Jonghwan Kim, Ph.D. - Publications

Affiliations: 
2011- Molecular Biosciences University of Texas at Austin, Austin, Texas, U.S.A. 
Area:
Stem cells, Genomics

68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 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. Nature Communications. 10: 4749. PMID 31628347 DOI: 10.1038/s41467-019-12720-6  0.96
2019 Jin G, Lee CS, Liao X, Kim J, Wang Z, Okello OFN, Park B, Park J, Han C, Heo H, Kim J, Oh SH, Choi SY, Park H, Jo MH. Atomically thin three-dimensional membranes of van der Waals semiconductors by wafer-scale growth. Science Advances. 5: eaaw3180. PMID 31360767 DOI: 10.1126/sciadv.aaw3180  0.48
2019 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, et al. TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network. Molecular Cell. PMID 31005419 DOI: 10.1016/j.molcel.2019.03.025  0.88
2019 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, ... ... Kim J, et al. Author Correction: ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors. Nature Cell Biology. PMID 30643186 DOI: 10.1038/s41556-018-0269-y  0.96
2018 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. 7. PMID 30561326 DOI: 10.7554/eLife.40167  0.96
2018 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, ... ... Kim J, et al. miRNA-mediated TUSC3 deficiency enhances UPR and ERAD to promote metastatic potential of NSCLC. Nature Communications. 9: 5110. PMID 30504895 DOI: 10.1038/s41467-018-07561-8  0.96
2018 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 Reports. 24: 1471-1483. PMID 30089259 DOI: 10.1016/j.celrep.2018.06.089  0.6
2018 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. PMID 30076412 DOI: 10.1038/s41388-018-0421-y  0.96
2018 Lindlau J, Selig M, Neumann A, Colombier L, Förste J, Funk V, Förg M, Kim J, Berghäuser G, Taniguchi T, Watanabe K, Wang F, Malic E, Högele A. The role of momentum-dark excitons in the elementary optical response of bilayer WSe. Nature Communications. 9: 2586. PMID 29968708 DOI: 10.1038/s41467-018-04877-3  0.32
2018 Jin C, Kim J, Utama MIB, Regan EC, Kleemann H, Cai H, Shen Y, Shinner MJ, Sengupta A, Watanabe K, Taniguchi T, Tongay S, Zettl A, Wang F. Imaging of pure spin-valley diffusion current in WS-WSe heterostructures. Science (New York, N.Y.). 360: 893-896. PMID 29798880 DOI: 10.1126/science.aao3503  0.32
2018 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 Research. PMID 29529258 DOI: 10.1093/nar/gky147  0.96
2018 Suh J, Tan TL, Zhao W, Park J, Lin DY, Park TE, Kim J, Jin C, Saigal N, Ghosh S, Wong ZM, Chen Y, Wang F, Walukiewicz W, Eda G, et al. Reconfiguring crystal and electronic structures of MoS2 by substitutional doping. Nature Communications. 9: 199. PMID 29335411 DOI: 10.1038/s41467-017-02631-9  0.48
2017 Rhee C, Kim J, Tucker HO. Transcriptional Regulation of the First Cell Fate Decision. Journal of Developmental Biology & Regenerative Medicine. 1. PMID 29658952  0.84
2017 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 Research. 26: 95-102. PMID 29272857 DOI: 10.1016/j.scr.2017.12.004  0.96
2017 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 Research. 45: 10103-10114. PMID 28973471 DOI: 10.1093/nar/gkx692  0.96
2017 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, ... ... Kim J, et al. ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors. Nature Cell Biology. PMID 28846095 DOI: 10.1038/ncb3598  0.96
2017 Kim J, Jin C, Chen B, Cai H, Zhao T, Lee P, Kahn S, Watanabe K, Taniguchi T, Tongay S, Crommie MF, Wang F. Observation of ultralong valley lifetime in WSe2/MoS2 heterostructures. Science Advances. 3: e1700518. PMID 28782025 DOI: 10.1126/sciadv.1700518  0.32
2017 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. 18: 538. PMID 28716006 DOI: 10.1186/s12864-017-3929-6  0.72
2017 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 Research. PMID 28453857 DOI: 10.1093/nar/gkx310  0.96
2016 Rhee C, Edwards M, Dang C, Harris J, Brown M, Kim J, Tucker HO. ARID3A is required for mammalian placenta development. Developmental Biology. PMID 27965054 DOI: 10.1016/j.ydbio.2016.12.003  0.84
2016 Sun T, Kim J, Yuk JM, Zettl A, Wang F, Chang-Hasnain C. Surface-normal electro-optic spatial light modulator using graphene integrated on a high-contrast grating resonator. Optics Express. 24: 26035-26043. PMID 27857342  0.32
2016 Sanchez A, De Vivo A, Uprety N, Kim J, Stevens SM, Kee Y. BMI1-UBR5 axis regulates transcriptional repression at damaged chromatin. Proceedings of the National Academy of Sciences of the United States of America. PMID 27647897 DOI: 10.1073/pnas.1610735113  0.96
2016 Li L, Kim J, Jin C, Ye GJ, Qiu DY, da Jornada FH, Shi Z, Chen L, Zhang Z, Yang F, Watanabe K, Taniguchi T, Ren W, Louie SG, Chen XH, et al. Direct observation of the layer-dependent electronic structure in phosphorene. Nature Nanotechnology. PMID 27643457 DOI: 10.1038/nnano.2016.171  0.32
2016 Bordiya Y, Zheng Y, Nam JC, Bonnard AC, Choi HW, Lee BK, Kim JK, Klessig D, Fei Z, Kang HG. Pathogen Infection and MORC proteins Affect Chromatin Accessibility of Transposable Elements and Expression of Their Proximal Genes in Arabidopsis. Molecular Plant-Microbe Interactions : Mpmi. PMID 27482822 DOI: 10.1094/MPMI-01-16-0023-R  0.96
2016 Jiang L, Shi Z, Zeng B, Wang S, Kang JH, Joshi T, Jin C, Ju L, Kim J, Lyu T, Shen YR, Crommie M, Gao HJ, Wang F. Soliton-dependent plasmon reflection at bilayer graphene domain walls. Nature Materials. PMID 27240109 DOI: 10.1038/nmat4653  0.32
2016 Zhang Y, Moreno Ugeda M, Jin C, Shi SF, Bradley A, Martin-Recio A, Ryu H, Kim J, Tang S, Kim Y, Zhou B, Hwang C, Chen Y, Wang F, Crommie MF, et al. Electronic Structure, Surface Doping and Optical Response in Epitaxial WSe2 Thin Films. Nano Letters. PMID 26974978 DOI: 10.1021/acs.nanolett.6b00059  0.32
2016 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 Reports. PMID 26917425 DOI: 10.15252/embr.201540933  0.96
2016 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, ... ... Kim J, et al. Serine/Threonine Kinase MLK4 Determines Mesenchymal Identity in Glioma Stem Cells in an NF-κB-dependent Manner. Cancer Cell. 29: 201-213. PMID 26859459 DOI: 10.1016/j.ccell.2016.01.005  0.96
2016 Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA. NANOG binds to GLI proteins and represses Hedgehog-mediated transcription. The Journal of Biological Chemistry. PMID 26797124 DOI: 10.1074/jbc.M116.714857  0.96
2015 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 Reports. PMID 26411691 DOI: 10.1016/j.celrep.2015.08.067  0.96
2015 Rhee C, Lee BK, Beck S, Anjum A, Cook KR, Popowski M, Tucker HO, Kim J. Corrigendum: Arid3a is essential to execution of the first cell fate decision via direct embryonic and extraembryonic transcriptional regulation. Genes & Development. 29: 1890. PMID 26341560  0.96
2015 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, ... ... Kim J, et al. 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: 1456-1470. PMID 26299972 DOI: 10.1016/j.celrep.2015.07.053  0.96
2015 Beck S, Lee BK, Kim J. Multi-layered global gene regulation in mouse embryonic stem cells. Cellular and Molecular Life Sciences : Cmls. 72: 199-216. PMID 25227241 DOI: 10.1007/s00018-014-1734-9  0.96
2014 Kim J, Hong X, Jin C, Shi SF, Chang CY, Chiu MH, Li LJ, Wang F. Ultrafast generation of pseudo-magnetic field for valley excitons in WSe₂ monolayers. Science (New York, N.Y.). 346: 1205-8. PMID 25477455 DOI: 10.1126/science.1258122  0.32
2014 Beck S, Lee BK, Rhee C, Song J, Woo AJ, Kim J. CpG island-mediated global gene regulatory modes in mouse embryonic stem cells. Nature Communications. 5: 5490. PMID 25405324 DOI: 10.1038/ncomms6490  0.96
2014 Zhang L, Liu K, Wong AB, Kim J, Hong X, Liu C, Cao T, Louie SG, Wang F, Yang P. Three-dimensional spirals of atomic layered MoS2. Nano Letters. 14: 6418-23. PMID 25343743 DOI: 10.1021/nl502961e  0.32
2014 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 & Development. 28: 2219-32. PMID 25319825 DOI: 10.1101/gad.247163.114  0.96
2014 Ki S, Park D, Selden HJ, Seita J, Chung H, Kim J, Iyer VR, Ehrlich LI. Global transcriptional profiling reveals distinct functions of thymic stromal subsets and age-related changes during thymic involution. Cell Reports. 9: 402-15. PMID 25284794 DOI: 10.1016/j.celrep.2014.08.070  0.96
2014 Hong X, Kim J, Shi SF, Zhang Y, Jin C, Sun Y, Tongay S, Wu J, Zhang Y, Wang F. Ultrafast charge transfer in atomically thin MoS₂/WS₂ heterostructures. Nature Nanotechnology. 9: 682-6. PMID 25150718 DOI: 10.1038/nnano.2014.167  0.32
2014 Sun Y, Liu K, Hong X, Chen M, Kim J, Shi S, Wu J, Zettl A, Wang F. Probing local strain at MX(2)-metal boundaries with surface plasmon-enhanced Raman scattering. Nano Letters. 14: 5329-34. PMID 25133959 DOI: 10.1021/nl5023767  0.32
2014 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 Research. 42: 6999-7011. PMID 24799437 DOI: 10.1093/nar/gku388  0.48
2014 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, ... ... Kim J, et al. Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Molecular Cell. 53: 32-48. PMID 24361252 DOI: 10.1016/j.molcel.2013.11.011  0.88
2013 Woo AJ, Wieland K, Huang H, Akie TE, Piers T, Kim J, Cantor AB. Developmental differences in IFN signaling affect GATA1s-induced megakaryocyte hyperproliferation. The Journal of Clinical Investigation. PMID 23863621 DOI: 10.1172/JCI40609  0.96
2013 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, et al. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes & Development. 27: 683-98. PMID 23512661 DOI: 10.1101/gad.211011.112  0.96
2013 Majumdar A, Kim J, Vuckovic J, Wang F. Electrical control of silicon photonic crystal cavity by graphene. Nano Letters. 13: 515-8. PMID 23286896 DOI: 10.1021/nl3039212  0.32
2013 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. American Journal of Respiratory Cell and Molecular Biology. 48: 288-98. PMID 23204392 DOI: 10.1165/rcmb.2011-0403OC  0.96
2013 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, et al. Transcription elongation factor Tcea3 regulates the pluripotent differentiation potential of mouse embryonic stem cells via the Lefty1-Nodal-Smad2 pathway. Stem Cells (Dayton, Ohio). 31: 282-92. PMID 23169579 DOI: 10.1002/stem.1284  0.72
2012 Kim J, Son H, Cho DJ, Geng B, Regan W, Shi S, Kim K, Zettl A, Shen YR, Wang F. Electrical control of optical plasmon resonance with graphene. Nano Letters. 12: 5598-602. PMID 23025816 DOI: 10.1021/nl302656d  0.32
2012 Kim J, Di Vizio D, Kim TK, Kim J, Kim M, Pelton K, Clinton SK, Hai T, Hwang D, Solomon KR, Freeman MR. 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: e39448. PMID 22768301 DOI: 10.1371/journal.pone.0039448  0.64
2011 Kim J, Orkin SH. Embryonic stem cell-specific signatures in cancer: insights into genomic regulatory networks and implications for medicine. Genome Medicine. 3: 75. PMID 22126538 DOI: 10.1186/gm291  0.96
2011 Woo AJ, Kim J, Xu J, Huang H, Cantor AB. Role of ZBP-89 in human globin gene regulation and erythroid differentiation. Blood. 118: 3684-93. PMID 21828133 DOI: 10.1182/blood-2011-03-341446  0.96
2010 Kim J, Woo AJ, Chu J, Snow JW, Fujiwara Y, Kim CG, Cantor AB, Orkin SH. A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell. 143: 313-24. PMID 20946988 DOI: 10.1016/j.cell.2010.09.010  0.96
2010 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, et al. TIF1gamma controls erythroid cell fate by regulating transcription elongation. Cell. 142: 133-43. PMID 20603019 DOI: 10.1016/j.cell.2010.05.028  0.96
2010 Snow JW, Kim J, Currie CR, Xu J, Orkin SH. Sumoylation regulates interaction of FOG1 with C-terminal-binding protein (CTBP). The Journal of Biological Chemistry. 285: 28064-75. PMID 20587419 DOI: 10.1074/jbc.M109.096909  0.96
2010 Splendiani A, Sun L, Zhang Y, Li T, Kim J, Chim CY, Galli G, Wang F. Emerging photoluminescence in monolayer MoS2. Nano Letters. 10: 1271-5. PMID 20229981 DOI: 10.1021/nl903868w  0.32
2010 Kim J, Orkin SH. Systematic tracking of cell fate changes. Nature Biotechnology. 28: 146-7. PMID 20139953 DOI: 10.1038/nbt0210-146  0.96
2009 Trowbridge JJ, Snow JW, Kim J, Orkin SH. DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells. Cell Stem Cell. 5: 442-9. PMID 19796624 DOI: 10.1016/j.stem.2009.08.016  0.96
2009 Hu G, Kim J, Xu Q, Leng Y, Orkin SH, Elledge SJ. A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal Genes and Development. 23: 837-848. PMID 19339689 DOI: 10.1101/gad.1769609  0.96
2009 Kim J, Cantor AB, Orkin SH, Wang J. Use of in vivo biotinylation to study protein-protein and protein-DNA interactions in mouse embryonic stem cells. Nature Protocols. 4: 506-17. PMID 19325547 DOI: 10.1038/nprot.2009.23  0.96
2008 Shen X, Liu Y, Hsu YJ, Fujiwara Y, Kim J, Mao X, Yuan GC, Orkin SH. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Molecular Cell. 32: 491-502. PMID 19026780 DOI: 10.1016/j.molcel.2008.10.016  0.88
2008 Kim J, Chu J, Shen X, Wang J, Orkin SH. An extended transcriptional network for pluripotency of embryonic stem cells. Cell. 132: 1049-61. PMID 18358816 DOI: 10.1016/j.cell.2008.02.039  0.88
2008 Kim J, Lee JH, Iyer VR. Global identification of Myc target genes reveals its direct role in mitochondrial biogenesis and its E-box usage in vivo. Plos One. 3: e1798. PMID 18335064 DOI: 10.1371/journal.pone.0001798  0.96
2007 Saleque S, Kim J, Rooke HM, Orkin SH. Epigenetic regulation of hematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by the cofactors CoREST and LSD1. Molecular Cell. 27: 562-72. PMID 17707228 DOI: 10.1016/j.molcel.2007.06.039  0.88
2007 Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Research. 17: 910-6. PMID 17568006 DOI: 10.1101/gr.5574907  0.96
2007 Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research. 17: 877-85. PMID 17179217 DOI: 10.1101/gr.5533506  0.96
2005 Kim J, Iyer VR. Identifying chromosomal targets of DNA-binding proteins by Sequence Tag Analysis of Genomic Enrichment (STAGE). Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.10. PMID 18265357 DOI: 10.1002/0471142727.mb2110s72  0.96
2005 Kim J, Bhinge AA, Morgan XC, Iyer VR. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nature Methods. 2: 47-53. PMID 15782160 DOI: 10.1038/nmeth726  0.96
2004 Kim J, Iyer VR. Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles. Molecular and Cellular Biology. 24: 8104-12. PMID 15340072 DOI: 10.1128/MCB.24.18.8104-8112.2004  0.96
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