Summary

The Alkek Center for Metagenomics and Microbiome Research Center (CMMR) is an integral part of the Baylor College of Medicine strategic plan and serves as a hub for translational microbiome and virome research by: 1) providing sequencing, informatics, and microbiological expertise and resources to drive and support clinical and basic research microbial genomics studies, 2) providing the infrastructure and critical mass of expertise to explore host-microbe interactions, 3) driving technology and analytical development to improve metagenomic capabilities for characterizing bacterial, viral, and fungal communities, and 4) translating new discoveries into the realm of personalized medicine where new therapeutics and diagnostics may be implemented. Over the past 10 years, we’ve collaborated on more than 1000 projects with over 300 research groups from around the world. 

The CMMR is seeking a highly motivated Senior Scientific Programmer for the Metagenomics and Microbiome Research Center to develop and apply computational approaches supporting microbiome and viral genomics research. This individual will develop scalable bioinformatics workflows, analyze high-throughput sequencing datasets, and collaborate with investigators and research staff to support translational microbiome and virome studies. The successful candidate will combine expertise in bioinformatics, software development, and scientific computing to support innovative research projects, core service activities, and method development initiatives.

Job Duties

Collaboration and Technical Contributions

• 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.

Minimum Qualifications

• Bachelor's degree in Management Information Systems, Computer Science, or a related field. Four years of related experience may substitute for degree requirement.
• Three years of relevant experience.

Preferred Qualifications

• Ph.D. in Bioinformatics, Computational Biology, Computer Science, Biology, or a related discipline.
• Familiarity with cloud computing platforms or Trusted Research Environments (AWS, Azure, or Google Cloud).
• Experience managing large biological datasets and databases, including proficiency with relational databases such as SQL.
• Experience with Amazon DynamoDB or equivalent NoSQL database technologies.
• Demonstrated contributions to peer-reviewed publications, software projects, or grant applications.
• Experience developing web-based scientific applications, interactive data visualization tools, or researcher-facing analytical resources.