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Boemo Group

Publications

*equal contribution

†correspondence

PhD Opportunities Open

A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells

2025

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.†

Nature Communications

ecDNA replication is disorganised and vulnerable to replication stress

2025

Jaworski, J. J., Pfuderer, P.L., Czyz, P., Petris, G.†, Boemo, M.A.†, Sale, J.†

Nucleic Acids Research

Regulation of replication timing in Saccharomyces cerevisiae

2025

Berners-Lee, R., Gilmore, E., Berkemeier, F.†, Boemo, M.A.†

PLOS Computational Biology

DNA replication timing reveals genome-wide features of transcription and fragility

2025

Berkemeier, F.†, Cook, P.R., Boemo, M.A.†

Nature Communications

DNA replication dynamics are associated with genome composition in Plasmodium species

2025

Totanes, F.I.G., Chapman, S.E., Rai, S.K., Jones, M.J.K., Boemo, M.A.†, Merrick, C.J.†

Nucleic Acids Research

High levels of DNA replication initiation factors indicate ATRi sensitivity via excessive origin firing

2025

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.†

Available as a bioRxiv preprint

A genome-wide map of DNA replication at single-molecule resolution in the malaria parasite Plasmodium falciparum

2023

Totanes, F.I.G., Gockel, J., Chapman, S.E., Bartfai, R., Boemo, M.A.†, Merrick, C.J.†

Nucleic Acids Research

DNA replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses

2022

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.†

Genome Biology

DNAscent v2: Detecting replication forks in nanopore sequencing data with deep learning

2021

Boemo, M.A.†

BMC Genomics

A free-running oscillator times and executes centriole biogenesis

2020

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.†

Cell

The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems

2020

Boemo, M.A.†, Cardelli, L., Nieduszynski, C.A.

PLoS Computational Biology

Capturing the dynamics of genome replication on individual ultra-long nanopore sequencing reads

2019

Mueller, C.A., Boemo, M.A., Spingardi, P., Kessler, B. Kriaucionis, S. Simpson, J.T., Nieduszynski, C.A.†

Nature Methods

Mathematical modelling of a hypoxia-regulated oncolytic virus delivered by tumour-associated macrophages

2018

Boemo, M.A.†, Byrne, H.M.†

Journal of Theoretical Biology

The formal language and design principles of autonomous DNA walker circuits

2016

Boemo, M.A., Lucas, A.E., Turberfield, A.J.†, Cardelli, L.†

ACS Synthetic Biology

Automated design and verification of localized DNA computation circuits

2015

Boemo, M.A.†, Turberfield, A.J., Cardelli, L.

DNA 2015. LNCS, vol. 9211, p. 1-13. Springer, Heidelberg

Lactase persistence and lipid pathway selection in the Maasai

2012

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.†

PLOS ONE

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