Postdoctoral Research Scientist (Novel statistics and bioinformatics for microbiome analysis)
Post Details
Job Title
Postdoctoral Research Scientist (Novel statistics and bioinformatics for microbiome analysis)
Post Number
1004087
Closing Date
3 Nov 2022
Grade
SC6
Starting Salary
£33,050 - £40,750
Hours per week
37
Project Title
Novel statistics and bioinformatics for microbiome analysis
Expected/Ideal Start Date
12 Dec 2022
Months Duration
36
Interview Date
18 Nov 2022

Job Description

Main Purpose of the Job

We are looking for an individual with a high-level of quantitative skills to develop novel statistics and bioinformatics for the analysis of microbiome data. The position will be based within Dr Quince’s group at the Earlham Institute (https://www.earlham.ac.uk/quince-group).

The individual will be given considerable freedom but the overall aim will be to improve methods for de novo strain level analysis from metagenome data. Potential areas of research include Bayesian reconstruction of strain level genomes from metagenomes using probabilistic graphs and development of predictive mechanistic strain-level microbial community models through integration of other 'omics data.

To address these problems the individual will be expected to apply methods from Bayesian statistics and machine learning including variational inference and MCMC. The development of predictive models may incorporate aspects of dynamical systems e.g. ODEs and SDEs in addition to metabolic modelling.

These new tools will be applied to a variety of microbiome data sets studied in the group including coupled metagenome metabolome samples to understand the role of therapeutic diets in the treatment of Crohn’s disease, the transmission of AMR through the human and murine gut and the phyllosphere microbiome.

Key Relationships

Dr Quince (PI) and Drs Gaetan Benoit, Rob James and Seb Raguideau (co-workers).

Main Activities & Responsibilities

Develop statistical methods for strain resolution
Develop bioinformatics pipelines for the analysis of microbiome data
Develop new tools for statistical analysis of integrated 'omics data sets
Manage pipeline software on repositories
Collaborate with colleagues within and outside the Institute to apply these methods to metagenome studies
Disseminate research findings through attendance at international conferences
Regularly publish results as manuscripts in leading scientific journals or through other relevant media
Organise generation of new integrated 'omics data sets
As agreed with line manager, any other duties relevant to and commensurate with the nature of the role

Person Profile

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
Command line bioinformatics
Essential
Basic understanding of statistics
Essential
Knowledge of software programming in at least one language e.g. R, Python, C/C++
Essential
Bioinformatics of metagenomics or metabolomics
Desirable
Bayesian statistics and probabilistic modelling
Desirable
Biological understanding of microbial communities
Desirable
Understanding of metabolism
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 verbal
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 Essential required
Essential

Who We Are

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

The Quince group at EI focusses on experimental methods and bioinformatics for high resolution microbiomics.

Management and Leadership

Requirement
Importance
Ability to manage junior team members such as graduate students
Desirable

Living in Norfolk

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Postdoctoral Research Scientist (Novel statistics and bioinformatics for microbiome analysis)

Applications are invited for a Postdoctoral Research Scientist to join the Laboratory of Dr Quince in the High-Resolution Microbiomics group at the Earlham Institute, based in Norwich, UK.

Background:

The position will be based within Dr Quince’s High Resolution Microbiomics group at the Earlham Institute (https://www.earlham.ac.uk/quince-group). The group uniquely focusses on both theoretical and experimental methods for microbial community analysis. Combining statistical bioinformatics with technological developments in sequencing and ‘omics data generation to resolve both the microbes present in a community and their functional roles and interactions.  

The role:

The aim will be to improve methods for de novo strain level analysis from metagenome data. Potential areas of research include Bayesian reconstruction of strain level genomes from metagenomes and development of predictive mechanistic microbial community models through integration of other 'omics data. To address these problems the individual will be expected to apply methods from Bayesian statistics and machine learning. The development of predictive models may incorporate aspects of dynamical systems in addition to metabolic modelling. 

These new tools will be applied to a variety of microbiome data sets studied in the group including coupled metagenome metabolome samples to understand the role of therapeutic diets in the treatment of Crohn’s disease, the transmission of AMR through the human and murine gut and the phyllosphere microbiome. 

The ideal candidate:

The ideal candidate will have PhD in bioinformatics or statistics, or a related subject area with strong element of statistical modelling. They will also have a First-class degree in any area of science. 

Knowledge of command line bioinformatics, software programming in at least one language (e.g. R, Python, C/C++) and a basic understanding of statistics are essential requirements for this role. 

A proven record in scientific writing with experience of oral research presentations are also essential. 

Knowledge of Bayesian statistics and probabilistic modelling, bioinformatics of metagenomics or metabolomics and a biological understanding of microbial communities and metabolism would be advantageous.

Additional information:

Salary on appointment will be within the range £33,050 to £40,750 per annum depending on qualifications and experience.  This is a full-time post for a contract of 36 months.

Interviews will be held on 18th November 2022.

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 3 November 2022.