Bioinformatician

European Bioinformatics Institute; Cambridge; Hybrid; GBP 40,000 - 44,000; Full time

Benefits offered by this job

Hybrid working

Relocation package

Annual leave

Pension scheme

Private medical insurance

On-site facilities

Job summary

EMBL-EBI's Velankar team seeks a Bioinformatician to connect molecular dynamics data with structural biology resources and biological knowledge bases. You will build AI-driven literature mining to enrich MD datasets and extend SIFTS mappings to enable wider data interoperability.

You will work at the intersection of structural bioinformatics, MD data, and scientific software development, creating workflows, APIs, and annotations to improve data reuse across resources.

Qualifications

• PhD in bioinformatics, computational biology, structural biology, computer science, data science, or related field.
• Familiarity with structural biology and molecular simulation data.
• Experience with NLP/LLM-based scientific literature mining.
• Demonstrated experience with FAIR data principles, metadata standards, and scientific repositories.
• Understanding of sequence, structure, and functional annotations of proteins.
• Experience in scientific software development, preferably in Python.
• Experience with Linux environments, Git, and CI/CD practices.
• Scientific publications relevant to structural biology, bioinformatics, or protein annotations.

Responsibilities

• Design and implement data integration pipelines that connect MDDB with major life science resources like PDBe, UniProt, PDBe-KB.
• Develop AI- and ML-based approaches for extracting metadata from literature to enrich MDDB datasets.
• Extend and maintain the SIFTS infrastructure to support MD data integration.
• Develop tools, APIs, workflows, and documentation for FAIR data integration and accessible data.
• Collaborate with domain experts and data providers to integrate MD-derived insights across resources.
• Support FAIRification, standardisation and interoperability of MD datasets and annotations.
• Collaborate with international partners across ELIXIR, Instruct-ERIC, EU-OPENSCREEN, HPC centres, and industry.
• Participate in community standards development, technical documentation, training, and outreach.

Skills

Python programming

Git

CI/CD

Nextflow

REST APIs

Neo4J

Education

PhD in Bioinformatics or related field

Tools

Python

Neo4J

REST APIs

Nextflow

Git

CI/CD

Job description

About the team

We are seeking a Bioinformatician with expertise in data integration and experience in structural biology and molecular dynamics (MD) data to join the Velankar team at the European Bioinformatics Institute (EMBL-EBI). The Protein Data Bank in Europe (PDBe) team develops essential macromolecular structure resources and tools for biologists and other life scientists. As a founding partner of the Worldwide Protein Data Bank, we are responsible for maintaining the global archive of experimentally determined macromolecular structures, the Protein Data Bank (PDB). We also manage the community-led PDBe Knowledge Base (PDBe-KB) resource and the AlphaFold Protein Structure Database (AFDB), a collaboration with Google DeepMind. The PDBe team consists of an international and interdisciplinary group of scientists, software engineers, and data engineers who develop a range of tools and services that support structure deposition, data integration, and advanced search capabilities for structural biologists and the wider life sciences community.

This position offers an exciting opportunity to contribute to the Horizon Europe-funded MD4SB (Molecular Dynamics for Structure-Based Biology) project. MD4SB is a major European research infrastructure initiative aiming to transform structural biology by integrating molecular dynamics simulation data into the wider life sciences ecosystem. The project brings together ELIXIR, Instruct-ERIC, EU-OPENSCREEN, HPC centres, AI factories, and pharmaceutical industry partners to develop FAIR, AI-ready infrastructure for structural ensemble data and molecular simulations.

Your role

You will contribute to the development of infrastructure connecting molecular dynamics simulations with structural biology resources and biological knowledge bases. A major component of the role will be developing AI-driven approaches to mine scientific literature and automatically extract experimental and biological metadata to enrich MD datasets. You will develop and extend SIFTS (Structure Integration with Function, Taxonomy and Sequence), a core PDBe resource that provides residue-level mappings between PDB structures, UniProtKB sequences, and other biological resources, to facilitate the integration of MD-derived insights across the wider life sciences data ecosystem.

This is an interdisciplinary role combining structural bioinformatics, molecular dynamics, and scientific software development. You will apply both scientific understanding and technical expertise to develop data integration workflows, APIs, and biological annotations that improve interoperability and reuse of structural and molecular simulation data across various resources.

Primary responsibilities

• Design and implement data integration pipelines that connect MDDB with major life science resources, including PDBe, UniProt, PDBe-KB, and other relevant knowledge bases and databases
• Develop and deploy AI- and machine learning-based approaches for extracting experimental and biological metadata from scientific literature to enrich MDDB datasets and support downstream biological interpretation.
• Extending and maintaining the SIFTS infrastructure and codebase to support integration of molecular dynamics and other data resources
• Develop and maintain software tools, APIs, workflows, and documentation that facilitate FAIR data integration, metadata enrichment, and integrated data access
• Collaborating with domain experts, software engineers, and data resource providers to enable the integration of MD-derived biological insights into the wider life sciences data ecosystem.
• Supporting FAIRification, standardisation, and interoperability of MD datasets and associated annotations
• Collaborating with international partners across ELIXIR, Instruct-ERIC, EU-OPENSCREEN, HPC centres, and industry
• Participating in community standards development, technical documentation, training, outreach, and dissemination activities

You have

• PhD in Bioinformatics, Computational Biology, Structural Biology, Computer Science, Data Science, or a related field
• Familiarity with structural biology and molecular simulation data
• Experience with NLP/LLM-based scientific literature mining
• Demonstrated experience with FAIR data principles, metadata standards, and scientific repositories.
• Understanding of sequence, structure, and functional annotations of proteins
• Experience in scientific software development, preferably in Python
• Experience with Linux environments, Git, and CI/CD practices
• Scientific publications relevant to structural biology, bioinformatics, or protein annotations
• Strong communication, collaboration, and problem-solving skills

You may also have

• Postdoctoral research experience in a relevant field
• Experience with graph databases (e.g. Neo4J), REST APIs, containerisation technologies, and workflow management systems such as Nextflow
• Experience in data visualisation and analysis
• Understanding of FAIR data principles and the biological data lifecycle
• Experience in reporting and presenting scientific topics
• Experience working in international and interdisciplinary teams

Contract length: 3 years grant based contract (with a possibility of extension for another year).

Salary: Grade 5 or 6 depending on relevant experience. Monthly salary starting from £3,303 - £3,695 after tax plus generous benefits and financial allowances depending on family circumstances. Excluding personal pension and insurance contributions.

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. Watch this video to see how EMBL-EBI makes an impact.

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.

What else you need to know

• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Please take a look at our International Applicants page for further information.
• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.
• Diversity and inclusion: At EMBL, 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.

Closing Date

04/09/2026