2026 Antanaviciute Group (iCase): The Gut Chronicle project: Exploring intestinal epithelial and immune function across the lifespan

Dr Michael FitzPatrick, Dr A Antanaviciute

Friday, June 12, 2026

Funded PhD Project (UK Students Only)

About the Project

We have a fantastic doctoral training opportunity in human immunology, multiomics approaches, and computational biology, due to start in October 2026.

Funding for this project covers stipend and fees for students with a home fee status only.

The small intestine is the largest epithelial surface in contact with the external environment, and is not only the key site of nutrient absorption and endocrine function, but a highly active immune organ which shapes immune responses throughout the body. The effect of age, disease, and the exposome on small intestinal absorbative, metabolic, and immune function has not been well-studied. Little is understood about how the broad and complex functions of the small intestine, including digestion and the expression/activity of digestive enzymes produced by the brush border membrane, alter, either during the human lifespan, with a range of environmental factors, or in human disease.

This project seeks to understand how human small intestinal function changes with age. We hypothesise that there are broad changes in digestive, absorptive, metabolic, and immunological pathways in the small intestine which occur during growth, development and aging in healthy human subjects.

The Gut Chronicle project will generate a richly annotated, integrated multi-omic (bulk, single-cell and spatial transcriptomics, proteomics and epigenetics) chronicle of the small intestinal epithelium across the lifespan. This DPhil project will establish a foundation for understanding age-associated variation in intestinal function and its relevance to health, disorders, and disease.

The DPhil student will work at the interface of computational biology, gastroenterology and molecular medicine, using state-of-the-art transcriptomic, proteomic and epigenomic profiling techniques to map how intestinal epithelial and immune functions evolve across the human lifespan. This project offers an exceptional opportunity to integrate advanced bioinformatics, wet-lab and translational research within a multidisciplinary academic-industry environment. The student will gain experience in both experimental and computational methods, contributing to foundational datasets that will inform future studies on intestinal health, aging and enteropathies.

This project will be supported by Dr Mourabit from AMYRA biosciences. The successful candidate will have the opportunity to join the Enteropathy Consortium, which brings together other AMYRA-funded/co-funded international PhD students to support innovation and collaboration. There may be opportunities to collaborate and travel to Switzerland or Finland as part of the consortium.

Interested candidates should contact the supervisors for an informal discussion (michael.fitzpatrick@ndm.ox.ac.uk and agne.antanaviciute@rdm.ox.ac.uk).

Further information about the groups’ research can be found here:

• Antanaviciute Group
• Oxford Coeliac Network
• Michael FitzPatrick

Training Opportunities

Students will have access to a wide variety of training and courses within Oxford University teaching and training schemes. As part of this project, the student will split their time between the groups of Dr. Michael FitzPatrick and Dr. Agne Antanaviciute due to interdisciplinary nature of the work. As such, the successful applicant will have access to training in the following techniques: NGS data analysis, single cell and bulk multi-omics, including scRNA-Seq, CITE-Seq, scATAC-Seq, TCR/BCR repertoire analysis, spatial ‘omics and imaging, intestinal organoids, statistical inference and machine learning. The interdisciplinary nature of this project means students will interact with and learn from experts in both wet- and dry-lab research, gaining experience in experimental design, data generation and computational data integration and modelling. In addition, opportunities will be provided for attendance at national and international workshops and conferences, as well as regularly interface with industry collaborators at AMYRA, and the opportunity to visit and collaborate with other labs within the Enteropathy Consortium.

Students will be enrolled on the MRC Weatherall Institute of Molecular Medicine DPhil Course, which takes place in the autumn of their first year. Running over several days, this course helps students to develop basic research and presentation skills, as well as introducing them to a wide range of scientific techniques and principles, ensuring that students have the opportunity to build a broad-based understanding of differing research methodologies.

Generic skills training is offered through the Medical Sciences Division's Skills Training Programme. This programme offers a comprehensive range of courses covering many important areas of researcher development: knowledge and intellectual abilities, personal effectiveness, research governance and organisation, and engagement, influence, and impact. Students are actively encouraged to take advantage of the training opportunities available to them.

As well as the specific training detailed above, students will have access to a wide range of seminars and training opportunities through the many research institutes and centres based in Oxford.

The Department has a successful mentoring scheme, open to graduate students, which provides an additional possible channel for personal and professional development outside the regular supervisory framework. We hold an Athena SWAN Silver Award in recognition of our efforts to build a happy and rewarding environment where all staff and students are supported to achieve their full potential.

How to apply

All applications must be made using the University's online application form.

Find out more