Charlie Lees Research Group: Edinburgh IBD

Professor of Gastroenterology, University of Edinburgh; Honorary Consultant Gastroenterologist, NHS Lothian (Edinburgh IBD Unit); UKRI Future Leaders Fellow; Adjunct Professor, Aalborg University (PREDICT Center).

Charlie trained in London (UCL, MBBS 2000), moved to Edinburgh in 2001 for medical and gastroenterology training, completed a PhD in IBD genetics in 2009, and has been an NHS consultant since 2009 and a UKRI Future Leaders Fellow since 2019. He maintains a large, complex IBD clinic while leading a translational research programme focused on prediction, prevention and practical care impact.

Inflammatory bowel disease care is still too often reactive: patients flare, inflammation accumulates and important treatment decisions can come late. Edinburgh IBD is building a different model — one that sees disease earlier, understands where it is going and turns that insight into better decisions with patients.

We are a fully integrated IBD research programme at the University of Edinburgh’s Institute of Genetics and Cancer, working alongside the NHS Lothian IBD clinical service. Our team brings together clinical research, data science, laboratory discovery, clinical trials and patient partnership to build proactive, predictive and whole-person IBD medicine.

Our work integrates longitudinal biomarkers and electronic health record data with prospective cohort science, multi-omics, digital monitoring and machine learning. The practical end-point is SENTINEL: an AI-enabled, clinician-supervised platform for proactive monitoring and clinical decision support in routine IBD care.

Edinburgh is a uniquely powerful place to build this model. The Institute of Genetics and Cancer brings world-class data science, statistical genomics and translational discovery. NHS Lothian brings a large, deeply characterised IBD population and a clinical service embedded beside the research team. Together, they let us move from signal, to model, to trial, to implementation.

The programme builds on more than two decades of Edinburgh IBD genetics, epidemiology and real-world data leadership. The Lothian IBD Registry includes around 10,000 patients and more than 20 years of longitudinal clinical data, now being integrated with DataLoch to support real-time risk stratification and action prompts in routine care.

• Mapping disease in motion — using longitudinal faecal calprotectin, CRP and multimodal biomarkers to understand inflammatory burden, trajectories and risk over time.
• Proactive intelligence and observability — defining how to observe an IBD population across clinical states, and building the algorithmic layer that helps clinical teams see what needs attention sooner.
• Whole-person, whole-course care — diet, lifestyle, microbiome, genetics, comorbidity, ageing, women’s health and quality of life across the full arc of disease, anchored in deep phenotyping through PREdiCCt and linked data.
• Therapy positioning and outcomes — comparative effectiveness, sequencing, treatment persistence and outcomes of advanced therapies using real-world data and partner-centre collaborations.
• Patient partnership and public involvement — patients helping to shape priorities, tools, trial design and how proactive monitoring should work in practice.

• PREdiCCt — UK-wide prospective cohort of 2,629 participants across 49 sites, with deep dietary, lifestyle, microbiome and biomarker phenotyping.
• Lothian IBD Registry (LIBDR) — comprehensive longitudinal cohort of approximately 10,000 patients with more than 20 years of data, integrated with DataLoch.
• SENTINEL — flagship AI-enabled, clinician-supervised clinical decision-support and proactive-monitoring platform for IBD, built to transform care in Lothian and to scale.

The group delivers an active programme of commercial and non-commercial IBD trials — including new molecules, combinations of advanced therapies, head-to-head studies, strategy trials and intestinal ultrasound studies — giving local patients access to tomorrow’s care and keeping the research programme close to frontline therapeutic decision-making.

• Currently recruiting or in set-up: GONDOMAR, UK IBD BioResource, OPEN-IBD, IBD-RESPONSE, PROFILE, TARGET, VICTRIVA, VECTORS and ICONIC-UC.

• Biomedical Data Science — with Dr Catalina A. Vallejos (Vallejos Group, MRC HGU / IGC).
• PREDICT Center, Aalborg University, Denmark — with Professor Tine Jess; Charlie is Adjunct Professor at PREDICT.
• National and international consortia — UK IBD BioResource; IIBDGC; PANTS; GIVES-21; and the Lancet Commission on Global IBD (2024–2026).

• We welcome data science PhD students and post-doctoral researchers, clinical research fellows and visiting researchers. Projects span dynamic risk prediction, longitudinal modelling, comparative effectiveness, clinical trials methodology, translational discovery and the implementation of proactive IBD care. Please contact Charlie to discuss opportunities.

• Global evolution of inflammatory bowel disease across the epidemiologic stages. Nature (2025).
• PREdiCCt: baseline faecal calprotectin and environmental factors predict flare in IBD — a UK-wide prospective cohort (2,629 participants, 49 sites). Gut (2026).
• HLA-DRB1*01:03 in inflammatory bowel disease: a genotype–phenotype association study. Lancet Gastroenterology & Hepatology (2026).
• Twenty-year trends in colectomy and advanced therapy use in Lothian. Alimentary Pharmacology & Therapeutics (2025).
• Inflammatory bowel disease and more than 1,500 comorbidities: a disease-wide phenome association study. American Journal of Gastroenterology (2025).
• Large-scale clustering of longitudinal faecal calprotectin and C-reactive protein profiles in IBD. Clinical Gastroenterology and Hepatology (2025).
• HLA-DQA1*05 carriage and immunogenicity to anti-TNF therapy in Crohn’s disease (PANTS). Gastroenterology (2020).
• Disease monitoring in IBD: state of the art. Gastroenterology (2022).
• Comparative effectiveness of tofacitinib and vedolizumab in ulcerative colitis. Journal of Crohn’s and Colitis (2024).

A full publication list is available via PubMed: lees cw - Search Results - PubMed

UKRI Future Leaders Fellowship (2019–2027); Open Targets “Open IBD” (2025–2028); PREdiCCt funders (CSO Scotland, Cure Crohn’s & Colitis, Crohn’s & Colitis in Childhood, Lothian Health Endowment Fund); NHS Lothian Charity.

Help us move IBD care from reacting to flares to anticipating them.

Philanthropy accelerates the work that turns promising science into practical care: research nurse time, patient involvement, clinical research fellowships, early data-science build and the bridge from model to tool in the clinic. To support Edinburgh IBD, see our Support our research page or contact the Institute’s Development team.

We maintain open-source analytical pipelines. Access to the Lothian IBD Registry is via the NHS Lothian / DataLoch governance process.