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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 |
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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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2026 Journal Article hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics dataLiu, Ning, Martin, Jarryd, Bhuva, Dharmesh D., Chen, Jinjin, Li, Mengbo, Lee, Samuel C., Kharbanda, Malvika, Cheng, Jinming, Mohamed, Ahmed, Kulasinghe, Arutha, Chen, Yunshun, Tan, Chin Wee, Li, Fuyi, Polo, Jose M. and Davis, Melissa J. (2026). hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data. Bioinformatics btag609. doi: 10.1093/bioinformatics/btag609 |
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2026 Other Outputs pcf - Metabolic and Inflammatory Niches Driving Recurrence in Adjuvant-Treated NSCLCKulasinghe, Arutha, Monkman, James, Kilgallon, Aaron and Tan, Chin Wee (2026). pcf - Metabolic and Inflammatory Niches Driving Recurrence in Adjuvant-Treated NSCLC. The University of Queensland. (Dataset) doi: 10.48610/0e4890f |
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2026 Other Outputs GeoMX : Metabolic and Inflammatory Niches Driving Recurrence in Adjuvant-Treated NSCLCKulasinghe, Arutha, Monkman, James, Kilgallon, Aaron and Tan, Chin Wee (2026). GeoMX : Metabolic and Inflammatory Niches Driving Recurrence in Adjuvant-Treated NSCLC. The University of Queensland. (Dataset) doi: 10.48610/dc02c80 |
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2026 Journal Article Spatial multiomics approaches for antibody-drug conjugate target discoveryWijerathna-Yapa, Akila, Mansfield, James, Vasaturo, Angela, Sheng Yeong, Joe Poh and Kulasinghe, Arutha (2026). Spatial multiomics approaches for antibody-drug conjugate target discovery. Cell Press Blue 100085, 100085. doi: 10.1016/j.cpblue.2026.100085 |
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2026 Journal Article Agentic <scp>AI</scp> for Spatial OmicsPavilion, Gianna, Mbigidde, Cathrine, Tubelleza, Rafael, Ramarao‐Milne, Priya and Kulasinghe, Arutha (2026). Agentic AI for Spatial Omics. Immunology & Cell Biology imcb.70146. doi: 10.1111/imcb.70146 |
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2026 Journal Article Tertiary lymphoid structures in head and neck squamous cell carcinoma as predictors of response to immunotherapyGriffin, Cara, Donovan, Meg L., Lawler, Clara, Da Gama Duarte, Jessica, Ladwa, Rahul, Barnett, Catherine M. E. and Kulasinghe, Arutha (2026). Tertiary lymphoid structures in head and neck squamous cell carcinoma as predictors of response to immunotherapy. Oral Oncology, 178 107998, 1-8. doi: 10.1016/j.oraloncology.2026.107998 |
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2026 Journal Article Dissecting non-small cell lung cancer (NSCLC) with blood proteomics—from surgical to immunotherapeutic responsesYaghoubi Naei, Vahid, Kilgallon, Aaron, Mendes, Gwendoline, Wijerathna-Yapa, Akila, Dutta, Sanjay, Lawler, Clara, O’Leary, Connor, Mullally, William, Monkman, James, Mansfield, James, Hedou, Julien, Adams, Mark N., O’Byrne, Ken, Warkiani, Majid E. and Kulasinghe, Arutha (2026). Dissecting non-small cell lung cancer (NSCLC) with blood proteomics—from surgical to immunotherapeutic responses. npj Precision Oncology, 10 (1) 221. doi: 10.1038/s41698-026-01469-z |
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2026 Journal Article Defining the tumor microenvironment of non‐small cell lung cancerEmbaye, Kidane Siele, Blick, Tony, Naei, Vahid Yaghoubi, O'Byrne, Ken, Hughes, Brett G. M. and Kulasinghe, Arutha (2026). Defining the tumor microenvironment of non‐small cell lung cancer. Immunology and Cell Biology, 104 (5) imcb.70114, 499-518. doi: 10.1111/imcb.70114 |
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2026 Journal Article Early-stage multi-cancer detection through a plasma extracellular vesicle protein signatureLobb, Richard J., Zhou, Quan, Fielding, David, Visan, Kekoolani S., Wuethrich, Alain, Wang, Jing, Hu, Youran, Norris, Emma L., Hastie, Marcus L., Everitt, Sarah, Parris, Brielle, Aoude, Lauren G., Bonazzi, Vanessa F., Nixon, Elizabeth, Mooi, Jennifer, Koo, Kevin M., O'Byrne, Kenneth, Kulasinghe, Arutha, Bowman, Rayleen V., Yang, Ian A., Corcoran, Niall M., Hovens, Christopher M., MacManus, Michael, Gorman, Jeffrey J., Day, Bryan W., Hartel, Gunter, Whiteman, David C., Tebbutt, Niall, Mariadason, John M. ... Möller, Andreas (2026). Early-stage multi-cancer detection through a plasma extracellular vesicle protein signature. Cell Reports Medicine, 7 (4) 102694, 1-20. doi: 10.1016/j.xcrm.2026.102694 |
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2026 Conference Publication Plasma proteomic profiling of lung cancer blood samples reveals immune-related inflammatory signatures as prognostic biomarkersWijerathna-Yapa, Akila, Kilgallon, Aaron, Lawler, Clara, Monkman, James, Robichaud, Nathaniel, Rosebloom, Alyssa, Mullaly, William, O'Byrne, Ken and Kulasinghe, Arutha (2026). Plasma proteomic profiling of lung cancer blood samples reveals immune-related inflammatory signatures as prognostic biomarkers. AACR Annual Meeting, San Diego Ca, Apr 17-22, 2026. PHILADELPHIA: AMER ASSOC CANCER RESEARCH. doi: 10.1158/1538-7445.AM2026-1186 |
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2026 Conference Publication Cellular decomposition and metabolic profiling of the tumor microenvironment tumor-stroma interface using high-dimensional spatial proteomics and image analyticsKulasinghe, Arutha, Roland, Felicia, Poulin, Michelle, Mihani, Ritu, Hales, Katherine and Winkowski, Daniel (2026). Cellular decomposition and metabolic profiling of the tumor microenvironment tumor-stroma interface using high-dimensional spatial proteomics and image analytics. AACR Annual Meeting, San Diego Ca, Apr 17-22, 2026. PHILADELPHIA: AMER ASSOC CANCER RESEARCH. doi: 10.1158/1538-7445.AM2026-790 |
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2026 Journal Article Spatial multi-omics characterization of neuroblastoma reveals ferroptosis-associated metabolic features in high-risk tumorsTu, Cui, Tan, Chin Wee, Monkman, James, Almeida, Ana Clara, Antonio-Carreon, Gabrielle, Omer, Natacha, Hull, Giaan, Chung, Kimberly, Mehdi, Ahmed M., Salerno, Antonietta, Vittorio, Orazio, Mayer, Aaron, Machado-Souza, Cleber, Jayabalan, Nanthini, Toh, Yi-Chin, Hon, Hui Nee, de Almeida Brehm Pinhatti, Fernanda, Elifio-Esposito, Selene, Nicholls, Wayne, de Noronha, Lucia, Kulasinghe, Arutha and Souza-Fonseca-Guimaraes, Fernando (2026). Spatial multi-omics characterization of neuroblastoma reveals ferroptosis-associated metabolic features in high-risk tumors. Genome Medicine, 18 (1) 35. doi: 10.1186/s13073-026-01622-0 |
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2026 Journal Article Tumour microenvironment diversity of HNSCC and the molecular landscape of recurrent diseaseSteele, Katelyn, Barnett, Catherine, Ladwa, Rahul, Donovan, Meg L, Lawler, Clara and Kulasinghe, Arutha (2026). Tumour microenvironment diversity of HNSCC and the molecular landscape of recurrent disease. Oral Oncology, 174 107864, 1-8. doi: 10.1016/j.oraloncology.2026.107864 |
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2026 Journal Article Metabolic characterization of tumor-immune interactions by multiplexed immunofluorescence reveals spatial mechanisms of immunotherapy response in non-small cell lung carcinoma (NSCLC)Monkman, James, Kilgallon, Aaron, Lawler, Clara, Tubelleza, Rafael, Aung, Thazin Nwe, Warrell, Jonathan H., Vathiotis, Ioannis, Trontzas, Ioannis P., Gavrielatou, Niki, Nyein Chan, Nay Nwe, Czertok, Rotem, Bookstein, Shai, O’Byrne, Ken, Markovits, Ettai, Rimm, David L. and Kulasinghe, Arutha (2026). Metabolic characterization of tumor-immune interactions by multiplexed immunofluorescence reveals spatial mechanisms of immunotherapy response in non-small cell lung carcinoma (NSCLC). Nature Communications, 17 (1) 837, 1-16. doi: 10.1038/s41467-026-68633-8 |
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2026 Journal Article Large-scale spatial profiling of the tumor microenvironmentKilgallon, Aaron, Tubelleza, Rafael and Kulasinghe, Arutha (2026). Large-scale spatial profiling of the tumor microenvironment. Cell, 189 (2) PMID 413066, 343-344. doi: 10.1016/j.cell.2025.12.028 |
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2026 Journal Article SM3DD with segmented PCA: a comprehensive method for interpreting 3D spatial transcriptomicsBlick, Tony, Kilgallon, Aaron, Monkman, James, Cooper, Caroline, Tan, Chin Wee, Killingbeck, Emily E., Pan, Liuliu, Kim, Youngmi, Liang, Yan, Nam, Andy, Leon, Michael, Guimaraes, Paulo S. F., Nagashima, Seigo, Martins, Ana P. C., Machado-Souza, Cleber, de Noronha, Lucia, Fraser, John F., Belz, Gabrielle T., Souza-Fonseca-Guimaraes, Fernando and Kulasinghe, Arutha (2026). SM3DD with segmented PCA: a comprehensive method for interpreting 3D spatial transcriptomics. NAR Genomics and Bioinformatics, 8 (1) lqag007, 1-10. doi: 10.1093/nargab/lqag007 |
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2026 Journal Article Integrating mass spectrometry‐based multi‐omic signatures of extracellular vesicles: from discovery to clinical translationWijerathna‐Yapa, Akila, Aubert, Dimitri and Kulasinghe, Arutha (2026). Integrating mass spectrometry‐based multi‐omic signatures of extracellular vesicles: from discovery to clinical translation. Clinical and Translational Immunology, 15 (1) e70078. doi: 10.1002/cti2.70078 |
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2025 Journal Article Society for Immunotherapy of Cancer: Standards for Reporting of Multiplex Immunohistochemistry/Immunofluorescence Assays (STORMI)Sater, Sam, Bifulco, Carlo B., Rodriguez-Canales, Jaime, Yeong, Joe, Akturk, Guray, Angelo, Michael, Ballesteros-Merino, Carmen, Bankhead, Peter, Basu, Subham, Blando, Jorge M., Brajkovic, Saska, Cassano, Marco, Chen, Benjamin J., Coskun, Ahmet F., Cottrell, Tricia R., De Andrea, Carlos E., Edwards, Robin H., Egelston, Colt, Engle, Logan L., Ernstoff, Marc S., Fan, Rong, Feldman, Michael, Fox, Bernard A., Galon, Jerome, Gartrell, Robyn, Gnjatic, Sacha, Green, Benjamin F., Gulley, James L., Hellebust, Anne ... Taube, Janis M. (2025). Society for Immunotherapy of Cancer: Standards for Reporting of Multiplex Immunohistochemistry/Immunofluorescence Assays (STORMI). Journal for ImmunoTherapy of Cancer, 13 (12) e012280, 1-16. doi: 10.1136/jitc-2025-012280 |
