Main Purpose of the Job

We are looking for an individual with a high-level of quantitative skills to develop novel algorithms for analysing metagenomics data. The study of microbiomes has revolutionised our understanding of the microbial world but tools capable of extracting individual genomes from complex communities are still lacking. Methods for genome binning can use shared features of contigs from metagenome assemblies to generate species bins but these will be composites of multiple closely related organisms. Instead we will develop methods that work directly on assembly graphs, exploit a combination of novel sequencing technologies, correlations in time series, and recent algorithmic developments to resolve genomes to the strain level. We will also explore the incorporation of Hi-C and single cell data to enable plasmids to be linked to genomes. The ideal candidate would combine a knowledge of metagenomics assembly, Bayesian modelling and software development but excellence in any of these areas would be sufficient.

Key Relationships

Internal: Dr Christopher Quince and additional group members to be recruited.
External: Collaborators, funders, scientists in UK and international academia.

Main Activities & Responsibilities

Develop novel algorithms for metagenomics strain resolution.

Maintain and create software pipelines for metagenome analysis.

Incorporate long reads and other novel technologies into metagenomics assembly and binning.

Collaborate with colleagues within and outside the Institute to apply these methods to metagenome studies.

Maintain an in-depth knowledge of the bioinformatics literature applied to metagenomics.

Disseminate research findings through attendance at international conferences.

Regularly publish results as manuscripts in leading scientific journals or through over relevant media.

As agreed with line manager, any other duties relevant to and commensurate with the nature of the role.

Education & Qualifications

Requirement

Importance

PhD in bioinformatics or statistics or related subject area with strong element of statistical modelling

Essential

First degree in any area of science

Essential

Specialist Knowledge & Skills

Requirement

Importance

Knowledge of software programming in at least one language e.g. R, Python, C/C++

Essential

Understanding of basic statistics

Essential

Bayesian probability

Desirable

Experience with genome/metagenome assembly

Desirable

Command line bioinformatics in Linux and shell

Desirable

Relevant Experience

Requirement

Importance

Proven record in scientific writing

Essential

Experience of oral research presentations

Essential

Preparing data / information for grant proposals

Desirable

Experience developing software for genomics or metagenomics

Desirable

Interpersonal & Communication Skills

Requirement

Importance

Excellent communication skills both written and oral

Essential

Good interpersonal skills, with the ability to work as part of a team

Essential

Demonstrated ability to work independently, using initiative and applying problem solving skills

Essential

Ability to follow instructions/Standard Operating Procedures

Essential

Additional Requirements

Requirement

Importance

Attention to detail

Essential

Promotes equality and values diversity

Essential

Able to present a positive image of self and the Institute, promoting both the international reputation and public engagement aims of the Institute

Essential

Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to work

Essential

Willingness to work outside standard working hours when required

Essential

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.

Department

Organisms and Ecosystems

Group Details

Dr Quince's group focusses on bioinformatics and experimental methods for microbial community analysis. Combining statistical bioinformatics for problems such as strain resolution, and integrating multiple sources of 'omics data with technological developments in sequencing. These methods are applied to both simple bench top experiments with microbial communities and large scale 'omics studies. These studies span a range of environment from host associated to biotechnology applications.

Management and Leadership

Requirement

Importance

Experience managing junior group members, students etc.

Desirable

Advert Text

Postdoctoral Research Scientist (Metagenome Bioinformatics)

Applications are invited for a Postdoctoral Research Scientist to join the Laboratory of Dr Quince in the Organisms and Ecosystems Programme at the Earlham Institute, based in Norwich, UK.

Background:

The Quince group focusses on both theoretical and experimental methods for microbial community analysis. Combining statistical bioinformatics with technological developments in sequencing and ‘omics data generation to address problems such as metagenome strain resolution and trait inference. These methods are applied to both simple bench top experiments with microbial communities and large scale 'omics studies. These studies span a range of environments from host associated to biotechnology applications.

The role:

We are looking for an individual with a high-level of quantitative skills to join a project resolving strain genomes from metagenomes. The study of microbiomes has revolutionised our understanding of the microbial world but tools capable of extracting individual genomes from complex communities are still lacking. Methods for genome binning can use shared features of contigs from metagenome assemblies to generate species bins but these will be composites of multiple closely related organisms. Instead, we will develop methods that work directly on assembly graphs, exploit a combination of novel sequencing technologies, correlations in time series, and recent algorithmic developments to resolve genomes to the strain level.

The ideal candidate:

The ideal candidate would combine a knowledge of metagenomics assembly, Bayesian statistics and software development but excellence in any of these areas would be sufficient. You will have a PhD in bioinformatics or statistics or related subject area with a strong element of statistical modelling. Knowledge of software programming in at least one language e.g. R, Python, C/C++ is essential.

Additional information:

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 contract 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 28 February 2021.