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2026 Journal Article The GFI1-FOXO1 axis regulates NK cell maturation and functionHuang, Qiutong, Chaudhry, M. Zeeshan, Dight, James, Alim, Louisa, Yu, Huiyang, Denman, Renae, Man, Hiu On, Schreuder, Jaring, Garnham, Alexandra L., Tuong, Zewen K., Souza-Fonseca-Guimaraes, Fernando, Jacquelot, Nicolas and Belz, Gabrielle T. (2026). The GFI1-FOXO1 axis regulates NK cell maturation and function. Nature Communications. doi: 10.1038/s41467-026-72022-6 |
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2026 Journal Article Feature-preserving manifold approximation and projection to analyze single-cell dataYang, Yang, Gong, Jialei, Sun, Hongjian, Choo, Amos, Mar, Jessica Cara, Wei, Yunbo, Zhang, Yu, Zhang, Wenjie, Shu, Minglei, Tuong, Zewen Kelvin and Yu, Di (2026). Feature-preserving manifold approximation and projection to analyze single-cell data. Nature Computational Science. doi: 10.1038/s43588-026-00970-6 |
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2026 Journal Article Subclinical fields of BRAF V600E-mutant melanocytes populate human skin and are enriched around melanoma and naeviLee, Katie J., Kao, Yung-Ching, Jiang, Amanda, Prokofyeva, Anastasia, Tom, Lisa N., Jagirdar, Kasturee, Smit, Darren J., Oey, Harald M., Tan, Jean-Marie, Ainger, Stephen A., Huang, Nancy, Tuong, Zewen Kelvin, Andersen, Stacey, Senabouth, Anne, Powell, Joseph E., Lambie, Duncan, Schaider, Helmut, Soyer, H. Peter, Sturm, Richard A., Welm, Alana L., Grossman, Douglas, Judson-Torres, Robert L. and Stark, Mitchell S. (2026). Subclinical fields of BRAF V600E-mutant melanocytes populate human skin and are enriched around melanoma and naevi. British Journal of Dermatology, 194 (2), 301-310. doi: 10.1093/bjd/ljaf412 |
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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 In vivo labelling resolves distinct temporal, spatial, and functional properties of tumour macrophages, and identifies subset-specific effects of PD-L1 blockadeLee, Colin Y. C., Dean, Isaac, Richoz, Nathan, Li, Zhi, Kennedy, Bethany C., Vettore, Lisa A., Samarakoon, Youhani, Gilroy, Kathryn L., Hasegawa, Tetsuo, Carlesso, Gianluca, Hammond, Scott A., Dovedi, Simon J., Sansom, Owen J., Tuong, Zewen K., Halim, Timotheus YF., Withers, David R. and Clatworthy, Menna R. (2025). In vivo labelling resolves distinct temporal, spatial, and functional properties of tumour macrophages, and identifies subset-specific effects of PD-L1 blockade. Cancer Immunology Research, 13 (9), 1453-1470. doi: 10.1158/2326-6066.cir-24-1233 |
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2025 Journal Article scRepertoire 2: Enhanced and efficient toolkit for single-cell immune profilingYang, Qile, Safina, Ksenia R., Nguyen, Kieu Diem Quynh, Tuong, Zewen Kelvin and Borcherding, Nicholas (2025). scRepertoire 2: Enhanced and efficient toolkit for single-cell immune profiling. PLOS Computational Biology, 21 (6) e1012760, 1-10. doi: 10.1371/journal.pcbi.1012760 |
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2025 Journal Article Temporal multi-omics analysis of COVID-19 in end-stage kidney diseaseStephenson, Emily, Macdonald-Dunlop, Erin, Dratva, Lisa M., Lindeboom, Rik G.H., Tuong, Zewen Kelvin, Tun, Win Min, Kretschmer, Lorenz, Buang, Norzawani B., Ballereau, Stephane, Cabantaus, Mia, Peñalver, Ana, Prigmore, Elena, Ferdinand, John R., Stewart, Benjamin J., Gisby, Jack, Malik, Talat H., Clarke, Candice L., Medjeral-Thomas, Nicholas, Prendecki, Maria, McAdoo, Stephen, Portet, Anais, Willicombe, Michelle, Sandhu, Eleanor, Pickering, Matthew C., Botto, Marina, Teichmann, Sarah A., Haniffa, Muzlifah, Clatworthy, Menna R., Thomas, David C. and Peters, James E. (2025). Temporal multi-omics analysis of COVID-19 in end-stage kidney disease. Cell Genomics, 5 (8) 100918. doi: 10.1016/j.xgen.2025.100918 |
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2025 Journal Article Low-dose interleukin-2 induces clonal expansion of BACH2-repressed effector regulatory T cells following acute coronary syndromeCase, A. G., O’Brien, J. W., Lu, Y., Charlier, F. T. W., Zhao, X., Weng, Y., Masters, L., Tuong, Z. K., Sriranjan, R., Cheriyan, J., Kemper, C., Clatworthy, M. R., Mallat, Z. and Zhao, T. X. (2025). Low-dose interleukin-2 induces clonal expansion of BACH2-repressed effector regulatory T cells following acute coronary syndrome. Nature Cardiovascular Research, 4 (6) 40, 727-739. doi: 10.1038/s44161-025-00652-y |
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2025 Journal Article GFI1-driven transcriptional and epigenetic programs maintain CD8+ T cell stemness and persistenceChaudhry, M. Zeeshan, Chen, Evelyn, Man, Hiu On, Jones, Aneesha, Denman, Renae, Yu, Huiyang, Huang, Qiutong, Ilich, Adrian, Schreuder, Jaring, Navarro, Severine, Tuong, Zewen K. and Belz, Gabrielle T. (2025). GFI1-driven transcriptional and epigenetic programs maintain CD8+ T cell stemness and persistence. Nature Immunology, 26 (6) 1418, 894-907. doi: 10.1038/s41590-025-02151-5 |
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2025 Journal Article Data standards for single‐cell RNA‐sequencing of paediatric cancerXu, Xiaohan, Saxon, John, Soon, Megan Sioe Fei, Lee, Colin Y. C. and Tuong, Zewen Kelvin (2025). Data standards for single‐cell RNA‐sequencing of paediatric cancer. Clinical & Translational Immunology, 14 (5) e70033, e70033-5. doi: 10.1002/cti2.70033 |
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2025 Journal Article CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics dataTroulé, Kevin, Petryszak, Robert, Cakir, Batuhan, Cranley, James, Harasty, Alicia, Prete, Martin, Tuong, Zewen Kelvin, Teichmann, Sarah A., Garcia-Alonso, Luz and Vento-Tormo, Roser (2025). CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data. Nature Protocols, 20 (12), 3412-3440. doi: 10.1038/s41596-024-01137-1 |
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2025 Journal Article Temporal profiling of human lymphoid tissues reveals coordinated defense against viral challengeCoates, Matthew L., Richoz, Nathan, Tuong, Zewen K., Bowyer, Georgina S., Lee, Colin Y. C., Ferdinand, John R., Gillman, Eleanor, McClure, Mark, Dratva, Lisa, Teichmann, Sarah A., Jayne, David R., Di Marco Barros, Rafael, Stewart, Benjamin J. and Clatworthy, Menna R. (2025). Temporal profiling of human lymphoid tissues reveals coordinated defense against viral challenge. Nature Immunology, 26 (2) 838328, 215-229. doi: 10.1038/s41590-024-02064-9 |
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2025 Journal Article Enhancement of anti-sarcoma immunity by NK cells engineered with mRNA for expression of a EphA2-targeted CARLam, Pui Yeng, Omer, Natacha, Wong, Josh K. M., Tu, Cui, Alim, Louisa, Rossi, Gustavo R., Victorova, Maria, Tompkins, Hannah, Lin, Cheng-Yu, Mehdi, Ahmed M., Choo, Amos, Elliott, Melissa R., Coleborn, Elaina, Sun, Jane, Mercer, Timothy, Vittorio, Orazio, Dobson, Lachlan J., Mclellan, Alexander D., Brooks, Andrew, Tuong, Zewen Kelvin, Cheetham, Seth W., Nicholls, Wayne and Souza-Fonseca-Guimaraes, Fernando (2025). Enhancement of anti-sarcoma immunity by NK cells engineered with mRNA for expression of a EphA2-targeted CAR. Clinical and Translational Medicine, 15 (1) e70140, 1-21. doi: 10.1002/ctm2.70140 |
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2025 Journal Article dandelionR: single-cell immune repertoire trajectory analysis in RYu, Jiawei, Xu, Xiaohan, Borcherding, Nicholas and Tuong, Zewen Kelvin (2025). dandelionR: single-cell immune repertoire trajectory analysis in R. Computational and Structural Biotechnology Journal, 27, 2890-2897. doi: 10.1016/j.csbj.2025.06.047 |
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2024 Journal Article An organotypic atlas of human vascular cellsBarnett, Sam N., Cujba, Ana-Maria, Yang, Lu, Maceiras, Ana Raquel, Li, Shuang, Kedlian, Veronika, Pett, J. Patrick, Polanski, Krzysztof, Miranda, Antonio M. A., Xu, Chuan, Cranley, James, Kanemaru, Kazumasa, Lee, Michael, Mach, Lukas, Perera, Shani, Tudor, Catherine, Joseph, Philomeena D., Pritchard, Sophie, Toscano-Rivalta, Rebecca, Tuong, Kelvin, Bolt, Liam, Petryszak, Robert, Prete, Martin, Cakir, Batuhan, Huseynov, Alik, Sarropoulos, Ioannis, Chowdhury, Rasheda A., Elmentaite, Rasa, Madissoon, Elo ... Teichmann, Sarah A. (2024). An organotypic atlas of human vascular cells. Nature Medicine, 30 (12), 3468-3481. doi: 10.1038/s41591-024-03376-x |
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2024 Journal Article Computational estimation of clonal diversity in autoimmunityTuong, Zewen Kelvin, van der Merwe, Rohan, Canete, Pablo F and Roco, Jonathan A (2024). Computational estimation of clonal diversity in autoimmunity. Immunology and Cell Biology, 102 (8), 692-701. doi: 10.1111/imcb.12801 |
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2024 Journal Article Embracing computational immunologyCañete, Pablo F and Tuong, Zewen Kelvin (2024). Embracing computational immunology. Immunology & Cell Biology, 102 (8), 663-664. doi: 10.1111/imcb.12817 |
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2024 Journal Article Measuring single-cell immune clonality to track haematological cancersChoo, Amos and Tuong, Zewen Kelvin (2024). Measuring single-cell immune clonality to track haematological cancers. Clinical and Translational Medicine, 14 (8) e1780, e1780. doi: 10.1002/ctm2.1780 |
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2024 Journal Article TGF-β signalling limits effector function capacity of NK cell anti-tumour immunity in human bladder cancerWong, Joshua K. M., McCulloch, Timothy R., Alim, Louisa, Omer, Natacha, Mehdi, Ahmed M., Tuong, Zewen Kelvin, Bonfim-Melo, Alexis, Chung, Eric, Nicol, Alice, Simpson, Fiona, Rhee, Handoo, Rossi, Gustavo Rodrigues and Souza-Fonseca-Guimaraes, Fernando (2024). TGF-β signalling limits effector function capacity of NK cell anti-tumour immunity in human bladder cancer. EBioMedicine, 104 105176, 1-15. doi: 10.1016/j.ebiom.2024.105176 |
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2024 Journal Article Single-cell immune repertoire analysisIrac, Sergio E., Soon, Megan Sioe Fei, Borcherding, Nicholas and Tuong, Zewen Kelvin (2024). Single-cell immune repertoire analysis. Nature Methods, 21 (5), 777-792. doi: 10.1038/s41592-024-02243-4 |
