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Publications
*equal contribution
†correspondence
CAD-C reveals centromere pairing and near-perfect alignment of sister chromatids
Delamarre, A., Reveil, M. Pichon, D.P., Boemo, M.A., Whitehouse, I.†
2025
Available as a bioRxiv preprint
2025
Available as a bioRxiv preprint
Stalling of elongating Pol II triggers Ser7 phosphorylation in trans to drive transcription recovery
Shlamovitz, I.*, Bao, Y.*, Toteva, T.*, Crisp, A.*, Ye, S., Wingett, S.W., Cacioppo, R., Edmonson, A., Castiblanco, D., Boemo, M.A., Tufegdžić Vidaković, A.†
2025
Available as a bioRxiv preprint
2025
Available as a bioRxiv preprint
A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells
Jones, M.J.K.†, Rai, S.K., Pfuderer, P.L., Bonfim-Melo, A., Pagan, J.K., Clarke, P.R., Totanes, F.I.G., Merrick, C.J., McClelland, S.E., Boemo, M.A.†
2025
Nature Communications
2025
Nature Communications
ecDNA replication is disorganised and vulnerable to replication stress
Jaworski, J. J.*, Pfuderer, P.L.*, Czyz, P., Petris, G.†, Boemo, M.A.†, Sale, J.†
2025
Nucleic Acids Research
2025
Nucleic Acids Research
Regulation of replication timing in Saccharomyces cerevisiae
Berners-Lee, R., Gilmore, E., Berkemeier, F.†, Boemo, M.A.†
2025
PLOS Computational Biology
2025
PLOS Computational Biology
DNA replication timing reveals genome-wide features of transcription and fragility
Berkemeier, F.†, Cook, P.R., Boemo, M.A.†
2025
Nature Communications
2025
Nature Communications
DNA replication dynamics are associated with genome composition in Plasmodium species
Totanes, F.I.G., Chapman, S.E., Rai, S.K., Jones, M.J.K., Boemo, M.A.†, Merrick, C.J.†
2025
Nucleic Acids Research
2025
Nucleic Acids Research
High levels of DNA replication initiation factors indicate ATRi sensitivity via excessive origin firing
Lumeau, A., Pfuderer, P.L., De Angelis, S., Scarth, J.A., Guscott, M.A., Shaikh, N., Copley, F.B., Gerdes, H., Alard, E.L., Cutillas, P.R., Mardakheh, F., Boemo, M.A., Forment, J.V.†, McClelland, S.E.†
2025
Available as a bioRxiv preprint
2025
Available as a bioRxiv preprint
A genome-wide map of DNA replication at single-molecule resolution in the malaria parasite Plasmodium falciparum
Totanes, F.I.G., Gockel, J., Chapman, S.E., Bartfai, R., Boemo, M.A.†, Merrick, C.J.†
2023
Nucleic Acids Research
2023
Nucleic Acids Research
DNA replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses
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
Genome Biology
2022
Genome Biology
DNAscent v2: Detecting replication forks in nanopore sequencing data with deep learning
Boemo, M.A.†
2021
BMC Genomics
2021
BMC Genomics
A free-running oscillator times and executes centriole biogenesis
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
Cell
2020
Cell
The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems
Boemo, M.A.†, Cardelli, L., Nieduszynski, C.A.
2020
PLOS Computational Biology
2020
PLOS Computational Biology
Capturing the dynamics of genome replication on individual ultra-long nanopore sequencing reads
Mueller, C.A.*, Boemo, M.A.*, Spingardi, P., Kessler, B. Kriaucionis, S. Simpson, J.T., Nieduszynski, C.A.†
2019
Nature Methods
2019
Nature Methods
Mathematical modelling of a hypoxia-regulated oncolytic virus delivered by tumour-associated macrophages
Boemo, M.A.†, Byrne, H.M.†
2018
Journal of Theoretical Biology
2018
Journal of Theoretical Biology
The formal language and design principles of autonomous DNA walker circuits
Boemo, M.A., Lucas, A.E., Turberfield, A.J.†, Cardelli, L.†
2016
ACS Synthetic Biology
2016
ACS Synthetic Biology
Automated design and verification of localized DNA computation circuits
Boemo, M.A.†, Turberfield, A.J., Cardelli, L.
2015
DNA 2015. LNCS, vol. 9211.
2015
DNA 2015. LNCS, vol. 9211.
Lactase persistence and lipid pathway selection in the Maasai
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
PLOS ONE
2012
PLOS ONE
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