Dr Woo Jun Shim
Postdoctoral Research Fellow
Institute for Molecular Bioscience
+61 7 344 33564
Researcher biography
Dr Shim's research revolves around developing computational methods to understand determinants of cell identity by analysing various genomic data. Trained in bioinformatics, pharmacy and biomedical science (majoring in biochemistry and immunology), Dr Shim incorporates inter-disciplinary knowledge to solve research questions in both basic science and translational medicine.
| Featured projects | Duration |
|---|---|
| Building tools to predict how the genome controls cells |
Journal Articles
Sun, Yuliangzi, Shim, Woo Jun, Shen, Sophie, Sinniah, Enakshi, Pham, Duy, Su, Zezhuo, Mizikovsky, Dalia, White, Melanie D., Ho, Joshua W. K., Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J (2023). Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity. Nucleic Acids Research, 51 (11), e62-e62. doi: 10.1093/nar/gkad307
Hume, Robert D., Deshmukh, Tejas, Doan, Tram, Shim, Woo Jun, Kanagalingam, Shaan, Tallapragada, Vikram, Rashid, Fairooj, Marcuello, Maria, Blessing, Daniel, Selvakumar, Dinesh, Raguram, Kalyan, Pathan, Faraz, Graham, Dinny, Ounzain, Samir, Kizana, Eddy, Harvey, Richard P., Palpant, Nathan J. and Chong, James J.H. (2023). PDGF-AB Reduces Myofibroblast Differentiation Without Increasing Proliferation After Myocardial Infarction. JACC: Basic to Translational Science, 8 (6), 658-674. doi: 10.1016/j.jacbts.2022.11.006
Afonso, Juliana, Shim, Woo Jun, Boden, Mikael, Salinas Fortes, Marina Rufino, da Silva Diniz, Wellison Jarles, de Lima, Andressa Oliveira, Rocha, Marina Ibelli Pereira, Cardoso, Tainã Figueiredo, Bruscadin, Jennifer Jessica, Gromboni, Caio Fernando, Nogueira, Ana Rita Araujo, Mourão, Gerson Barreto, Zerlotini, Adhemar, Coutinho, Luiz Lehmann and de Almeida Regitano, Luciana Correia (2023). Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle. Biochemistry and Biophysics Reports, 33 101420, 1-9. doi: 10.1016/j.bbrep.2023.101420
Plaisance, Isabelle, Chouvardas, Panagiotis, Sun, Yuliangzi, Nemir, Mohamed, Aghagolzadeh, Parisa, Aminfar, Farhang, Shen, Sophie, Shim, Woo Jun, Rochais, Francesca, Johnson, Rory, Palpant, Nathan and Pedrazzini, Thierry (2023). A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification. Cardiovascular Research, 119 (6), 1361-1376. doi: 10.1093/cvr/cvac191
Plaisance, Isabelle, Chouvardas, Panagiotis, Sun, Yuliangzi, Nemir, Mohamed, Aghagolzadeh, Parisa, Aminfar, Farhang, Shen, Sophie, Shim, Woo Jun, Rochais, Francesca, Johnson, Rory and Pedrazzini, Thierry (2022). Alternative splicing of a transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification. Journal of Molecular and Cellular Cardiology, 173, S182-S182. doi: 10.1016/j.yjmcc.2022.08.344
Shen, Sophie, Sun, Yuliangzi, Matsumoto, Maika, Shim, Woo Jun, Sinniah, Enakshi, Wilson, Sean B., Werner, Tessa, Wu, Zhixuan, Bradford, Stephen T., Hudson, James, Little, Melissa H., Powell, Joseph, Nguyen, Quan and Palpant, Nathan J. (2021). Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation. Trends in Molecular Medicine, 27 (12), 1135-1158. doi: 10.1016/j.molmed.2021.09.006
Kojic, Marija, Gawda, Tomasz, Gaik, Monika, Begg, Alexander, Salerno-Kochan, Anna, Kurniawan, Nyoman D., Jones, Alun, Drożdżyk, Katarzyna, Kościelniak, Anna, Chramiec-Głąbik, Andrzej, Hediyeh-Zadeh, Soroor, Kasherman, Maria, Shim, Woo Jun, Sinniah, Enakshi, Genovesi, Laura A., Abrahamsen, Rannvá K., Fenger, Christina D., Madsen, Camilla G., Cohen, Julie S., Fatemi, Ali, Stark, Zornitza, Lunke, Sebastian, Lee, Joy, Hansen, Jonas K., Boxill, Martin F., Keren, Boris, Marey, Isabelle, Saenz, Margarita S., Brown, Kathleen ... Wainwright, Brandon J. (2021). Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype. Nature Communications, 12 (1) 2678, 2678. doi: 10.1038/s41467-021-22888-5
Shim, Woo Jun, Sinniah, Enakshi, Xu, Jun, Vitrinel, Burcu, Alexanian, Michael, Andreoletti, Gaia, Shen, Sophie, Sun, Yuliangzi, Balderson, Brad, Boix, Carles, Peng, Guangdun, Jing, Naihe, Wang, Yuliang, Kellis, Manolis, Tam, Patrick P L, Smith, Aaron, Piper, Michael, Christiaen, Lionel, Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J. (2020). Conserved epigenetic regulatory logic infers genes governing cell identity. Cell Systems, 11 (6), 625-639.e13. doi: 10.1016/j.cels.2020.11.001
Conference Papers
Cao, Yuanzhao, Redd, Meredith A., Shim, Woo Jun, Fang, Chen, Chiu, Han, Azofeifa, Daniela Rojas, Thomas, Ulrich, Lemme, Marta, Dragicevic, Elena, Stoelzle-Feix, Sonja and Palpant, Nathan J. (2023). Disease modeling utilizing human pluripotent stem cell-derived cardiomyocytes and physiological characterization. Safety Pharmacology Society Annual Meeting, Brussels, Belgium, 18-21 September 2023. Philadelphia, PA United States: Elsevier. doi: 10.1016/j.vascn.2023.107267
Afonso, J., Shim, W.J., Boden, M., Palpant, N., Fortes, M.R.S., Diniz, W.J.S., Lima, A.O., Rocha, M.I.P., Cardoso, T.F., Bruscadin, J.J., Gromboni, C.F., Nogueira, A.R.A., Mourão, G.B., Zerlotini, A., Coutinho, L.L. and Regitano, L.C.A. (2022). 553. H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscle. The Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_553
Shim, W. J. and Firth, S. I. (2009). Sortilin localisation in the rat retina during early postnatal development. 29th Annual Meeting Australian Neuroscience Society, Canberra, ACT, Australia, 27-30 January 2009.
Thesis
Shim, Woo Jun (2021). Identifying genetic regulators of cell fate through computational analysis of epigenetic repression. PhD Thesis, School of Chemistry and Molecular Biosciences, The University of Queensland. doi: 10.14264/4d7b321