A conversation with Dr Rufus Daw about CellTypeAI. As single-cell datasets grow from thousands to hundreds of thousands of cells, accurate cell annotation is becoming a major bottleneck in biomedical research. In this episode, bioinformatician Rufus Daw discusses CellTypeAI, a new locally deployable AI framework that uses large language models to automate cell-type identification from single-cell RNA sequencing data. We explore how privacy-preserving AI tools, retrieval-augmented generation, and ensemble prompting can match or exceed conventional annotation approaches while keeping sensitive research data entirely in-house, and what this means for the future of AI-assisted immunology and systems biology. Further resources: Rufus H. Daw, Harry R. Deijnen, Magnus Rattray, John R. Grainger, ‘CellTypeAI: Automated cell identification for scRNA-seq using local generative-AI’, preprinted posted on bioRxiv March 05, 2026. https://doi.org/10.64898/2026.03.03.709253 [doi.org] Rufus Daw talk: LLMs in the Laboratory: practical tools for AI-assisted research. https://www.youtube.com/watch?v=I7AlwgYnu9c [youtube.com]
A conversation with Professor Sheena Cruickshank about the new MRC Centre of Research Excellence in Exposome Immunology. To mark World Immunology Day, we’re joined by Professor Sheena Cruickshank from the MRC Centre of Research Excellence in Exposome Immunology. Sheena and Paul discuss how environmental and lifestyle exposures, from pollution to microbiome and socioeconomic factors, shape immune responses across the life course and contribute to disease. They explore the Centre’s integrated three-pillar approach, combining large-scale population data, mechanistic studies, and human experimental medicine to link exposure to immune function. The conversation also covers interdisciplinary team science, patient and community involvement, and how the Centre is building datasets and infrastructure that can support future discovery. Finally, they discuss the implications of climate change, eco-immunology, and how this work could inform drug repurposing, target identification, and evidence-based policy. The MRC Centre of Research Excellence in Exposome Immunology is supported by the Medical Research Council Centre of Research Excellence in Exposome Immunology [grant number UKRI/MR/B000935/1]. Further reading: • Sheena M Cruickshank, Kathryn J Else, Iris Mair, Holly Shiels, Susanne Shultz, How (Eco)immunology can augment global EcoHealth programmes: opportunities, needs, and challenges, Discovery Immunology, Volume 3, Issue 1, 2024, kyae015, https://doi.org/10.1093/discim/kyae015 • Markel Vigo, Lamiece Hassan, William Vance, Caroline Jay, Andrew Brass, Sheena Cruickshank, Britain Breathing: using the experience sampling method to collect the seasonal allergy symptoms of a country, Journal of the American Medical Informatics Association, Volume 25, Issue 1, January 2018, Pages 88–92, https://doi.org/10.1093/jamia/ocx148 • Community consultation on health, air quality and active travel in Hulme and Ardwick: https://research.manchester.ac.uk/en/activities/community-consultation-on-health-air-quality-and-active-travel-in/ • Report of a case study in exploring barriers and developing solutions to encourage take up of active travel in Ardwick, Greater Manchester: https://research.manchester.ac.uk/en/activities/report-of-a-case-study-in-exploring-barriers-and-developing-solut/
A conversation with Professor Hashem Koohy about possibilities for use of AI in driving forward T cell research. In the first To Immunity and Beyond episode of 2026, Paul Klenerman speaks with systems biologist Hashem Koohy, whose career journey from pure mathematics to immunology offers a fresh lens on T cell research. Hashem describes how advances in genomics, data science, and AI led him to focus on one of immunology’s central challenges: understanding how T cells recognise their targets, a process critical to infections, cancer, and immunotherapy. The discussion explores why predicting T cell–antigen interactions remains difficult despite vast datasets and powerful AI tools. Hashem argues that progress requires more than better predictions—it demands clearer biological concepts, realistic expectations, and data designed to answer the right questions. He highlights the importance of cross-disciplinary collaboration and calls for AI to be used not just to generate results, but to reveal the underlying rules of immune recognition. Further reading: T Cell Recognition Community LinkedIn page: https://www.linkedin.com/groups/15319051/ Hudson, D., Fernandes, R.A., Basham, M. et al. Can we predict T cell specificity with digital biology and machine learning? Nat Rev Immunol 23, 511–521 (2023). https://doi.org/10.1038/s41577-023-00835-3 McMaster, B., Thorpe, C., Ogg, G. et al. Can AlphaFold’s breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity? Nat Methods 21, 766–776 (2024). https://doi.org/10.1038/s41592-024-02240-7 Hashem’s website: https://www.immunointelligence.co.uk/ ImmSilico: https://www.immsilico.com/
A conversation with Professor Andrew McMichael, Professor Tomáš Hanke, and Dr Fon Acho about current priorities in HIV treatment and prevention. In this episode of To Immunity and Beyond, we talk to HIV immunologist Professor Andrew McMichael, vaccinologist Professor Tomáš Hanke, and Dr Fon Acho, a Cameroonian doctor and Oxford MSc immunology graduate. We discuss the global burden of HIV, and the possibilities offered by current and future vaccines and treatments. We also explore challenges in research funding and the importance of community engagement in intervention uptake. Further reading: Chanda, Chama et al. ‘Safety and broad immunogenicity of HIVconsvX conserved mosaic candidate T-cell vaccines vectored by ChAdOx1 and MVA in HIV-CORE 006: a double-blind, randomised, placebo-controlled phase 1 trial in healthy adults living without HIV-1 in eastern and southern Africa’. The Lancet Microbe, Volume 6, Issue 6, 101041. https://doi.org/10.1016/j.lanmic.2024.101041 Haynes, Barton et al. ‘Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies.’ Nat Rev Immunol. 2023 Mar;23(3):142-158. https://doi.org/10.1038/s41577-022-00753-w
A conversation with Philip Goulder about the recent article ‘Sustained aviremia despite anti-retroviral therapy non-adherence in male children after in utero HIV transmission’. In this episode of To Immunity and Beyond, we discuss a prospective study of 284 children from KwaZulu-Natal, South Africa, who were treated very early with antiretroviral therapy (ART) after mother-to-child transmission of HIV. Unexpectedly, female fetuses were more susceptible to in utero transmission, but of 5 children identified who maintained undetectable levels of HIV despite unscheduled ART interruption, all were males. Distinct viruses were transmitted to males and females - females but not males being susceptible to type I interferon-resistant, low fitness viruses. These findings indicate the central role that early life innate immune sex differences play in HIV cure/remission in children. Full article: Bengu, N., Cromhout, G., Adland, E. et al. Sustained aviremia despite anti-retroviral therapy non-adherence in male children after in utero HIV transmission. Nat Med 30, 2796–2804 (2024). https://doi.org/10.1038/s41591-024-03105-4