Boemo Group
Our Research
Before a cell divides, it must copy (or “replicate”) its genome exactly once, but errors along the way can lead to cancer or other genetic diseases. An important error occurs when DNA replication forks stall. This may happen due to nucleotide shortages from abnormal cell cycle entry or when the fork encounters an obstacle that it cannot pass such as actively transcribing genes, DNA lesions, or difficult-to-replicate sequences. The frequent slowing or stalling of replication forks, termed “replication stress”, can lead to the rapid acquisition of mutations that results in genomic instability, but replication stress also presents an attractive therapeutic target for both human cancer cells and parasites. The purpose of our research is to determine how cells replicate and repair their DNA, the causes and consequences of any errors in DNA replication and repair, and how we can best exploit these errors with therapies.
We are a computational biology lab that studies DNA replication and repair by developing high-performance mathematical modelling methods and AI models that analyse large genomic sequencing datasets. We then engineer these methods into scalable, easy-to-use software that is deployed by our lab, our collaborating labs, and a broad userbase around the world. While our work is computational, our lab members have a wide range of academic backgrounds including medicine, mathematics, biochemistry, computer science, theoretical physics, and engineering. We are always interested in enquiries from prospective students and postdocs; candidates are encouraged to visit our lab webpage at www.boemogroup.org for further information.
Our Current Projects include
DNAScent - Algorithms that detect replication fork movement in single molecules
Cancer Diganostics - Deep learning algorithms that debug cancer cells
Simulation and Verification - Programming languages that make simulations safe, fast, and easy
Key Publications
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]
