Bioinformatics Engineer II

Experience- 2+ Years

Location- Bangalore/ Delhi (3days a week)

About the Company:

Elucidata is an AI Solutions Tech Data-centric AI company on a mission to make life sciences AI-ready. Headquartered in San Francisco with a 120+ member team across the US and India, we're building the future of data-centric AI for drug discovery. Our flagship AI-Agentic powered platform, Polly, helps research teams wrangle, harmonize, and analyze massive volumes of biomedical data, accelerating discoveries and making precision medicine a reality.

Recognized by Fast Company as the Most Innovative Biotech Company of 2024, Elucidata partners with 25+ leading organizations, including Pfizer, Novo Nordisk, Google DeepMind, Alnylam Therapeutics, and the Bill & Melinda Gates Research Institute. Backed by top VCs like Eight Roads, F-Prime, IvyCap, and Hyperplane.

With over 200 data products and AI solutions co-developed by 100+ domain experts, we've helped our partners achieve 4X faster R&D milestones and contribute to 16 therapies advancing toward FDA approval. At Elucidata, you'll work at the intersection of AI, biology and impact while solving real-world challenges that accelerate the journey from data to discovery.

About the Role

Elucidata is seeking a skilled and motivated Bioinformatics Engineer II to join our Customer Delivery Team. In this role, you will be responsible for developing scalable bioinformatics applications and pipelines for efficient data processing and consumption. You will also maintain and enhance existing pipelines, adding new features to improve performance and usability. This role offers an opportunity to collaborate with multidisciplinary teams, apply data science and engineering principles to solve complex problems, and leverage AI/ML to accelerate drug discovery and biomedical research.

What You'll Own

• Design, develop, and maintain robust and reproducible bioinformatics workflows using tools like Nextflow.
• Process and analyze bulk RNA-seq and single-cell RNA-seq data using tools such as STAR, Kallisto, Cell Ranger, and others.
• Collaborate with scientists and analysts to validate workflows and ensure high-quality data outputs for client delivery.
• Perform quality control checks, troubleshoot pipeline issues, and optimize performance for large-scale datasets.

What Makes You a Great Fit

• Master's degree in Computer Science, Bioinformatics, Computational Biology, or a related field with 2+ years of experience developing bioinformatics workflows and performing NGS data analysis.
• Experience with workflow managers (e.g., Nextflow), containerization technologies (e.g., Docker), and deploying workflows on AWS or HPC environments.
• Proficient in Python and R, including experience with data wrangling and visualization libraries.
• Familiarity with biological databases (e.g. Ensembl, NCBI) and experience retrieving data files (e.g. downloading FASTQ files from the SRA or obtaining count files for pipeline ingestion).
• Experience in NGS raw data processing (e.g bulk RNAseq, scRNAseq) using tools such as STAR, kallisto, CellRanger and an understanding of typical QC and downstream analysis steps.
• Excellent communication and strong problem solving and collaboration skills. Ability to write clear technical documentation and share knowledge.

Good to have skills

• Experience with version control and CI/CD systems, including Git/GitHub for collaborative development and GitHub Actions or GitLab CI for workflow testing and automation.
• Experience developing interactive dashboards using R Shiny and/or enterprise tools like Spotfire is a plus.
• Basic understanding of ML/statistical modeling in bioinformatics is a plus.
• Agile: Exposure to Agile/Scrum methodologies and tools like Jira.

Why Join Elucidata

• Opportunity to shape the future of biomedical data ecosystems by building partnerships at the frontier of science and healthcare.
• Direct visibility with the CEO and leadership team.
• High-impact role - the partnerships you establish will directly translate into Elucidata's growth and customer success.
• Work with global leaders and contribute to data-driven drug discovery.
• We are proud to be an equal-opportunity workplace and are an affirmative action employer. We are committed to equal employment opportunities regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, caste, citizenship, marital status, disability, gender identity, or Veteran status.