Applications Bioinformatician

Oxford Nanopore Technologies; Oxford; Hybrid; GBP 55,000 - 85,000; Full time

Benefits offered by this job

Bonus

Private healthcare

Pension contributions

Job summary

Oxford Nanopore Technologies seeks an Applications Bioinformatician to join the Proof of Concept Clinical Applications team in Oxford. You will interpret sequencing data from lab scientists and develop proof-of-concept workflows across human disease contexts, collaborating with the wider Applications group to share expertise.

The role is hybrid with in-office presence required at least two days per week, supporting the nanpore sensing platform and advancing sequencing analytics for clinical

Qualifications

• MSc or equivalent with DNA/RNA sequence data analysis experience.
• Undergraduate degree in Biological Science or Computer Science; PhD beneficial.
• Track record of bioinformatics sequence analyses on multiple projects.
• Experience handling large human datasets, preferably clinical research data.

Responsibilities

• Initial investigations of sequencing data to evaluate experimental designs.
• Evaluate bioinformatics tools for applications and perform custom analyses as needed.
• Independently deliver analysis tasks while escalating blockers as needed.
• Support development of proof-of-concept analyses and provide guidance on design and interpretation.
• Develop initial proof-of-concept pipelines for DNA, cDNA and direct RNA sequencing data.
• Collaborate with lab scientists to interpret data and report results to stakeholders.

Skills

Python

R

Data visualization

HPC

Bioinformatics

Sequence analysis

Terminology: file formats

Git

Education

MSc in Bioinformatics

Biological Science degree

Undergraduate in CS or Biology

PhD beneficial

Tools

samtools

bedtools

IGV

Conda

Git/GitHub/GitLab

Job description

About Us

Our goal is to bring the widest benefits to society through enabling the analysis of anything, by anyone, anywhere.

Job Description

Oxford Nanopore Technologies

Location: Oxford, UK

Role Type: Full time, hybrid

Our goal is to bring the widest benefits to society through enabling the analysis of anything, by anyone, anywhere. The company has developed a new generation of nanopore-based sensing technology for faster, information rich, accessible and affordable molecular analysis. The first application is DNA/RNA sequencing, and the technology is in development for the analysis of other types of molecules including proteins. The technology is used to understand and characterise the biology of humans and diseases such as cancer, plants, animals, bacteria, viruses, and whole environments.

With a thriving culture of ambition and strong innovation goals, Oxford Nanopore is a UK headquartered company with global operations and customers in more than 125 countries.

We are looking for an individual with expertise in bioinformatics, with particular experience of working with human sequencing data, to join our Applications team as an Applications Bioinformatician.

The Role

The Proof of Concept Clinical Applications team works within R&D to evaluate the feasibility of novel applications of Oxford Nanopore sequencing examining human disease, with a particular focus on rare disease.

As a member of the Proof of Concept Clinical Applications team, the successful candidate will primarily interpret sequencing data generated by lab scientists within the team, in a range of biological contexts aiming to showcase the abilities of the technology and develop proof of concept workflows to fill market niches. You should also be prepared to work with others across the wider Applications group to share expertise and collaborate where appropriate and to communicate your findings to internal stakeholders through presentations, reports and discussions in meetings.

As this role is within a multi-disciplinary team, the position is offered as hybrid, with an expectation of being in the Oxford office at least two days a week.

Main Responsibilities Include

• Initial investigations of sequencing data to identify the potential of an experimental design.
• Performing evaluation of appropriate bioinformatics tools for a given application, and carrying out defined custom analysis where needed.
• Independently deliver assigned analysis tasks while escalating priorities, design decisions and blockers.
• Support evaluation and development of defined proof-of-concept analyses; seek guidance on analysis design, interpretation and roadblocks.
• Developing initial proof-of-concept pipelines for analysis of DNA, cDNA and direct RNA sequencing data using ONT's nanopore sensing platform, with regular guidance from a senior bioinformatician/manager, including task prioritization and mentoring.
• Working collaboratively with laboratory-based scientists in the group to contribute suggestions on experimental design, to interpret the data generated in the appropriate biological context, and to report the results clearly.
• Working with the team to make analysis and figure contributions to conference talks and posters.
• Working closely with other applications groups in different locations to keep up-to-date with the latest developments, provide feedback and incorporate them into analyses where appropriate.

What We're Looking For…

To be successful you'll have an MSc or equivalent experience, involving analysis and visualization of DNA and RNA sequence data, plus an undergraduate degree in a Biological Science or Computer Science. Additionally, having a PhD or job experience in a relevant field would be beneficial.

We'll expect you to have a track record of successfully performing appropriate bioinformatics sequence analyses for at least a couple of research projects and awareness of the whole experimental process, from the initial experimental concept to biologically meaningful results. In addition, you'll have some practical experience of handling and analysing large human datasets, ideally in a clinical research setting. An awareness of the concepts of assembly, phasing and variant calling, and how to perform them would be beneficial. You would be working closely with lab scientists to continually refine the experimental and analytical approaches. Therefore, the role is a mixture of collaboration for project design and independent analysis, though the bioinformatics will be supported as appropriate. An important part of the role is also keeping up to date with advances in genetics and genomics.

Specific technical experience that would be expected for the role:

• Programming experience (python, R)
• Graphical visualisation experience
• Experience of using a terminal interface, HPC and scheduling
• Familiarity with common bioinformatics file formats
• Experience with common bioinformatic tools (e.g. samtools, bedtools, IGV)
• Package management (conda)
• Version control (git, Github/Gitlab)

Specific technical experience that would be beneficial for the role:

• Experience with Oxford Nanopore sequencing data
• Experience with human clinical data regulations
• Experience with assembly, phasing and/or variant calling
• Claude or Codex experience
• Workflow management systems (nextflow, snakemake)
• Cloud usage (AWS EC2 and s3)
• Statistics

You're also someone with good communication and interpersonal skills with an enthusiasm for technology. You feel confident discussing and presenting data within the team and with other colleagues. You are versatile, have excellent problem-solving and time management skills and the ability to work on multiple projects simultaneously. It will be important to be able to work efficiently both independently, supported by regular check-ins, and as part of a team.

This role will suit a curious, organized individual with the ability to adapt based on changing business needs and looking for a supportive environment in which to further develop their skills.

We offer outstanding benefits to include an attractive bonus, generous pension contributions, private healthcare and an excellent starting salary. Based within beautiful, landscaped surroundings with tree-lined walks, water features and a lake, all of which make for a wonderful working environment.

Please note that no terminology in this advert is intended to discriminate on the grounds of a person's gender, marital status, race, religion, colour, age, disability or sexual orientation. Every candidate will be assessed only in accordance with their merits, qualifications and abilities to perform the duties of the job.

About Us

Oxford Nanopore Technologies: Our goal is to bring the widest benefits to society through enabling the analysis of anything, by anyone, anywhere. The company has developed a new generation of nanopore-based sensing technology for faster, information rich, accessible and affordable molecular analysis. The first application is DNA/RNA sequencing, and the technology is in development for the analysis of other types of molecules including proteins. The technology is used to understand and characterise the biology of humans and diseases such as cancer, plants, animals, bacteria, viruses, and whole environments. With a thriving culture of ambition and strong innovation goals, Oxford Nanopore is a UK headquartered company with global operations and customers in more than 125 countries.