Bioinformatics Research Assistant
About The Position
The Uterine Health Research Lab in the Department of Obstetrics and Gynecology is seeking an experienced Bioinformatics Research Assistant who will support research exploring the utility of the vaginal microbiome individually and in combination with cell-free DNA and DNA methylation markers, for improved screening and detection of endometrial cancer. The successful candidate will assist in analyzing high throughput sequencing data, focusing on single nucleotide variant (SNV) calling, benchmarking tools, and generating performance metrics. This position provides hands-on experience in computational genomics, reproducible research workflows, and literature-driven problem solving.
Requirements
- High school graduation, some additional training in a related field and a minimum two years of related experience or an equivalent combination of education and experience.
- Willingness to respect diverse perspectives, including perspectives in conflict with one’s own
- Demonstrates a commitment to enhancing one’s own awareness, knowledge, and skills related to equity, diversity, and inclusion
Nice To Haves
- Undergraduate in bioinformatics, computational biology, computer science, molecular biology, or related fields
- Foundational knowledge of genomics and bioinformatics concepts, particularly SNV calling using Mutect2, Strelka, LoFreq.
- Strong command of Bash scripting and experience with workflow management tools such as Snakemake.
- Ability to critically read and interpret scientific literature.
- Experience benchmarking computational tools and interpreting performance metrics.
- Clear written and verbal communication skills to document findings and present results, and strong attention to detail.
Responsibilities
- Assist in processing and quality-controlling high-throughput sequencing data, including read trimming, alignment, sorting, indexing, duplicate marking, and base quality score recalibration.
- Perform SNV calling and microbiome profiling from sequencing data using established bioinformatics pipelines.
- Benchmark variant calling tools by comparing performance, accuracy, and computational efficiency.
- Leverage databases and statistical tools to filter SNVs.
- Assist in generating and interpreting metrics to assess tool performance and data quality.
- Conduct literature reviews to identify best practices, tools, and methods relevant to the project.
- Assist in developing and maintaining reproducible analysis workflows using Bash and Snakemake.
- Document analyses and results clearly for both internal use and potential publications.
- Delegate responsibilities to undergraduate students and other junior members of the lab, providing guidance on bioinformatics pipelines protocols and reproducible workflows.
- Compile and interpret results and prepare a report of statistical findings.
- Attend team meetings and 1-on-1 meetings with the principal investigator and senior lab staff.
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What This Job Offers
Career Level
Entry Level
Education Level
High school or GED
