Bioinformatician

European Molecular Biology Laboratory; Saffron Walden; Hybrid; GBP 60,000 - 80,000; Full time

Job summary

A leading research organization in Saffron Walden is looking for a candidate to develop and deploy systems for producing reference-quality gene annotations. You will collaborate with genomic data analysts to enhance annotations and integrate cutting-edge data. An MSc or PhD in Computer Science, Bioinformatics, or Genetics is required. The role offers a hybrid working model and a competitive salary starting at £3,303 per month with generous benefits, including private medical insurance and 30 days annual leave.

Benefits

Private medical insurance

30 days annual leave

Flexible working arrangements

Relocation package

On-site nursery

Qualifications

• Experience in producing reference-quality annotations for genomes.
• Ability to integrate primary data for gene structure and function.
• Proficiency in developing pipelines for genome annotation.

Responsibilities

• Develop annotation systems for gene validation.
• Collaborate internationally on genome projects.
• Train users in annotation methods.

Skills

Genome annotation

Machine learning concepts

Strong communication skills

Interpersonal skills

Attention to detail

Problem-solving skills

Education

MSc or PhD in Computer Science or Bioinformatics

Tools

Relational databases

Job description

Your main responsibility will be the development and deployment of annotation systems to produce and validate reference-quality gene annotations. More specifically, you will:

Responsibilities

• Work alongside genomic data analysts in the team to produce and improve reference-quality, evidence-based annotation including protein-coding genes, noncoding RNA genes
• Integrate cutting edge primary data to create and validate gene structure and function annotation.
• Develop pipelines to extend GENCODE annotation from a single reference genome to the human and mouse pangenomes
• Develop pipelines to generate training sets for machine learning initiatives.
• Maintaining a version controlled code base
• Querying databases and helping maintain/expand associated schemas
• Operate in a release-based environment and coordinate with other teams.
• Collaborate with international partners on genome projects.
• Participate in training users in our annotation methods and workflows.

You should hold an MSc, PhD, or equivalent experience in Computer Science, Bioinformatics, Genetics, or a related field.

You will be expected to write, understand, and maintain complex code.

Domain experience

• Genome annotation
• Methods for DNA/RNA sequencing and sequence alignment
• Relational databases
• Scaling and optimization
• Machine learning concepts

Behaviours we look for in our team

• Strong communication and interpersonal skills
• Ability to manage your own time and balance multiple tasks
• Excellent attention to detail and problem‑solving skills
• Ability to work effectively in a team
• Willingness to learn, develop, and adapt in a fast‑moving research environment
• Confidence communicating both biological and computational concepts, orally and in writing

Desirable

• Previous experience processing large biological data sets in a production environment is advantageous. This includes an understanding of compute clusters, pipeline workflows, software design, and automation.
• Evidence of working in a dynamic, team‑based environment or contributing to a large, shared codebase is desirable. Experience with Riboseq data is also highly desirable.

Part of Ensembl, a world leading provider of genomics data resources and bioinformatics software tools, the HAVANA team produces reference quality gene annotation for the human and mouse genomes. As part of the GENCODE project we leverage cutting‑edge technologies and develop novel approaches to ensure GENCODE provides foundational reference genome annotation for human and mouse. A Global Core Biodata Resource, GENCODE has a wide range of users from internationally significant consortia and resources to individual researchers. Our role in the Primary Annotated Resources to Advance Discovery In Genomic Medicine (PARADIGM) consortium is to ensure that gene annotation is optimised to support genomic medicine, for example through our collaboration with NCBI RefSeq to produce the Matched Annotation from NCBI and EMBL-EBI (MANE) transcript set.

Our team comprises both genomic data analysts and bioinformatics developers, working together to incorporate cutting‑edge scientific knowledge and data into gene annotation. Hands‑on annotation of genes and transcripts by expert scientists is directly incorporated into the GENCODE and PARADIGM annotation products and also informs the development of manually supervised automated annotation pipelines that support the scaling of human‑expert‑quality annotation. We are looking for highly motivated candidates who possess scientific curiosity and initiative.

Diversity & Inclusion

At EMBL‑EBI, we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities, and/or any other diverse backgrounds.

Hybrid Working

At EMBL‑EBI we are pleased to offer hybrid working options for all our employees. A dedicated desk will be available everyday, our team work three days on site and two from home.

Interviews

We plan to hold introductory meetings with selected candidates remotely.

Contract

Contract length: 3 years (Grant Based Contract)

Salary

Grade 5 monthly salary starting at £3,303 per month after tax but excluding pension and insurance contributions. Plus generous benefits.

Why join us

Do something meaningful. At EMBL‑EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL‑EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.

Join a culture of innovation. We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential.

Enjoy lots of benefits:

• Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme, death benefit, long-term care, accident‑at‑work and unemployment insurances
• Flexible working arrangements — including hybrid working patterns
• Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
• Generous time off: 30 days annual leave per year, in addition public holidays
• Relocation package including installation grant (if required)
• Campus life: Free shuttle bus to and from work, on‑site library, subsidised on‑site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)
• Family benefits: On‑site nursery, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
• Benefits for non‑UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non‑resident allowance.