Reconstructing the immune response: from molecules to cells to systems

Reconstructing the immune response: from molecules to cells to systems

Project details

Lymphocyte responses are complex processes whereby B and T cells undergo programmed rounds of proliferation and death triggered by pathogenic stimuli. Adequate timing and magnitude of the response are essential for effective pathogen clearance. 

The collective behavior of a population of cells emerges from gene regulatory networks controlling individual cells. However, transcriptional regulation of lymphocyte responses is poorly understood.

In this interdisciplinary project we will use bioinformatics methods to develop predictive mathematical models of lymphocyte responses. We will experimentally establish transcriptional profiles at different stages of the response, and interrogate these data using advanced statistical methods. 

The student will learn both “wet lab” experimental techniques, such as cell proliferation assays and DNA sequencing, and “dry lab” skills for data analysis, such as developing statistical models using R and Python.


About our research group

We are an interdisciplinary team that combines expertise from Hodgkin and Shi labs. Professor Philip Hodgkin and his group have pioneered methods of quantitative description and mathematical modelling of lymphocyte responses (Nat Immunol 2000, PNAS 2007). This group has established that the kinetics of lymphocyte responses is largely pre-programmed at the time of activation and that there is a high concordance in kinetics within each clone (PNAS 2009, Science 2012, Science 2014). 

The group of Dr Wei Shi specialises in developing computational statistical methods for analysing sequencing data especially in application to immunological questions. These methods have been instrumental for a large number of recent immunological studies (J Immunol 2014, Nat Immunol 2015, Nat Immunol 2016, Science 2016).




Dr Wei Shi

Profile photo of Dr Wei Shi
Laboratory Head
Andrey Kan in the office
Immunology division

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