Bioinformatician – Microbial Genomics


Based at East Malling in Kent, NIAB EMR is an internationally renowned plant science organisation conducting research on horticultural crops and their interactions with the environment, with particular emphasis on perennial and clonally propagated fruit crops. NIAB EMR is part of The NIAB Group, the UK’s fastest growing crop science organisation, with rapidly expanding research capabilities in plant genetics, agronomy, farming systems and data science, the largest national field trials capability, and strong research links with industry, Government and academia. Employing more than 400 people across the UK, NIAB provides scientific research, technical services and practical advice to improve the yield, efficiency and resilience of crop production across the arable, forage and horticulture sectors.

(Fixed Term for 3 years with the possibility of becoming a permanent post)

NIAB EMR carries out research across the supply chain in perennial crop species and their pests and pathogens. We are seeking an innovative, motivated and enthusiastic individual to contribute microbial genomics and bioinformatics analysis to BBSRC-funded multidisciplinary research into microbes and plant-microbe interactions. Specifically, projects include analysis of growth responses to light and temperature in the fungal pathogen, Verticillium dahliae, and analysis of secondary metabolism in the fungus, Fusarium venenatum.

The appointee will join the Genetics, Genomics and Breeding (GGB) Department; one of three research departments within NIAB EMR. In the wider department there is a strong emphasis on using statistical genomics approaches to understand the genetic basis of complex traits in plants, and functional genomics approaches to characterise pathways important in virulence and metabolism in bacterial, fungal and oomycete pathogens.

The GGB department is a collaborative environment and scientists are multidisciplinary (genetics, breeding, imaging, biochemistry, pathology and physiology). The post holder will be expected to collaborate, integrate, and communicate with the wet-lab scientists conducting experiments and generating the data. This post holder will play a full role in hypothesis generation and collaborative experimental design.

This post is a three year position at NIAB Band D (postdoctoral level) and is subject to a six month probationary period. The minimum requirement for this post is a PhD in bioinformatics (or a heavily informatics-based PhD), or another computational discipline (with additional experience in biology/informatics). An understanding of working on a high performance computer cluster, use of version control and scripting in python (or another appropriate language) are key.

The successful applicant will work across two BBSRC-funded projects in the area of microbial functional genomics and plant-microbe interactions. Key tasks include:

• Genome annotation of fungal genomes – metabolic pathway annotation
• Analysis of RNA-seq transcriptome timecourse and multiple treatment data
• Structural analysis of genomes and identification of regions of the genome undergoing rapid re-arrangement
• Analysis of ChIP-Seq datasets

The successful candidate will also assist with national and international collaborations and in time (subject to performance), be given the opportunity to prepare grant proposals at appropriate levels to attract research funding and develop their own independent research path. The desire to prepare high quality submissions to journals will be expected and an ability to communicate and present to both scientific and industry audiences is also essential.

Job Summary

A bioinformatician is required to undertake genomics research on a range of filamentous fungi. Much of the research undertaken will work towards investigating the regulatory networks involved in the virulence of pathogens and regulation of secondary metabolism. The successful applicant will work across a number of BBSRC funded research including:

BBSRC grant – BB/P020364/1 Mycoprotein 2.0- a project aimed at characterising transcriptional regulation in response to changing carbon and nitrogen sources in the fungus Fusarium venenatum.

BBSRC grant – BB/R008191/1 How do light and temperature affect lifecycle, development and pathogenicity in Verticillium? – aimed at characterising the circadian clock and regulation of perception of light and temperature.

BBSRC grant – BB/P000851/1- The nature of resistance to Neonectria ditissima in apple species- a project to characterise pathogen virulence factors and host responses in Malus species.

An interest in the evolutionary dynamics of host-pathogen interactions would be highly desirable.

The principal duties of the appointee will include:

• Analysis of RNA-seq transcriptome timecourse data in order to identify genes and regulatory motifs which are implicated in perception of light, temperature, carbon and nitrogen. Analysis of gene regulatory networks is an important component of this work, linking expression to transcription factor.
• Analysis of ChIP-seq data.
• Protein function prediction and genome annotation through comparative genomics approaches- a focus on promoter motif analysis and metabolic pathways analysis will be major tasks.
• Developing national and international collaborations with other organisations involved in genomics and bioinformatics research on horticultural crops.
• Publishing results in high impact refereed journals and giving presentations at national and international conferences.

Proficiency in: Python is essential as well as knowledge of the R statistic environment. Experience with mySQL is desirable.

It is not expected that candidates will meet all of the skills in these key areas, however a keen desire to learn is essential.

Job Requirements and Person Specification

Attainments and qualifications

Essential Elements:
• Good honours degree and PhD in Bioinformatics (or a heavily informatics-based PhD, or other computational discipline (with additional experience in biology/informatics).
• Proficiency in:
Maintaining code (version control)
• Good publication record in quality referred journals.

Desirable Elements:
• Experience in project management.
• Experience in writing successful grant proposals

Experience and Knowledge

Essential Elements:

• Skills and experience in bioinformatics techniques including genome assembly, gene prediction and RNA-seq.
• Sound understanding of next generation sequencing and its applications.
• Understanding of theoretical underpinning of sequence alignment and population genetics analysis of sequence variation.
• Linux expertise including file systems, shell, hardware/software monitoring etc.
• An understanding of working on a high performance computer cluster, use of version control and scripting in python (or another appropriate language).

Desirable Elements:

• Population genetics experience.
• Detailed understanding of frequentist and Bayesian statistics and its application to population genetics and/or sequencing data.

Skills and Attributes

Essential Elements:
• Ability to innovate and develop ideas into grant proposals.
• Ability to write concise and timely scientific papers and reports.
• Must be able to plan and prioritise work effectively to meet deadlines.

Desirable Elements:

• Good presentation skills and talent for technology and knowledge transfer.
• Aptitude for international collaboration.
• Ability to interact with industry partners and explain complex ideas to non-scientists in an understandable way.

Special Requirements

Essential Elements:
• Willingness to travel overseas as required for international collaboration.
• Willingness to work flexibly to deal with seasonal peaks in activity.

The full time appointment will be on Pay Band 6 £28,125 to £32,422 or Pay Band 5 £33,696 to £35,915 per annum, dependent on qualifications and experience, 25 days annual leave plus 8 days public holidays, work in a pleasant collegial environment and have eligibility to join the company pension scheme upon appointment.

Further details and an application form can be obtained by e-mail from Please include a detailed CV with your application. Please contact Richard Harrison for informal enquiries. Closing date: 23rd March 2018

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