Totanes, F.I.G., Chapman, S.E., Rai, S.K., Jones, M.J.K., Boemo, M.A.†, Merrick, C.J.† (2024) DNA replication dynamics are associated with genome composition in Plasmodium species.

[bioRxiv]

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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.

[bioRxiv]

[DOI:10.1093/nar/gkad093]

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Jones, M.J.K.†, Rai, S.K., Pfuderer, P.L., Bonfim-Melo, A., Pagan, J.K., Clarke, P.R., McClelland, S.E., Boemo, M.A.† (2022) A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells.

[bioRxiv]

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Shaikh, N.*, Mazzagatti, A.*, Bakker, B., Spierings, D.C.J.E., Wardenaar, R., Maniati, E., Larsson, P., Wang, J., Boemo, M.A., Foijer, F., McClelland, S.E.† (2022) DNA replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses. Genome Biology 23:223.

[bioRxiv]

[DOI:10.1186/s13059-022-02781-0]

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Boemo, M.A.† (2021) DNAscent v2: Detecting replication forks in nanopore sequencing data with deep learning. BMC Genomics 22:430.

[bioRxiv]

[DOI:10.1186/s12864-021-07736-6]

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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]

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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]

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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]

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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]

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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]

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Boemo, M.A.†, Turberfield, A.J., Cardelli, L. (2015) Automated design and verification of localized DNA computation circuits. In: Phillips, A., Yin, P. (eds.) DNA 2015. LNCS, vol. 9211, p. 1-13. Springer, Heidelberg. 

[DOI:10.1007/978-3-319-21999-8_11]

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Wagh, K.*, Bhatia, A.*, Alexe, G., Reddy, A., Ravikumar, V., Seiler, M., Boemo, M., Yao, M., Cronk, L., Naqvi, A., Ganesan, S., Levine, A.J.†, Bhanot, G.† (2012) Lactase persistence and lipid pathway selection in the Maasai. PLoS ONE 7: e44751. 

[DOI:10.1371/journal.pone.0044751]