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2025 Journal Article SpaNorm: spatially-aware normalization for spatial transcriptomics dataSalim, 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 |
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2025 Journal Article mastR: an R package for automated identification of tissue-specific gene signatures in multi-group differential expression analysisChen, 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 |
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2024 Journal Article Library size confounds biology in spatial transcriptomics dataBhuva, 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 |
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2024 Journal Article In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infectionTan, 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 |
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2024 Journal Article vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysisBhuva, 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 |
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2023 Journal Article Discovery of a highly potent, selective, orally bioavailable inhibitor of KAT6A/B histone acetyltransferases with efficacy against KAT6A-high ER+ breast cancerSharma, 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 |
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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 StudyWhite, 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 |
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2023 Journal Article vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysisMohamed, 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 |
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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 inhibitionVo, 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 |
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2023 Journal Article Transcriptomic profiling of cardiac tissues from SARS‐CoV ‐2 patients identifies DNA damageKulasinghe, 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 |
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2022 Conference Publication Deep single-cell, proteogenomic insights from SARS-CoV-2 infected lung tissuesKulasinghe, 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 |
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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 inhibitionVo, 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 |
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2022 Journal Article Computational screening of anti-cancer drugs identifies a new BRCA independent gene expression signature to predict breast cancer sensitivity to cisplatinBerthelet, 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 |
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2022 Journal Article Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signaturesKulasinghe, 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 |
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2021 Journal Article Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastomaGenovesi, 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 |
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2020 Journal Article Stable gene expression for normalisation and single-sample scoringBhuva, 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 |
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2019 Journal Article Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancerBhuva, 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 |
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2019 Journal Article Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signaturesBhuva, 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 |
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2018 Journal Article Single sample scoring of molecular phenotypesForoutan, 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 |
