Francis Crick Institute

Postdoctoral Training Fellow x2: Immunology and Computational Biology

Francis Crick Institute

London, United Kingdom

Salary for this Role:

From £38,300, subject to skills and experience

Reports to:

Moritz Treeck

Job Description:


4 years with the possibility to extend to 5 years.


2 Wellcome Trust funded postdoctoral research posts (immunology and computational biology) in the laboratory of Moritz Treeck ( are available. We are looking for curious researchers to investigate the complex interaction of effector proteins that one of the most successful parasite, Toxoplasma gondii, injects into its host cells. Novel single-cell sequencing methods that combine CRISPR screens in the parasite and analysis of transcriptional responses in host cells will be employed to map all Toxoplasma effector proteins that alter host cell behaviour in various hosts and cell types. The function of the effector proteins will be studied in cell culture and in vivo to investigate how effector proteins injected into a host cell can lead to systemic changes of the immune response. This project will appeal to those with an interest in the cell biology and innate immunology of host-pathogen interaction and the complex analysis of single cell sequencing datasets. Extensive collaborations with immunology and cell biology groups within the Francis Crick institute, and co-supervision of the computational work by Prof. Manfred Claassen using machine learning approaches provides a stimulating and diverse framework. 

Toxoplasma is remarkable for a pathogen, as it is a true generalist that infects any nucleated cell of any warm-blooded animal, including ~30% of the human population. To do that, the parasite secretes effector proteins into the host cells to rewire their normal behaviour in the parasites’ favour, ranging from the cell autonomous immune response within the infected cell to altered cytokine secretion, thus creating a favourable infection environment. How it achieves that across species and cell types is not known.

Only a few of the ~220 predicted effector proteins and their effects on the host have been characterized, often leading to important and novel insights into host-pathogen interaction. However, the majority of the effectors are of unknown function and hold great promise to uncover novel mechanisms as to how the parasite subverts the host immune response. Novel methods have been developed in the lab to address this question, such as the PerturbSEQ technology that combines parasite CRISPR screens (Young J, et al., 2019, PMID: 31481656) and single-cell RNAseq experiments of the infected host cell.

To perform this work, we are looking for 2 motivated postdocs with a strong interest in infection biology and host-pathogen interaction. We are particularly interested in hearing from candidates with a background in either of the following:

  • Cellular immunology of the innate immune system. A very good understanding of the innate immune system and how its components function together is desirable. Experience in working with mice is essential.

  • Computational biology. A solid background in bioinformatics/statistics and enthusiasm to tackle highly complex biological problems is essential. Experience in analysis of single-cell sequencing data would be a plus. The primary role will be to develop analysis methods for multi-model single-cell sequencing in a novel host-pathogen interaction context, but there may also be opportunities to be involved in wet-lab data generation. This position will be co-supervised by Prof. Manfred Claassen, a specialist in advanced single cell analysis methods (

Postdoctoral Training Fellows are expected to lead their own projects, contribute to other projects on a collaborative basis (both in the lab and with external collaborators) and guide PhD students in their research.

About us

The project complements ongoing research in the lab to identify effector proteins of the parasite which are essential for survival within an infected cell. Within the lab, we foster a diverse group of scientists coming from various scientific backgrounds and employ a range of techniques to answer our questions including quantitative proteomics, CRISPR screens, single-cell RNA seq, immunology, cell biology and biochemical methods. See for an overview of the lab and projects. For the computational part of this work, we closely collaborate with the laboratory of Prof Manfred Claassen at the University of Tuebingen, who applies machine learning methods to complex single cell analysis. As such, we have a diverse team of like-minded scientists that can learn from each other and tackle questions in a collaborative and fun way, while providing substantial room to build an independent niche within the team.

The Crick has a wide research portfolio. Since there are no divisions or departments, our research groups have the freedom to establish research programmes within broad areas. We are collaborative and outward-looking, reflecting our status as a partnership of six organisations aiming to pool knowledge, ideas and resources.

We’re conducting research of the highest quality right at the forefront of biomedical research. We combine this rigour with an open and interactive culture, bringing together people with varied research interests and expertise, including clinicians, physical scientists and applied scientists from our pharmaceutical partners.

We aim to attract the most talented researchers and support them to tackle innovative research questions, sharing resources across laboratories. Our range of science technology platforms provide our researchers with access to state-of-the-art technology and expertise. We provide an excellent learning environment with dedicated education programmes in scientific outreach, education and personal development and a postdoc training programme that prepares scientists for leadership roles in academia and industry.

  • If you are interested in applying for this role, please apply via our website.
  • A cover letter detailing for which of the 2 positions you are applying for and how your research skills and interests align with the aims of this project is absolutely essential.
  • There is no closing date: positions will be filled when a suitable candidate has been identified. The anticipated start is from February 2022 until all positions are filled.

Interested candidates are encouraged to enquire whether the position of interest is still available.

  • All offers of employment are subject to successful security screening and continuous eligibility to work in the United Kingdom.
  • Informal requests can be made to

Essential Qualifications, experience and competencies

  • PhD in a field related to the above, or in the final stages of PhD submission
  • Good knowledge and experience in a field as described above
  • Technical expertise in a field as described above
  • Track record of writing papers as evidenced by publications or submitted manuscripts in referred journals. It is understood that COVID has led to disruptions in manuscript submissions.
  • Evidence of data presentation at scientific meetings
  • Experience of experimental design
  • Ability to work independently and also capable of interacting within a group

Please apply via recruiter’s website.