
Overview
Background
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.
Availability
- Dr Dharmesh Bhuva is:
- Available for supervision
Fields of research
Qualifications
- Bachelor of Computer Science, University of Southampton
- Masters (Coursework) of Bioinformatics, University of Melbourne
- Doctor of Philosophy of Mathematics and Statistics, University of Melbourne
- Honorary Fellow, University of Adelaide, University of Adelaide
Research impacts
Dr Bhuva is an expert in developing and implementing novel computational methods that have been widely used in the field to advance knowledge of disease systems. He is a well-rounded early career researcher who has led teams to develop innovative solutions to complex analytics problems that enhance biological insight from data.
Contributions to science: Bhuva has worked in the fields of computational and systems biology for over 5 years with a focus on developing approaches to decipher complex molecular phenotypes and the regulatory mechanisms from various cancer data types, including single-cell and spatial transcriptomics. His recent work highlighted a wide-spread issue with analysing spatial ‘omics datasets and resulted in recommended best practices to address it. He has disseminated his work through 28 conferences, seminar talks and workshops (14 invitations).
Supervision, mentoring and teaching: Bhuva has delivered guest workshops to the University of Melbourne masters students for 4 consecutive years. He has also been invited to deliver 6 workshops, including one international workshop. He has successfully supervised 2 MSc students that have gone on to PhDs and has mentored 2 PhD students in his lab. He is currently supervising a PhD student (2023-present).
Professional engagement: Bhuva is a member of the Australian Bioinformatics and Computational Biology Society (ABACBS). He was on the organising committee of the annual ABACBS conference (2022, Melbourne). He has helped organise the WEHI Bioinformatics and Computational masterclass (Online, 2021) that had attendees from 15 countries. He formed the post-doctoral committee at the newly established South Australian Immunogenomics Cancer Institute (SAiGENCI) and served on the committee from 2024-2025.
Works
Search Professor Dharmesh Bhuva’s works on UQ eSpace
2025
Journal Article
SpaNorm: spatially-aware normalization for spatial transcriptomics data
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
2025
Journal Article
mastR: an R package for automated identification of tissue-specific gene signatures in multi-group differential expression analysis
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
2024
Journal Article
Library size confounds biology in spatial transcriptomics data
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
2024
Journal Article
In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection
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
2024
Journal Article
vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis
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
2023
Journal Article
Discovery of a highly potent, selective, orally bioavailable inhibitor of KAT6A/B histone acetyltransferases with efficacy against KAT6A-high ER+ breast cancer
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
2023
Journal Article
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
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
2023
Journal Article
vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis
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
2023
Journal Article
Spatial transcriptomic analysis of Sonic hedgehog medulloblastoma identifies that the loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibition
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
2023
Journal Article
Transcriptomic profiling of cardiac tissues from SARS‐CoV ‐2 patients identifies DNA damage
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
2022
Conference Publication
Deep single-cell, proteogenomic insights from SARS-CoV-2 infected lung tissues
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
2022
Conference Publication
MEDB-06. Spatial transcriptomic analysis of Sonic Hedgehog Medulloblastoma identifies that loss of heterogeneity and induced differentiation underlies the response to CDK4/6 inhibition
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
2022
Journal Article
Computational screening of anti-cancer drugs identifies a new BRCA independent gene expression signature to predict breast cancer sensitivity to cisplatin
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
2022
Journal Article
Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures
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
2021
Journal Article
Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma
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
2020
Journal Article
Stable gene expression for normalisation and single-sample scoring
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
2019
Journal Article
Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer
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
2019
Journal Article
Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
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
2018
Journal Article
Single sample scoring of molecular phenotypes
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
Supervision
Availability
- Dr Dharmesh Bhuva is:
- Available for supervision
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