Antanaviciute Group: Decrypting human intestinal development

Supervisor: Agne Antanaviciute

About the Research 

The human intestine undergoes rapid and complex developmental changes before and after birth, establishing a functional epithelial barrier and a diverse local immune system essential for maintaining tissue homeostasis and supporting healthy host-microbe interactions. This process involves coordinated immune cell colonisation, epithelial differentiation, barrier maturation and the establishment of spatially organised tissue niches. Premature birth interrupts these critical developmental windows, often resulting in impaired barrier integrity, dysregulated immune responses and increased susceptibility to severe inflammatory diseases such as necrotising enterocolitis, a leading cause of neonatal morbidity and mortality worldwide. Despite the clinical significance, the cellular and molecular mechanisms underpinning early-life intestinal barrier development and immune-epithelial crosstalk remain poorly understood. Understanding how these tissue niches form, and how prematurity alters their structure and function, is essential to inform strategies for preventing or mitigating early-life intestinal disease and its long-term consequences on immune health.

Our research group sits at the interface of tissue immunology and data science. We combine single-cell and spatial multi-omics technologies, complex in vitro tissue models with high-dimensional patient data and advanced computational approaches, including statistical modelling, network inference and machine learning, to better understand tissue immunity during development and in disease. This data-driven approach enables us to explore how tissues develop, adapt and remodel in response to developmental cues or pathological insults. Our work is inherently interdisciplinary, bringing together expertise in immunology, developmental biology, computational biology and data science to address complex biological questions with translational relevance.

Various research opportunities are currently available within the group, broadly focusing either on: a) Computational method and model development in the area of spatial transcriptomics and integrative approaches with single cell multi-omics data; or b) applying complex in vitro tissue models, such as organoid and co-culture systems, and multi-omics and spatial technologies to explore human intestinal immune system development and early childhood diseases at single cell resolution. Options include wet-lab projects focused on functional exploration of immune-epithelial interactions; half-wet/half-dry projects combining experimental perturbations with computational analysis of multi-omics and imaging data; and purely dry lab computational projects dedicated to advanced model and method development for analysing high-dimensional datasets and biological inference.  Therefore, we are interested in hearing from students from diverse backgrounds, including molecular and cellular biology, computational biology or computer science. Interested candidates are encouraged to reach out for an informal discussion (agne.antanaviciute@rdm.ox.ac.uk).

This project is not suitable for part-time research. 

Training Opportunities 

Students will have access to a wide variety of training and courses within Oxford University's teaching and training schemes.  Specifically within the group, the successful applicant will have access to training in the following techniques: spatial ‘omics and imaging, intestinal organoids, NGS data analysis, single cell multi-omics, including scRNA-Seq, CITE-Seq, scATAC-Seq, TCR/BCR repertoire analysis, statistical inference and machine learning. The interdisciplinary nature of our group 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.

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.

 Additional Supervisors 

1. Alison Simmons

2. David Fawkner-Corbett

3. Marella de Bruijn 

Publications