Computational Biology of DNA Replication and Repair
Key words
Computational Biology, AI, DNA Replication, DNA Repair, Genomic Instability
Research interests
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.
Selected publications
- Totanes, F.I.G., Gockel, J., Chapman, S.E., Bartfai, R., Boemo, M.A.†, Merrick, C.J.† (2023) A genome-wide map of DNA replication at single-molecule resolution in the malaria parasite Plasmodium falciparum. Nucleic Acids Research.
- 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.
- 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.