Research
I am interested in developing new computational methods and software to study how the dysregulation or faults in cell cycle mechanisms can lead to genome instability and cancer. A selection of recent and ongoing projects are:
- machine learning software called DNAscent that infers replication fork movement on individual molecules from Oxford Nanopore sequencing data,
- mathematical modelling of centriole growth and regulation,
- development of the Beacon Calculus, a process algebra for the simulation of biological systems,
- software that analyses the copy number variations in cancer genomes to infer disrupted cell cycle mechanisms.
This research lies at the interface of biology and computer science, and employs methods from machine learning, software verification, bioinformatics, and computational modelling.
Publications
Aydogan, M.G.*†, Steinacker, T.L.*, Mofatteh, M., Wilmott, Z.M., Zhou, F.Y., Gartenmann, L., Wainman, A., Saurya, S., Novak, Z.A., Wong, S., Goriely, A., Boemo, M.A.†, Raff, J.W.† (2020) A free-running oscillator times and executes centriole biogenesis. Cell 181:1-16.
[bioRxiv] DOI:10.1016/j.cell.2020.05.018
Boemo, M.A.†, Cardelli, L., Nieduszynski, C.A. (2020) The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems. PLoS Computational Biology 16:e1007651.
[bioRxiv] DOI:10.1371/journal.pcbi.1007651
Mueller, C.A.*, Boemo, M.A.*, Spingardi, P., Kessler, B. Kriaucionis, S. Simpson, J.T., Nieduszynski, C.A.† (2019) Capturing the dynamics of genome replication on individual ultra-long nanopore sequencing reads. Nature Methods 16:429-436. [bioRxiv] DOI:10.1038/s41592-019-0394-y
Boemo, M.A.†, Byrne, H.M.† (2018) Mathematical modelling of a hypoxia-regulated oncolytic virus delivered by tumour-associated macrophages. Journal of Theoretical Biology 461:102-116.
DOI:10.1016/j.jtbi.2018.10.044
Boemo, M.A., Lucas, A.E., Turberfield, A.J.†, Cardelli, L.† (2016) The formal language and design principles of autonomous DNA walker circuits. ACS Synthetic Biology 5:878-884.
DOI:10.1021/acssynbio.5b00275
