Improving and applying repeat expansion detection methods to identify causes of disease

• PhD

Short tandem repeat expansions are known to cause more than 50 diseases. The Bahlo lab has developed several bioinformatic methods for detecting expansions of short tandem repeats in short-read next generation sequencing data (Tankard et al AJHG 2018, Fearnley et al Sci Rep 2022, Dolzhenko & Bennett et al Genome Biol 2020). These have been used to identify novel repeat expansions (Rafehi et al AJHG 2019 & 2023) and novel motifs for known repeat expansions (Bennett et al Brain Comms 2025).

Aim 1: Continue development of repeat expansion bioinformatic methods
Aim 2: Search for novel pathogenic repeat expansions in epilepsy, ataxia and MND patient cohorts

Ony suitable for students with a strong quantitative background in computational biology, computer science, data science or statistics.

The Bahlo lab’s work is focused on the identification and understanding of genetic risk factors involved in neurological and retinal disorders. We are a computational biology lab (dry lab only, no lab work) with about 17 members from diverse backgrounds. We have lab meetings every week on Tuesdays at 1 pm and all students speak several times a year.

We are a highly collaborative group and we have regular lab lunches. We have access and experience with multiple large-scale biobanks and maintain a lab GitHub page with our tools (https://github.com/bahlolab). We work highly collaboratively with clinicians and molecular biologists and have access to whole genome sequencing from several large scale patient cohorts, particularly in ataxia and epilepsy.