bioinformatics-Clinical Microbiome

Excelra Knowledge Solutions Pvt. Ltd.; Oost-Vlaanderen; Hybrid; EUR 60,000 - 90,000; Full time

Benefits offered by this job

Flexible hybrid work

International team

Ambitious vision

Job summary

Excelra Knowledge Solutions Pvt. Ltd. is hiring a Clinical Microbiome R&D Bioinformatician to develop and maintain microbiome analytics pipelines and reference resources.

You will work across the full research lifecycle, from pipeline development on the Seven Bridges platform to benchmarking and method development in a collaborative, multidisciplinary environment. The role emphasizes scalable data integration, reproducible workflows, and communicating complex results to stakeholders.

Qualifications

• Experience with microbiome sequencing data and bioinformatics workflows.
• Hands-on experience with Illumina and/or Oxford Nanopore data.
• Experience developing and maintaining bioinformatics pipelines.
• Proficient in Python, R, Bash; strong analytical skills.
• Excellent communication and collaboration abilities.

Responsibilities

• Develop and maintain CWL pipelines on the Seven Bridges platform for microbiome data.
• Build and maintain CI/CD pipelines to automate testing and deployment of workflows.
• Build and curate microbiome reference databases for host species and environments.
• Benchmark microbiome tools and assess their strengths and limitations.
• Keep up with new computational methods to improve workflows.

Skills

Python

R

Bash

Nextflow

Snakemake

Data analysis

Education

PhD in Bioscience engineering / Bioinformatics

MSc with 5+ years experience in related field

Tools

Docker

Cloud platforms

CI/CD pipelines

Seven Bridges platform

Job description

Location: Europe
Work Mode: Hybrid

Who are we?

Excelra is a leader in biopharma data and analytics, that uniquely blends scientific understanding with technological expertise. This dual mastery empowers innovative drug discovery and development, transforming research data into actionable insights for groundbreaking discovery.

We have locations in Hyderabad (head offices – India), Ghent (Belgium), London (UK), Utrecht (The Netherlands), and Boston/SFO (US).

We are hiring a Clinical Microbiome R&D Bioinformatician to support the development of next-generation microbiome analytics, workflows, and reference resources that enable the interpretation of complex microbial sequencing data from clinical studies.

This role combines microbiome bioinformatics, workflow engineering, computational method development, and large-scale data integration. You will work across the full research lifecycle, from developing and maintaining analysis pipelines on the Seven Bridges platform to evaluating emerging computational methods and building reusable microbiome data resources.

You will play a key role in advancing microbiome research capabilities through robust workflow development, reference database curation, benchmarking studies, and innovative approaches for analysing microbiome datasets generated from Illumina and/or Oxford Nanopore sequencing technologies.

Key Responsibilities

Seven Bridges Platform & Workflow Development

• Develop and maintain Common Workflow Language (CWL) pipelines on the Seven Bridges platform for preprocessing, analysing, and interpreting microbiome data from Illumina and/or Oxford Nanopore sequencing.
• Build and maintain CI/CD pipelines to automate the testing and deployment of bioinformatics workflows to Seven Bridges.
• Build and curate microbiome reference databases for different host species, mainly human and mouse, and a range of environments such as the gut, skin, and rumen.
• Support the ongoing maintenance, optimisation, and scalability of microbiome analysis workflows.

Microbiome Research & Method Development

• Explore and develop new approaches to improve how we analyse and interpret microbiome data.
• Develop methods to identify and characterise putative microbial subspecies from sequencing data.
• Benchmark microbiome tools, including taxonomic profilers and functional annotation tools, to understand their strengths, limitations, and suitability for different research questions.
• Keep up with new computational methods and assess whether they can improve existing microbiome workflows and analyses.

Data Integration and Scientific Computing

• Develop data-ingestion pipelines for public sequencing datasets, making it easier to find, process, standardise, and reuse external microbiome data.
• Support the integration and harmonisation of microbiome datasets from multiple sources.
• Contribute to the development of reproducible and scalable bioinformatics workflows.
• Maintain high-quality documentation, version control, and workflow reproducibility standards.

Scientific Collaboration

• Collaborate closely with bioinformaticians, microbiome scientists, and multidisciplinary research teams.
• Translate scientific requirements into practical computational solutions.
• Communicate analytical findings and technical recommendations to both technical and non-technical stakeholders.
• Contribute to continuous improvement of microbiome analytics platforms, methodologies, and best practices.

You Bring

• A PhD in Bioscience engineering, Bioinformatics, computer science, Computational Biology, Data Science, Computer Science, Genomics, Systems Biology, or a related discipline– or an MSc with 5+ years of equivalent experience. You can demonstrate this through peer-reviewed publications, contributions to public code repositories, or relevant project work.
• Experience working with microbiome sequencing data and bioinformatics workflows.
• Hands-on experience with next-generation sequencing (NGS) datasets, including Illumina and/or Oxford Nanopore sequencing.
• Experience developing and maintaining bioinformatics pipelines.
• Strong programming skills in Python, R, Bash, or related scripting languages.
• Experience working with workflow technologies such as Nextflow, Snakemake, or similar frameworks.
• Strong analytical and problem-solving skills.
• Excellent communication and collaboration skills.
• Ability to work independently while partnering effectively with multidisciplinary teams.

Preferred

• Experience working with the Seven Bridges platform or similar cloud-based workflow platforms.
• Experience developing CI/CD pipelines for scientific software and bioinformatics workflows.
• Experience building and curating microbiome reference databases.
• Experience benchmarking taxonomic profilers, functional annotation tools, or other microbiome analysis software.
• Knowledge of microbial genomics, metagenomics, and microbiome data interpretation.
• Experience working with public sequencing repositories and large-scale biological datasets.
• Experience with cloud-based or HPC computing environments.
• Experience with Docker, containerised deployments, and workflow reproducibility practices.
• Experience supporting research, biotechnology, pharmaceutical, or life sciences environments.

What Do We Offer?

• A challenging job environment with advancement opportunities.
• Flexible hybrid working in an international setting.
• A dynamic company with an open culture, easy communication, and an ambitious vision.
• A rich and global team with a mix of backgrounds, experiences, and expertise.
• Independence and flexibility.
• Opportunities to work on cutting-edge microbiome research, workflow development, and computational method innovation.
• An attractive salary package with extra-legal benefits.