At a Glance
- Tasks: Join the Velankar team to enhance biological data processing and develop web applications.
- Company: EMBL-EBI, a leader in biological data analysis and innovation.
- Benefits: Flexible working, generous leave, private medical insurance, and relocation support.
- Other info: Collaborative culture with excellent career growth opportunities in a beautiful campus setting.
- Why this job: Make a real impact on global health and biodiversity through innovative bioinformatics.
- Qualifications: MSc or PhD in bioinformatics, Python proficiency, and experience in data analysis.
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.
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
- Extend and maintain 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
- Collaborate 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
- Support FAIRification, standardisation, and interoperability of MD datasets and associated annotations
- Collaborate with international partners across ELIXIR, Instruct‑ERIC, EU‑OPENSCREEN, HPC centres, and industry
- Participate in community standards development, technical documentation, training, outreach, and dissemination activities
Qualifications
- 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
Additional Preferred Experience
- 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).
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
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 any other diverse backgrounds.
International applicants
We recruit internationally and successful candidates are offered visa exemptions. Please see our International Applicants page for further information.
Closing Date: 19/07/2026
Bioinformatician employer: European Bioinformatics Institute | EMBL-EBI
At EMBL-EBI, we offer a unique opportunity for Bioinformaticians to engage in meaningful work that accelerates scientific discovery and addresses global challenges. Our collaborative and inclusive culture, set within the picturesque Wellcome Genome Campus, fosters innovation and professional growth, supported by generous benefits such as flexible working arrangements, extensive leave, and comprehensive family support. Join us to be part of a leading institution where your contributions will have a lasting impact on the future of biological research.
Contact Details:
European Bioinformatics Institute | EMBL-EBI Recruitment Team
StudySmarter Expert Advice🤫
We think this is how you could land Bioinformatician
✨Network Like a Pro
Get out there and connect with people in the bioinformatics field! Attend conferences, workshops, or even local meetups. You never know who might have a lead on your dream job or can introduce you to someone at EMBL-EBI.
✨Show Off Your Skills
When you get the chance to chat with potential employers, make sure to highlight your experience with Python and data pipelines. Share specific examples of projects you've worked on that relate to protein domain analysis or web applications.
✨Be Curious and Ask Questions
During interviews or networking events, don’t hesitate to ask questions about the team’s current projects or challenges. This shows your genuine interest and helps you understand how you can contribute to their goals at EMBL-EBI.
✨Apply Through Our Website
Make sure to submit your application through our website. It’s the best way to ensure your CV gets seen by the right people. Plus, it shows you’re serious about joining the innovative team at EMBL-EBI!
We think you need these skills to ace Bioinformatician
Some tips for your application 🫡
Craft a Compelling Cover Letter:Your cover letter is your chance to shine! Make sure to highlight your passion for bioinformatics and how your skills align with the role. Be creative and show us why you're the perfect fit for the Velankar team!
Tailor Your CV:Don’t just send a generic CV! Tailor it to showcase your experience in protein domain analysis and data pipelines. Highlight any relevant projects or publications that demonstrate your expertise in Python and bioinformatics.
Show Off Your Communication Skills:Since excellent written and oral English skills are key, make sure your application is clear and concise. Use straightforward language and avoid jargon unless necessary. We want to see how well you can communicate complex ideas!
Apply Through Our Website:Remember, the best way to apply is through our online system. It’s super easy and ensures your application gets to the right place. Don’t miss out on this fantastic opportunity – hit that apply button!
How to prepare for a job interview at European Bioinformatics Institute | EMBL-EBI
✨Know Your Bioinformatics Basics
Make sure you brush up on your bioinformatics fundamentals, especially around protein domains and data analysis. Be ready to discuss your experience with Python libraries and how you've used them in past projects.
✨Showcase Your Creativity
Since the role requires a creative mindset, think of examples where you've innovated or improved processes in your previous work. Prepare to share specific instances where your curiosity led to impactful results.
✨Familiarise Yourself with PDBe and SCOP
Do some research on the PDBe and SCOP teams, their projects, and how they contribute to the field. Being able to discuss their work and how you can add value will show your genuine interest in the role.
✨Prepare for Technical Questions
Expect technical questions related to data pipelines and web applications. Brush up on your knowledge of PDB data formats and be ready to explain your approach to creating and improving biological data processing pipelines.
