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Dr Kelvin Tuong
Dr

Kelvin Tuong

Email: 
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+61 7 3069 7506

Overview

Background

Dr. Kelvin Tuong is a Senior Research Fellow/Group Leader at the Ian Frazer Centre for Children’s Immunotherapy Research (IFCCIR), Child Health Research Centre. He is interested in single-cell analysis of immune cells and harnessing adaptive immune receptors for understanding immune cell development and function in health and in cancer.

Dr. Tuong was born and raised in Singapore and moved to Brisbane, Australia, after completing national service in Singapore and obtaining a Diploma in Biomedical Laboratory Technology (Ngee Ann Polytechnic).

Dr. Tuong was originally trained as a molecular cell biologist and gradually transitioned into bioinformatics during his post-doctoral training. He has been very prolific for an early career researcher, having published >70 articles since 2013, with nearly a third of them as first/co-first or last author and has a stellar track record of pushing out highly collaborative work in prestigious journals including Nature, Cell, Science, Nature Medicine, Nature Biotechnology J Exp Med etc. He has the rare combination of having excellent laboratory and bioinformatics skill sets which provide him a strong command of both fundamental immunology and computational approaches.

Dr. Tuong completed his undergraduate Bachelor's degree in Biomedical science with Class I Honours, followed by his PhD in macrophage cell biology and endocrinology at UQ (Prof. Jenny Stow lab and Emiritus Prof. George Muscat lab, IMB, UQ). He then went on to a post-doc position with Emiritus Prof. Ian Frazer (co-inventor of the Gardasil cervical cancer vaccine, UQ Frazer Institute, Translational Research Institute) where he worked on HPV immunology, cervical cancer and skin cancer. In his time in the Frazer lab, he developed an interest in bioinformatics analyses as a means to tackle and understanding immunology problems in health and disease. He then moved to the UK and joined Prof. Menna Clatworthy's lab at the University of Cambridge and Dr. Sarah Teichmann's lab at the Wellcome Trust Sanger Institute. He has focused his interests on single-cell analyses of tissue immune cells, including T and B cells and their specific receptors (TCR/BCR). He has developed bespoke bioinformatics software, including one tailored for single-cell B Cell Receptor sequencing analysis, Dandelion, which he used in one of the largest combined single-cell transcriptomic, surface proteomic and TCR/BCR sequencing dataset in the world, published in Nature Medicine, and more recently in Nature Biotechnology where we introduced a TCR-based pseudotime trajectory analysis method.

Dr. Tuong is now leading the Computational Immunology group at the IFCCIR and his lab is focused on investigating how pediatric immunity is perturbed during cancer at the cellular level and how this information can be used for creating novel warning systems for children with cancer. For potential students/post-docs/trainees interested in joining the team, please contact Dr. Tuong at z.tuong@uq.edu.au.

Availability

Dr Kelvin Tuong is:
Available for supervision
Media expert

Qualifications

  • Doctor of Philosophy, The University of Queensland

Research interests

  • Deep learning of immune repertoires

    T cells and B cells play a critical role in recognizing and eliminating cancer cells through their highly specific adaptive immune receptors. Our vision is to harness the power of these receptors to enable early cancer detection and real-time disease monitoring, particularly in children. These receptors act as natural "time-keepers" of the immune system’s engagement with tumors, capturing a molecular history of the immune response as cancer progresses. Our research focuses on understanding the properties that make these immune cells effective in the context of childhood cancers. Using high-resolution single-cell gene expression profiling, we aim to uncover how T and B cells behave in pediatric patients and how their receptors evolve during disease and treatment. To achieve this, we are developing new computational tools and algorithms designed to analyze immune receptor sequences and their expression patterns. Using deep learning, we aim to identify receptor signatures that are specific to cancer, and use these patterns to predict therapeutic responses and monitor disease progression in children with blood cancers. This approach offers a path toward highly sensitive tool for early detection and long-term monitoring of pediatric immunity and cancer.

  • Single-cell prediction of cancer cells

    We’re interested in using deep learning to make sense of single-cell RNA sequencing (scRNA-seq) data, especially to uncover copy number variations (CNVs) that are often hidden in the noise of single-cell measurements. CNVs are a key feature in many cancers, but detecting them reliably at the single-cell level is still a challenge. Rather than relying on traditional approaches that often struggle with the sparse and noisy nature of scRNA-seq, we’re exploring how deep learning models can be trained to recognize subtle patterns in gene expression that point to underlying genomic alterations. Our goal is to build tools that can separate cancer cells from normal cells based on these inferred CNVs, helping us better understand tumor composition, heterogeneity, and evolution. This work has implications not just for identifying malignant cells, but also for tracking how tumors change over time or respond to treatment. We’re also interested in combining this with other data types—like epigenomic or spatial information—to build a more complete picture of what’s happening inside tumors at the single-cell level. We approach this work from both a computational and biological perspective, and we’re motivated by the potential for these methods to contribute to more personalized and effective cancer diagnostics.

  • Paediatric Immune Cell Atlas

    We’re building the largest immune cell atlas of Australian children to date, profiling blood samples from over 1,000 healthy and disease-affected children using single-cell RNA sequencing (scRNA-seq). Our goal is to create a high-resolution map of the developing immune system in early life—a period when immune function is still maturing and highly dynamic. Children’s immune systems differ significantly from those of adults, yet they remain understudied in immunology. By analyzing immune cell populations at single-cell resolution, we’re uncovering how these cells change with age, how they respond to infections or immune-related diseases, and how early-life immunity is shaped by both genetic and environmental factors. To fully capture the complexity of the pediatric immune system, we’re incorporating machine learning and deep learning approaches to uncover subtle patterns and rare cell states across this large and diverse dataset. We’re also applying integrative methods to link scRNA-seq data with immune repertoire sequencing, enabling us to explore how T and B cell clonality and diversity contribute to immune development and disease. This work has important implications for understanding pediatric diseases, identifying early biomarkers of immune dysregulation, and designing age-specific diagnostics and therapies. In addition to its clinical relevance, the atlas will serve as a foundational reference for researchers working in pediatric immunology and systems biology.

Works

Search Professor Kelvin Tuong’s works on UQ eSpace

89 works between 2013 and 2025

1 - 20 of 89 works

2025

Journal Article

CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data

Troulé, 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

CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data

2025

Journal Article

Temporal profiling of human lymphoid tissues reveals coordinated defense against viral challenge

Coates, 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

Temporal profiling of human lymphoid tissues reveals coordinated defense against viral challenge

2025

Journal Article

Enhancement of anti-sarcoma immunity by NK cells engineered with mRNA for expression of a EphA2-targeted CAR

Lam, 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

Enhancement of anti-sarcoma immunity by NK cells engineered with mRNA for expression of a EphA2-targeted CAR

2024

Journal Article

An organotypic atlas of human vascular cells

Barnett, 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), 1-1. doi: 10.1038/s41591-024-03376-x

An organotypic atlas of human vascular cells

2024

Conference Publication

Early human lung immune cell development and its role in epithelial cell fate

Barnes, Josephine, Yoshida, Masahiro, He, Peng, Worlock, Kaylee, Lindeboom, Rik, Suo, Chenqu, Pett, J. Patrick, Wilbrey-Clark, Anna, Dann, Emma, Mamanova, Lira, Richardson, Laura, Polanski, Krzysztof, Pennycuick, Adam, Allen-Hytinnen, Jessica, Herczeg, Iván, Arzili, Romina, Hynds, Robert, Teixeira, Vitor, Haniffa, Muzlifah, Lim, Kyungtae, Sun, Dawei, Rawlins, Emma, Oliver, Amanda, Lyons, Paul, Marioni, John, Ruhrberg, Christiana, Tuong, Zewen, Clatworthy, Menna, Reading, James ... Nikolić, Marko (2024). Early human lung immune cell development and its role in epithelial cell fate. SHEFFIELD: European Respiratory Society. doi: 10.1183/13993003.congress-2024.oa1893

Early human lung immune cell development and its role in epithelial cell fate

2024

Conference Publication

Self or Bacteria-reactive Th17 Expand from Conventional and Regulatory T Cells in Parabacteroides Goldsteinii Gnotobiotic Arthritic SKG Mice, in Context of Interferon-driven Synovial Inflammatory Macrophages and Reduced Bacterial Immune Regulation

Cai, Benjamin, Tuong, Zewen Kelvin, Morrison, Mark, Bergot, Anne-Sophie and Thomas, Ranjeny (2024). Self or Bacteria-reactive Th17 Expand from Conventional and Regulatory T Cells in Parabacteroides Goldsteinii Gnotobiotic Arthritic SKG Mice, in Context of Interferon-driven Synovial Inflammatory Macrophages and Reduced Bacterial Immune Regulation. ACR Convergence 2024, Washington, DC United States, 15–19 November 2024. Hoboken, NJ United States: John Wiley & Sons.

Self or Bacteria-reactive Th17 Expand from Conventional and Regulatory T Cells in Parabacteroides Goldsteinii Gnotobiotic Arthritic SKG Mice, in Context of Interferon-driven Synovial Inflammatory Macrophages and Reduced Bacterial Immune Regulation

2024

Journal Article

Computational estimation of clonal diversity in autoimmunity

Tuong, 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

Computational estimation of clonal diversity in autoimmunity

2024

Journal Article

Embracing computational immunology

Cañete, Pablo F and Tuong, Zewen Kelvin (2024). Embracing computational immunology. Immunology & Cell Biology, 102 (8), 663-664. doi: 10.1111/imcb.12817

Embracing computational immunology

2024

Conference Publication

The effect of low-dose interleukin-2 on the T cell receptor landscape in patients with acute myocardial infarction

Case, Ayden, O'Brien, James, Sriranjan, Rochelle, Tuong, Zewen Kelvin, Cheriyan, Joseph, Clatworthy, Menna, Mallat, Ziad and Zhao, Tian (2024). The effect of low-dose interleukin-2 on the T cell receptor landscape in patients with acute myocardial infarction. EAS Congress 2024, Lyon, France, 26-29 May 2024. Elsevier. doi: 10.1016/j.atherosclerosis.2024.118476

The effect of low-dose interleukin-2 on the T cell receptor landscape in patients with acute myocardial infarction

2024

Conference Publication

LOW DOSE INTERLEUKIN 2 EXPANDS PLASMABLASTS WITH A REGULATORY B CELL PHENOTYPE POST-MT

O'Brien, James, Case, Ayden, Sriranjan, Rochelle, Tuong, Zewen Kelvin, Cheriyan, Joseph, Clatworthy, Menna, Mallat, Ziad and Zhao, Tian (2024). LOW DOSE INTERLEUKIN 2 EXPANDS PLASMABLASTS WITH A REGULATORY B CELL PHENOTYPE POST-MT. 92nd Congress of the European-Atherosclerosis-Society (EAS), Lyon France, May 26-29, 2024. CLARE: ELSEVIER IRELAND LTD.

LOW DOSE INTERLEUKIN 2 EXPANDS PLASMABLASTS WITH A REGULATORY B CELL PHENOTYPE POST-MT

2024

Conference Publication

Low dose interleukin 2 expands plasmablasts with a regulatory b cell phenotype post-MI

O'Brien, James, Case, Ayden, Sriranjan, Rochelle, Tuong, Zewen Kelvin, Cheriyan, Joseph, Clatworthy, Menna, Mallat, Ziad and Zhao, Tian (2024). Low dose interleukin 2 expands plasmablasts with a regulatory b cell phenotype post-MI. EAS Congress 2024, Lyon, France, 26-29 May 2024. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.atherosclerosis.2024.118287

Low dose interleukin 2 expands plasmablasts with a regulatory b cell phenotype post-MI

2024

Journal Article

Measuring single-cell immune clonality to track haematological cancers

Choo, 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

Measuring single-cell immune clonality to track haematological cancers

2024

Conference Publication

THE EFFECT OF LOW-DOSE INTERLEUKIN-2 ON THE T CELL RECEPTOR LANDSCAPE IN PATIENTS WITH ACUTE MYOCARDIAL INFARCTION

Case, Ayden, O'Brien, James, Sriranjan, Rochelle, Tuong, Zewen Kelvin, Cheriyan, Joseph, Clatworthy, Menna, Mallat, Ziad and Zhao, Tian (2024). THE EFFECT OF LOW-DOSE INTERLEUKIN-2 ON THE T CELL RECEPTOR LANDSCAPE IN PATIENTS WITH ACUTE MYOCARDIAL INFARCTION. 92nd Congress of the European-Atherosclerosis-Society (EAS), Lyon France, May 26-29, 2024. CLARE: ELSEVIER IRELAND LTD.

THE EFFECT OF LOW-DOSE INTERLEUKIN-2 ON THE T CELL RECEPTOR LANDSCAPE IN PATIENTS WITH ACUTE MYOCARDIAL INFARCTION

2024

Journal Article

TGF-β signalling limits effector function capacity of NK cell anti-tumour immunity in human bladder cancer

Wong, 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. doi: 10.1016/j.ebiom.2024.105176

TGF-β signalling limits effector function capacity of NK cell anti-tumour immunity in human bladder cancer

2024

Conference Publication

Early Human Lung Immune Cell Development and Its Role in Epithelial Cell Fate

Nikolic, M., Barnes, J. L., Yoshida, M., He, P., Worlock, K. B., Lindeboom, R. G. H., Suo, C., Pett, J. P., Wilbrey-Clark, A., Dann, E., Mamanova, L., Richardson, L., Polanski, K., Pennycuick, A., Allen-Hyttinen, J., Herczeg, I., Arzili, R., Hynds, R. E., Teixeira, V. H., Haniffa, M., Lim, K., Sun, D., Rawlins, E. L., Oliver, A., Lyons, P. A., Marioni, J. C., Ruhrberg, C., Tuong, Z. K., Clatworthy, M. R. ... Meyer, K. B. (2024). Early Human Lung Immune Cell Development and Its Role in Epithelial Cell Fate. International Conference of the American-Thoracic-Society (ATS), San Diego Ca, May 17-22, 2024. NEW YORK: AMER THORACIC SOC.

Early Human Lung Immune Cell Development and Its Role in Epithelial Cell Fate

2024

Conference Publication

Early Human Lung Immune Cell Development and Its Role in Epithelial Cell Fate

Nikolic, M., Barnes, J.L., Yoshida, M., He, P., Worlock, K.B., Lindeboom, R.G.H., Suo, C., Pett, J.P., Wilbrey-Clark, A., Dann, E., Mamanova, L., Richardson, L., Polanski, K., Pennycuick, A., Allen-Hyttinen, J., Herczeg, I., Arzili, R., Hynds, R.E., Teixeira, V.H., Haniffa, M., Lim, K., Sun, D., Rawlins, E.L., Oliver, A., Lyons, P.A., Marioni, J.C., Ruhrberg, C., Tuong, Z.K., Clatworthy, M.R. ... Meyer, K.B. (2024). Early Human Lung Immune Cell Development and Its Role in Epithelial Cell Fate. American Thoracic Society 2024 International Conference, San Diego, CA United States, 17-22 May 2024. New York, NY United States: American Thoracic Society. doi: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a7456

Early Human Lung Immune Cell Development and Its Role in Epithelial Cell Fate

2024

Journal Article

Single-cell immune repertoire analysis

Irac, 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

Single-cell immune repertoire analysis

2024

Journal Article

Venous-plexus-associated lymphoid hubs support meningeal humoral immunity

Fitzpatrick, 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

Venous-plexus-associated lymphoid hubs support meningeal humoral immunity

2024

Journal Article

Rapid functional impairment of natural killer cells following tumor entry limits anti-tumor immunity

Dean, 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

Rapid functional impairment of natural killer cells following tumor entry limits anti-tumor immunity

2024

Journal Article

Tumour-retained activated CCR7+ dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activity

Lee, 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

Tumour-retained activated CCR7+ dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activity

Funding

Current funding

  • 2024 - 2029
    Paediatric Immune Cell Atlas for Immunotherapy Innovation (PICACHIU)
    MRFF - National Critical Infrastructure Initiative
    Open grant
  • 2024 - 2026
    A novel approach to engineer personalized vaccines to prevent cutaneous Squamous Cell Carcinoma.
    TRI Leading Innovations through New Collaborations Scheme
    Open grant
  • 2024 - 2026
    Deciphering interleukin-21 agonism in boosting CD8+ T cell mediated anti-tumour immunity to engineer next-generation immunotherapies
    Cure Cancer Early Career Research Grants
    Open grant

Past funding

  • 2017 - 2018
    Is there really a viral cause for skin cancer?
    Australasian College of Dermatologists Scientific Research Fund
    Open grant
  • 2017 - 2019
    Approaching antigen-presenting cell immunotherapy for cervical cancers using single-cell transcriptomics
    Advance Queensland Research Fellowships
    Open grant

Supervision

Availability

Dr Kelvin Tuong is:
Available for supervision

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Available projects

  • Developing single-cell analysis methods harnessing adaptive immune receptors

    The direct linkage of adaptive immune receptor repertoire with cellular phenotypes from single-cell sequencing technology has proven to be a powerful tool in understanding lymphocyte development and function in healthy and disease contexts. Multi-omics analysis leverages data from different modalities e.g. transcriptomics, epigenetics, proteomics. Recent advances has successfully integrated the data modalities to study cellular biology at an unprecedented resolution. However, unlike the other data modalities, which are largely continuous data, single-cell adaptive immune receptor sequencing (scVDJ-seq) data are a mixture of categorical and continuous data which poses additional challenges for integration. It consists of annotations of variable (V), diversity (D) and joining (J) genes, which are selected and recombined during B/T-cell development. The technology to profile this at the single cell level with paired gene expression data is relatively new. I have led the development of Dandelion, a scVDJ-seq software framework which has been used to deeply profile single-cell lymphocyte biology and I aim to expand on the its capabilities for immunology research.

  • Developing single-cell analysis methods harnessing adaptive immune receptors

    The direct linkage of adaptive immune receptor repertoire with cellular phenotypes from single-cell sequencing technology has proven to be a powerful tool in understanding lymphocyte development and function in healthy and disease contexts. Multi-omics analysis leverages data from different modalities e.g. transcriptomics, epigenetics, proteomics. Recent advances has successfully integrated the data modalities to study cellular biology at an unprecedented resolution. However, unlike the other data modalities, which are largely continuous data, single-cell adaptive immune receptor sequencing (scVDJ-seq) data are a mixture of categorical and continuous data which poses additional challenges for integration. It consists of annotations of variable (V), diversity (D) and joining (J) genes, which are selected and recombined during B/T-cell development. The technology to profile this at the single cell level with paired gene expression data is relatively new. I have led the development of Dandelion, a scVDJ-seq software framework which has been used to deeply profile single-cell lymphocyte biology and I aim to expand on the its capabilities for immunology research.

  • Building Australia’s Largest Single-Cell Atlas of the Pediatric Immune System

    The immune system in early life undergoes rapid and unique developmental changes that are not well captured by adult immune profiling studies. This project aims to generate the most comprehensive single-cell atlas of the pediatric immune system in Australia, based on over 1,000 blood samples from both healthy children and those affected by various diseases, including immune disorders and infections.

    We use single-cell RNA sequencing (scRNA-seq) to capture the diversity of immune cells in unprecedented detail, allowing us to map how these cells evolve with age and in response to disease. Importantly, we are integrating scRNA-seq with adaptive immune receptor sequencing (scVDJ-seq) and clinical metadata to uncover how immune repertoires develop and function across different pediatric cohorts.

    To analyze this complex dataset, we are developing advanced machine learning and deep learning frameworks capable of identifying age- and disease-specific immune states. We are also applying integrative computational approaches to connect transcriptional states with immune clonotypes and repertoire diversity. This atlas will serve as a key resource for pediatric immunology, providing foundational insights that can inform early diagnostics, vaccine strategies, and targeted therapies for children.

  • Deep Learning Approaches for Inferring Copy Number Variation from Single-Cell Transcriptomics in Cancer

    Copy number variations (CNVs) are a hallmark of cancer, but detecting them accurately at the single-cell level remains a major challenge due to the noisy and sparse nature of single-cell RNA-seq (scRNA-seq) data. This project focuses on the development of deep learning models capable of inferring CNVs directly from transcriptomic profiles, with the ultimate goal of identifying cancer cells within heterogeneous tissues.

    By applying neural network architectures tailored to single-cell data, we aim to model the underlying gene dosage effects reflected in gene expression patterns. Our models will be trained to distinguish malignant from normal cells and to identify patterns of genomic instability across tumor subclones. These methods will allow us to reconstruct the evolutionary dynamics of tumors and better understand the relationship between transcriptomic signatures and chromosomal alterations.

    This work has direct applications in cancer diagnostics, especially in improving the resolution of tumor profiling for early detection and minimal residual disease monitoring. We also aim to make these methods publicly available as open-source tools to support the broader community studying tumor heterogeneity through single-cell approaches.

  • Deep Learning of T-Cell Receptor Signatures for Monitoring Pediatric Cancer Immunity

    T cells play a crucial role in recognizing and attacking cancer cells through their highly specific T-cell receptors (TCRs). These receptors carry detailed information about the immune system’s engagement with tumors, offering a rich but complex source of data for understanding immune responses in childhood cancers. This project focuses on developing deep learning models to decode TCR sequences, with the aim of identifying cancer-specific immune responses and predicting therapeutic outcomes in pediatric patients.

    Using immune receptor sequencing data, we are characterizing the clonal landscape of T cells in children with cancers. By integrating this data, we aim to learn predictive features of TCR sequences associated with anti-tumor activity, treatment response, and disease progression. These models will be trained to recognize subtle sequence motifs, clonal expansions, and phenotype-receptor relationships that are often missed by conventional approaches.

    A central goal of this project is to develop tools that allow for immune-based monitoring of pediatric cancers over time. By identifying cancer-associated TCRs, we aim to build sensitive and specific assays for early detection, residual disease tracking, and treatment monitoring. Ultimately, this work will help uncover how the developing immune system interacts with cancer and contribute to more personalized, immune-informed approaches to treating childhood cancers.

Supervision history

Current supervision

  • Doctor Philosophy

    Advancing Paediatric Cancer Immunotherapy with Antigen Receptors and Artificial Intelligence

    Principal Advisor

    Other advisors: Dr Yang Yang

  • Doctor Philosophy

    A Comprehensive Paediatric Immune Cell Atlas for Children's Immunotherapy Innovation

    Principal Advisor

    Other advisors: Dr Quan Nguyen, Professor Di Yu

  • Doctor Philosophy

    Harnessing adaptive immune receptors to monitor paediatric immunity in cancer and enhance neoantigen vaccine pipeline

    Principal Advisor

    Other advisors: Professor Di Yu, Dr Jazmina Gonzalez Cruz

  • Doctor Philosophy

    Decipher interleukin-21 signaling and engineer next generation immunotherapies

    Associate Advisor

    Other advisors: Dr Zhian Chen

  • Doctor Philosophy

    Development of novel vaccines for cancer immunotherapy

    Associate Advisor

    Other advisors: Professor Maher Gandhi, Honorary Professor Kristen Radford

  • Doctor Philosophy

    Investigate T cell specificity and function in immune responses by systems immunology

    Associate Advisor

    Other advisors: Dr Yang Yang, Professor Di Yu

Completed supervision

Media

Enquiries

Contact Dr Kelvin Tuong directly for media enquiries about:

  • Cancer
  • Genomics
  • Immunology

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