Wellcome Trust Sanger Institute

Senior Bioinformaticians x 4 - Tree of Life

Wellcome Sanger Institute

Cambridge, United Kingdom

The Tree of life is a new programme at the Wellcome Sanger Institute that will explore the evolutionary biology of genomes from across eukaryote diversity to understand pattern and process in the generation of diversity. To do this, we will generate many thousands of high quality genomes, chromosomally-resolved wherever possible, of protists, fungi, plants and animals. We are looking for up to four postdoctoral bioinformatics researchers to join Mark Blaxter’s group to work on diverse aspects of the evolution of genomes, their structure, their analysis and their presentation to the wider world.

Post 1: Phylogenomics
We aim to build a continually updated tree of life from the genomes generated in the Tree of Life programme at Sanger and elsewhere. This post will deliver software solutions to identify orthology, build alignments and compute phylogenies across all sequenced genomes. In addition to resolving a species-level tree, these data will be used to understand the dynamics of gene family change through evolution, and map the conflicting roles of introgression, hybridisation and horizontal gene transfer in producing conflict in tree estimation. The ideal applicant will have experience in both software pipe-lining in a production environment and in large scale phylogenetic inference. A keen interest in the diversity of life and understanding of the nuances of genome evolution would be desirable.

Post 2: Chromosome evolution
While organisms and genes evolve rapidly, karyotypes appear to be relatively stable. In addition, chromosomes have internal structure that persists through phylogenetic time, such that many genes have been linked on the same chromosome for many millions of years. What maintains chromosome structures through time? What does karyotypic conservatism mean for linked gene coevolution? These questions will be explored using the breadth of genomes sequenced in the Tree of Life programme across a range of evolutionary distances. The ideal applicant for this post would be a computational biologist comfortable with large data and able to develop algorithms to describe and model chromosome evolution.

Post 3: Genomes within genomes
Nearly one third of eukaryotic species are parasites, and many eukaryotes host prokaryotic endosymbionts. We have built toolkits for effective separation of cobiont genomes from their hosts, and this post will use these tools to survey and describe the diversity of symbionts within the thousands of genomes delivered by the Tree of Life programme. Do these cobionts cospeciate with their hosts, or do they jump regularly? What novel symbionts are there in the majority of unsequenced life? How do symbiont genomes evolve? The ideal applicant would be comfortable with genome assembly and interpretation, and in particular have an interest in investigating pattern and process in symbiont genome evolution.

Post 4: GenomeHubs
We are developing a genome databasing package, GenomeHubs (see https://genomehubs.org) based on Ensembl, that communities of researchers can use to deliver custom solutions for sharing and analysis of genome data. This post is for a curator/developer who will support our several taxon-oriented communities in installing and maintaining their instances of GenomeHubs, train users (including generating online training materials), and assist in the development of new functionality. The post will involve considerable travel and collaborative working, and so the ideal applicant will have experience in programming and genomics databasing and a desire to communicate and train a diversity of fellow scientists worldwide. This position is funded in part by the UK BBSRC.

General
The post holders will work closely with others in the Tree of Life programme and Mark Blaxter’s evolutionary genomics group. Within the underpinning need to deliver a whole solution to their overarching goals, all the posts will have independence in defining research focus and in establishing key collaborations.
All posts are for 3 years in the first instance, with prospect for extension.
For informal enquiries please email mark.blaxter@sanger.ac.uk

Essential Skills
• Experienced in independently solving bioinformatics problems, either as part of PhD work or demonstrated by several years of on-the-job training
• Good programming skills, preferably Python; Proficiency in Unix/Linux operating system
• Experience with managing and processing next-generation sequencing data
• Experience in genome assembly and quality assessment, and in genome interpretation
• Experience and understanding of large-scale phylogenetic inference
• Strong grounding in evolutionary genomics, genome biology and population genetics
• Excellent communication skills
• Attention to detail and highly developed problem solving skills

Ideal Skills
• Experience with using relational database systems
• Experience with using compute cluster and batch queuing systems
• Experience with workflow engines and languages
• Experience with software version control systems
• Knowledge of biodiversity and comparative evolutionary analysis of sequence data
• Experience with genome annotation methodologies and pipelines
• Proficient in writing research manuscripts and reports

Other information
Closing Date: 30th November 2019

About Us
The Wellcome Sanger Institute is a world leading genomics research centre. We undertake large-scale research that forms the foundations of knowledge in biology and medicine. Our findings are used to improve health and to understand life on Earth. Find out more at www.sanger.ac.uk or follow us on Twitter, Facebook, LinkedIn, Youtube and on our Blog.

Our campus
Set across 130 acres, just outside of Cambridge, The Sanger Institute is located on the stunning Wellcome Genome Campus. Home to some of the world’s foremost institutes and organisations in genomics and computational biology, committed to delivering life-changing science with the reach, scale, and creativity to solve some of humanity’s greatest challenges.

Our benefits:
There’s an attractive benefits package on offer at the Genome Wellcome Campus. We appreciate the importance of achieving work-life balance and support this with a number of family and carer-friendly policies. Plus a flexible working policy for those who may wish to amend their working pattern or arrangement.
As well as the usual benefits you would expect, we go much further:
• 25 days annual leave (extra 1 day to a maximum of 30 days for every year you work)
• Auto-enrolment into a generous Group Defined Contribution Pension Scheme, with enhanced company contribution (for more information, see our Pensions page)
• Up to 2 days annual paid volunteering leave
• Up to 10 days paid Emergency Carers Leave per year
• Family friendly environment including options for flexible and part-time working, an on-site Workplace Nursery salary Sacrifice Schemes for pre-school children and Summer holiday club
• Life Assurance Cover and a Group Income Protection Scheme (if on a contract of 12 months or more)
• Enhanced maternity leave and parental leave
• Access to substantial number of courses and training events onsite
• Private Healthcare Scheme (after 6 months service)
• Eyecare and Dental payment plans
• Concessions and discounts from our corporate perks site

Being part of the Genome Wellcome Campus you will be part of the beautiful working environment with an impressive range of benefits, services and facilities also including:
• Free bus service to and from Campus, covering various routes around Cambridge, Saffron Walden and surrounding villages
• A car-share initiative
• Free parking
• A number of on-site venues where you can meet, eat and socialise with colleagues
• A thriving Sports and Social Club which provides members with subsidised access to a gym, tennis courts, sports hall, fitness classes and a vibrant social calendar of events

Find out more about our Genome Wellcome Campus.

We hold an Athena SWAN Bronze Award and will consider all individuals without discrimination and are committed to creating an inclusive environment for all employees, where everyone can thrive.

Please apply via recruiter’s website.

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