biomarkers. 4:11. doi: 10.5772/61822. LINK
36.
Lee BK, Shen W, Lee J, Rhee C, Chung H, Kim K, Park IH, Kim J (2015)
Tgif1 Counterbalances the Activity of Core Pluripotency Factors in Mouse Embryonic Stem Cells.
Cell Reports. 13(1):52-60. LINK
35.
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 (2015)
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 Reports. 12(9):1456-70. LINK
34.
Beck S*, Lee BK*, Kim J (2015)
Multi-Layered Global Gene Regulation in Mouse Embryonic Stem Cells.
Cell Mol Life Sci. 72(2):199-216. LINK
33.
Beck S, Lee BK, Rhee C, Song J, Woo AJ, Kim J (2014)
CpG Island-Mediated Global Gene Regulatory Modes in Mouse Embryonic Stem Cells.
Nature Communications. 5:5490. LINK
32.
Rhee C, Lee BK, Beck S, Cook KR, Anjum A, Tucker HO, Kim J (2014)
Arid3a is Essential to Execution of the First Cell Fate Decision via Direct Embryonic and Extraembryonic Transcriptional Regulation.
Genes and Development. 28(20):2219-32. LINK
31.
Ki S*, Park D*, Selden HJ, Seita J, Chung H, Kim J, Iyer VR, Ehrlich L (2014)
Global Transcriptional Profiling Reveals Distinct Functions of Thymic Stromal Subsets and Age-Related Changes During Thymic Involution.
Cell Reports. 9:402-415. LINK
30.
Kim MY, Park J, Lee JJ, Ha DH, Kim J, Kim CG, Hwang J, Kim CG (2014)
Staufen1-Mediated mRNA Decay Induces Requiem mRNA Decay through Binding of Staufen1 to the Requiem 3’UTR.
Nucleic Acids Res. 42(11):6999-7011. LINK
29.
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 AJ, Yuan GC, Onder T, Daley GQ, Hochedlinger K, Kim J, Orkin SH (2014)
Distinct and Combinatorial Functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in Mouse Embryonic Stem Cells Identity.
Mol Cell. 53(1):1–17. LINK
28.
Kim J, Chen JK, Kim J, Jeong S, Ohn T (2013)
Splicing Factor SRSF3 Represses the Translation of Programmed Cell Death 4 mRNA by Associating with the 5’UTR Region.
Cell Death Differ. 21(3):481-90. LINK
27.
Woo AJ, Wieland K, Huang H, Akie TE, Piers T, Fleming MD, Boyd T, Kim J, Cantor AB (2013)
Developmental Differences in IFN Signaling Affect GATA1s-Induced Megakaryocyte Hyperproliferation.
J Clin Invest. 123(8):3292–3304. LINK
26.
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 (2013)
ETV1 Directs Androgen Metabolism and Confers Aggressive Prostate Cancer in Targeted Mice and Patients.
Genes and Development. 5;27(6):683-98. LINK
25.
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. (2013)
Transcription Elongation Factor Tcea3 Regulates the Pluripotent Differentiation Potential of Mouse Embryonic Stem Cells, via the Lefty1-Nodal-Smad2 Pathway.
Stem Cells. 31(2):282-92. LINK
24.
Lee JH, Kim J, Gludish D, Roach RR, Saunders AH, Chen H, Conner DA, Fujiwara Y, Stripp BR, Kim CF (2013)
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. 48(3):288-98. LINK
23.
Kim J, Di Vizio D, Kim TK, Kim J, Kim M, Pelton K, Clinton SK, Hai T, Hwang D, Solomon KR, Freeman MR (2012)
The response of the prostate to circulating cholesterol: activating transcription factor 3 (ATF3) as a prominent node in a cholesterol-sensing network.
PLoS One. 7(7):e39448. LINK
22.
Kim J, Orkin SH (2011)
Embryonic Stem Cell-Specific Signatures in Cancer: Insights into Genomic Regulatory Networks and Implications for Medicine.
Genome Medicine. 3(11):75. LINK
21.
Woo AJ, Kim J, Xu J, Huang H, Cantor AB (2011)
Role of ZBP-89 in Human Globin Gene Regulation and Erythroid Differentiation.
Blood. 29;118(13):3684-93. LINK
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As a postdoctoral fellow
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20.
Kim J, Woo AJ, Chu J, Snow JW, Fujiwara Y, Kim CG, Cantor AB, Orkin SH (2010)
A Myc Network Accounts for Similarities between Embryonic Stem and Cancer Cell Transcription Programs.
Cell. 143(2): 313-324. LINK
19.
Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Ji H, Ehrlich L, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, Mckinney-Freeman S, Naveiras O, Yoon T, Hanna J, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg A, and Daley GQ (2010)
Epigenetic Memory in Induced Pluripotent Stem Cells.
Nature. 467(7313):285-90. LINK
18.
Bai X, Kim J, Yang Z, Jurynec MJ, Akie TE, Lee J, LeBlanc J, Sessa A, Jiang H, DiBiase A, Zhou Y, Grunwald DJ, Lin S, Cantor AB, Orkin SH, Zon LI (2010)
TIF1gamma Controls Erythroid Cell Fate by Regulating Transcriptional Elongation.
Cell. 142(1):133-143. LINK
17.
Snow JW, Kim J, Currie CR, Xu J, Orkin SH (2010)
Sumoylation Regulates Interaction of FOG1 with CTBP.
J Biol Chem. 3;285(36):28064-75. LINK
16.
Kim J, Orkin SH (2010)
Systematic Tracking of Cell Fate Changes.
Nature Biotechnology. 28(2) 146-147. LINK
15.
Trowbridge JJ, Snow JW, Kim J, Orkin SH (2009)
DNA Methyltransferase 1 is Essential for and Uniquely Regulates Hematopoietic Stem and Progenitor Cells.
Cell Stem Cell. 5(4) 442-449. LINK
14.
Hu G, Kim J, Xu Q, Leng Y, Orkin SH, Elledge SJ (2009)
A Genome-Wide RNAi Screen Identifies a New Transcriptional Module Required for Self-Renewal.
Genes and Development. 23(7): 837-848. LINK
13.
Kim J, Cantor AB, Orkin SH, Wang J (2009)
Use of In Vivo Biotinylation to Study Protein–Protein and Protein–DNA Interactions in Mouse Embryonic Stem Cells.
Nature Protocols. 4(4) : 506-517. LINK
12.
Orkin SH, Wang J, Kim J, Chu J, Rao S, Theunissen TW, Shen X, Levasseur DN (2008)
The Transcriptional Network Controlling Pluripotency in ES Cells.
Cold Spring Harb Symp Quant Biol. 73:195-202. LINK
11.
Shen X, Liu Y, Hsu YJ, Fujiwara Y, Kim J, Mao X, Yuan GC, Orkin SH (2008)
EZH1 Mediates Methylation on Histone H3 Lysine 27 and Complements EZH2 in Maintaining Stem Cell Identity and Executing Pluripotency.
Mol Cell. 32(4): 491-502. LINK
10.
Kim J, Chu J, Shen X, Wang J, Orkin SH (2008)
An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells.
Cell. 132: 1049-1061. LINK
9.
Kim J, Lee JH, Iyer VR (2008)
Global Identification of Myc Target Genes Reveals Its Direct Role in Mitochondrial Biogenesis and Its E-Box Usage In Vivo.
PLoS ONE. 3(3):e1798. LINK
8.
Saleque S, Kim J, Rooke HM, Orkin SH (2007)
Epigenetic Regulation of Hematopoietic Differentiation by Gfi-1 and Gfi-1b Is Mediated by the Cofactors CoREST and LSD1.
Mol Cell. 27(4):562-72. LINK
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As a graduate student
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7.
Bhinge AA*, Kim J*, Euskirchen G, Snyder M, Iyer VR (2007)
Mapping the Chromosomal Targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).
Genome Research. 17: 910-916 (*equally contributed). LINK
6.
The ENCODE Project Consortium (2007).
Identification and Analysis of Functional Elements in 1% of the Human Genome by the ENCODE Pilot Project.
Nature. 447, 799–816. LINK
5.
Giresi PG, Kim J, McDaniell R, Iyer VR, Lieb JD. (2007)
FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) Isolates Nucleosome-Depleted DNA from Human Chromatin.
Genome Research. 17: 877-885. LINK
4.
Kim J, Iyer VR (2005)
Identifying Chromosomal Targets of DNA-Binding Proteins by Sequence Tag Analysis of Genomic Enrichment (STAGE).
Curr Protoc Mol Biol. Chapter 21:Unit 21.10. LINK
3.
Kim J, Bhinge AA, Morgan XC, Iyer VR (2005)
Mapping DNA-Protein Interactions in Large Genomes by Sequence Tag Analysis of Genomic Enrichment.
Nature Methods. 2(1): 47-53 (Epub 2004 Dec 21). LINK
2.
Kim J, Iyer VR (2004)
Global Role of TATA Box-Binding Protein Recruitment to Promoters in Mediating Gene Expression Profiles.
Mol Cell Biol. 24(18):8104-12. LINK
1.
Kim SJ, Shin JH, Kim J, Kim SH, Chae JH, Park EJ, Seong RH, Hong SH, Park SD, Jeong S, Kim CG (1999)
Isolation of Developmentally Regulated Novel Genes Based on Sequence Identity and Gene Expression Pattern.
Mol Cells. 9(2):207-18. LINK