Publications

<2014>

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

Wang W, Kissig M, Rajakumari S, Huang L, Lim HW, Won KJ, Seale P (2014) Ebf2 is a selective marker of brown and beige adipogenic precursor cells PNAS

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, 306-319

Nguyen, N., An Vo, Won, K.J. (2014) A wavelet approach to detect enriched regions and explore epigenomic landscapes. Journal of Computational Biology, In Press

Step SE*, Lim HW*, Marinis JM, Prokesch A, Steger DJ, You SH, Won KJ, Lazar MA (2014) Anti-diabetic rosiglitazone remodels the adipocyte transcriptome by redistributing transcription to PPARĪ³-driven enhancers" Genes Dev. 28(9), 1018-1028

ISMB 2014 SIG: Genome-wide analysis of enhancer-RNA transcription reveals regulatory mechanisms by an anti-diabetic drug in adipocyte. Lim HW, Step SE, Marinis JM, Prokesch A, Steger DJ, You SH, Lazar MA, and Won KJ

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.

Nguyen, N., Won, K.J. (2014) Gaussian derivative wavelets identify dynamic changes in histone modification. IEEE Confereence on Computational Intelligence in Bioinformatics and Computational Biology

Lake R, Tsai PF, Choi I, Won KJ**, Fan HY** (2014) RBPJ, the major transcriptional effector of notch signaling, remains associated with chromatin throughout mitosis, suggesting a role in mitotic bookmarking. PLoS Genetics,10(3), e1004204, **:co-corresponding authors

Nguyen, N, Vo A, Won, KJ (2014) A wavelet-based method to exploit epigenomic language in the regulatory region. Bioinformatics, 30(7), 908-914

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 Islets Cell Metabolism, 19(1), 135-145

<2013>

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

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, K. J. Lazar MA, Artis D (2013) Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis , Nature, 504, 153-157

Shen, L., Choi, I, Nestler, E.J., Won, K. J. (2013) Human transcriptome and chromatin modification: An ENCODE perspective Genomics & Informatics, 11(2), 60-67

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

Kim J, Hoffman JP, Alpaugh RK, Rhimm AD, Reichert M, Stanger BZ, Furth EE, Sepulveda AR, 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),2088-99

Won, K. J.*, 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

Rajakumari S., Wu J., Ishibashi J, Lim H.W., Won K.J. Reed, RR, Seale P. (2013) EBF2 determines and maintains brown adipocyte identity, Cell Metabolism, 17:4, 562-574

Xie R., Everett L.J.,Lim H.W., Patel N.A., Schug J, Kroon E., Kelly O.G., Wang A., D'Amour K.A., Robins A.J., Won K.J., Kaestner K.H. Sander M. (2013) Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells, Cell Stem Cell, vol. 12, no., 2, pp. 224-237

You S.H., Lim H.W., Sun Z., Broache M., Won K.J., Lazar M.A. (2013) Nuclear receptor corepressors are required for the histone-deacetylase activity of HDAC3 in vivo, Nature Structural & Molecular Biology, vol. 20, pp. 182-187

Won, K. J.*, Prugel-Bennett, A., Sounders, C. (2013) Evolving Fisher Kernels for Biological Sequence Analysis, Evolutionary Computation, vol. 21, No. 1, pp. 83-105

<2012>

Wozniak M.A., Cheng C.Q., Shen C.J., Gao L., Olarerin-George A.O., Won K. J., Hogenesch J.B., Chen C.S (2012) Adhesion Regulates MAP Kinase/Ternary Complex Factor Exchange to Control a Proliferative Transcription Switch, Current Biology, vol. 22, no. 21, pp. 2017-2016.

Won K. J.*, Xu Z.*, Zhang X.*, Whitaker J.W., Shoemaker R., Ren B., Xu Y., Wang W. (2012) Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells , Nucleic Acid Research, vol.40, no.17,pp.8199-8209 (Supple) Human Embryonic Stem cell Transcription Network

< Before 2011 >

Won, K. J., Ren, B., Wang, W. (2010) Integrating chromatin modification and sequence information to identify functional transcription factor binding sites. Genome Biology , vol. 11:R7, presented in the HighLight Track in the ISMB 2010

Won, K. J., Argarwal, S.,Shen, L.,Shoemaker, R., Ren, B., Wang, W. (2009) An integrated approach to identify cis-regularoty modules in human genome. PLoS ONE , vol. 4, no. 5, pp.e5501, doi:10.1371/journal.pone.0005501

Won, K. J., Chepelev, I., Ren, B., Wang, W. (2008) Prediction of Regulatory Elements in Mammalian Genomes Using Chromatin Structure. BMC Bioinformatics, 9:547

Won, K. J., Sandelin, A., Marstrand, T., and Krogh, A. (2008) Modeling Promoter Grammars with Evolving Hidden Markov Models, Bioinformatics , vol.24, no.15,pp.1669-1675

Won, K. J., Hamelryck, T, Prugel-Bennett, A. and Krogh, A. (2007) An evolving method for learning HMM Structure: prediction of protein secondary structure. BMC Bioinformatics, 8:357

Won, K. J., Prugel-Bennett, A. and Krogh, A. (2006) Evolving the structure of Hidden Markov Models. IEEE Transactions on Evolutionary computation, vol. 10, no 1, pp.39-49

Won, K. J., Hamelryck, T, Prugel-Bennett, A. and Krogh, A. (2005) Evolving Hidden Markov Models for Protein Secondary Structure Prediction. Proceedings of the 2005 IEEE Congress on Evolutionary Computation, pp.33-40.

Won, K. J., Prugel-Bennett, A. and Krogh, A. (2004) The Block Hidden Markov Model for Biological Sequence Analysis. Lecture Notes in Artificial Intelligence. vol. 3213, pp.64-70.

Won, K. J., Prugel-Bennett, A. and Krogh, A. (2004) Training HMM Structure with Genetic Algorithm for Biological Sequence Analysis. Bioinformatics. vol. 20, no. 18, pp:3613-3619