European Bioinformatics Institute | EMBL-EBI

www.ebi.ac.uk

5 Jobs

826 Employees

About the Company

Working at EMBL-EBI gives you the opportunity to focus your energy and skills on something that really matters: using technology to contribute to discoveries that benefit humankind. We empower researchers everywhere to realise the potential of 'big data' in biology, and build sophisticated tools for exploring life at the atomic level.

Listed Jobs

Company Name: European Bioinformatics Institute | EMBL-EBI
Job Title: Bioinformatics Developer
Job Description: **Job Title:** Bioinformatics Developer **Role Summary:** Develop next-generation genome annotation tools for large-scale biodiversity projects, focusing on scalability, reproducibility, and sustainability. Collaborate on a global effort to annotate diverse eukaryotic species. **Expectations:** Design and implement scalable workflows, modernize legacy tools, integrate multi-omics data (transcriptomics, proteomics), and standardize methods with international partners. **Key Responsibilities:** - Develop and optimize genome annotation pipelines using Nextflow/Snakemake. - Integrate transcriptomics, proteomics, and comparative genomics data to refine annotations. - Modernize legacy tools with modular, maintainable code aligning with best practices. - Collaborate internationally to harmonize data standards and methodologies. - Leverage high-performance computing environments (cloud, cluster, GPU) for workflow optimization. **Required Skills:** - Proficiency in Python for bioinformatics tool development. - Experience with workflow managers (Nextflow, Snakemake). - Algorithm development for large-scale genomic data. - Understanding of eukaryotic genome annotation and comparative genomics. - Linux command-line expertise, Git version control, software testing practices. - High-performance computing (HPC) and workflow optimization. - Strong communication and problem-solving skills for cross-functional collaboration. **Required Education & Certifications:** Not specified.

England, United kingdom

Hybrid

Junior

12-11-2025

Company Name: European Bioinformatics Institute | EMBL-EBI
Job Title: Postdoctoral fellow - Petsalaki Group - NetworkCommons
Job Description: **Job Title** Postdoctoral Fellow – NetworkCommons (Petsalaki & Saez‑Rodriguez Groups) **Role Summary** Execute computational and AI‑driven research to connect multi‑omics data with disease mechanisms, building next‑generation tools for the NetworkCommons open platform. Collaborate with academic and industry partners on the Open Targets initiative. **Expectations** - PhD (or final‑year PhD) in computational biology, bioinformatics, computer science, or a related quantitative discipline. - Demonstrated ability in omics data analysis and development of computational methods. - Proficiency in Python or R; familiarity with reproducible workflow engines (Nextflow, Snakemake). - Strong grasp of systems/molecular biology and capacity to translate data into actionable insights. - Excellent communication and teamwork skills; eagerness to contribute to interdisciplinary projects. **Key Responsibilities** - Design, benchmark, and integrate state‑of‑the‑art network contextualisation methods across transcriptomics, proteomics, and single‑cell data for oncology, inflammatory bowel disease, and neuroinflammation. - Construct reproducible pipelines with Nextflow/Snakemake, containerise workflows using Docker or Singularity. - Contribute to the open‑source NetworkCommons platform, ensuring data quality, scalability, and user‑friendly interfaces. - Collaborate with developers, industry partners, and consortium members to translate computational methods into translational research workflows. - Prepare manuscripts, conference presentations, and technical reports. - Mentor junior team members and maintain comprehensive project documentation. **Required Skills** - Programming: Python and/or R; workflow management (Nextflow, Snakemake). - Containerisation: Docker, Singularity. - Network biology, graph algorithms, or causal inference (preferred). - Benchmarking bioinformatics tools; multi‑omics data integration. - Systems biology understanding; analytical and problem‑solving expertise. - Written and verbal communication; collaborative research mindset. **Required Education & Certifications** - PhD (or PhD‑candidate) in computational biology, bioinformatics, computer science, or equivalent quantitative field. - No mandatory external certifications; prior open‑science or reproducible‑science experience is advantageous.

England, United kingdom

On site

Junior

26-11-2025

Company Name: European Bioinformatics Institute | EMBL-EBI
Job Title: Software Developer
Job Description: Job Title: Software Developer Role Summary: Design, develop, and maintain the DECIPHER web platform, a human genetics tool built on Node.js, Vue/Nuxt.js, and PostgreSQL. Work on data structures, user interfaces, performance tuning, and new feature delivery while keeping the system aligned with scientific advances. Collaborate with internal and external stakeholders to refine requirements and ensure high‑quality, user‑friendly software. Expectations: 4–5 years of professional software development experience, strong command of modern JavaScript (Node), reactive front‑end frameworks, relational databases, and Unix/Linux tooling. Demonstrated commitment to code quality, CI/CD, automated testing, linting, and performance benchmarking. Ability to learn or apply knowledge of human genetics and deliver polished user experiences. Deliver reliably on time with attention to detail. Key Responsibilities - Design and implement data models and UI components for genomic and disorder data. - Retrieve, transform, and integrate data from external resources. - Review peer code, enforce coding standards, and propose improvements. - Respond to bug reports, support requests, and feature requests; engage stakeholders to clarify requirements. - Identify performance bottlenecks and develop optimizations to keep the service responsive. - Evaluate new technologies and champion beneficial adoption in team planning. - Coordinate with EMBL‑EBI groups and external partners on data representation standards. Required Skills - Proficiency in JavaScript (Node.js) and front‑end frameworks (Vue, React, or Angular). - Experience with PostgreSQL, Sequelize (or similar) ORM, and relational database design. - Unix/Linux proficiency, command‑line tools, and Git version control. - Familiarity with CI/CD pipelines, automated testing, linting, and performance profiling. - Strong communication skills for code reviews, stakeholder interaction, and cross‑group liaison. - Ability to produce intuitive, responsive user interfaces. - Knowledge or enthusiasm for human genetics data and bioinformatics is highly desirable. Required Education & Certifications - Bachelor’s degree (or equivalent) in Computer Science, Software Engineering, or related technical field. - No mandatory certifications required.

England, United kingdom

Hybrid

Junior

27-11-2025

Company Name: European Bioinformatics Institute | EMBL-EBI
Job Title: Bioinformatician
Job Description: **Job title** Bioinformatician **Role Summary** Design, develop, and maintain scalable bioinformatics pipelines that produce reference‑quality gene annotations for human and mouse genomes. Work closely with genomic data analysts to integrate primary sequencing data, validate gene models, and support automated annotation workflows used globally in research and clinical genomics. **Expectations** - Deliver robust, version‑controlled code in a release‑driven environment. - Collaborate with international partners and cross‑functional teams. - Communicate complex biological and computational concepts clearly to both technical and non‑technical audiences. **Key Responsibilities** - Develop and deploy annotation pipelines for protein‑coding and non‑coding RNA genes. - Integrate cutting‑edge primary data (e.g., RNA‑seq, Ribo‑seq, long‑read sequencing) to refine gene structure and function. - Extend GENCODE annotation to human and mouse pangenomes and generate training datasets for machine‑learning initiatives. - Maintain relational database schemas and perform efficient queries for annotation data. - Operate within a version‑controlled codebase, ensuring code quality and documentation. - Coordinate releases, troubleshoot pipeline failures, and optimize computational performance. - Participate in user training and provide technical support for annotation methods. **Required Skills** - Proficiency in scripting/programming languages (Python, Perl, or similar). - Experience designing and maintaining large‑scale data pipelines (e.g., Nextflow, Snakemake, WDL). - Strong understanding of genome annotation principles and DNA/RNA sequencing methods. - Knowledge of relational databases (SQL) and schema design. - Familiarity with compute clusters, job scheduling, and performance tuning. - Basic machine‑learning concepts and ability to generate training data. - Excellent problem‑solving, attention to detail, and independent work capability. - Effective communication and teamwork skills in an international setting. **Required Education & Certifications** - MSc, PhD, or equivalent in Computer Science, Bioinformatics, Genetics, or related field. - Demonstrated experience writing, understanding, and maintaining complex code.

England, United kingdom

On site

10-01-2026

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