Francis Crick Institute

Postdoctoral Training Fellow in Computational Biology/Bioinformatics (Host-Pathogen Interaction)

Francis Crick Institute

London, United Kingdom

Salary for this Role:

From £38,300, subject to skills and experience

Job Description:


Fixed term, 4 years with the possibility to extend to 5 years.

We are looking for a computational biologist/ bioinformatician to develop machine learning methodology to interpret PerturbSequencing and scRNAseq experiments in host-pathogen interaction.

We are trying to solve the question how the most successful parasite on earth, Toxoplasma gondii, subverts the host cell to establish a favourable immune response. Toxoplasma is special as it is a true generalist, infecting almost any nucleated cell in any warm blooded animal, including humans. To alter the host immune response, it secretes ~200 effector proteins into the host cell, some of which directly alter the host cells’ transcriptional profile changing the host cell behaviour. Which of these 200+ effectors function in which cell type and species, and how this leads to changes in the overall immune response however is only understood for a handful of effectors, some of which antagonize each other. The picture becomes more complicated as parasite strains of different virulence exist and differential expression of effectors and SNPs between them lead to different disease outcomes. Comprehensive elucidation of effector functions and mechanisms requires an integrated system wide monitoring and machine learning approach.

We have now developed a method that combines Toxoplasma CRISPR screens (PMID: 31481656) with host single cell RNA sequencing methods to identify transcriptional regulators of Toxoplasma and their effect of host cells (unpublished). We will apply this method to identify transcriptional regulators and the host cell transcriptome across parasite strains that differ in virulence in various hosts and cell types.

Your Role: You will play a central role in this project to apply and develop computational methods, co-supervised by the laboratory of Prof. Manfred Claassen, to analyse PerturbSequencing and scRNAseq data in complex experimental settings. The aim is to identify all transcriptional regulators of Toxoplasma that function across species, analyse the transcriptional responses in various cells and hosts and measure interdependencies between effector proteins. A second goal of this project is to understand how the effectors function within the cell, and their role in controlling the immune response. For this you will analyse immune cell populations across the course of an infection in vivo using scRNAseq and RNA velocity based trajectory inference of the natural cellular immune response to infection and the role of individual effector proteins. You will work alongside 3 researchers that will lead the wetlab aspect of this work, and have the opportunity to engage with other members of the lab.

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 will also be opportunities to be involved in wet-lab data generation.

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.

The laboratory of Prof Manfred Claassen at the University of Tuebingen develops and 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 with 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.
  • 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 relevant field or in the final stages of PhD submission with experience in the analysis of transcriptomics data, ideally scRNAseq. 
  • Technical expertise in coding (R!, Python)
  • 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.
  • Ability to work independently and also capable of interacting within a group

Equality, Diversity & Inclusion

We welcome applications from all backgrounds. We are committed to providing equal employment opportunities, regardless of ethnicity, nationality, gender, sexual orientation, gender identity, religion, pregnancy, age, disability, or civil partnership, marital or family status. We particularly welcome applications from people who are Minority Ethnic as they are currently underrepresented in the Crick at this level.

Diversity is essential to excellence in scientific endeavour. It increases breadth and perspective, leading to more innovation and creativity. We want the Crick to be a place where everyone feels valued and where diversity is celebrated and seen as part of the foundation for our Institute’s success.

The Crick is committed to creating equality of opportunity and promoting diversity and inclusivity. We all share in the responsibility to actively promote dignity, respect, inclusivity and equal treatment and it is our aim to ensure that these principles are reflected and implemented in all strategies, policies and practices.

Read more on our website:

Please apply via recruiter’s website.