Bioinformatician (Single Cell Analysis)

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Earlham Institute

Earlham Institute is a vibrant, contemporary research institute and registered charity, working in an area of rapid technological development and innovation.

Earlham Institute is strategically funded by the BBSRC to lead the development of a skill base in bioinformatics and a genomics technology platform for UK bioscience. The Institute is located on the Norwich Research Park, together with its partners: the John Innes Centre, the Institute of Food Research, The Sainsbury Laboratory, the University of East Anglia and the Norfolk and Norwich University Hospital. The research park has an excellent reputation for research in plant and microbial sciences, interdisciplinary environmental science and food, diet and health, to which Earlham Institute contributes strengths in genomics and bioinformatics. Close links exist between the NRP partners and new opportunities for collaboration in exciting new initiatives are under development. The NRP recently received £26M of government investment to facilitate innovation and further develop infrastructure to attract science and technology companies to the Park to enhance the vibrant environment and realise economic impact from research investment.

Earlham Institute is a UK hub for innovative Bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. This has been boosted recently by an e-Infrastructure grant to expand the data storage capacity to a multi-petabyte unit, deploying a high performance cluster and large-memory server enabling the allocation of processes requiring several terabytes of computing memory.

Earlham Institute’s state of the art DNA sequencing facility operates multiple complementary technologies for data generation that provide the foundation for analyses furthering our fundamental understanding of genomes and how they function. We aim to be at the forefront of technological advances and are developing and implementing technologies to generate and analyse new types of data. We also develop novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational bioscience. Earlham Institute has one fully owned subsidiary, Genome Enterprise Ltd (GEL) via which it offers genomic and bioinformatics services on a trading basis and works with commercial providers on a partnership basis. Earlham Institute also receives specific funding to enable knowledge exchange programmes which are supported across the institute teams.

Post Details

Job Title
Bioinformatician (Single Cell Analysis)
Post Number
1003438
Closing Date
16 Sep 2018
Grade
SC6
Starting Salary
£31,250 - £38,100
Hours per week
37
Project Title
Single Cell Analysis
Expected/Ideal Start Date
01 Oct 2018
Months Duration
24

Main Purpose of the Job

Establishing pipelines to analyse single cell genomic, epigenomic and transcriptomic sequencing data. Working alongside faculty groups, the genomic pipelines team and external collaborators to deliver single cell analysis on a diverse array of biological systems, including plant, microbial and animal studies. Contributing to the preparation of manuscripts for submission. Supporting technical development in single cell genomics and working with datasets arising from novel experimental techniques including multi-omics analysis.

Department

Digital Biology

Group Details

The Core Bioinformatics Group led by David Swarbreck provides high quality computational analyses of a range of sequence data types and develops software and analysis pipelines that support the Institute's Core Strategic Programmes and National Capability in Genomics and Single Cell Analysis (NCGS). The National Capability provides access to state of the art genomics technologies for research groups throughout the UK as well as delivering sequencing and genomics services to the associated Science Faculty groups and commercial customers. The group are involved in the analysis of sequence data from a wide variety of sequencing platforms and work alongside Earlham research groups to establish new software tools and analysis methods.

Advert Text

Applications are invited for an enthusiastic and dedicated Bioinformatician to join the Core Bioinformatics Group at the Earlham Institute (EI).

Background:

Earlham Institute is a research institute focused on exploring living systems by applying computational science and biotechnology to answer ambitious biological questions and generate enabling resources.

EI employs cutting edge technologies and computational approaches to deliver high-quality data analysis and develop software and analysis pipelines that support the Institute’s Core Research Programmes and UK Research community via the National Capability in Genomics and Single Cell Analysis (NCGS).

The role:

This position provides an opportunity to gain expertise in new sequencing technologies and their application in an exciting and emerging field. The successful candidate will work closely with our technical development team to develop and apply new technology to a variety of single cell applications.

The post-holder will analyse data from cutting edge technologies, establish and implement pipelines and methods for the analysis of single cell genome, epigenome and transcriptome data across a wide variety of biological systems. The post holder will deliver single cell data analysis in conjunction with faculty groups, the genomic pipelines team and external collaborators.

This is a collaborative project with the successful candidate joining the group of Dr. David Swarbreck and working closely with wet and dry lab scientists in the groups of Dr. Iain Macaulay and Dr. Wilfried Haerty.

The ideal candidate:

The successful candidate will possess a PhD or equivalent experience in computational biology, bioinformatics or similar, with a strong background in large scale data analysis, and will have demonstrated experience of transcriptomics, genomics or epigenomics data analysis. They will also possess a high level of skill and demonstrable experience of Python (preferable), Java, or C++, along with R and Bash scripting.

The ideal candidate will also be highly collaborative and have demonstrable experience of successfully managing their time to deliver analyses and input into multiple projects.

Additional information:

Salary on appointment will be within the range £31,250 to £38,100 per annum depending on qualifications and experience. This is a fulltime post for a contract for a period of 2 years

For further information and details of how to apply, please visit our web site http://jobs.earlham.ac.uk/ or contact the Human Resources team on 01603 450462 or nbi.recruitment@nbi.ac.uk quoting reference 1003438.

As a Disability Confident employer, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy.

Key Relationships

Reporting to the Core Bioinformatics group leader and interacting on a daily basis with members of the Swarbreck group, the Technical Development group leader and lab members (Macaulay group), faculty computational biologists, including the Haerty group, the Genomics Pipelines team, as well as other institute and external collaborators.

Main Activities & Responsibilities

Percentage
Analysis and interpretation of next generation sequencing data derived from single cells. This will include developing and assessing methods for quality control, mapping and subsequent analysis of single cell genome, epigenome and transcriptome sequencing data.
35
Development of novel tools to analyse and integrate data from single cell genome sequencing, single cell transcriptomics (short and long read sequencing) and various single cell epigenetic approaches.
35
Building analysis pipelines using open source and in-house developed tools as well as running commercially available analytical pipelines (e.g 10X genomics)
15
Working with EI researchers and collaborators to deliver timely analysis of single cell datasets and being involved at all stages, from inception to completion and publication.
15
As agreed with line manager, any other duties commensurate with the nature of the post

Education & Qualifications

Requirement
Importance
PhD in bioinformatics, computational biology or related subject with experience of working on genomics and transcriptomics data and bioinformatics
Essential

Specialist Knowledge & Skills

Requirement
Importance
Demonstrated skills in at least one of the following programming languages: Python (preferable), Java, C++, R
Essential
Transcriptomics, genomics or epigenomics analysis skills
Essential
Pertinent experience in Linux and in shell scripting
Essential
Excellent problem solving skills with the ability to solve problems with numerous and complex variables
Essential
Solid understanding of statistics for biology
Essential
Excellent record-keeping and time management skills to work on several different projects at the same time
Essential
Experience with Pipeline workflow programming (e.g. snakemake)
Desirable

Relevant Experience

Requirement
Importance
Genomics or genetics projects
Essential
Next generation sequencing (RNA-Seq, DNA-Seq) and large-scale data analysis
Essential
Working on externally funded projects
Essential
Single cell analysis
Desirable

Interpersonal & Communication Skills

Requirement
Importance
Excellent oral and written communication skills
Essential
Excellent interpersonal skills with the ability to work well in a team
Essential
Good organisational skills
Essential
Able to communicate with an interdisciplinary group including data analysts, computer scientists and biologists
Essential
Networking and influencing skills and the ability to build effective collaborative links
Desirable
Evidence of presenting research findings to internal and external audiences
Desirable

Additional Requirements

Requirement
Importance
Attention to detail
Essential
Promotes equality and values diversity
Essential
Must be able to travel and work a non-conventional work pattern on occasion
Essential
Willingness to interact with laboratory scientists to develop a thorough understanding of the computational challenges of single cell analysis, arising at all stages from sample collection and processing through to data QC and analysis
Essential
Willingness to participate in occasional training of other institute members and visitors, and as part of formal training programmes hosted at the institute
Essential