(* co-first, **co-senior)

Publications with lab members as a lead author

1. Emmett, M.J*., Lim, H.-W*., Jager, J., Richter, H.J., Adlanmerini, M., Peed, L.C., Briggs, E.R., Steger, D.J., Ma, T., Sims, C.A., Baur, J.A., Pei, L., Won, KJ, Seale, P., Gerhart-Hines, Z., Lazar M.A. (2017) Histone Deacetylase 3 prepares brown adipose tissue for acute thermogenic challenge. Nature. In Press.

2. Stanescu DE, Yu R, Won KJ**, Stoffers DA** (2017). Single cell transcriptomic profiling of mouse pancreatic progenitors. Physiol Genomics. 2017 Feb 1;49(2):105-114. PMID:28011883

3. Gonzales-Cope M, Sidoli S, Bhanu NV, Won KJ**, Garcia BA** (2016) Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells. BMC Genomics 4;17(1):95 PMID: 26847871

4. Lu F, Chen HS, Kossenkov AV, DeWispeleare K, Won KJ**, Lieberman PM**. (2016) EBNA2 Drives Formation of New Chromosome Binding Sites and Target Genes for B-Cell Master Regulatory Transcription Factors RBP-jκ and EBF1. PLoS Pathogen 12(1):e1005339. PMID: 26752713

5. Won KJ, Choi I, LeRoy G, Zee BM, Sidoli S, Gonzales-Cope M, Garcia BA (2015) Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants. Chromatin & Epigenetics, 10;8:13. PMID: 25878728. PMCID: PMC4397702.

6. Harms MJ*, Lim HW*, Ho Y, Ishibashi J, Rajakumari S, Steger DJ, Lazar MA, Won KJ**, Seale P** (2015), Prdm16 controls chromatin architecture to determine a brown fat transcriptional program, Gene and Development, 29(3), 298-307. PMID: 24703692; PubMed Central PMCID: PMC4012340. (Co-corresponding).

7. Lim HW*, Uhlenhaut NH*, Rauch A, Weiner J, Hübner S, Hübner N, Won KJ, Lazar MA, Tuckermann J, Steger DJ. (2015) Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo. Genome Research, 25(6):836-44. PMID: 25957148. PMCID: PMC4448680.

8. Nguyen N, Vo A, Won KJ (2014), A wavelet approach to detect enriched regions and explore epigenomic landscapes, Journal of Computational Biology. 21(11):846-54. PMID: 25072902, PMCID: PMC4224055.

9. Choi I, Kim R, Lim HW, Kaestner KH, Won KJ (2014), 5-hydroxymethylcytosine represses the activity of enhancers in embryonic stem cells: a new epigenetic signature for gene regulation, BMC Genomics, 15:670. PMID: 25106691. PMCID: PMC4133056.

10. Nguyen N, Vo A, Won KJ (2014). A wavelet-based method to exploit epigenomic language in the regulatory regions, Bioinformatics, 30:7, 179-190. PMID: 24096080. PMC3983404

11. Lake R, Tsai, PF, Choi I, Won KJ**, Fan HY** (2014). Specific mitotic chromatin association of the major notch effector RBPJ and its implication for transcriptional memory, PLoS Genetics, 10(3):e1004204. (co-corresponding author) PMID:24603501. PMCID: PMC3945225.

12. Step SE*, Lim HW*, Marinis JM, Prokesch A, Steger DJ, You SH, Won KJ, Lazar MA (2014),Antidiabetic rosiglitazone remodels the adipocyte transcriptome by redistributing transcription to PPARγ-driven enhancers (2014) Genes & Development, 28:9, 1018-1028, PMID: 24788520.

13. Shen L, Choi I, Nestler EJ, Won KJ* (2013) Human transcriptome and chromatin modification: An ENCODE perspective, Genomics & Informatics, 11(2), 60-67. PMID: 23843771. PMCID: PMC3704928.

14. Won KJ*, Saunders C, Prugel-Bennett A (2013) Evolving Fisher kernels for biological sequence classification. Evolutionary Computation, 21:1, 83-105. PMID: 22181969.

15. Won KJ, Zhang X, Wang T, Raha D, Snyder M, Ren B, Wang W. (2013). Comparative annotation of functional regions in the human genome using epigenomic data, Nucleic Acid Research, 41(8), 4423-4432. PMID: 23482391. PMCID: PMC3632130

16. Won KJ, Xu Z, Zhang X, Whitaker JW, Shoemaker R, Ren B, Xu Y, Wang W (2012) Global transcription network reconstruction using epigenomic data in pluripotent and fibroblast cells. Nucleic Acid Research, 40:17, 8199-8208. PMID: 22730289. PMCID: PMC3458541.

17. Won KJ, Ren B, Wang W (2010): Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biology, 11:R7. PMID: 20096096. PMCID: PMC2847719.

18. Won KJ, Argarwal S, Shen L, Shoemaker R, Ren B, Wang W (2009): An integrated approach to identify cis-regulatory modules in human genome. PLoS ONE, 4:5, e5501,

19. Won KJ, Chevelev I, Ren B, Wang W (2008):
Prediction of regulatory elements in mammalian genomes using chromatin structure. BMC Bioinformatics, 9:547. PMID: 19434238. PMCID: PMC2677454.

20. Won KJ, Sandelin A, Marstrand T, Krogh A (2008): Modeling promoter grammars with evolving hidden Markov models. Bioinformatics, 24:1669-1675. PMID: 18535083

21. Won KJ*, Hamelryck T, Prugel-Bennett A, Krogh A (2007): An evolving method for learning HMM structure: prediction of protein secondary structure. BMC
Bioinformatics, 8:357. PMID: 17888163. PMCID: PMC2072961.

22. Won KJ, Prugel-Bennett A, Krogh A (2006): Evolving the structure of hidden Markov Models. IEEE Transactions on Evolutionary Computation, 10:39-49.

23. Won KJ, Prugel-Bennett A, Krogh A (2005): Evolving hidden Markov models for protein secondary structure prediction. Proceedings of the 2005 IEEE Congress on Evolutionary Computation, pp.33-40.

24. Won KJ*, Prugel-Bennett A, Krogh A (2004): The block hidden Markov model for biological sequence analysis. Lecture Notes in Artificial Intelligence, 3213:64-70.

25. Won KJ*, Prugel-Bennett A, Krogh A (2004): Training HMM structure with genetic algorithm for biological sequence analysis. Bioinformatics, 1:3613-3619. PMID: 15297297.

Other collaborative works

1. Soccio RE, Li Z, Chen ER, Foong YH, Benson KK, Dispirito JR, Mullican SE, Emmett MJ, Briggs ER, Peed LC, Dzeng RK, Medina CJ, Jolivert JF, Kissig M, Rajapurkar SR, Damle M, Lim HW, Won KJ, Seale P, Steger DJ, Lazar MA. Targeting PPARγ in the epigenome rescues genetic metabolic defects in mice. J Clin Invest. 2017 Apr 3;127(4):1451-1462. PMID:28240605

2. Ediger BN, Lim HW, Juliana C, Groff DN, Williams LT, Dominguez G, Liu JH, Taylor BL, Walp ER, Kameswaran V, Yang J, Liu C, Hunter CS, Kaestner KH, Naji A, Li C, Sander M, Stein R, Sussel L, Won KJ, May CL, Stoffers DA. LIM domain-binding 1 maintains the terminally differentiated state of pancreatic β cells. J Clin Invest. 2017 Jan 3;127(1):215-229 PMID:27941246

3. Shin HJ, Kim H, Oh S, Lee JG, Kee M, Ko HJ, Kweon MN, Won KJ, Baek SH. (2016) AMPK-SKP2-CARM1 signaling cascade in transcriptional regulation of autophagy. Nature. 2016 Jun 15;534(7608):553-7

4. Kim R, Sheaffer KL, Choi I, Won KJ, Kaestner KH (2016) Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation. Genes Dev. 2016 Nov 1;30(21):2433-2442. PMID:27856615

5. Wang YJ, Schug J, Won KJ, Liu C, Naji A, Avrahami D, Golson ML, Kaestner KH (2016) Single-Cell Transcriptomics of the Human Endocrine Pancreas. Diabetes. 2016 Oct;65(10):3028-38. doi: 10.2337/db16-0405. PMID:27364731

6. Henley KD, Stanescu DE, Kropp PA, Wright CV, Won KJ, Stoffers DA, Gannon M (2016) Threshold-Dependent Cooperativity of Pdx1 and Oc1 in Pancreatic Progenitors Establishes Competency for Endocrine Differentiation and β-Cell Function. Cell Rep. 2016 Jun 21;15(12):2637-50. doi: 10.1016/j.celrep.2016.05.040. Epub 2016 Jun 9. PMID:27292642

7. Shah S, Carriveau WJ, Li J, Campbell SL, Kopinski PK, Lim HW, Daurio N, Trefely S, Won KJ, Wallace DC, Koumenis C, Mancuso A, Wellen KE (2016) Targeting ACLY sensitizes castration-resistant prostate cancer cells to AR antagonism by impinging on an ACLY-AMPK-AR feedback mechanism. Oncotarget. PMID:27248322

8. Jager J, Wang F, Fang B, Lim HW, Peed LC, Steger DJ, Won KJ, Kharitonenkov A, Adams AC, Lazar MA. (2016) The Nuclear Receptor Rev-erbα Regulates Adipose Tissue-Specific Fibroblast Growth Factor 21 (FGF21) Signaling. Journal of Biological Chemistry, PMID:27002153

9. Tran PV, Kennedy BC, Pisansky MT, Won KJ, Gewirtz JC, Simmons RA, Georgieff MK (2016) Prenatal Choline Supplementation Diminishes Early-Life Iron Deficiency-Induced Reprogramming of Molecular Networks Associated with Behavioral Abnormalities in the Adult Rat Hippocampus. J Nutr. PMID:26865644

10. Stine RR, Shapira SN, Lim HW, Ishibashi J, Harms M, Won KJ, Seale P. EBF2 promotes the recruitment of beige adipocytes in white adipose tissue. (2016) Mol Metab 14;5(1):57-65. PMID: 26844207

11. Roadmap Epigenomics Consortium (2015) Integrative analysis of 111 reference human epigenomes, Nature, 518(7539), 317-330. PMID: 25693563.
12. Wu Q, Won KJ, Li H (2015) Nonparametric tests for differential histone enrichment with ChIP-seq Data, Cancer Informatics, 14 (Suppl 1), 11. PMID: 25657574; PubMed Central PMCID: PMC4310510.

13. Jain R, Li D, Gupta M, Manderfield LJ, Ifkovits JL, Wang Q, Liu F, Liu Y, Poleshko A, Padmanabhan A, Raum JC, Li L, Morrisey EE, Lu MM, Won KJ, Epstein JA (2015) Integration of Bmp and Wnt signaling by Hopx specifies commitment of cardiomyoblasts. Science, 348(6242). PMID: 26113728.

14. Cohen DM, Won KJ, Nguyen N, Lazar MA, Chen CS, Steger DJ (2015) ATF4 licenses C/EBPβ activity in human mesenchymal stem cells primed for adipogenesis. Elife. doi: 10.7554/eLife.06821. PMID: 26111340

15. Soccio RE, Chen ER, Rajapurkar SR, Safabakhsh P, Marinis JM, Dispirito JR, Emmett MJ, Briggs ER, Fang B, Everett LJ, Lim HW, Won KJ, Steger DJ, Wu Y, Civelek M, Voight BF, Lazar MA (2015) Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo. Cell, 162(1):33-44. PMID: 26140591. PMCID: PMC4493773

16. SC Kang, SK Kim, JC Chai, SH Kim, KJ Won, YS Lee, KH Jung, YG Chai. Tanscriptomic Profiling and H3K27me3 Distribution Reveal Both Demethylase-Dependent and Independent Regulation of Developmental Gene Transcription in Cell Differentiation, PLoS one. 10(8), e0135276. PMID: 26263556.

17. Lake RJ, Boetefuer EL, Won KJ, Fan HY (2015) The CSB chromatin remodeler and CTCF architectural protein cooperate in response to oxidative stress. Nucleic Acids Res. gkv1219 PMID: 26578602

18. Wang W, Kissing M, Rajakumari S, Huang L, Lim HW, Won KJ, Seale P (2014), Ebf2 is a selective marker of brown and beige adipogenic precursor cells, Proceedings of the National Academy of Sciences, 111(40):14466-71. PMID:25197048. PMCID: PMC4209986

19. Lee JV, Carrer A, Shah S, Snyder NW, Wei S, Venneti S, Worth AJ, Yuan ZF, Lim HW, Liu S, Jackson E, Aiello NM, Haas NB, Rebbeck TR, Judkins A, Won KJ, Chodosh LA, Garcia BA, Stanger BZ, Feldman MD, Blair IA, Wellen KE (2014) Akt-Dependent Metabolic Reprogramming Regulates Tumor Cell Histone Acetylation. Cell Metabolism, 20(2):306-19 PMID:24998913. PMCID: PMC4151270

20. Lake R, Boetefuer E, Tsai, PF, Jeong J, Choi I, Won KJ, Fan HY (2014) The sequence-specific transcription factor c-Jun targets Cockayne syndrome protein B to regulate transcription and chromatin structure, PLoS Genetics, 10:4, 1018-1028. PMID: 24788520

21. Harms MJ, Ishibashi J, Wang W, Lim HW, Goyama S, Sato T, Kurokawa M, Won KJ, Seale P (2014) Prdm16 is required for the maintenance of brown adipocyte identity and function in adult mice. Cell Metabolism, 19:4, 593-604. PMID:24703692. PMCID: PMC4018489

22. Kameswaran V, Bramswig NC, Mckenna LB, Penn M, Schug J, Hand NJ, Chen Y, Choi I, Vourekas A, Won KJ, Liu C, Vivek K, Naji A, Friedman JR, Kaestner KH (2014) Epigenetic Regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islet, Cell Metabolism, 19(1), 135-145. PMID: 24374217. PMCID: PMC3932527

23. Sun Z, Feng D, Fang B, Mullican SE, You SH, Lim HW, Everett LJ, Nabel CS, Li Y, Selvakumaran VS, Won KJ, Lazar MA (2013) Deacetylase-Independent Function of HDAC3 in Transcription and Metabolism Requires Nuclear Receptor Corepressor, Molecular Cell, 52 (6), 769-782. PMID: 24268577. PMC3877208.

24. Alenghat T, Osborne LC, Saenz SA, Kobuley D, Ziegler CGK, Mullican SE, Choi I, Grunberg S, Sinha R, Wynosky-Dolfi M, Snyder A, Giacomin, PR, Joyce, KL, Hoang TB, Bewtra M, Brodsky IE, Sonnenberg GF, Bushman FD, Won KJ, Lazar MA, Artis D (2013) Histone Deacetylase 3 orchestrates commensal bacteria-dependent intestinal homeostasis, Nature, 504(7478), 153-157. PMID: 24185009. PMCID: PMC3949438.

25. Cho YW, Hong CJ, Hou A, Gent PM, Zhang K, Won KJ, Hamilton BA (2013) Zfp423 binds autoregulatory sites in P19 cell culture model, PLoS One, 8(6), e66514. PMID: 23762491. PMCID: PMC3675209.

26. Kim J, Hoffman JP, Alpaugh RK, Reichert M, Furth EE, Sepulveda AR, Rhim AD, Stanger BZ, Yuan CX, Won KJ, Donahue G, Sands J, Gumbs A, Zaret K (2013) An iPSC Line from Human Pancreatic Ductal Adenocarcinoma Undergoes Early to Invasive Stages of Pancreatic Cancer Progression, Cell Reports, 3(6), 2088-2-99. PMID: 23791528. PMCID: PMC3726210

27. Rajakumari S, Wu J, Ishibashi J, Lim HW, Won KJ, Reed RR, Seale P. (2013). EBF2 determines and maintains brown adipocyte identity, Cell Metabolism, 17(4), 562-574. PMID: 23499423. PMCID: PMC3622114

28. Xie R, Everett LJ, Lim HW, Patel NA, Schug J, Kroon E, Kelly OG, Wang A, D’Amour KA, Robins AJ, Won KJ, Kaestner KH, Sander M (2013) Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells, Cell Stem Cells, 12:2, 224-237. PMID: 23318056. PMCID: PMC3619036.

29. You SH, Lim HW, Sun Z, Broache M, Won KJ, Lazar MA (2013) Nuclear Receptor co-repressors are required for the histone-deacetylase activity of HDAC3 in vivo, Nature Structural & Molecular Biology, 20, 182-187. PMID: 23292142, PMCID: PMC3565028

30. Wozniak MA, Cheng CQ, Shen CJ, Gao L, Olarerin-George AO, Won KJ, Hogenesch J.B., Chen C.S (2012) Adhesion Regulates MAP Kinase/Ternary Complex Factor Exchange to Control a Proliferative Transcription Switch, Current Biology, 22:21, 2017-2016. PMID: 23063436. PMCID: PMC3586562.

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