NIH Bibliography: https://www.ncbi.nlm.nih.gov/sites/myncbi/jonghwan.kim.1/bibliography/40768405/public/?sort=date&direction=descending

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).

71. 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 M, Sykes DB, Sadreyev R, Scadden DT (2023) Limited plasticity of monocyte fate and function associated with epigenetic scripting at the level of progenitors. Blood. 142(7):658-674.

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.

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. ​

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. 

67. 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. 

66. 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. ​

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. ​

64. Choi J*, Jang YJ*, Dabrowska C, Iich E, Evans KV, Simons BD, Koo BK, Kim J*, Lee JH* (2021) Release of Notch activity coordinated by IL-1β signalling confers differentiation plasticity of airway progenitors via Fosl2 during alveolar regeneration. Nature Cell Biology. 23(9): 953–966​

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. ​

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. 

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. 

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. 

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.

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

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.

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

55. 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.

54. 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.

53. 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.

52. 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 (2018) Tumour penetrating peptides inhibiting Myc as a potent targeted therapeutic strategy for triple-negative breast cancers. Oncogene. 38(1):140-150.

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.

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.

49. Rhee C, Kim J, Tucker HO (2018) Transcriptional regulation of the first fate decision. J Dev Biol Regen Med. 1(1). pii: 102.

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.

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) Recovery of Genomic Stability by ZSCAN10 in Induced Pluripotent Stem Cells from Aged Donors. Nature Cell Biology. 19(9):1037-1048.

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.

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.

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.

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.

Mr. and Mrs. Isaac Arnold, Sr. Regents Chair in Molecular Biology (Fellow), 2023
Burroughs Wellcome Fund (BWF), Preterm Birth Initiative Award, 2017
Cancer Prevention Research Institute of Texas (CPRIT). Award for Recruitment of First-Time,
Tenure-Track Faculty Members, 2011-2016.
Institute for Cellular and Molecular Biology Fellow, University of Texas, 2011-2017
The 22nd Annual Meeting of the Korean Society for Molecular and Cellular Biology (KSMCB), Travel Award, 2010.
NIH Pathway to Independence (PI) Award, 2009-2014.
International Society for Stem Cell Research (ISSCR), Travel Award, 2008.
William S. Livingston Outstanding Employee Award Honorable Mention, UT-Austin, 2005.
The A. P. Bradie Endowed Fellowship, UT-Austin, 2002.

BIO337, Systems Biology of Stem Cells, 2024-present.
BIO344, Molecular Biology. Spring, 2013 - 2023.
BIO383K, Current Literature in Cell and Developmental Biology. Spring, 2012.
BIO397H, Dean’s Scholar’s Honors Thesis Program, Supervising Professor. Spring, 2012-present.

Positions Available (2024-2025)

1 Graduate Student
1 Postdoctoral Fellow