PhD Position in Computational Genomics

The Pipes Laboratory at the Pacific Bioscines Research Center (PBRC) is looking for a PhD student to join the Information and Computer Sciences (ICS) graduate program. We develop computational tools to analyze environmental DNA (eDNA).

We are looking for a student interested in Computer Science applications within genomics. The projects involve:

• Big Data: Handling terabytes of raw sequencing data.
• Algorithms: Designing efficient methods for string matching and clustering.
• Machine Learning: Building models to classify species from noisy biological data.
• Performance: Optimizing pipelines for memory efficiency and parallel processing.

The student will have access to significant hardware for their research:

• Two in-house, high-memory servers dedicated to the lab.
• The University of Hawaiʻi "KOA" High-Performance Computing cluster.
• National supercomputing resources (such as ACCESS) for large-scale jobs.

• BS or MS in Computer Science, Mathematics, or Data Science.
• Proficiency in Python, C/C++, Java, or Rust.
• Experience working in a Linux/Unix environment.
• Interest in biology is required, but prior coursework in biology is not.

The position includes a Graduate Research Assistantship (GRA). This provides a full tuition waiver, a monthly stipend, and benefits.

Please email Dr. Lenore Pipes (lpipes) with the following:

• CV or Resume.
• A brief note about your research interests and coding experience.
• Admission to the UH Manoa ICS PhD Program will be required for the position.