DAF-seq (Deaminase-Assisted single-molecule chromatin Fiber sequencing) is a recently developed long-read sequencing method (Swanson, Nature Biotechnology 2025) that directly measures chromatin accessibility and transcription factor footprints on individual DNA molecules. As a single-molecule approach, DAF-seq enables detailed exploration of regulatory landscapes across any genomic region and organism.
This PhD project will optimise and extend both the DAF-seq wet-lab protocol and its computational analysis pipeline. Students will gain experience in nucleic acid chemistry, library preparation, and Nanopore sequencing, alongside computational development using R/Python, Nextflow, and high-performance computing.
The balance between laboratory and computational work will be tailored to the student’s interests and project needs. The project would suit candidates with backgrounds in molecular biology, genomics, or bioinformatics, and an enthusiasm for developing complementary wet- and dry-lab skills. Programming experience is advantageous.
This project is open to students in the Metcalf Scholarship program.
