Publication successes for our Masters students
Three of our recent Master of Science (Bioinformatics) students – Seren Adachi, Hanyu Lu, and Alex Ringeri – already have peer-reviewed publications to their name, as the result of research undertaken during the capstone research project component of their degree. This is a fantastic result, reflecting both the hard work of these student researchers and the indispensable contribution of academic supervisors who provide our students with mentorship, excellent training and an authentic research experience. And, as Lu's supervisor Neil Young (Melbourne Veterinary School) notes, it 'highlights the real-world impact of strong bioinformatics training at the University of Melbourne'.
For example, Seren implemented ML/AI methods to analyse tear fluid proteomics data from both ALS patients and control subjects, mentored by Michael Menden (Department of Biochemistry and Pharmacology), and then validated these models to test the usefulness of tear fluid as a biomarker source for improved ALS diagnosis. Alex reviewed existing metabarcoding methods, which contributed to a study with supervisor Camille Truong and colleagues (Royal Botanic Gardens Victoria) comparing different classification algorithms to identify fungal species from long DNA sequences. And Lu used ATAC-seq to map accessible chromatin regions in embryonic roundworms, which he then compared with transcriptomic data from both embryonic and larval stages to identify which genes are essential for development.
Like all students in the Masters of Science (Bioinformatics) program, Seren, Lu and Alex benefitted from working closely with their academic supervisors. Lu says he is grateful for the dedicated support he received from Neil Young and Tulio Campos (Melbourne Veterinary School), 'including organizing presentation opportunities, helping me connect with other members of the team, supervising my progress, teaching me relevant skills, and carefully revising the manuscript in great detail'.
The papers are:
- Graetz, A., Feng, J., Ringeri, A., Bird, A., Vu, D., Truong, C., Schwessinger, B., 2025. Benchmarking fungal species classification using Oxford Nanopore Technologies long-read ITS metabarcodes. Fungal Genetics and Biology 181, 104042. https://doi.org/10.1016/j.fgb.2025.104042
- Lu, H., Campos, T., Sumanam, S.B., Wang, T., Zheng, Y., Gasser, R.B., Young, N.D., 2025. Chromatin accessibility landscape of a parasitic nematode during embryogenesis. BMC Genomics 27, 116. https://doi.org/10.1186/s12864-025-12473-1
- Scholl, L.-S., Demleitner, A.F., Riedel, J., Adachi, S., Neuenroth, L., Meijs, C., Tzeplaeff, L., Caldi Gomes, L., Galhoz, A., Cordts, I., Lenz, C., Menden, M., Lingor, P., 2025. Identification and validation of a tear fluid-derived protein biomarker signature in patients with amyotrophic lateral sclerosis. Acta Neuropathol Commun 13, 187. https://doi.org/10.1186/s40478-025-02109-6
Congratulations, Seren, Lu, and Alex, your supervisors, and all researchers contributing to these publications.