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 Bioinformatics Programmer II to join the Bioinformatics Service Center team. The candidate will support the development and maintenance of automated analysis pipelines, data management systems, and computational infrastructure for microbiome and viral genomics research. The successful candidate will work closely with researchers and collaborators to streamline data processing, improve reproducibility, and contribute to tool development and implementation.

Job Duties

• Design, implement, and maintain automated bioinformatics pipelines for processing and analyzing high-throughput sequencing data.
• Manage and version-control conda environments to ensure software reproducibility and dependency stability across projects.
• Support cluster setup, configuration, and data transfer between computing environments.
• Collaborate with research staff to develop and test alternative approaches to existing tools.
• Manage and curate large datasets, ensuring data integrity and accessibility.
• Develop and maintain databases to organize and query genomic and microbiome data.
• Contribute to genome assembly, annotation, and comparative genomics analyses.
• Provide coding and computational support in Python, R, and Bash.
• Collaborate with interdisciplinary teams to support ongoing microbiome and virome research initiatives.

Minimum Qualifications

• Bachelor's degree in Computer Science, Biological Science, or a related field. 
• Two years of relevant experience. 

Preferred Qualifications

• Master’s degree in a related field.
• Demonstrated proficiency in programming (e.g., Python, R, Bash).
• Experience with automated pipelines and workflow management tools (e.g., Snakemake).
• Familiarity with high-performance computing (HPC) environments and data transfer tools.
• Experience with database management systems (e.g., SQL, NoSQL).
• Previous experience in microbiome or virome research.
• Experience with large microbial genomic data sets (e.g., Metagenomes)
• Hands-on experience with viral and metagenomic genome assembly and annotation tools.
• Demonstrated ability to document and communicate technical workflows effectively.
• Experience maintaining Git-based repositories for collaborative development.
• Familiarity with AWS and cloud computing systems.