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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, e1012760-6. doi: 10.1371/journal.pcbi.1012760 |
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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 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 100918, 100918. doi: 10.1016/j.xgen.2025.100918 |
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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 6619, 1-29. 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 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 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 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, 105176. 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 |
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2024 Journal Article Venous-plexus-associated lymphoid hubs support meningeal humoral immunityFitzpatrick, Zachary, Ghabdan Zanluqui, Nagela, Rosenblum, Jared S., Tuong, Zewen Kelvin, Lee, Colin Y. C., Chandrashekhar, Vikram, Negro-Demontel, Maria Luciana, Stewart, Andrew P., Posner, David A., Buckley, Monica, Allinson, Kieren S. J., Mastorakos, Panagiotis, Chittiboina, Prashant, Maric, Dragan, Donahue, Danielle, Helmy, Adel, Tajsic, Tamara, Ferdinand, John R., Portet, Anais, Peñalver, Ana, Gillman, Eleanor, Zhuang, Zhengping, Clatworthy, Menna R. and McGavern, Dorian B. (2024). Venous-plexus-associated lymphoid hubs support meningeal humoral immunity. Nature, 628 (8008) s41586-024-07202-9, 612-619. doi: 10.1038/s41586-024-07202-9 |
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2024 Journal Article Rapid functional impairment of natural killer cells following tumor entry limits anti-tumor immunityDean, Isaac, Lee, Colin Y. C., Tuong, Zewen K., Li, Zhi, Tibbitt, Christopher A., Willis, Claire, Gaspal, Fabrina, Kennedy, Bethany C., Matei-Rascu, Veronika, Fiancette, Rémi, Nordenvall, Caroline, Lindforss, Ulrik, Baker, Syed Murtuza, Stockmann, Christian, Sexl, Veronika, Hammond, Scott A., Dovedi, Simon J., Mjösberg, Jenny, Hepworth, Matthew R., Carlesso, Gianluca, Clatworthy, Menna R. and Withers, David R. (2024). Rapid functional impairment of natural killer cells following tumor entry limits anti-tumor immunity. Nature Communications, 15 (1) 683, 1-18. doi: 10.1038/s41467-024-44789-z |
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2024 Journal Article Tumour-retained activated CCR7+ dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activityLee, Colin Y. C., Kennedy, Bethany C., Richoz, Nathan, Dean, Isaac, Tuong, Zewen K., Gaspal, Fabrina, Li, Zhi, Willis, Claire, Hasegawa, Tetsuo, Whiteside, Sarah K., Posner, David A., Carlesso, Gianluca, Hammond, Scott A., Dovedi, Simon J., Roychoudhuri, Rahul, Withers, David R. and Clatworthy, Menna R. (2024). Tumour-retained activated CCR7+ dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activity. Nature Communications, 15 (1) 682, 1-18. doi: 10.1038/s41467-024-44787-1 |
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2023 Journal Article Early human lung immune cell development and its role in epithelial cell fateBarnes, Josephine L., Yoshida, Masahiro, He, Peng, Worlock, Kaylee B., Lindeboom, Rik G. H., Suo, Chenqu, Pett, J. Patrick, Wilbrey-Clark, Anna, Dann, Emma, Mamanova, Lira, Richardson, Laura, Polanski, Krzysztof, Pennycuick, Adam, Allen-Hyttinen, Jessica, Herczeg, Iván T., Arzili, Romina, Hynds, Robert E., Teixeira, Vitor H., Haniffa, Muzlifah, Lim, Kyungtae, Sun, Dawei, Rawlins, Emma L., Oliver, Amanda J., Lyons, Paul A., Marioni, John C., Ruhrberg, Christiana, Tuong, Zewen Kelvin, Clatworthy, Menna R., Reading, James L. ... Nikolić, Marko Z. (2023). Early human lung immune cell development and its role in epithelial cell fate. Science Immunology, 8 (90) eadf9988, 1-18. doi: 10.1126/sciimmunol.adf9988 |
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2023 Journal Article Tissue-resident B cells orchestrate macrophage polarisation and functionSuchanek, Ondrej, Ferdinand, John R., Tuong, Zewen K., Wijeyesinghe, Sathi, Chandra, Anita, Clauder, Ann-Katrin, Almeida, Larissa N., Clare, Simon, Harcourt, Katherine, Ward, Christopher J., Bashford-Rogers, Rachael, Lawley, Trevor, Manz, Rudolf A., Okkenhaug, Klaus, Masopust, David and Clatworthy, Menna R. (2023). Tissue-resident B cells orchestrate macrophage polarisation and function. Nature Communications, 14 (1) 7081, 1-20. doi: 10.1038/s41467-023-42625-4 |
