Dr Dharmesh Bhuva
NHMRC Emerging Leadership Fellow
Frazer Institute
Researcher biography
Dr Dharmesh D Bhuva is a NHMRC Emerging Leadership Fellow (EL1) on a mission to understand how complex systems of gene regulation and signalling produce diverse tissue phenotypes in health, disease, and development. He completed his PhD in Oct 2020 through the Department of Mathematics and Statistics, University of Melbourne, focusing on developing novel systems biology approaches to study molecular function and gene regulation in cancer systems. His current work focuses on extending these ideas to biological tissues through the development of computational methods to generate accurate biological insights from spatial molecular datasets.
Whilst being an early career researcher, he has developed high quality bioinformatics software that have been downloaded more than 160,000 times, has received >$3.25M in funding support, including NHMRC and MRFF, and has published in Genome biology and Nucleic Acids Research, some of the highest-ranking journals in his field. Dr Bhuva has organised and run various computational biology workshops at the University of Melbourne as well as the WEHI Bioinformatics and Computational Biology Masterclass (2021) that was delivered to the Asia-Pacific region. He currently supervises a PhD student and has co-supervised 2 successful MSc Bioinformatics students.
Journal Articles
Salim, Agus, Bhuva, Dharmesh D., Chen, Carissa, Tan, Chin Wee, Yang, Pengyi, Davis, Melissa J. and Yang, Jean Y. H. (2025). SpaNorm: spatially-aware normalization for spatial transcriptomics data. Genome Biology, 26 (1) 109. doi: 10.1186/s13059-025-03565-y
Chen, Jinjin, Mohamed, Ahmed, Bhuva, Dharmesh D., Davis, Melissa J. and Tan, Chin Wee (2025). mastR: an R package for automated identification of tissue-specific gene signatures in multi-group differential expression analysis. Bioinformatics, 41 (3) btaf114, 3. doi: 10.1093/bioinformatics/btaf114
Bhuva, Dharmesh D., Tan, Chin Wee, Salim, Agus, Marceaux, Claire, Pickering, Marie A., Chen, Jinjin, Kharbanda, Malvika, Jin, Xinyi, Liu, Ning, Feher, Kristen, Putri, Givanna, Tilley, Wayne D., Hickey, Theresa E., Asselin-Labat, Marie-Liesse, Phipson, Belinda and Davis, Melissa J. (2024). Library size confounds biology in spatial transcriptomics data. Genome Biology, 25 (1) 99. doi: 10.1186/s13059-024-03241-7
Tan, Chin Wee, Chen, Jinjin, Liu, Ning, Bhuva, Dharmesh D., Blick, Tony, Monkman, James, Cooper, Caroline, Kharbanda, Malvika, Feher, Kristen, Phipson, Belinda, Killingbeck, Emily E., Pan, Liuliu, Kim, Youngmi, Liang, Yan, Nam, Andy, Leon, Michael, Souza-Fonseca-Guimaraes, Paulo, Nagashima, Seigo, Camargo Martins, Ana Paula, Machado-Souza, Cleber, de Noronha, Lucia, Tang, Benjamin, Short, Kirsty, Fraser, John, Belz, Gabrielle T., Souza-Fonseca-Guimaraes, Fernando, Kulasinghe, Arutha and Davis, Melissa J. (2024). In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection. eBioMedicine, 101 105016, 1-4. doi: 10.1016/j.ebiom.2024.105016
Bhuva, Dharmesh D., Tan, Chin Wee, Liu, Ning, Whitfield, Holly J., Papachristos, Nicholas, Lee, Samuel C., Kharbanda, Malvika, Mohamed, Ahmed and Davis, Melissa J. (2024). vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis. BMC Bioinformatics, 25 (1) 64. doi: 10.1186/s12859-024-05676-y
Sharma, Shikhar, Chung, Chi-Yeh, Uryu, Sean, Petrovic, Jelena, Cao, Joan, Rickard, Amanda, Nady, Nataliya, Greasley, Samantha, Johnson, Eric, Brodsky, Oleg, Khan, Showkhin, Wang, Hui, Wang, Zhenxiong, Zhang, Yong, Tsaparikos, Konstantinos, Chen, Lei, Mazurek, Anthony, Lapek, John, Kung, Pei-Pei, Sutton, Scott, Richardson, Paul F., Greenwald, Eric C., Yamazaki, Shinji, Jones, Rhys, Maegley, Karen A., Bingham, Patrick, Lam, Hieu, Stupple, Alexandra E., Kamal, Aileen ... Paul, Thomas A. (2023). Discovery of a highly potent, selective, orally bioavailable inhibitor of KAT6A/B histone acetyltransferases with efficacy against KAT6A-high ER+ breast cancer. Cell Chemical Biology, 30 (10), 1191-1210.e20. doi: 10.1016/j.chembiol.2023.07.005
White, Christine L., Kinross, Kathryn M., Moore, Molly K., Rasouli, Elnaz, Strong, Robyn, Jones, Janelle M., Cain, Jason E., Sturm, Dominik, Sahm, Felix, Jones, David T.W., Pfister, Stefan M., Robertson, Thomas, D'Arcy, Colleen, Rodriguez, Michael L., Dyke, Jason M., Junckerstorff, Reimar, Bhuva, Dharmesh D., Davis, Melissa J., Wood, Paul, Hassall, Tim, Ziegler, David S., Kellie, Stewart, McCowage, Geoffrey, Alvaro, Frank, Kirby, Maria, Heath, John A., Tsui, Karen, Dodgshun, Andrew, Eisenstat, David D. ... Hansford, Jordan R. (2023). Implementation of DNA methylation array profiling in pediatric central nervous system tumors: The AIM BRAIN Project: An Australian and New Zealand Children's Haematology/Oncology Group Study. Journal of Molecular Diagnostics, 25 (10), 709-728. doi: 10.1016/j.jmoldx.2023.06.013
Mohamed, Ahmed, Bhuva, Dharmesh D., Lee, Sam, Liu, Ning, Tan, Chin Wee and Davis, Melissa J. (2023). vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis. Nucleic Acids Research, 51 (W1), W593-W600. doi: 10.1093/nar/gkad337
Vo, Tuan, Balderson, Brad, Jones, Kahli, Ni, Guiyan, Crawford, Joanna, Millar, Amanda, Tolson, Elissa, Singleton, Matthew, Kojic, Marija, Robertson, Thomas, Walters, Shaun, Mulay, Onkar, Bhuva, Dharmesh D., Davis, Melissa J., Wainwright, Brandon J., Nguyen, Quan and Genovesi, Laura A. (2023). Spatial transcriptomic analysis of Sonic hedgehog medulloblastoma identifies that the loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibition. Genome Medicine, 15 (1) 29, 29. doi: 10.1186/s13073-023-01185-4
Kulasinghe, Arutha, Liu, Ning, Tan, Chin Wee, Monkman, James, Sinclair, Jane E., Bhuva, Dharmesh D., Godbolt, David, Pan, Liuliu, Nam, Andy, Sadeghirad, Habib, Sato, Kei, Bassi, Gianluigi Li, O'Byrne, Ken, Hartmann, Camila, Miggiolaro, Anna Flavia Ribeiro dos Santos, Marques, Gustavo Lenci, Moura, Lidia Zytynski, Richard, Derek, Adams, Mark, Noronha, Lucia de, Baena, Cristina Pellegrino, Suen, Jacky Y., Arora, Rakesh, Belz, Gabrielle T., Short, Kirsty R., Davis, Melissa J., Souza‐Fonseca Guimaraes, Fernando and Fraser, John F. (2023). Transcriptomic profiling of cardiac tissues from
SARS‐CoV
‐2 patients identifies
DNA
damage. Immunology, 168 (3), 403-419. doi: 10.1111/imm.13577
Berthelet, Jean, Foroutan, Momeneh, Bhuva, Dharmesh D., Whitfield, Holly J., El-Saafin, Farrah, Cursons, Joseph, Serrano, Antonin, Merdas, Michal, Lim, Elgene, Charafe-Jauffret, Emmanuelle, Ginestier, Christophe, Ernst, Matthias, Hollande, Frédéric, Anderson, Robin L., Pal, Bhupinder, Yeo, Belinda, Davis, Melissa J. and Merino, Delphine (2022). Computational screening of anti-cancer drugs identifies a new BRCA independent gene expression signature to predict breast cancer sensitivity to cisplatin. Cancers, 14 (10) 2404, 1-18. doi: 10.3390/cancers14102404
Kulasinghe, Arutha, Tan, Chin Wee, dos Santos Miggiolaro, Anna Flavia Ribeiro, Monkman, James, SadeghiRad, Habib, Bhuva, Dharmesh D., da Silva Motta Junior, Jarbas, Vaz de Paula, Caroline Busatta, Nagashima, Seigo, Baena, Cristina Pellegrino, Souza-Fonseca-Guimaraes, Paulo, de Noronha, Lucia, McCulloch, Timothy, Rodrigues Rossi, Gustavo, Cooper, Caroline, Tang, Benjamin, Short, Kirsty R., Davis, Melissa J., Souza-Fonseca-Guimaraes, Fernando, Belz, Gabrielle T. and O'Byrne, Ken (2022). Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures. European Respiratory Journal, 59 (6) 2101881, 1-19. doi: 10.1183/13993003.01881-2021
Genovesi, Laura A., Millar, Amanda, Tolson, Elissa, Singleton, Matthew, Hassall, Emily, Kojic, Marija, Brighi, Caterina, Girard, Emily, Andradas, Clara, Kuchibhotla, Mani, Bhuva, Dharmesh D., Endersby, Raelene, Gottardo, Nicholas G., Bernard, Anne, Adolphe, Christelle, Olson, James M., Taylor, Michael D., Davis, Melissa J. and Wainwright, Brandon J. (2021). Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma. Genome Medicine, 13 (1) 103, 103. doi: 10.1186/s13073-021-00920-z
Bhuva, Dharmesh D., Cursons, Joseph and Davis, Melissa J. (2020). Stable gene expression for normalisation and single-sample scoring. Nucleic Acids Research, 48 (19) e113, 1-14. doi: 10.1093/nar/gkaa802
Bhuva, Dharmesh D., Cursons, Joseph, Smyth, Gordon K. and Davis, Melissa J. (2019). Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer. Genome Biology, 20 (1) 236, 1-21. doi: 10.1186/s13059-019-1851-8
Bhuva, Dharmesh D., Foroutan, Momeneh, Xie, Yi, Lyu, Ruqian, Cursons, Joseph and Davis, Melissa J. (2019). Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures. F1000Research, 8 776, 1-43. doi: 10.12688/f1000research.19236.3
Foroutan, Momeneh, Bhuva, Dharmesh D., Lyu, Ruqian, Horan, Kristy, Cursons, Joseph and Davis, Melissa J. (2018). Single sample scoring of molecular phenotypes. BMC Bioinformatics, 19 (1) 404, 1-10. doi: 10.1186/s12859-018-2435-4
Conference Papers
Kulasinghe, Arutha, Tan, Chin Wee, Liu, Ning, Monkman, James, Killingbeck, Emily, Kim, Youngmi, Pan, Liuliu, Blick, Tony, Bhuva, Dharmesh, Feher, Kristen, Leon, Michael, Gregory, Mark, Short, Kirsty, Guimaraes, Fernando, Rhodes, Michael, Belz, Gabrielle and Davis, Melissa (2022). Deep single-cell, proteogenomic insights from SARS-CoV-2 infected lung tissues. SITC 37th Annual Meeting (SITC 2022), Boston, MA USA, 8-12 November 2022. London, United Kingdom: BMJ Publishing Group. doi: 10.1136/jitc-2022-sitc2022.0923
Vo, Tuan, Balderson, Brad, Jones, Kahli, Crawford, Joanna, Millar, Amanda, Tolson, Elissa, Ruitenberg, Marc, Robertson, Thomas, Bhuva, Dharmesh, Davis, Melissa, Wainwright, Brandon, Nguyen, Quan and Genovesi, Laura (2022). MEDB-06. Spatial transcriptomic analysis of Sonic Hedgehog Medulloblastoma identifies that loss of heterogeneity and induced differentiation underlies the response to CDK4/6 inhibition. International Symposium on Pediatric Neuro-Oncology, Hamburg, Germany, 12–15 June 2022. Cary, NC, United States: Oxford University Press. doi: 10.1093/neuonc/noac079.381