Overview
Background
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.
Availability
- Dr Woo Jun Shim is:
- Available for supervision
Qualifications
- Bachelor of Biomedical Science, University of Adelaide
- Bachelor (Honours), The University of Queensland
- Masters (Coursework), The University of Queensland
- Doctor of Philosophy, The University of Queensland
Research impacts
Dr Shim's discovery has helped address an area of unmet need in genetic analysis pipelines as evidenced by significant international uptake. Working with UQ’s main commercialisation company UniQuest, Dr Shim's work formed the basis for successful contracts with industry partners including HAYA Therapeutics (Switzerland), Merck (Germany), Mogrify (UK), and ConcR (UK) to improve the accuracy and efficiency of clinical diagnostic and drug discovery pipelines. Dr Shim was awarded a UQ Early-Mid Career Researcher (EMCR) Industry Engagement Award in 2022 for his successful engagement with HAYA Therapeutics and EMMA Whitelaw ECR publication award in 2022 for his work on a highly scalable computational framework to discover key regulatory genes.
Works
Search Professor Woo Jun Shim’s works on UQ eSpace
2026
Journal Article
Glycaemic variability underlies myocyte dysfunction and myocardial injury risk in diabetes
Cao, Yuanzhao, Redd, Meredith A., Outhwaite, Jennifer E., Mizikovsky, Dalia, Shim, Woo Jun, Fang, Chen, Vedelago, Courtney, Tan, Clarissa, Wu, Zhixuan, Daygon, Dara, Stark, Terra, Palfreyman, Robin, Chiu, Han Sheng, Thomas, Ulrich, Dragicevic, Elena, Sng, Julian D. J., Saez, Natalie J., Barrett, Helen L., Dorey, Emily S., King, Glenn F., Wuethrich, Alain, Trau, Matt, Shah, Sonia, Short, Kirsty R. and Palpant, Nathan J. (2026). Glycaemic variability underlies myocyte dysfunction and myocardial injury risk in diabetes. Nature Communications. doi: 10.1038/s41467-026-71809-x
2026
Other Outputs
Protocol-dependent cardiomyocyte states determine disease modelling capacity of human iPSCs
Sophie Shen, Clarissa Tan, Yuanzhao Cao, Chris Siu Yeung Chow, Dalia Mizikovsky, Janice Reid, Steve Dingwall, Andrew Prowse, Yuliangzi Sun, Zhixuan Wu, Sumedha Negi, Shaine Chenxin Bao, Enakshi Sinniah, Woo Jun Shim, Qiongyi Zhao, Jordan Thorpe, Azadeh Zahabi, Amy Hanna, Trishia Cheng, Adam Hill, James Hudson, James J. H. Chong and Nathan J. Palpant (2026). Protocol-dependent cardiomyocyte states determine disease modelling capacity of human iPSCs. doi: 10.64898/2026.03.29.715135
2026
Other Outputs
Hierarchical control of cardiomyocyte maturation and ischaemia sensitivity by metabolic culture conditions
Yuanzhao Cao, Chris Siu Yeung Chow, Sumedha Negi, Woo Jun Shim, Sophie Shen, Chen Fang and Nathan J. Palpant (2026). Hierarchical control of cardiomyocyte maturation and ischaemia sensitivity by metabolic culture conditions. doi: 10.64898/2026.03.12.711459
2026
Journal Article
The changing landscape of gene expression analysis
Zhao, Qiongyi, Shen, Sophie, Shim, Woo Jun and Palpant, Nathan J. (2026). The changing landscape of gene expression analysis. Briefings in Bioinformatics, 27 (2) bbag185, 2. doi: 10.1093/bib/bbag185
2025
Journal Article
Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and disease
Sinniah, Enakshi, Mizikovsky, Dalia, Shim, Woo Jun, Chow, Chris Siu Yeung, Souilmi, Yassine, Cheng, Fei-Fei, Zeng, Zhili, Laurie, Jordan, Foster, Matthew, Shah, Sonia, Bodén, Mikael, Zeng, Jian, Llamas, Bastien and Palpant, Nathan J. (2025). Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and disease. Nucleic Acids Research, 53 (20) gkaf971, 1-23. doi: 10.1093/nar/gkaf971
2025
Conference Publication
Human Hearts Intrinsically Increase Cardiomyocyte Mitosis Following Myocardial Infarction
Hume, R., Warwick, J., Shim, W., Malecki, C., Li, M., Harney, D., Slaughter, E., Wang, X., Nguyen, L., Cole, L., Edelman, J., Rashid, F., Houlahan, C., Gao, A., Ferguson, A., Chong, J., Larance, M., O’Sullivan, J., Palpant, N., Bannon, P. and Lal, S. (2025). Human Hearts Intrinsically Increase Cardiomyocyte Mitosis Following Myocardial Infarction. 73rd Annual Scientific Meeting of the Cardiac Society of Australia and New Zealand, Sydney, NSW Australia, 14-17 August 2025. Chatswood, NSW Australia: Elsevier. doi: 10.1016/j.hlc.2025.06.332
2025
Conference Publication
Glycaemic variability underlies myocyte dysfunction and myocardial injury risk in diabetes
Cao, Y., Redd, M., Outhwaite, J., Mizikovsky, D., Shim, W., Fang, C., Wu, Z., Daygon, D., Stark, T., Palfreyman, R., Chiu, H., Tan, C., Thomas, U., Dragicevic, E., Sng, J., Barrett, H., Dorey, E., Shah, S., Short, K. and Palpant, N. (2025). Glycaemic variability underlies myocyte dysfunction and myocardial injury risk in diabetes. 73rd Annual Scientific Meeting ofthe Cardiac Society of Australia and New Zealand, Brisbane, QLD Australia, 14-17 August 2025. Chatswood, NSW Australia: Elsevier Australia. doi: 10.1016/j.hlc.2025.06.821
2025
Journal Article
Putative epigenetic regulation mechanisms related to production, carcass and beef quality traits in Nelore cattle
Afonso, Juliana, Jun Shim, Woo, Figueiredo Cardoso, Tainã, Bruscadin, Jennifer Jéssica, Oliveira de Lima, Andressa, Jarles da Silva Diniz, Wellison, Silva-Vignato, Bárbara, Soares Garcia, Ingrid, Liang Andre Tan, Wei, Silva Neubern de Oliveira, Priscila, Silva Mello Cesar, Aline, Barreto Mourão, Gerson, Zerlotini, Adhemar, Lehmann Coutinho, Luiz, Rufino Salinas Fortes, Marina and Correia de Almeida Regitano, Luciana (2025). Putative epigenetic regulation mechanisms related to production, carcass and beef quality traits in Nelore cattle. Frontiers in Genetics, 16 1593444, 1593444. doi: 10.3389/fgene.2025.1593444
2025
Journal Article
Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure
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, 1-19. doi: 10.1038/s41467-025-56533-2
2025
Journal Article
Glycaemic variability underlies myocyte dysfunction and myocardial injury risk in diabetes
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
2025
Journal Article
Human hearts intrinsically increase cardiomyocyte mitosis after myocardial infarction
Hume, Robert D., Warwick, Jessica, Shim, Woo Jun, Malecki, Cassandra, Li, Mengbo, Seth, Lakshay, Harney, Dylan, Dagher, Julien, Lum, Trina, Tierney, Geraldine, Cooper, Wendy, Slaughter, Eugene, Wang, Xiaosuo, Nguyen, Lisa, Cole, Louise, Edelman, James, Rashid, Fairooj, Houlahan, Callum, Gao, Antony, Ferguson, Angela L., Chong, James J.H., Larance, Mark, O’Sullivan, John, Palpant, Nathan J., Bannon, Paul and Lal, Sean (2025). Human hearts intrinsically increase cardiomyocyte mitosis after myocardial infarction. Circulation Research, 138 (2) e327486, 367-382. doi: 10.1161/circresaha.125.327486
2025
Journal Article
TRIAGE: an R package for regulatory gene analysis
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
2024
Journal Article
A community-oriented, data-driven resource to improve protocol design for cardiac modelling from human pluripotent stem cells
Chow, Chris Siu Yeung, Negi, Sumedha, Bao, Shaine, Fang, Chen, Hudson, James, Shim, Woo Jun, Yuanzhao Cao and Palpant, Nathan (2024). A community-oriented, data-driven resource to improve protocol design for cardiac modelling from human pluripotent stem cells. doi: 10.1101/2024.09.04.611313
2024
Conference Publication
Preclinical models of Glycaemic variability recapitulate Clinical Cardiovascular outcomes in Diabetes
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
2023
Conference Publication
Disease modeling utilizing human pluripotent stem cell-derived cardiomyocytes and physiological characterization
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
2023
Journal Article
Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity
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
2023
Journal Article
Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle
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
2023
Journal Article
PDGF-AB Reduces Myofibroblast Differentiation Without Increasing Proliferation After Myocardial Infarction
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
2023
Journal Article
A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification
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
2022
Conference Publication
H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscle
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
Supervision
Availability
- Dr Woo Jun Shim is:
- Available for supervision
Looking for a supervisor? Read our advice on how to choose a supervisor.
Supervision history
Current supervision
-
Doctor Philosophy
Bioinformatics of epigenetics at multiple scales: from evolution of epigenetic factors to tracing their marks in organellar development
Associate Advisor
Other advisors: Professor Mikael Boden
-
Doctor Philosophy
Machine learning analysis of clinical data to improve diagnosis and treatment of heart disease
Associate Advisor
Other advisors: Professor Nathan Palpant
Completed supervision
-
2024
Doctor Philosophy
Using signatures of cell identity to improve cell type prediction in single cell analysis pipelines
Associate Advisor
Other advisors: Dr Quan Nguyen, Professor Nathan Palpant
Media
Enquiries
For media enquiries about Dr Woo Jun Shim's areas of expertise, story ideas and help finding experts, contact our Media team: