The Sabeti Lab at the Broad Institute seeks a Postdoctoral Associate to contribute to the development of novel computational approaches for pathogen genomic sequencing. The fellow will develop bioinformatics methods and pipelines for viral genomic sequencing data, working in close collaboration with the Institute of Genomics and Global Health (IGH) team in Nigeria to implement and deploy these tools in the field.
This position combines methods development, pipeline implementation, and direct international collaboration. The fellow will be expected to travel to Nigeria to work on-site with the IGH team; at minimum this involves periodic short-term visits, with the possibility of longer stints depending on program needs and funding.
Beyond pipeline support, the fellow is expected to develop an independent research program in computational genomics or genomic epidemiology that aligns with Sentinel Connect's broader goals of strengthening pathogen surveillance and outbreak preparedness in resource-variable settings.
Key Responsibilities
1. Bioinformatics Method and Pipeline Development
● Design, develop, and implement bioinformatics pipelines for viral genomic sequencing data, including assembly, variant calling, and lineage or phylogenetic analysis, in support of Sentinel Connect surveillance activities.
● Apply computational and machine learning approaches to genomic surveillance data to improve pathogen detection, characterization, and outbreak analysis.
● Build pipelines that are robust, scalable, and reproducible, with attention to deployment in resource-variable settings, including partner sites in Nigeria.
● Maintain clear documentation and version control practices that support reproducibility and knowledge transfer to partner teams.
2. International Collaboration and On-Site Support
● Collaborate directly with the IGH team in Nigeria on pipeline deployment, troubleshooting, and adaptation to local infrastructure and sample types.
● Travel to Nigeria to work on-site with the IGH team; at minimum, periodic short-term visits are expected, with longer stints possible depending on program needs and funding.
● Contribute to training and knowledge transfer with in-country partners to help build sustainable local computational capacity.
3. Independent Research Program Development
● Develop an independent research program in computational genomics or genomic epidemiology that aligns with Sentinel Connect's goals and mission.
● Identify, propose, and pursue research questions using data generated through the Sentinel Connect program.
● Publish findings in peer-reviewed journals and contribute to the lab's broader scientific strategy.
Qualifications
Education & Experience
● PhD in bioinformatics, computational biology, genomics, computer science, statistics, or a related discipline.
● Demonstrated experience developing bioinformatics pipelines for genomic sequencing data; experience with viral genomics is preferred.
● Experience working in global health or low- and middle-income country settings is preferred but not required.
● Willingness and ability to travel internationally, including to Nigeria, as required by the position.
Required Skills & Competencies
● Pipeline Development: Proficiency in workflow languages (e.g., Nextflow, Snakemake) and programming languages (e.g., Python, R) for building and maintaining bioinformatics pipelines.
● Genomic Analysis: Experience with viral genome assembly, variant calling, and phylogenetic analysis using tools such as Nextstrain, IQ-TREE, or BEAST.
● Computational and Statistical Methods: Familiarity with machine learning or statistical genomics approaches applied to sequencing or epidemiological data.
● Independent Research: Demonstrated ability to define, execute, and communicate an independent research agenda.
● Collaboration: Comfortable working across disciplinary and international teams, including partners operating with varying infrastructure and resources.
● Scientific Communication: Ability to present technical results clearly to both specialist and non-specialist audiences and contribute to manuscripts.
● Documentation and Reproducibility: Maintains clear, well-documented, version- controlled code to support reproducibility and continuity across teams.
