3-year tenure track Bioinformatician/Computational Biologist (Band D) The James Hutton Institute - Information and Computational Sciences Group (ICS) United Kingdom

The work undertaken by The James Hutton Group is right at the top of the global agenda tackling problems such as the impact of climate change and threats to food and water security.

Our Information and Computational Science Group comprises a wide portfolio of skills, working at a range of scales from molecular to global.  The Group exploits expertise in bioinformatics, geoinformatics, soil science, community planning, policy analysis, risk assessment and integrated complex systems modelling, as well as research computing and high-performance computing (HPC). The skills and experience embodied in the ICS teams enable the Group to act as leaders, integrators and enablers of complex interdisciplinary and transdisciplinary projects.

This is an exciting opportunity for a skilled and motivated bioinformatician/computational biologist to join a world-class team on a 3-year tenure track position to develop novel RNA-seq analysis methods and tools. In the first two years, the successful candidate will work within an interdisciplinary team that interacts closely with top plant research groups in University of Dundee, University of York and University of Cambridge on a BBSRC funded project to 1) develop an automated pipeline to construct comprehensive and high-quality transcriptomes for plant species using Illumina short-read sequence and single molecule long sequence data; 2) develop a transcript evaluation software suite that employs comprehensive metrics to measure and assess transcript assembly quality to identify and remove/correct mis-annotated and mis-assembled transcripts. To demonstrate the utility of the pipeline and software, the candidate will work with leading potato, tomato and lettuce research groups as exemplar crop species to improve and test the pipelines. The successful candidate will have the opportunity to become involved in a portfolio of projects funded by the Scottish Government involving RNA-seq analysis and will be encouraged to apply for their own research funding and develop their own network of collaborators to pursue their research interests. More information on the post and post holder can be found below.


Main Purpose of Job

To develop an automated pipeline (RTDBox) to construct and evaluate comprehensive RTDs for any plant species with a genome reference using Illumina short sequencing and single molecule long sequencing data.  The aim is to produce an automated pipeline which requires minimal bioinformatics expertise and computational infrastructure to run.

To develop a transcript evaluation suite (TES) that employs comprehensive metrics to measure and assess transcript annotation quality to identify and remove/correct mis-annotated and mis-assembled transcripts.

To demonstrate the utility of the pipeline and software (Purpose 1 and 2) using potato, tomato and lettuce as exemplar crop species to develop and apply RTDs.


Main Duties of Postholder

  • Coding, testing, optimization of the top performing transcript assembly tools, parameters and processes. Constructing an automated computational pipeline to construct the RTDs
  • Development of the Transcript Evaluation Suite (TES) to evaluate the transcript assemblies; Removal of mis-annotated and mis-assembled transcripts
  • Construction of RTDs for exemplary species (tomato, lettuce and potato) using the automated pipeline to test and refine the pipeline


Education/Experience/Skills

Essential

  • PhD in a related subject
  • A solid background in computational biology. 
  • Extensive experience on RNA transcript assembly, transcript quantification, differential expression analysis, alternative splicing analysis using RNA-seq for eukaryotes with in-depth understanding of the mechanism and issues of current state of art RNA-seq analysis methods.
  • Good understanding and hands-on experience with transcript assembly using long single molecule sequencing technologies, such as PacBio and Oxford nanopore sequencing
  • Proficient in running, installing and managing analysis tools under Unix system
  • Proficient programming skills to carry out customized sequence analysis using Python, R or shell scripts, with a track record in producing publicly available analytical software tools.
  • Able to work in a team


Desirable

  • Experience of handling large and complex RNA-seq datasets.
  • Strong interest and prior evidence of developing novel mathematical and computational approaches for RNA-seq analysis would be advantageous.
  • Good communication and project management skills


Additional Information

This post is available for 36 months, start date from Oct 1, 2019, after which it will migrate to a permanent position subject to evaluation.

Informal enquiries are welcome: Dr. Runxuan Zhang,

e-mail:  Runxuan.Zhang@hutton.ac.uk

Prof Robbie Waugh, e-mail: Robbie.waugh@hutton.ac.uk


The James Hutton Institute is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees. As they are under-represented in this area of our work we would particularly welcome applications from women.


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