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2026 Journal Article Intra- and inter-organ communications in aging and cancer: Local and global spatial perspectivesMulay, Onkar, Benedicto, Aitor, Murata, Yui, Ng, Monica Suet Ying, Gonzalez Cruz, Jazmina L. and Nguyen, Quan (2026). Intra- and inter-organ communications in aging and cancer: Local and global spatial perspectives. Seminars in Cell & Developmental Biology, 179-180 103672, 103672-179. doi: 10.1016/j.semcdb.2026.103672 |
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2026 Journal Article Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung diseaseZhang, Lai-Ying, Allen, Peter C., Lutzky, Viviana P., Apte, Simon H., Groves, Penny L., Tan, Maxine E., De Silva, Tharushi, Spenceley, Eleanor R., McCloy, Rachael A., Nguyen, Quan H., Powell, Joseph E., Chambers, Daniel C. and O’Sullivan, Brendan J. (2026). Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung disease. PLOS One, 21 (4), e0347852. doi: 10.1371/journal.pone.0347852 |
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2026 Journal Article A tissue multiplexing approach to maximize spatial omics output from pathology specimensKao, Yung-Ching, Lee, Katie J., Zhou, Chenhao, Causer, Andrew, Oey, Harald, Khosrotehrani, Kiarash, O’Brien, Blake, Collins, Angus, Nguyen, Quan, Soyer, H. Peter and Stark, Mitchell S. (2026). A tissue multiplexing approach to maximize spatial omics output from pathology specimens. Frontiers in Medicine, 13 1749401, 13. doi: 10.3389/fmed.2026.1749401 |
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2026 Journal Article Spatial omics for profiling the dynamic tumor microenvironmentNguyen, Hao, Eapen, Merrin Mary, Nguyen, Quan and Sharma, Ankur (2026). Spatial omics for profiling the dynamic tumor microenvironment. Clinical & Translational Immunology, 15 (4) e70084, 4. doi: 10.1002/cti2.70084 |
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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, 17. 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. doi: 10.1038/s41467-026-70911-4 |
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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 Journal Article <i>BRRIAR</i> lncRNA alters breast cancer risk by modulating interferon signaling <i>in cis</i> and <i>in trans</i>Sivakumaran, Haran, Nair, Sneha, Bitar, Maina, Lu, Xue, Wang, Lu, Liu, Ji, Karunarathne, Deshapriya S., Prakrithi, P., Jacquelin, Sebastien, Rivera, Isela Sarahi, Hillman, Kristine M., Kaufmann, Susanne, Ziegman, Rebekah, 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. doi: 10.1186/s12943-025-02510-8 |
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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 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 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 |
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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 |
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2025 Journal Article Integrated profiling of metaplastic breast cancer identifies putative master regulators of intratumoral heterogeneityFeng, Yufan, Xiong, Albert, Mulay, Onkar, Sokolova, Anna, Lim, Malcolm, Van Haeringen, Benjamin, McGuire, Natasha, de Luca, Xavier, Simpson, Peter T., Nguyen, Quan, Lakhani, Sunil R. and McCart Reed, Amy E. (2025). Integrated profiling of metaplastic breast cancer identifies putative master regulators of intratumoral heterogeneity. npj Breast Cancer, 11 (1) 89. doi: 10.1038/s41523-025-00807-x |
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2025 Journal Article Transcriptomic plasticity of human alveolar macrophages revealed by single-cell RNA sequencing following drug exposure: implications for therapeutic developmentGroves, Penny L., Hockey, Levi, O’Sullivan, Brendan J., Zhang, Lai-Ying, Xiong, Zherui, Nguyen, Quan H., Tan, Maxine E., Lutzky, Viviana P., Davis, Rohan A., Chambers, Daniel C. and Apte, Simon H. (2025). Transcriptomic plasticity of human alveolar macrophages revealed by single-cell RNA sequencing following drug exposure: implications for therapeutic development. International Journal of Molecular Sciences, 26 (9) 4439, 4439. doi: 10.3390/ijms26094439 |
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2025 Journal Article Corrigendum to “Tolerogenic dendritic cells protect against acute kidney injury.” Kidney International 2023;104:492–507 (Kidney International (2023) 104(3) (492–507), (S0085253823003782), (10.1016/j.kint.2023.05.008))Li, Jennifer S.Y., Robertson, Harry, Trinh, Katie, Raghubar, Arti M., Nguyen, Quan, Matigian, Nicholas, Patrick, Ellis, Thomson, Angus W., Mallett, Andrew J. and Rogers, Natasha M. (2025). Corrigendum to “Tolerogenic dendritic cells protect against acute kidney injury.” Kidney International 2023;104:492–507 (Kidney International (2023) 104(3) (492–507), (S0085253823003782), (10.1016/j.kint.2023.05.008)). Kidney International, 107 (5), 949-949. doi: 10.1016/j.kint.2025.02.001 |
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2025 Journal Article The single-cell spatial landscape of stage III colorectal cancersSu, Andrew, Lee, HoJoon, Tran, Minh, dela Cruz, Richard C., Sathe, Anuja, Bai, Xiangqi, Wichmann, Ignacio, Pflieger, Lance, Moulton, Bryce, Barker, Tyler, Haslem, Derrick, Jones, David, Nadauld, Lincoln, Nguyen, Quan, Ji, Hanlee P. and Rhodes, Terence (2025). The single-cell spatial landscape of stage III colorectal cancers. Npj Precision Oncology, 9 (1) 101, 1-13. doi: 10.1038/s41698-025-00853-5 |
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2025 Journal Article A spatial transcriptomic signature of 26 genes resolved at single-cell resolution characterizes high-risk gastric cancer precursorsHuang, Robert J., Wichmann, Ignacio A., Su, Andrew, Sathe, Anuja, Shum, Miranda V., Grimes, Susan M., Meka, Rithika, Almeda, Alison, Bai, Xiangqi, Shen, Jeanne, Nguyen, Quan, Luo, Ingrid, Han, Summer S., Amieva, Manuel R., Hwang, Joo Ha and Ji, Hanlee P. (2025). A spatial transcriptomic signature of 26 genes resolved at single-cell resolution characterizes high-risk gastric cancer precursors. npj Precision Oncology, 9 (1) 52, 1-13. doi: 10.1038/s41698-025-00816-w |
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2025 Journal Article Spatial analysis of a complete DIPG-infiltrated brainstem reveals novel ligand-receptor mediators of tumour-to-TME crosstalkKordowski, Anja, Mulay, Onkar, Tan, Xiao, Vo, Tuan, Baumgartner, Ulrich, Maybury, Mellissa K., Hassall, Timothy, Harris, Lachlan, Nguyen, Quan and Day, Bryan W. (2025). Spatial analysis of a complete DIPG-infiltrated brainstem reveals novel ligand-receptor mediators of tumour-to-TME crosstalk. Acta Neuropathologica Communications, 13 (1) 35, 35. doi: 10.1186/s40478-025-01952-x |
