- Job Title
- Bioinformatician (Analysis pipelines)
- Post Number
- Closing Date
- 3 Aug 2021
- Starting Salary
- £32,255 - £39,345
- Hours per week
- Project Title
- Single Cell Analysis
- Expected/Ideal Start Date
- 23 Aug 2021
- Months Duration
Main Purpose of the Job
Establish pipelines to assess data quality and provide analysis of single cell genomic, epigenomic and transcriptomic sequencing data. Working with faculty groups, the genomic pipelines team and external collaborators to deliver analysis on a diverse array of biological systems, including plant, microbial and animal studies. Supporting technical development in single cell genomics and working with datasets arising from novel experimental techniques including multi-omics analysis.
Reporting to the Core Bioinformatics group leader and interacting on a daily basis with members of the Swarbreck group. Technical Development group leader and lab members (Macaulay group) Faculty computational biologists including the Haerty group. Genomics Pipelines team, Institute and Faculty collaborators.
Main Activities & Responsibilities
- Analysis of next generation sequencing data derived from single cells. This will include developing, testing and optimisation of methods for quality control, mapping and subsequent analysis of single cell genome, epigenome and transcriptome sequencing data.
- Working with faculty to deliver timely analysis of datasets on projects at all stages, from inception to completion and publication.
- Installation and setup of analytical pipelines (e.g 10x genomics) as well as open source and in-house developed tools.
- Participate in the development of novel tools and pipelines to analyse single cell and bulk sequencing data.
- The role will be involved in designing, building, extending and automating pipelines, performing high-quality bespoke data analysis across a range of applications and species and expanding our sequencing QC workflows.
- As agreed with line manager, any other duties commensurate with the nature of the post
Education & Qualifications
- PhD in bioinformatics, computational biology or related subject
- Strong background in large scale data analysis
Specialist Knowledge & Skills
- Good knowledge of programming languages including Perl, R, Linux and/or Python
- Transcriptomics, genomics or epigenomics analysis skills
- Excellent problem solving skills with the ability to solve problems with numerous and complex variables
- Familiarity with statistics
- Excellent record-keeping and time management skills to work on several different projects at the same time
- Knowledge of pipeline frameworks such as Snakemake, Nextflow or Cromwell
- Working on genomics and transcriptomics data and bioinformatics
- Next generation sequencing (RNA-Seq, DNA-Seq) and large-scale data analysis
- Working on externally funded projects
- Experience with Pipeline workflow programming
- Familiarity with working in a high-performance computing environment
- Single cell analysis
Interpersonal & Communication Skills
- Excellent oral and written communication skills
- Excellent interpersonal skills with the ability to work well in a team
- Good organisational skills
- Able to communicate with an interdisciplinary group including data analysts, computer scientists and biologists
- Networking and influencing skills and the ability to build effective collaborative links
- Evidence of presenting research findings to internal and external audiences
- Attention to detail
- Promotes equality and values diversity
- 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
- Willingness to participate in occasional training of other institute members and visitors, and as part of formal training programmes hosted at the institute
- Must be able to travel and work a non-conventional work pattern on occasion
Who We Are
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.
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 is involved in the analysis of sequence data from a wide variety of sequencing platforms and works alongside Earlham research groups to establish new software tools and analysis methods.
Living in Norfolk
Bioinformatician (Analysis pipelines)
The Core Bioinformatics Group at the Earlham Institute (EI, Norwich, UK) is looking for an enthusiastic and dedicated Bioinformatician 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 successful candidate will join the group of Dr. David Swarbreck and work closely with wet and dry lab scientists in the groups of Dr. Iain Macaulay and Dr. Wilfried Haerty. The post-holder will establish and implement pipelines and processes for the analysis of genome, epigenome and transcriptome data from a wide variety of biological systems and technology platforms. The role will be involved in designing, building, extending and automating pipelines, performing high-quality bespoke data analysis across a range of applications and species and expanding our sequencing QC workflows.
The role will have a specific focus on delivering and growing the single-cell data analysis capability in conjunction with faculty groups, the genomic pipelines team and external collaborators. The postholder will be able to contribute to established and upcoming projects at the institute, and be involved in experimental design, data analysis and preparation of manuscripts for publication. Examples of some of our recent single-cell work can be found here:
Combined single-cell gene and isoform expression analysis in haematopoietic stem and progenitor cells (Laura Mincarelli, Vladimir Uzun, Stuart A. Rushworth, Wilfried Haerty, Iain C. Macaulay)
Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies (Matt Bawn, Johana Hernandez, Eleftheria Trampari, Gaetan Thilliez, Mark A. Webber, Robert A. Kingsley, Neil Hall, Iain C. Macaulay)
The ideal candidate:
The successful candidate will possess a PhD in computational biology, ideally having a strong background in large scale data analysis and be highly motivated to contribute to the development of single-cell platforms and analysis at the institute.
They will have demonstrated experience of transcriptomic, genomic or epigenomic data analysis, experience of single-cell data analysis is beneficial but is not a requirement. They will also possess a good knowledge and demonstrable experience of Perl, Python and R scripting, familiarity with working in a high-performance computing environment and knowledge of pipeline frameworks such as Snakemake, Nextflow or Cromwell is desirable. The ideal candidate will also be highly collaborative, comfortable working with diverse projects and datasets, and have experience of successfully managing their time to deliver analysis and input into multiple projects.
Salary on appointment will be within the range £32,255 to £39,345 per annum depending on qualifications and experience. This is a full-time post for a period of 3 years.
As a Disability Confident employer, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy.
The closing date for applications will be 3rd August 2021.