Pixu Shi

PreMiEr at Duke University is offering a postdoctoral research opportunity in precision microbiome engineering. The project sits at the intersection of artificial intelligence, microbial genomics, and microbiome science, with a strong emphasis on computational method development for complex microbial communities. The postdoctoral associate will work on large-scale DNA sequencing data to identify health-relevant patterns in built-environment microbiomes. The research includes developing and applying DNA language model approaches, designing machine learning methods for prediction and classification from metagenomic sequence data, and comparing representation-learning strategies with conventional bioinformatics workflows. A further goal is to evaluate how well these approaches generalize across independent studies, sequencing platforms, and environmental settings. The role is embedded in PreMiEr and connected to broader efforts in microbiome monitoring, risk assessment, and precision microbiome engineering. The selected researcher will collaborate with biologists, engineers, microbiologists, and data scientists, contributing to reproducible computational workflows, benchmarking analyses, and collaborative interdisciplinary projects. There may also be opportunities to mentor graduate and undergraduate researchers and to participate in educational and training activities within the Duke research community. The position is supervised by Dr. Joshua Granek and Dr. Pixu Shi in the Duke University School of Medicine.