|
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 |
|
2025 Journal Article Cell-cell interactions as predictive and prognostic markers for drug responses in cancerLu, Xuehan, Tan, Xiao, Kim, Eun Ju, Jin, Xinnan, Donovan, Meg L, Gonzalez Cruz, Jazmina L., Xiong, Zherui, de Los Reyes Becerra Perez, Maria Reyes Becerra, Gong, Jialei, Monkman, James, Agrawal, Divya, Kulasinghe, Arutha, U. Q. CellOmics Innovation Forum, Nguyen, Quan and Tuong, Zewen Kelvin (2025). Cell-cell interactions as predictive and prognostic markers for drug responses in cancer. Genome Medicine, 17 (1) 117, 1-20. doi: 10.1186/s13073-025-01518-5 |
|
2025 Journal Article Spatial signatures for predicting immunotherapy outcomes using multi-omics in non-small cell lung cancerAung, Thazin N., Monkman, James, Warrell, Jonathan, Vathiotis, Ioannis, Bates, Katherine M., Gavrielatou, Niki, Trontzas, Ioannis P., Tan, Chin Wee, Fernandez, Aileen I., Moutafi, Myrto, O’ Byrne, Ken, Schalper, Kurt A., Syrigos, Konstantinos, Herbst, Roy S., Kulasinghe, Arutha and Rimm, David L. (2025). Spatial signatures for predicting immunotherapy outcomes using multi-omics in non-small cell lung cancer. Nature Genetics, 57 (10), 2482-2493. doi: 10.1038/s41588-025-02351-7 |
|
2025 Journal Article Response-adapted surgical and radiotherapy de-escalation in resectable cutaneous squamous cell cancer using pembrolizumab: the De-Squamate studyLadwa, Rahul, Lee, Jenny H., McGrath, Margaret, Cooper, Caroline, Liu, Howard, Bowman, James, Gupta, Ruta, Cuscaden, Claire, Nottage, Michelle, Clark, Jonathan R., Le, Dieu, Pauley, Marketa, Kulasinghe, Arutha, Gonzalez-Cruz, Jazmina, Porceddu, Sandro V., Hughes, Brett G.M. and Panizza, Benedict (2025). Response-adapted surgical and radiotherapy de-escalation in resectable cutaneous squamous cell cancer using pembrolizumab: the De-Squamate study. Journal of Clinical Oncology, 43 (26) JCO-25-00387, 2888-2896. doi: 10.1200/jco-25-00387 |
|
2025 Journal Article Proximity and metabolic activity proxies in the Tumour Microenvironment as predictors of survival in High Grade Serous Ovarian Cancer (HGSOC)Berrell, Naomi, Kilgallon, Aaron, Donovan, Meg L., Lawler, Clara, Tan, Chin Wee, Embaye, Kidane S., Tubelleza, Rafael, Monkman, James, Fraser, John F., O’Byrne, Ken, Huang, Ruby and Kulasinghe, Arutha (2025). Proximity and metabolic activity proxies in the Tumour Microenvironment as predictors of survival in High Grade Serous Ovarian Cancer (HGSOC). iScience, 28 (10) 113572, 113572. doi: 10.1016/j.isci.2025.113572 |
|
2025 Journal Article PRISM: a Python package for interactive and integrated analysis of multiplexed tissue microarraysTubelleza, Rafael, Kilgallon, Aaron, Tan, Chin Wee, Monkman, James, Fraser, John F and Kulasinghe, Arutha (2025). PRISM: a Python package for interactive and integrated analysis of multiplexed tissue microarrays. NAR Genomics and Bioinformatics, 7 (3) lqaf114, lqaf114-3. doi: 10.1093/nargab/lqaf114 |
|
2025 Journal Article The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironmentTan, Chin Wee, Berrell, Naomi, Donovan, Meg L., Monkman, James, Lawler, Clara, Sadeghirad, Habib, Naei, Vahid Yaghoubi, Chen, Jinjin, Rossenbloom, Alyssa, Bonnett, Shilah, Conner, Mark, Filanoski, Brian, Kang, Christine, Beechem, Joseph M., Fraser, John F., Barnett, Catherine, Ladwa, Rahul, Hughes, Brett G. M. and Kulasinghe, Arutha (2025). The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironment. npj Precision Oncology, 9 (1) 191, 1. doi: 10.1038/s41698-025-00963-0 |
|
2025 Other Outputs Metabolic microenvironment predictors of NSCLC immunotherapy responseKulasinghe, Arutha, Monkman, James, Tubelleza, Rafael, Kilgallon, Aaron and Lawler, Clara (2025). Metabolic microenvironment predictors of NSCLC immunotherapy response. The University of Queensland. (Dataset) doi: 10.48610/73b218c |
|
2025 Conference Publication Spatial profiling of tumor microenvironment uncovers potential novel therapeutic approach in pediatric neuroblastomaTu, Cui, Tan, Chin Wee, Monkman, James, Almeida, Ana Clara, Antonio-Carreon, Gabrielle, Omer, Natacha, Hull, Giaan, Chung, Kimberly, Mehdi, Ahmed, Salerno, Antonietta, Vittorio, Orazio, Mayer, Aaron, Machado de Souza, Cleber, de Almeida Brehm Pinhati, Fernanda, Elifio-Esposito, Selene, Nicholls, Wayne, de Noronha, Lucia, Kulasinghe, Arutha and Souza-Fonseca-Guimaraes, Fernando (2025). Spatial profiling of tumor microenvironment uncovers potential novel therapeutic approach in pediatric neuroblastoma. AACR Annual Meeting 2025, Chicago, IL United States, 25-30 April 2025. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2025-2705 |
|
2025 Conference Publication Tumor microenvironment profiling of multiplexed images in head and neck cancer reveals spatial features associated with immunotherapy responseMarkovits, Ettai, Monkman, James, Kilgallon, Aaron, Aung, Thazin Nwe, Rimm, David and Kulasinghe, Arutha (2025). Tumor microenvironment profiling of multiplexed images in head and neck cancer reveals spatial features associated with immunotherapy response. AACR Annual Meeting 2025, Chicago, IL United States, 25-30 April 2025. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2025-156 |
|
2025 Conference Publication A Bayesian framework for unraveling disease biology from spatially resolved single-cell omics datasets by combining unbiased approaches with biological priors for cell-based microdomain discoveryFalkenstein, Brian, Yan, Raymond, Quinn, Shannon, Tosun, Akif Burak, Chennubhotla, S. Chakra, Kulasinghe, Arutha and Pullara, Filippo (2025). A Bayesian framework for unraveling disease biology from spatially resolved single-cell omics datasets by combining unbiased approaches with biological priors for cell-based microdomain discovery. AACR Annual Meeting 2025, Chicago, IL United States, 25-30 April 2025. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2025-2485 |
|
2025 Conference Publication Unravelling melanoma brain metastasis tumor microenvironment characteristics using spatial transcriptomicsBelle, Clemence J., Brosda, Sandra, Bonazzi, Vanessa F., Bulteau, Victor, Stuart, Thomas, Xiong, Zherui, Lambie, Duncan, Johansson, Peter A., Aoude, Lauren G., Patel, Kalpana, Stehbens, Samantha J., Stark, Mitchell S., Haass, Nikolas K., Xu, Wen, Pinkham, Mark B., Foote, Matthew C., Olson, Sarah, Atkinson, Victoria, Kulasinghe, Arutha, Nguyen, Quan H. and Barbour, Andrew (2025). Unravelling melanoma brain metastasis tumor microenvironment characteristics using spatial transcriptomics. AACR Annual Meeting 2025, Chicago, IL United States, 25-30 April 2025. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2025-5076 |
|
2025 Conference Publication Exploring PD1/PDL1 interactions and macrophage-tumor barriers in head and neck cancer: A spatial approach to immunotherapy responseNaei, Vahid Yaghoubi, Tubelleza, Rafael, Monkman, James, Sadeghirad, Habib, Donovan, Meg L., Blick, Tony, Wicher, Agata, Bodbin, Sara, Basu, Subham, Stad, Robert, Barnett, Catherine, O’Byrne, Ken, Ladwa, Rahul, Cooper, Caroline, Warkiani, Majid Ebrahimi, Hughes, Brett G.M. and Kulasinghe, Arutha (2025). Exploring PD1/PDL1 interactions and macrophage-tumor barriers in head and neck cancer: A spatial approach to immunotherapy response. AACR Annual Meeting 2025, Chicago, IL United States, 25-30 April 2025. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2025-750 |
|
2025 Conference Publication Spatial deconvolution of non-small-cell lung cancer tissues prior to immune checkpoint inhibitor therapyMonkman, James, Tan, Chin Wee, Tubelleza, Rafael, OByrne, Ken and Kulasinghe, Arutha (2025). Spatial deconvolution of non-small-cell lung cancer tissues prior to immune checkpoint inhibitor therapy. AACR Annual Meeting 2025, Chicago, IL United States, 25-30 April 2025. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2025-2082 |
|
2025 Conference Publication 2D and 3D spatial characterisation of tertiary lymphoid structures in head and neck cancer patients receiving immune checkpoint blockade therapyDonovan, Meg L., Sadeghirad, Habib, Berrell, Naomi, Monkman, James, Naei, Vahid Yaghoubi, Tan, Chin Wee, Yunis, Joseph, West, Zoe, Warkiani, Majid E., Ladwa, Rahul, Hughes, Brett G., Da Gama Duarte, Jessica and Kulasinghe, Arutha (2025). 2D and 3D spatial characterisation of tertiary lymphoid structures in head and neck cancer patients receiving immune checkpoint blockade therapy. AACR Annual Meeting 2025, Chicago, IL United States, 25-30 April 2025. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2025-5252 |
|
2025 Conference Publication Characterising head and neck tumour microenvironment using high plex spatial omics technologies and analysesTan, Chin Wee, Berrell, Naomi, Donovan, Meg L., Monkman, James, Sadeghirad, Habib, Naei, Vahid Yaghoubi, Chen, Jinjin, Rossenbloom, Alyssa, Bonnett, Shilah, Conner, Mark, Filanoski, Brian, Kang, Christine, Beechem, Joseph M., Fraser, John F., Barnett, Catherine, Ladwa, Rahul, Hughes, Brett G. and Kulasinghe, Arutha (2025). Characterising head and neck tumour microenvironment using high plex spatial omics technologies and analyses. AACR Annual Meeting 2025, Chicago, IL United States, 25-30 April 2025. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2025-175 |
|
2025 Journal Article Spatial interaction mapping of PD-1/PD-L1 in head and neck cancer reveals the role of macrophage-tumour barriers associated with immunotherapy responseNaei, Vahid Yaghoubi, Tubelleza, Rafael, Monkman, James, Sadeghirad, Habib, Donovan, Meg L., Blick, Tony, Wicher, Agata, Bodbin, Sara, Viratham, Amelie, Stad, Robert, Basu, Subham, Cooper, Caroline, Barnett, Catherine, O’Byrne, Ken, Ladwa, Rahul, Warkiani, Majid Ebrahimi, Hughes, Brett G. M. and Kulasinghe, Arutha (2025). Spatial interaction mapping of PD-1/PD-L1 in head and neck cancer reveals the role of macrophage-tumour barriers associated with immunotherapy response. Journal of Translational Medicine, 23 (1) 177, 1-15. doi: 10.1186/s12967-025-06186-y |
|
2025 Other Outputs Metabolic and Inflammatory Niches Driving Recurrence in Adjuvant-Treated NSCLCKulasinghe, Arutha, Monkman, James, Berrell, Naomi Louise and Kilgallon, Aaron (2025). Metabolic and Inflammatory Niches Driving Recurrence in Adjuvant-Treated NSCLC. The University of Queensland. (Dataset) doi: 10.48610/3244c1b |
|
2025 Book Chapter Spatial-omics methods and applicationsKulasinghe, Arutha, Berrell, Naomi, Donovan, Meg L. and Nilges, Benedikt S. (2025). Spatial-omics methods and applications. Gene expression analysis: methods and protocols. (pp. 101-146) edited by Nalini Raghavachari and Natalia Garcia-Reyero. New York, NY, U.S.A.: Humana Press. doi: 10.1007/978-1-0716-4276-4_5 |
|
2024 Journal Article Copper chelation redirects neutrophil function to enhance anti-GD2 antibody therapy in neuroblastomaRouaen, Jourdin R. C., Salerno, Antonietta, Shai-Hee, Tyler, Murray, Jayne E., Castrogiovanni, Giulia, McHenry, Charlotte, Jue, Toni Rose, Pham, Vu, Bell, Jessica Lilian, Poursani, Ensieh, Valli, Emanuele, Cazzoli, Riccardo, Damstra, Naomi, Nelson, Delia J., Stevens, Kofi L. P., Chee, Jonathan, Slapetova, Iveta, Kasherman, Maria, Whan, Renee, Lin, Francis, Cochran, Blake J., Tedla, Nicodemus, Veli, Feyza Colakoglu, Yuksel, Aysen, Mayoh, Chelsea, Saletta, Federica, Mercatelli, Daniele, Chtanova, Tatyana, Kulasinghe, Arutha ... Vittorio, Orazio (2024). Copper chelation redirects neutrophil function to enhance anti-GD2 antibody therapy in neuroblastoma. Nature Communications, 15 (1) 10462, 1-20. doi: 10.1038/s41467-024-54689-x |
