Lead Bioinformatics Engineer

Description

The company invents and builds life sciences ventures. Since 2000 it has founded more than 100, and it has put over $4 billion into scientific discovery, including Moderna.

The Scientific Cloud team is the IT group that supplies cloud, data, research systems, lab systems and vendor management to the company's growing portfolio of new companies. It builds shared infrastructure that each venture can depend on from formation through growth.

This is an individual contributor role on the Scientific Cloud team within company IT, reporting to the Director, Scientific Cloud Engineering, and sitting inside a sub-team.

The role centres on owning the platform and enabling others to use it, rather than doing one-off consulting. The ideal person is strong technically, skilled at navigating an organization, and equally at home building production infrastructure and teaching scientists to use it alone.

Responsibilities

• Administer, configure and run the portfolio bioinformatics platform, including CodeOcean, Sequera (Nextflow Tower), Tamarind.bio and related tools, and act as the first escalation point for platform problems.
• Create and keep up a set of reusable, production-ready pipeline templates and starter setups that portfolio companies and the Pioneering Medicines teams can use without custom engineering each time.
• Turn code from the open-source bioinformatics library maintained by the enterprise's data science arm into documented workflows that scientists and informatics staff can run on their own.
• Set the rules for bioinformatics data formats, pipeline documentation and code contributions, so internal and externally contributed workflows meet the same standard for reproducibility and portability.
• Coach portfolio scientists and informatics staff to build and change pipelines themselves inside the platform. The aim is for each company to become self-sufficient, not for Scientific Cloud to own those pipelines long term.
• Work with Scientific Cloud Engineering so the bioinformatics platform follows enterprise cloud standards for identity management, security and cost control.
• Act as the main contact for external genomic and biomedical data consortia and repositories such as UK Biobank, the Francis Crick Institute, dbGaP, GTEx, ENCODE and other curated dataset providers.
• Handle every stage of data access agreements, including Data Access Committee applications, DUAs, renewals and compliance reports, working with the legal and compliance teams.
• Track the plans and new datasets of key consortium partners and flag access opportunities that match portfolio science needs.
• Bring new consortium datasets into the company's data environment with the data engineering team, covering ingestion, governance metadata and access controls.
• Build working relationships with data operations and scientific leads at partner institutions to make access smoother over time.
• Work with the Data and Informatics Engineering team, including architects, data engineers and software engineers, so bioinformatics workloads fit into shared data platforms, pipelines and catalogs.
• Work with Research Systems, Lab Systems and informatics colleagues across the company and portfolio to translate scientific needs into platform features.
• Work with the data science and machine learning teams at Pioneering Intelligence to make sure processed omics data is well formatted, annotated and easy to reach for analysis and AI work.
• Take part in cross-team technical reviews, architecture talks and sprint ceremonies as a working member of Scientific Cloud.
• Help write shared standards, playbooks and documentation for Scientific Cloud and the portfolio.
• Advise scientists and IT staff on genomics, transcriptomics and multi-omics data as the in-house subject expert, sharing good practice.
• Assess and recommend compute options (HPC, cloud batch and spot instances) for large genomic workloads.
• Keep up with changes in bioinformatics tools, reference datasets and public database standards, and feed them into platform development.
• Write technical documentation, onboarding material and knowledge-sharing content to grow bioinformatics skills across the company.

Requirements

• Required: a master's or PhD in bioinformatics, computational biology, genomics, computer science or a closely related field.
• Required: at least 7 years of hands-on bioinformatics engineering, including building and deploying production-grade pipelines.
• Required: deep knowledge of genomic data types and formats such as FASTQ, BAM/CRAM, VCF, BED, HDF5 and AnnData, and of the tools used to process them.
• Required: experience building and running cloud-native bioinformatics workflows with Nextflow, Snakemake or WDL. AWS is preferred; Azure or GCP is acceptable.
• Required: strong Python and/or R, plus shell scripting for pipeline automation.
• Required: familiarity with public genomic data repositories and the access and compliance rules behind them, such as dbGaP, UK Biobank and TCGA.
• Required: a proven record of managing complex external relationships and data access work, including DUAs, DAC applications and compliance reporting.
• Required: strong communication skills and a collaborative style, able to work with both scientific and technical audiences.
• Preferred: experience administering or deploying managed bioinformatics platforms such as CodeOcean, Sequera or Nextflow Tower, Tamarind.bio, or similar cloud-native workflow environments.
• Preferred: experience supporting varied scientific teams with different computing needs across several companies or a portfolio.
• Preferred: familiarity with single-cell omics platforms (10x Genomics, Seurat, Scanpy, scVelo) and spatial transcriptomics workflows.
• Preferred: experience with containers (Docker, Singularity) and orchestrating them across HPC and cloud environments.
• Preferred: knowledge of data governance frameworks, catalog tools such as DataHub or Collibra, and lineage tracking for scientific data.
• Preferred: experience contributing to or maintaining open-source bioinformatics libraries or shared code repositories.
• Preferred: prior work in a biotechnology, pharmaceutical or life sciences technology organization.

Conditions

Salary range is $128,000 - $176,000.

Pay depends on qualifications, skills, competencies and experience.

The company values diverse, inclusive teams and welcomes applicants who meet only some of the listed qualifications.

Benefits

• Healthcare coverage, an annual incentive program, retirement benefits and a broad range of other benefits are offered.
• Benefit and compensation details are a good-faith estimate as of publication and may change.