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2026 Conference Publication AI foundation model for single cell annotation from conventional histopathology images of cancerBai, Xiangqi, Lee, HoJoon, Tan, Xiao, Li, Chaoyi, Sathe, Anuja, Wang, Yan, Nguyen, Quan and Ji, Hanlee P. (2026). AI foundation model for single cell annotation from conventional histopathology images of cancer. AACR Annual Meeting, San Diego, CA United States, 17-22 April 2026. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.AM2026-5491 |
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2026 Journal Article Understanding heterogeneity in the pathogenesis and drug responses of ulcerative colitis through single-cell and spatial transcriptomicsPhillips, Jennifer, Tambakis, George, Kumar, Rina, Croft, Anthony, Brown, Ian, Rosty, Christophe, Anderson, Robert, Belz, Gabrielle, Oliver, Amanda J., Xiong, Albert, Nguyen, Quan, Radford-Smith, Graham and Walker, Gareth J. (2026). Understanding heterogeneity in the pathogenesis and drug responses of ulcerative colitis through single-cell and spatial transcriptomics. Frontiers in Immunology, 17 1794207, 1-21. doi: 10.3389/fimmu.2026.1794207 |
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2026 Journal Article CD8+ T cells sustain vaccination-induced immunity against dissemination of contained tuberculosis in immunosuppressed hostsMiranda-Hernandez, Socorro, Kumar, Manoharan, Henderson, Alec, Graham, Erin, Tan, Xiao, Taylor, Jim, Meehan, Michael T., Ceja, Zuriel, del Pozo-Ramos, Lidia, Pan, Yi, Tsui, Ellen, Donovan, Meg L., Rentería, Miguel E., Flores-Valdez, Mario Alberto, Blumenthal, Antje, Nguyen, Quan, Subbian, Selvakumar, Field, Matt A. and Kupz, Andreas (2026). CD8+ T cells sustain vaccination-induced immunity against dissemination of contained tuberculosis in immunosuppressed hosts. Nature Communications, 17 (1) 4476, 1-17. doi: 10.1038/s41467-026-70911-4 |
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2026 Other Outputs SPanC-Lnc raw sequencing dataPavithra, Prakrithi and Nguyen, Quan (2026). SPanC-Lnc raw sequencing data. The University of Queensland. (Dataset) doi: 10.48610/86039c7 |
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2026 Other Outputs SPanC-Lnc manuscript dataPavithra, Prakrithi and Nguyen, Quan (2026). SPanC-Lnc manuscript data. The University of Queensland. (Dataset) doi: 10.48610/4570a11 |
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2026 Conference Publication AI interpretation of broncho-alveolar lavage cytology for personalised pulmonary fibrosis careHockey, Levi, Xiong, Zherui, Kaur, Ashandeep, Apte, Simon H., Groves, Penny L., Tan, Maxine E., Lutzky, Viviana P., Knuckley, Kiara, Zhang, Lai-Ying, Timmins, Sjane, Carew, Alan, Nguyen, Quan and Chambers, Daniel C. (2026). AI interpretation of broncho-alveolar lavage cytology for personalised pulmonary fibrosis care. Unknown, Unknown, Unknown. Richmond, VIC Australia: John Wiley & Sons. |
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2026 Journal Article Robust and interpretable prediction of gene markers and cell types from spatial transcriptomics dataTan, Xiao, Mulay, Onkar, Xie, Jacky, MacDonald, Samual, Kim, Taehyun, Zhou, Chenhao, Xiong, Zherui, Tan, Samuel X., Ye, Nan, McCart Reed, Amy, Khosrotehrani, Kiarash, Roosta, Fred, Trzaskowski, Maciej, Simpson, Peter T. and Nguyen, Quan (2026). Robust and interpretable prediction of gene markers and cell types from spatial transcriptomics data. Nature Communications, 17 (1) 1781, 1781. doi: 10.1038/s41467-026-68487-0 |
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2026 Journal Article Integrative spatial omics and artificial intelligence: transforming cancer research with omics data and AIMcKenzie, Maddison, Irac, Sergio Erdel, Chen, Zhian, Moradi, Afshin, Jenner, Adrianne, Nguyen, Quan and Rashidieh, Behnam (2026). Integrative spatial omics and artificial intelligence: transforming cancer research with omics data and AI. Seminars in Cancer Biology, 119 PMID 9010218, 65-82. doi: 10.1016/j.semcancer.2026.01.002 |
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2026 Journal Article Progressive fibrosis in human MASLD is associated with spatially linked transcriptomic signatures of metabolic reprogramming and senescenceVu, Hani, Sun, Yuliangzi, Xiong, Zherui, Tan, Xiao, Radford-Smith, Daniel, Causer, Andrew, Dickens, Alex M., Hyötyläinen, Tuulia, Evstafev, Ilia, Oresic, Matej, Nefzger, Christian, O’Sullivan, Eoin D., Watt, Matthew J., Ramm, Grant A., Clouston, Andrew, Irvine, Katharine, Nguyen, Quan H. and Powell, Elizabeth E. (2026). Progressive fibrosis in human MASLD is associated with spatially linked transcriptomic signatures of metabolic reprogramming and senescence. JHEP Reports, 8 (2) 101657, 1-12. doi: 10.1016/j.jhepr.2025.101657 |
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2026 Conference Publication Transdiagnostic comparison of sleep measures across chronic physical and mental health disorders using fitbit data in the All Of Us datasetHuang, X., Hsieh, C., Nguyen, Q., Renteria, M. E. and Gharahkhani, P. (2026). Transdiagnostic comparison of sleep measures across chronic physical and mental health disorders using fitbit data in the All Of Us dataset. Unknown, Unknown, Unknown. Amsterdam, Netherlands: ELSEVIER. |
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2026 Journal Article BRRIAR lncRNA alters breast cancer risk by modulating interferon signaling in cis and in transSivakumaran, Haran, Nair, Sneha, Bitar, Maina, Lu, Xue, Wang, Lu, Liu, Ji, Karunarathne, Deshapriya S., Prakrithi, P., Jacquelin, Sebastien, Rivera, Isela Sarahi, Hillman, Kristine M., Ziegman, Rebekah, Kaufmann, Susanne, Shi, Wei, Alexandrou, Sarah, Caldon, C. Elizabeth, Veedu, Rakesh N., Nguyen, Quan H., Beesley, Jonathan, Wykes, Michelle N., French, Juliet D. and Edwards, Stacey L. (2026). BRRIAR lncRNA alters breast cancer risk by modulating interferon signaling in cis and in trans. Molecular Cancer, 25 (1) 5, 1-14. doi: 10.1186/s12943-025-02510-8 |
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2026 Other Outputs SMACsMulay, Onkar, Mulay, Onkar and Nguyen, Quan (2026). SMACs. The University of Queensland. (Dataset) doi: 10.48610/2f40a80 |
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2025 Other Outputs Spatial pharmaco-multiomics reveals drug distribution, metabolic niches, and spatially constrained resistance in medulloblastomaCui, Cedric, Lee, John, Fung, Jenny, Vu, Hani, Nguyen, Quan, Causer, Andrew, Vo, Quang Anh Tuan, Tan, Xiao and Chen, Yibi (2025). Spatial pharmaco-multiomics reveals drug distribution, metabolic niches, and spatially constrained resistance in medulloblastoma. The University of Queensland. (Dataset) doi: 10.48610/bba49ae |
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2025 Journal Article Spatial analysis of HPV ‐associated cervical intraepithelial neoplastic tissues demonstrate distinct immune signatures associated with cervical cancer progressionPavilion, Gianna, Vu, Hani, Xiong, Zherui, Dang, Thi Viet Trinh, O'Brien, Blake, Walsh, Michael, Causer, Andrew, Chandra, Janin, Nguyen, Quan and Frazer, Ian H. (2025). Spatial analysis of HPV ‐associated cervical intraepithelial neoplastic tissues demonstrate distinct immune signatures associated with cervical cancer progression. Journal of Pathology, 268 (2) path.70002, 200-214. doi: 10.1002/path.70002 |
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2025 Conference Publication Endothelial progenitor plasticity as a driver of immune suppression in melanomaSormani, L., Hashemi, G., Li, H., Tan, S., Zhou, C., Li, K., Muller, N., Nguyen, Q., Roy, E. and Khosrotehrani, K. (2025). Endothelial progenitor plasticity as a driver of immune suppression in melanoma. 54th Annual ESDR 2025 Meeting, Antwerp, Belgium, 10 - 13 September 2025. Oxford, United Kingdom: Elsevier. doi: 10.1016/j.jid.2025.10.407 |
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2025 Conference Publication Chronic UVB exposure induces early transcriptomic changes associated with skin cancer developmentZhou, C., Galbraith, J. A., Roy, E., Chandra, J., Nguyen, Q., Walker, G. and Khosrotehrani, K. (2025). Chronic UVB exposure induces early transcriptomic changes associated with skin cancer development. 54th Annual ESDR 2025 Meeting, Antwerp, Belgium, 10-13 September 2025. Oxford, United Kingdom: Elsevier. doi: 10.1016/j.jid.2025.10.412 |
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2025 Conference Publication Validating the Eph family of receptors as therapeutic targets using patient-derived Glioblastoma organoidsSkarne, Niclas, D'Souza, Rochelle, Martins, Paulo, Mulay, Onkar, Harris, Lachlan, Holton, Emily, Zaman, Ashraf, Akgul, Seckin, Palethorpe, Helen, Colditz, Michael, Alexander, Hamish, Jeffree, Rosalind, Powell, Joseph, Thurecht, Kris, Khanna, Rajiv, Nguyen, Quan, Boyd, Andrew, Gomez, Guillermo and Day, Bryan (2025). Validating the Eph family of receptors as therapeutic targets using patient-derived Glioblastoma organoids. 2025 WFNOS and SNO Annual Meeting, Honolulu, HI United States, 19-23 November 2025. Cary, NC United States: Oxford University Press. doi: 10.1093/neuonc/noaf201.1409 |
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2025 Journal Article MASLD fibrosis stage F3 is morphologically and transcriptomically diverse: implications for assessing therapeutic responseLi, Chaoyi, Nguyen, Quan H., Irvine, Katharine, Powell, Elizabeth E. and Clouston, Andrew (2025). MASLD fibrosis stage F3 is morphologically and transcriptomically diverse: implications for assessing therapeutic response. Journal of Hepatology, 84 (4), e135-e137. doi: 10.1016/j.jhep.2025.11.006 |
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2025 Conference Publication SMINT and SPAMTP: integrative spatial analysis tools reveal metabolic and transcriptional drivers of invasion in IDH-mutated gliomaFreytag, Saskia, Kriel, Jurgen, Moffet, Joel J. D., Lu, Tianyao, Causer, Andrew, Narayana, Vinod K., Nguyen, Quan, Whittle, James R. and Best, Sarah A. (2025). SMINT and SPAMTP: integrative spatial analysis tools reveal metabolic and transcriptional drivers of invasion in IDH-mutated glioma. 2025 WFNOS and SNO Annual Meeting, Honolulu, HI United States, 19-23 November 2025. Cary, NC United States: Oxford University Press. doi: 10.1093/neuonc/noaf201.0027 |
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2025 Journal Article Long-term fixation impact on archived human nervous tissues for sequencing-based transcriptomicsHowe, Stephanie, McCann, Heather, Xiong, Zherui, Nguyen, Quan, Steyn, Frederik J., Ngo, Shyuan T. and Chang, Jeryn (2025). Long-term fixation impact on archived human nervous tissues for sequencing-based transcriptomics. Brain Communications, 7 (6) fcaf428, fcaf428. doi: 10.1093/braincomms/fcaf428 |
