A photo of Hee Woong Lim.

Hee Woong Lim, PhD

  • Assistant Professor, UC Department of Pediatrics
  • UC Department of Biomedical Informatics



I trained to be a computational scientist. However, after obtaining my PhD, I had a fascination with the convoluted and multifaceted, yet very ordered, biological system. Therefore, I moved my career in the direction of the bioinformatics field for my postdoctoral training at the University of Pennsylvania.

During my postdoc, I studied transcriptional regulations in multiple metabolic systems, including liver, adipose tissues and pancreas. Then, I joined the team in the Division of Biomedical Informatics at the Cincinnati Children’s Hospital Medical Center as an assistant professor and started a regulatory genomics laboratory to further my research.

In my research lab, I study fundamental mechanisms of gene transcriptional regulations in various contexts, such as metabolism, general cellular or tissue development, pathogenesis, and pharmacogenomics. In particular, I focus on enhancer regulations to delineate their intrinsic heterogeneity of architectures and functions using a high-resolution landscape of transcription factor binding and enhancer RNA (eRNA). To this end, my lab actively utilizes multi-omics high-throughput data including GRO-seq, RNA-seq, ChIP-seq, ChIP-exo, CUT&RUN, csRNA-seq, etc.

The most notable discoveries I made over the years include using eRNAs for direct monitoring of enhancer activities to uncover a molecular mechanism of anti-diabetic rosiglitazone-driven gene transcriptional regulation and an unconventional role of HDAC3 to prepare a thermogenic program in brown fat. In addition, I have discovered distinct binding modes (dimeric and monomeric binding) of the glucocorticoid receptor (GR) by studying the high-resolution footprints of GR binding using ChIP-exo.

I have more than 10 years of experience in the biomedical informatics field and began working at Cincinnati Children’s Hospital Medical Center in 2019. My research has been published in respected journals, such as Nature, Cell, Genome Research, Genes and Development, Proceedings of the National Academy of Sciences of USA, and Genome Research.

BS: Seoul National University, Seoul, Korea.

MS: Seoul National University, Seoul, Korea.

PhD: Seoul National University, Seoul, Korea.

Postdoc: University of Pennsylvania, Philadelphia, PA.


Regulatory genomics; enhancer; transcription; metabolism; pharmacogenomics; machine learning

Research Areas

Biomedical Informatics



Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Matsui, S; Granitto, M; Buckley, M; Ludwig, K; Koigi, S; Shiley, J; Zacharias, WJ; Mayhew, CN; Lim, HW; Iwafuchi, M; Brown, E; Neuzil, KM; Munoz, FM; MOMI-Vax Study Group, . Molecular Cell. 2024; 84:476-489.e10.


Single-cell RNA-Seq of human esophageal epithelium in homeostasis and allergic inflammation. Rochman, M; Wen, T; Kotliar, M; Dexheimer, PJ; Morgenstern, NB B; Caldwell, JM; Lim, HW; Rothenberg, ME. JCI insight. 2022; 7:e159093.


Distinct macrophage populations direct inflammatory versus physiological changes in adipose tissue. Hill, DA; Lim, HW; Kim, YH; Ho, WY; Foong, YH; Nelson, VL; Nguyen, HC B; Chegireddy, K; Kim, J; Habertheuer, A; Vallabhajosyula, P; Kambayashi, T; Won, KJ; Lazar, MA. Proceedings of the National Academy of Sciences of USA. 2018; 115:E5096-E5105.


Histone deacetylase 3 prepares brown adipose tissue for acute thermogenic challenge. Emmett, MJ; Lim, H; Jager, J; Richter, HJ; Adlanmerini, M; Peed, LC; Briggs, ER; Steger, DJ; Ma, T; Sims, CA; Won, K; Seale, P; Gerhart-Hines, Z; Lazar, MA. Nature. 2017; 546:544-548.


Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo. Lim, H; Uhlenhaut, NH; Rauch, A; Weiner, J; Huebner, S; Huebner, N; Won, K; Lazar, MA; Tuckermann, J; Steger, DJ. Genome research. 2015; 25:836-844.

Microbiota-derived butyrate restricts tuft cell differentiation via histone deacetylase 3 to modulate intestinal type 2 immunity. Eshleman, EM; Rice, T; Potter, C; Waddell, A; Hashimoto-Hill, S; Woo, V; Field, S; Engleman, L; Lim, HW; Schumacher, MA; Frey, MR; Denson, LA; Finkelman, FD; Alenghat, T. Immunity. 2024; 57:319-332.e6.

Single-cell transcriptomics identifies adipose tissue CD271+ progenitors for enhanced angiogenesis in limb ischemia. Inoue, O; Goten, C; Hashimuko, D; Yamaguchi, K; Takeda, Y; Nomura, A; Ootsuji, H; Takashima, S; Iino, K; Takemura, H; Hwa, V; Sanchez-Gurmaches, J; Usui, S; Takamura, M. Cell Reports Medicine. 2023; 4:101337.

Sinus venosus adaptation models prolonged cardiovascular disease and reveals insights into evolutionary transitions of the vertebrate heart. Gafranek, JT; D’Aniello, E; Ravisankar, P; Thakkar, K; Vagnozzi, RJ; Lim, HW; Salomonis, N; Waxman, JS. Nature Communications. 2023; 14:5509.

The widely used Ucp1-CreEvdr transgene elicits complex developmental and metabolic phenotypes. Halurkar, MS; Inoue, O; Mukherjee, R; Paese, CL B; Duszynski, M; Brugmann, SA; Lim, H; Sanchez-Gurmaches, J. 2023; 4:2023.10.20.563165.

Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data. Cain, B; Webb, J; Yuan, Z; Cheung, D; Lim, HW; Kovall, RA; Weirauch, MT; Gebelein, B. Nucleic Acids Research. 2023; 51:6055-6072.

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How ‘Pioneers’ Blaze the One Trail that Determines Cell Fate

Hee Woong Lim, PhD, Makiko Iwafuchi, PhD1/10/2024