References and Links to Papers

PUBLICATIONS
 

At UT Austin

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

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

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

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

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

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

 

As a postdoctoral fellow

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

As a graduate student

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

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