Janet Thornton Fellowship

Janet Thornton Fellowship

At the Wellcome Trust Sanger Institute we are committed to enabling and opening routes back into science for those who have had a break from scientific research - for any reason.

The 2017 call is now closed
fellows.jpgSanger Institute, Genome Research Limited

We understand that even a short time out of research can have an impact on your career, which is why we have created a postdoctoral fellowship providing an additional opportunity specifically for those who have been out of scientific research for 12 months or more to return to high-quality postdoctoral training. One Fellowship will be awarded each year. Each Fellowship will last for three years and can be worked full time, part time or flexibly.

Fellowships will be awarded after a competitive selection process, with applicants developing their own project with prior agreement and in collaboration with a Sanger Institute Faculty member.

While the Sanger Institute provides the opportunity in its recruitment processes for job applicants to declare career breaks (taken for any reason) so that they can be taken into account when assessing applications for all roles, particularly in relation to the potential impact of time out on individuals' scientific and career outputs, this fellowship will be open exclusively to those who have taken a career break of 12 months or more.

What's included?

This postdoctoral Fellowship is for a duration of three years, can be worked full time, part time or flexibly at the Sanger Institute on the Wellcome Trust Genome Campus in Hinxton near Cambridge and includes:

  • Salary £31,115 - £39,004
  • Research expenses, including consumables and travel costs for conferences and training courses
  • Access to training and support resources at the Institute
  • Access to the University of Cambridge Careers Service
  • Generous benefits

One Janet Thornton Fellowship will be awarded each year following a competitive selection process.

If you have questions about what is included in the Fellowship please email fellowship@sanger.ac.uk

Eligibility

The Janet Thornton Fellowship is open to scientists who:

  • have had a break from scientific research, of 12 continuous months or more, for any reason
  • are not currently working in scientific research
  • have at least one years' postdoctoral experience

If you have questions about your eligibility for the Fellowship please contact fellowship@sanger.ac.uk.

Application Process

Eligible candidates are invited to apply to one of the project listed below.

All shortlisted candidates will be invited to an interview in December 2017 to discuss their application in more detail and to give a short presentation on their previous work.

Applications are to be made online. Candidates will be asked to provide:

  • a covering letter
  • a current CV
  • the names of two referees
  • the reason(s) for their break from scientific research.

Shortlisting decisions will be made based on the scientific excellence of the candidates.

The call is now open. Deadline for applications is Wedensday 4 October 2017.

If you have questions about the application process please contact fellowship@sanger.ac.uk.

Carl Anderson

Project 1 - Genomics of Immune response to vaccination

Supervisor: Dr. Carl Anderson

Contact: carl.anderson@sanger.ac.uk

The Genomics of Inflammation and Immunity group at the Wellcome Trust Sanger Institute is undertaking a large-scale study of rotavirus vaccine response. Rotavirus is the major cause of acute gastroenteritis in children under the age of five. In developed countries rotavirus vaccines are highly effective and have greatly reduced morbidity. However, in developing countries vaccine efficacy is significantly lower, despite minimal geographical variation in the circulating strains. In collaboration with Dr. Stephen Baker’s group at the OUCRU Vietnam, we are recruiting 1000 Vietnamese infants into a longitudinal systems vaccinology study to identify molecular markers of rotavirus vaccine response and the genetic variants that regulate these. We are seeking a Janet Thornton fellow to play a leading role in the project, combining genetic data with multi-omic data (transcriptomics, metagenomics, metabolomics and proteomics) collected both before and longitudinally after vaccination to understand the biological basis of vaccine response (antibody titre and vaccine failure) and develop predictive models of response. In addition to measuring antibody titres, we will capture vaccine failure events by longitudinally following the children for 18 months. This project will particularly suit individuals with statistical and computational skills (R, python etc.) and an interest in host response to immune challenge.

Project 2 - Using next-generation sequencing to understand inflammatory bowel disease

Supervisor: Dr Carl Anderson

Contact: carl.anderson@sanger.ac.uk

Our group has a long-standing interest in the genetics of inflammatory bowel disease (IBD). IBD is a chronic, debilitating disorder of the gastrointestinal tract that affects around 0.5% of the population, with a typical onset in early adulthood. Many IBD patients ultimately requiring major abdominal surgery, resulting in lifelong disability, because an appropriate drug either does not exist or is not administered soon enough. Total healthcare costs in the UK are estimated to be over £1 billion per year (Cummings et al., 2008). Disease pathogenesis is poorly understood but is likely driven by a dysregulated immune response to commensal gut microorganisms in genetically susceptible individuals. IBD is highly heritable and the group has played a leading role in the identification of 240 regions of the genome associated with disease susceptibility. These loci were predominantly detected via genome-wide association studies and are driven by common genetic variants. As part of the UK IBD Genetics Consortium we are currently whole-genome sequencing over 15,000 IBD cases and 20,000 population controls to powerfully test the entire allelic spectrum for association to IBD. In a subset of these patients we are using RNA-seq to identify eQTLs in disease relevant cell types (including immune cells isolated from the gastrointestinal tract) with the aim of using these to identify potential therapeutic targets within IBD associated loci. We are also embarking on large-scale metagenome sequencing of stool samples from IBD patients and controls in attempt to identify microbial species driving disease susceptibility and prognosis.

Mara Lawniczak

Project 3 - Reprogramming non-coding RNAs as a novel approach to vector control – Anopheles

Supervisors: Eric Miska and Mara Lawniczak

Contact: mara.lawniczak@sanger.ac.uk

Small RNA pathways act in eukaryotes to protect organisms from viral infection and transposable elements. In animals, PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. We recently found that somatic piRNAs were likely present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and mRNAs are common among arthropods. Our results call into question the view that the ancestral role of the piRNA pathway was to protect the germline and demonstrate that small RNA silencing pathways have been repurposed for both somatic and germline functions throughout arthropod evolution.

Here we propose to examine the piRNA populations in wild isolates of several species of African Anopheles malaria vector mosquitoes to assess their impact on viral infection, transposon mobility, and fertility. The eventual goal would be to reprogram piRNA pathways as a novel epigenetic control method of key vector species. The project will involve sequencing small RNAs and transcriptomes from different tissues of wild mosquitoes, as well as each mosquito’s genome to carry out a population study of piRNAs from different wild mosquito species. These data would also be used to test the hypothesis that endogenous RT in insects can generate RNA virus derived genomic piRNA clusters.

This project will involve DNA/RNA high-throughput sequencing, gene editing approaches, and possibly time in the field (though this is not required). Relevant expertise: computational biology, molecular biology, insect biology.

We would also be happy to work with interested candidates to develop self-proposed projects in the general area of transcriptomics, genomics, and Anopheles mosquitoes.

Carl Anderson and Jeff Barrett

Project 4 - High-throughput cellular screens for the genetic determinants of inflammatory bowel disease

Supervisors: Dr Carl Anderson and Dr Jeff Barrett

Contact: carl.anderson@sanger.ac.uk

The Anderson and Barrett groups at the Wellcome Trust Sanger Institute (WTSI) have a long-standing interest in the genetics of inflammatory bowel disease (IBD). IBD is a chronic, debilitating disorder of the gastrointestinal tract that affects around 0.5% of the population, with a typical onset in early adulthood. Many IBD patients ultimately requiring major abdominal surgery, resulting in lifelong disability, because an appropriate drug either does not exist or is not administered soon enough. Total healthcare costs in the UK are estimated to be over £1 billion per year (Cummings et al., 2008). IBD is highly heritable and the groups have played a leading role in the identification of 240 regions of the genome associated with disease susceptibility. These loci are predominantly driven by common non-coding genetic variants.

We are performing high throughput genetic screens to better understand the role of non-coding DNA in this complex disease, including massively parallel reporter assays and CRISPR-Cas9 genome editing in model immune cell lines. Screen hits will be validated using molecular, (e.g. transcriptomics and chromatin immunoprecipitation [ChIP] sequencing) and phenotypic (e.g. cell migration and degranulation) assays that we are currently establishing in model human immune cell lines. We will then determine the mechanistic effects of genetic variants on ex-vivo human primary cells obtained from the large cohorts of genotyped individuals that we have access to through local bioresources.

This is a really exciting opportunity to better understand the role of sequence variants and regulatory regions associated with predisposition to IBD and ultimately, to identify potential therapeutic targets. The successful candidate will work closely with Dr. Rebecca McIntyre who has herself returned successfully to experimental research after a two-year career break. Candidates with a strong background in cell biology, especially high throughput assays, are encouraged to apply.

Contact

Please send any queries about the Janet Thornton Fellowship to fellowship@sanger.ac.uk