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
Shen, Sophie, Werner, Tessa, Lukowski, Samuel W., Andersen, Stacey, Sun, Yuliangzi, Shim, Woo Jun, Mizikovsky, Dalia, Kobayashi, Sakurako, Outhwaite, Jennifer, Chiu, Han Sheng, Chen, Xiaoli, Chapman, Gavin, Martin, Ella M. M. A., Xia, Di, Pham, Duy, Su, Zezhuo, Kim, Daniel, Yang, Pengyi, Tan, Men Chee, Sinniah, Enakshi, Zhao, Qiongyi, Negi, Sumedha, Redd, Meredith A., Powell, Joseph E., Dunwoodie, Sally L., Tam, Patrick P. L., Bodén, Mikael, Ho, Joshua W. K., Nguyen, Quan and Palpant, Nathan J. (2025). Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure. Nature Communications, 16 (1) 1356, 1356-1. doi: 10.1038/s41467-025-56533-2
Zhao, Qiongyi, Shim, Woo Jun, Sun, Yuliangzi, Sinniah, Enakshi, Shen, Sophie, Boden, Mikael and Palpant, Nathan J. (2025). TRIAGE: an R package for regulatory gene analysis. Briefings in Bioinformatics, 26 (1) bbaf004, 1-13. doi: 10.1093/bib/bbaf004
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
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
Cho, Hyunju, Shim, Woo Jun, Liu, Yumeng and Shan, Shu-ou (2021). J-domain proteins promote client relay from Hsp70 during tail-anchored membrane protein targeting. Journal of Biological Chemistry, 296 100546, 1-15. doi: 10.1016/j.jbc.2021.100546
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, Y., Redd, M., Outhwaite, J., Shim, W., Fang, C., Negi, S., Shen, S., Mizikovsky, D., Chiu, H., Tan, C., Thomas, U., Dragicevic, E., Sng, J., Short, K. and Palpant, N. (2024). Preclinical models of Glycaemic variability recapitulate Clinical Cardiovascular outcomes in Diabetes. 72nd Annual Scientific Meeting of the Cardiac Society of Australia and New Zealand, Perth, WA Australia, 1-4 August 2024. Chatswood, NSW Australia: Elsevier. doi: 10.1016/j.hlc.2024.06.332
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). H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscle. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_553
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. XXIV World Congress of the International Society for Heart Research, Berlin, Germany, 12–15 June 2022. London, United Kingdom: Academic Press. doi: 10.1016/j.yjmcc.2022.08.344
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
Preprints
Cao, Yuanzhao, Redd, Meredith, Outhwaite, Jennifer, Mizikovsky, Dalia, Shim, Woo Jun, Fang, Chen, Wu, Zhixuan, Daygon, Dara, Stark, Terra, Palfreyman, Robin, Chiu, Han Sheng, Tan, Clarissa, Thomas, Ulrich, Dragicevic, Elena, Sng, Julian, Barrett, Helen, Dorey, Emily, Shah, Sonia, Short, Kirsty and Palpant, Nathan J. (2025). Glycaemic variability underlies myocyte dysfunction and myocardial injury risk in diabetes. doi: 10.1101/2025.01.29.635173