Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

  • Alison Simmons


The human intestinal tract is one of the most architecturally and functionally complex organs of the body. Contributions from a myriad of different highly specialised cell types are required to coordinate intestinal functions, including digestion, absorption and waste secretion, but also to maintain the delicate balance between immunity towards invading pathogens and tolerance towards commensals. Until recently the diversity of these cellular functions has remained unappreciated, but recent developments in single-cell modalities (single cell RNA-sequencing, ATAC profiling, and imaging methods such as spatial transcriptomics) have led to new insights into intestinal epithelial (1), mesenchymal (2), and immune cell (3) function in health and breakdown in adult inflammatory diseases such as inflammatory bowel disease.

The developmental circuits that underpin formation of a healthy intestinal barrier through fetal and early post-natal life into old age remain poorly charted. At birth, the neonatal gut experiences its first exposure to food antigens, pathogens and colonisation by commensals. The events driving infant intestinal immune maturation which is critical for intestinal barrier function through life remain unclear. Defining these will shed light on how lifelong immunity and tolerance are established and provide a foundation for exploring aging of the intestine. Furthermore, profiling the early intestine in term and premature babies will assist in  defining the molecular pathogenesis of necrotising enterocolitis, one of the major causes of mortality in premature neonates.

Previously, our group has revealed unappreciated facets of normal human intestinal development by generating a spatiotemporal single cell atlas of fetal gut development (4), sampling intestine from fetal development up to 22 post-conceptual weeks. This captured the transcriptional regulatory networks and intercellular signaling events responsible for epithelial crypt-villus formation, differentiation of mesenchymal cellular architecture, establishment of muscle layers, expansion of vascular circuitry, and immune cell colonisation with formation of gut associated lymphoid tissue (GALT) in preparation for birth (4).

Recently we have developed novel multi-omic, in vitro and computational methods to further explore intestinal aging. As part of a larger study we have collected surgical tissue from pre-term neonates born as early as 24 post-conceptual weeks, through to adulthood. The project will provide a unique opportunity to define the molecular networks operating at different stages of human intestinal development and aging. Paired samples are also available from rare paediatric surgical disorders characterised by breakdown in the epithelial barrier, immune tolerance or neural migration such as necrotising enterocolitis (the most common gastrointestinal emergency of pre-term infants) or Hirschsprung’s disease (a congenital bowel disorder characterised by abnormal intestinal motility and neural cell migration in utero).

Various research opportunities are available for a prospective student within the scope of this project. These include:

  • Understanding early gut immune cell colonisation and immune maturation
  • Investigating the molecular, cellular and epigenetic determinants of gut aging
  • Defining novel mechanisms of innate sensing and barrier protective function through life
  • Understanding epithelial barrier breakdown in necrotising enterocolitis
  • Understanding of in utero neuronal migration anomalies and effects on long term intestinal health in Hirschsprung’s disease

Applicants from biological, biomedical, clinical or computational biology backgrounds are encouraged to apply.  In addition to lab-based projects, there are further opportunities for half-wet half-dry computational, inter-disciplinary projects. Interested candidates are encouraged to reach out for an informal discussion (

Additional supervision may be provided by Dr Agne Antaniviciute and Dr David Fawkner-Corbett. 



Successful applicants will have access to training in the following techniques:

  • High resolution multi-omic techniques: Single cell RNA-sequencing, Single cell ATAC sequencing, CITE-Seq, multi-omic techniques, bulk RNA and ATAC sequencing, microfluidic PCR, quantitative PCR, RNA extraction, cDNA processing, 16S sequencing, proteomics
  • Spatial techniques: Spatial transcriptomics, in situ sequencing, immunohistochemistry, immunofluorescence, in situ hybridisation, imaging mass cytometry, sample processing / embedding / sectioning.
  • Tissue processing, culture and analysis: Immortalised cell culture, primary cell culture, organoids and co-cultures, lineage tracking, ex vivo T cell culture / Treg suppression assays, human cell isolation (surgical / biopsy/ fetal / blood), RNA extraction, protein extraction, mass spectrometry, western blot
  • Next generation sequencing: Library preparation, Illumina NGS (RNA/ ATAC / DNA libraries), TCR and BCR sequencing
  • Routine Molecular Biology and Immunological assays: eg. Flow cytometry and cell sorting, ELISA, mass cytometry, immune cell culture / stimulations.
  • In vivo murine work: access to training such as personal licence, design and use of genetic models, tissue processing and analysis.
  • Computational techniques: NGS data analysis, single cell multi-omics data analysis, spatial data analysis, TCR/BCR analysis, statistical analysis, machine learning. 

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.




Parikh K, Antanaviciute A, Fawkner-Corbett D, Jagielowicz M, Aulicino A, Lagerholm C, Davis S, Kinchen J, Chen HH, Alham NK, Ashley N, Johnson E, Hublitz P, Bao L, Lukomska J, Andev RS, Bjorklund E, Kessler BM, Fischer R, Goldin R, Koohy H, Simmons A. 2019. Colonic epithelial cell diversity in health and inflammatory bowel disease. Nature



Structural remodeling of the human colonic mesenchyme in inflammatory bowel disease

James Kinchen, Hannah H Chen, Kaushal Parikh, Agne Antanaviciute, Marta Jagielowicz, David Fawkner-Corbett, Neil Ashley, Laura Cubitt, Esther Mellado-Gomez, Moustafa Attar, Eshita Sharma, Quin Wills, Rory Bowden, Felix C Richter, David Ahern, Kamal D Puri, Jill Henault, Francois Gervais, Hashem Koohy, Alison Simmons, Cell



Corridoni D, Antanaviciute A, Gupta T, Fawkner-Corbett D, Aulicino A, Jagielowicz M, Parikh K, Repapi E, Taylor S, Ishikawa D, Hatano R, Yamada T, Xin W, Slawinski H, Bowden R, Napolitani G, Brain O, Morimoto C, Koohy H, Simmons A. 2020. Single-cell atlas of colonic CD8(+) T cells in ulcerative colitis. Nat Med 26: 1480-90


Fawkner-Corbett D, Antanaviciute A, Parikh K, Jagielowicz M, Geros AS, Gupta T, Ashley N, Khamis D, Fowler D, Morrissey E, Cunningham C, Johnson PRV, Koohy H, Simmons A. 2021. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell