Postdoctoral Fellow - Systems Immunology/Computational

Updated: 2 months ago
Location: Cambridge, ENGLAND
Job Type: FullTime
Deadline: 30 Nov 2021

The Opportunity:

We are looking to appoint a highly motivated postdoctoral fellow interested in systems immunology to join Menna Clatworthy’s group at the Wellcome Sanger Institute, working closely with the Sarah Teichmann’s lab.

About the Role:

You will lead a project focused on integrating single-cell multiomics and imaging datasets to understand tissue immunity in the kidney, working with colleagues in the Teichmann Lab. This project is part of the Chan-Zuckerberg Foundation-supported Kidney Seed Network , and international collaboration aimed at generating a comprehensive human kidney cell atlas across lifespan.

About Us:

Our research is focused on understanding what type of immune cells live within different organs in humans, and how the special environment within each tissues affects their function. We are particularly interested in the kidney and urinary tract. This research is part of the Human Cell Atlas initiative, which has set out to create a comprehensive reference map of all human cells as the basis for understanding human health and diagnosing, monitoring and treating disease. I also have a lab based at the University of Cambridge where we conduct complementary research http://www.med.cam.ac.uk/clatworthy/<>< a=""> />
About You:

You must be familiar with genomics, and will play a vital role in writing up studies. You will have the opportunity to be embedded in a large community of computational and experimental scientists. You will be integrated in the Clatworthy lab, a highly collaborative, international work environment with well-experience colleagues in single-cell and spatial data production, analysis and methods development

As a Postdoctoral Fellow in the Cellular Genetics Programme, you will be joining a collaborative and cutting-edge environment. The Programme encourages everyone to network and to showcase their research, including at our weekly seminar series. In addition to support from the Sanger core areas of Scientific Operations, Management Operations and ICT, within the Programme the Cellular Genetics Operations teams provide comprehensive multidisciplinary support to help with everything from processing samples, delivering analysis pipelines, to assistance with fellowship applications. The Sanger Institute also supports PDFs by offering various training opportunities, chances to network, and has a PDF committee in place to ensure our PDFs are supported throughout their posts.

For relevant publications of the team associated to this work, please, see:

Stewart BS, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL, Staniforth JU, Vieira Braga FA, Botting R, Popescu DM, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Polanski K, Efremova M, Green K, Velasco-Herrera M, Guzzo C, CollorD G, Mamanova L, Aho T, Armitage JN, Riddick AC, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, LisgoS, Lindsay S, Bajenoff M, Warren AY, Stewart GD, SebireN, Coleman N, Haniffa M*, Teichmann SA*, Behjati S*, Clatworthy MR*. Spatio-temporal immune zonation of the human kidney. Science 2019;365(6460):1461-1466.
Stewart BJ, Clatworthy MR. Applying single-cell technologies to clinical pathology: progress in nephropathology. J Pathol. 2020 Mar 3. doi: 10.1002/path.5417. PMID:32125696
Stewart BJ, Ferdinand JR, Clatworthy MR. Using single-cell technologies to map the human immune system - implications for nephrology. Nat Rev Nephrol. 2019 Dec 12. doi: 10.1038/s41581-019-0227-3.
Jing C, Castro-Dopico T, Richoz N, Tuong ZK, Ferdinand JR, Lok LSC, Loudon KW, Banham GD, Mathews RJ, Cader Z, Fitzpatrick S, Bashant KR, Kaplan MJ, Kaser A, Johnson RS, Murphy MP, Siegel RM, Clatworthy MR. Macrophage Metabolic Reprogramming Presents a Therapeutic Target in Lupus Nephritis. Proc Natl Acad Sci U S A. 2020 Jun 15:202000943.
5. Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu DM, Loudon KW, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Del Castillo Velasco-Herrera M, Guzzo C, Richoz N, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Maxwell PH, Lindsay S, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M*, Teichmann SA*, Clatworthy MR*, Behjati S*. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science. 2018 Aug 10;361(6402):594-599. *Co-corresponding authors.
Essential Skills
Technical Skills:

PhD in relevant discipline (e.g. Systems Immunology, Computational Biology, Genetics, Bioinformatics, Physics, Engineering or Mathematics)
Proven understanding and experience in the fields of genomics, data processing and high-throughput data analysis
Good experience in Single Cell Analysis and Spatial Genomics Tools
Good record of publications
Experience developing statistical methods for the analysis of large data sets, particularly constrained generalized linear models and machine learning methods such as regularised logistic regression, decision trees, or support vector machines
Behavioural Competencies:

Motivation and ambition to make a personal contribution to GRL research
Excellent communication skills to allow efficient interactions with collaborators
Team player with the ability to work with others in a collegiate and collaborative environment
Ability to effectively prioritise, multi-task and work independently
Demonstrates inclusivity and respect for all
Ideal Skills
Experience with single cell RNAseq and/or image data analysis

Other information
Application Process:

Please apply with your CV and a Cover letter outlining your suitability for the role, addressing the criteria set out above and in the job description.

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