Janet Thornton Fellowship

Janet Thornton Fellowship

At the Wellcome 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 2019 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 applying to one of the broad project outlines listed below. Applicants are encouraged to make contact with the named supervisor.

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.

If you would like to learn more about a day in a life of a Janet Thornton Fellow please click here 

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 Genome Campus in Hinxton near Cambridge and includes:

  • Salary £31,897 - £39,986
  • Research expenses, including generous consumables and travel costs for conferences and training courses
  • Access to training and support resources from across the organisation
  • Access to the University of Cambridge Careers Service
  • Generous and flexible benefits

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

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

Application Process

Applicants are asked to provide:

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

APPLICATION ARE NOW CLOSED

The project lead will short list candidates based on their skills and experience and will then work with the most suitable candidate to further develop the proposal, the deadline is now CLOSED for final submission.

If you have any questions about the application process please contact saher.ahmed@sanger.ac.uk 

Davenport project

2019 PROJECT EXAMPLES:

Davenport Project - Integrating functional genomics and clinical datasets to understand patient heterogeneity

Supervisor: Dr Emma Davenport

Our group integrates functional genomics with clinical data to understand why there can be substantial heterogeneity across cohorts of patients. Understanding this heterogeneity is necessary to improve patient stratification for precision medicine-based approaches to treat disease.

We focus on diseases that involve systemic inflammation such as sepsis and systemic lupus erythematosus (SLE). For both of these diseases, patients present with variable clinical features making diagnosis and treatment very challenging. We have previously used transcriptomic data (microarray and RNA-seq) to identify subgroups of patients with different disease severities and linked these to survival and treatment outcomes. We have recently set up exciting new projects to generate additional functional genomics datasets through clinical and industry collaborators. With BioAID, we are generating RNA-seq data for 1,800 patients presenting to the emergency room with suspected infections, a proportion of which will go on to develop sepsis, and with OpenTargets, we are generating single-cell RNA-seq for 300 SLE patients. The main aim of these projects is to identify gene expression signatures for predicting disease severity and treatment response as well as using expression quantitative trait locus (eQTL) mapping to understand the role of regulatory DNA in patient heterogeneity.

We are a computational group but welcome applications from those looking to develop their computational skills as well as those with experience of analysing functional genomics datasets. We are currently setting up a number of new projects in this area that would be ideal for a Janet Thornton Fellow to lead, but we can also support the Fellow to develop their own research project within the scope of the group’s research interests.

Ellis Project

Ellis Project - Developing and Employing CapTF Synthetic Sponge DNA Arrays

Supervisor: Dr Tom Ellis (Associate Faculty in Synthetic Genomics)

The classic model of transcription factor (TF) action sees the TF protein randomly diffuse to promoter DNA and bind tightly upon recognition of the DNA bases of its binding site motif. This is thought to occur for over 1000 TFs as they locate their targets in the 6 billion bases of the human genome. However, in reality most TFs are promiscuous, binding to many sequences that are broadly similar to their main target. Recent work in bacterial synthetic biology has exploited the promiscuity of TFs, by making synthetic DNA intentionally designed to be bound by TFs and using this DNA to titrate TFs away from their usual target when needed - effectively soaking them up like a sponge.

Here we plan to extend this approach and use it to understand promiscuous TF binding around the human genome, in the hope of quantifying how much TF binding occurs in non-promoter DNA regions. We will use synthetic DNA library generation to create Capture Transcription Factor (CapTF) Synthetic Sponge DNA Arrays. We will design and synthesise an array for each human TF, making around 1000 of these in parallel to get a library representing all known human TFs. These arrays will consist of tandem repeats of the predicted strong binding sites for the TF plus a barcoded region that is actively transcribed. The array plasmid library will be pooled and transfected into human cells (e.g. iPSCs) and the perturbation of gene expression from the action of each CapTF sponge array will be determined from single cell RNAseq measurements. The data from the CapTF experiment will be used to build a model of the levels of each TF in the cell and the anticipated number of off-target sites they usually bind around the human genome (e.g. within ‘junk’ DNA). Understanding the numbers of these sites and their necessity will be essential for future efforts that seek to recode, rearrange and reduce the human genome.

Lawniczak project

Lawniczak Project - Tree of Life Genomics

Supervisor: Mara Lawniczak, Matt Berriman, Mark Blaxter, Richard Durbin

Broad Project Outline: An exciting new Scientific Programme, the Tree of Life, has launched at the Wellcome Sanger Institute. At Sanger, we are leading the Darwin Tree of Life project, which is a decade long ambitious consortial project aiming to build high quality reference genomes for all eukaryotic species found in the British Isles. Alongside this, we are also carrying out population and evolutionary genomics research projects on organisms within focal ecosystems such as the intertidal, and on natural populations of molluscs, insects, fish, and worms both in the UK and abroad. These projects include examining the evolution of genome structure in specific branches of life, using genomics to define and understanding species interactions in ecosystems, investigating cryptic speciation, and more. We are looking for a candidate with a strong ecological genomics background to join our new Programme as a Janet Thornton research fellow and develop projects in this general area. If you are interested in this opportunity, and have had a career break for at least 12 months, please get in direct touch with us to develop a project in the general area of evolutionary genomics.

Teichmann Project

Teichmann Project - Genomic and computational dissection of tissue architectures

Supervisor: Sarah Teichmann

Single cell genomics and spatial gene expression technologies can now be combined to provide high-resolution maps of tissues. These methods are now routine, robust and scalable, and can be applied to mapping tissues in human development as well as mature adult tissues across the lifespan and across genders, and in health versus disease states. There are fundamental questions about cell lineages (e.g.in haematopoiesis, immunity, etc.), systems (e.g. skin, vasculature, immunity) and organs (e.g. kidney, lung, reproductive tissues, endometrium/decidua etc.) that can be addressed with these approaches.

We welcome postdoctoral projects that focus on specific biological tissues or systems, as well as on general overarching questions that span multiple tissues. We also value methods development projects (computational or experimental) that advance the study of tissue architectures using genomics technologies.

Thomson Project

Thomson Project – High-throughput mutagenesis of diarrhoeal pathogens to understand human colonisation and environmental persistence

Supervisor: Nicholas Thomson

Diarrhoeal disease is ranked as the fourth most important cause of death worldwide and the second cause of years of productive life lost due to premature mortality or disability (160 million cases and 750,000 fatalities in the under-fives alone). A small number of bacterial pathogens, including Vibrio cholerae, Shigella spp, enterotoxigenic Escherichia coli, Salmonella spp. and Campylobacter spp., account for a significant percentage of all diarrhoeal diseases in these countries. Cholera alone accounts for 3-5 million cases of diarrhoea and 120,000 fatalities per annum. We have shown in several global phylogeographic surveys1-6 how diarrhoeal diseases are spreading globally. It’s clear from these data that functions important in both the human and the environmental phase of their transmission cycle and ecology are critical for their sustained transmission. We propose to use high-throughput mutagenesis to identify genes associated with colonisation and survival within a human infection model system, as well as comparing the differing ability of successful epidemic lineages, of key enteric pathogens, to survive and persist in the environment or the contaminated environment.

TraDIS offers enormous potential to combine high-throughput genomics with functional screening. In essence it assay the whole genome for genes linked to a range of phenotypes important for disease, colonistation or survival: either in a host or in the environment. We will prepare TraDIS libraries from isolates selected to represent the full diversity of their species, from those isolates that have been clinically successful globally to those linked only to sporadic disease localised disease. The ability to select isolates across the species to assay in this way will allow us to chart the evolutionary changes that define the emergence of these modern successful lineages, more specifically for diarrhoeal pathogens to define the boundaries of human and environmental adaptation.

References

1. Ankur Mutreja*, Dong Wook Kim*, Nicholas Thomson*, Thomas R Connor, Je Hee Lee, et al., Gordon Dougan (2011) Evidence for multiple global transmission events within the seventh cholera pandemic. Nature. 24th August 2011. PMID21866102 PMC3736323 
2. François-Xavier Weill, Daryl Domman, Elisabeth Njamkepo, Chery Tarr, Jean Rauzier, et al., Nicholas R. Thomson. Genomic history of the seventh pandemic of cholera in Africa. Science. 2017 Nov 10;358(6364):785-789. doi: 10.1126/science.aad5901. PMID:29123067.
3. Daryl Domman, Marie-Laure Quilici, Matthew J. Dorman, Elisabeth Njamkepo, Ankur Mutreja, et al., Nicholas R. Thomson. Integrated view of Vibrio cholerae in the Americas. Science. 2017 Nov 10;358(6364):789-793. doi: 10.1126/science.aao2136. PMID: 29123068.
4.   Holt KE, Thieu Nga TV, Thanh DP, Vinh H, Kim DW, Vu Tra MP, Campbell JI, Hoang NV, Vinh NT, Minh PV, et al., Parkhill J, Dougan G, Thomson NR, Baker S. Tracking the establishment of local endemic populations of an emergent enteric pathogen Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):175227.
5.    Kathryn E. Holt, Stephen Baker, François-Xavier Weill, Edward C. Holmes, Andrew Kitchen, Jun Yu, Vartul Sangal, Derek J. Brown, et al., Nicholas R. Thomson (2012) Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nature Genetics. 2012 Sep; 44(9):1056-9.
6. Gemma C. Langridge, Minh-Duy Phan, Daniel J. Turner, Timothy T. Perkins, Leopold Parts, et al., A. Keith Turner. (2009) Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res. 2009 Dec;19(12):2308-16.