Senior Scientific Programmer

Job Duties

Collaborates with CMMR laboratory, informatics, and research teams to support project execution, core operations, and software development initiatives.

Contributes to best practices in bioinformatics tool development, reproducible research, scientific computing, data management, and collaborative code development.

Under limited supervision, works closely with investigators and researchers to understand project goals and develop computational solutions to address scientific questions.

Documents analytical workflows and provide guidance to researchers on the use of computational tools and resources.

Bioinformatics and Software Development

Develops, maintains, and optimizes automated bioinformatics pipelines for processing and analyzing high-throughput sequencing data.

Develops, tests, and maintains bioinformatics software tools, databases, and analytical applications supporting genomics, microbiome, and virome research.

Collaborate with research staff to evaluate, develop, and implement new computational methods, workflows, and analytical approaches.

Develops interactive applications, dashboards, and data exploration tools using technologies such as R Shiny and related frameworks.

Applies programming expertise in Python, R, Bash, and workflow management systems such as Snakemake or Nextflow.

Performs genome assembly, annotation, comparative genomics, metagenomics, and related analyses supporting microbiome and virome research.

Computational Infrastructure and Data Management

Utilizes and support high-performance computing (HPC) environments, including software deployment, pipeline configuration, troubleshooting, and data transfer processes.

Develops and maintain database-driven research applications and data management systems supporting laboratory operations, core services, and collaborative research projects.

Curates, manage, and analyze large-scale biological datasets while ensuring data integrity, accessibility, reproducibility, and long-term sustainability.

Contributes to the implementation and maintenance of computational workflows and software environments using modern development and deployment practices.

Research and Scientific Contributions

Collaborates with multidisciplinary research teams on genomics, metagenomics, microbiome, and virome research initiatives.

Contributes computational and analytical expertise to grant proposals, research planning, and new project development.

Contributes to scientific manuscripts, presentations, software documentation, technical reports, and user documentation for computational tools and research systems.

Stays informed of emerging bioinformatics methods, technologies, and best practices relevant to microbial genomics research.