*: first author, **: corresponding author

DE Stanescu, R Yu, KJ Won**, DA Stoffers** (2017) Single cell transcriptomic profiling of mouse pancreatic progenitors Physiological Genomics

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

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

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

Rinho Kim, Karyn L Sheaffer, Inchan Choi, Kyoung-Jae Won, Klaus H Kaestner (2016) Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation Genes & Development 30,21, 2433,2442

Benjamin N Ediger, Hee-Woong Lim, Christine Juliana, David N Groff, LaQueena T Williams, Giselle Dominguez, Jin-Hua Liu, Brandon L Taylor, Erik R Walp, Vasumathi Kameswaran, Juxiang Yang, Chengyang Liu, Chad S Hunter, Klaus H Kaestner, Ali Naji, Changhong Li, Maike Sander, Roland Stein, Lori Sussel, Kyoung-Jae Won, Catherine Lee May, Doris A Stoffers (2016), LIM domain–binding 1 maintains the terminally differentiated state of pancreatic β cells , The Journal of Clinical Investigation 127, 1

Yue J Wang, Jonathan Schug, Kyoung-Jae Won, Chengyang Liu, Ali Naji, Dana Avrahami, Maria L Golson, Klaus H Kaestner (2016) Single cell transcriptomics of the human endocrine pancreasDiabetes db160405

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. 15(12):2637-50.

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.

Jager J, Wang F, Fang B, Lim HW, Peed LC, Steger DJ, Won KJ, Kharitonenkov A, Adams AC, Lazar MA The Nuclear Receptor Rev-erbα Regulates Adipose Tissue-specific FGF21 Signaling. J Biol Chem 13;291(20):10867-75

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

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

Lake RJ, Boetefuer EL, Won KJ, Fan HY. (2016) The CSB chromatin remodeler and CTCF architectural protein cooperate in response to oxidative stress. Nucleic Acids Research, gkv1219 PMID: 26578602

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)

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.

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 Res. 25(6):836-44.

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

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 Epigenetics & Chromatin, 8:13

Lim HW, Uhlenhaut NH, Rauch A, Weiner J, Hübner S, Hübner N, Won KJ, Lazar MA, Tuckermann J, Steger DJ Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo. Genome Research

Nature, 518: 317-330

Harms MJ*, Lim HW* , Ho Y, Shapira NS, Ishibashi J, Rajakumari S, Steger DJ, Lazar MA, Won KJ**, Seale P** (2015) PRDM16 binds MED1 and controls chromatin architecture to determine a brown fat transcriptional program , Gene Dev, 29: 298-307

Wu Q, Won KJ , Li H (2015) Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data , Cancer Informatics, Suppl. 1 11-22

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,111(40):14466-71.

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, 21(10), 846-854

Nguyen, N., Choi I.,, An Vo, Won, K.J. (2014) A stationary wavelet entropy based clustering approach accurately predicts gene expression. 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 PPARγ-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.

Lake R, Boetefuer EL, 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), e1004284,

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

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

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

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