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Dr Renata Retkute

Research Interests and Publications

My research focuses on developing mathematical models for various biological problems at a range of spatial scales from the molecular to the population level.

Infectious Diseases


Minter A.*, Retkute R.* (2019) Approximate Bayesian Computation for infectious disease modelling, Epidemics, doi: 10.1016/j.epidem.2019.100368

Retkute R., Jewell C.P., Van Boeckel T., Zhang G., Xiao X., Thanapongtharm W., Keeling M., Gilbert M., Tildesley M.J. (2018) Dynamics of the 2004 avian influenza H5N1 outbreak in Thailand: the role of duck farming, sequential model fitting and control, Preventive Veterinary Medicine, 159: 171-181, doi:10.1016/j.prevetmed.2018.09.014


Retkute R., Townsend A.J., Murchie E.H., Jensen O.E., Preston S.P. (2018) Three-dimensional plant architecture and sunlit-shaded patterns: a stochastic model of light dynamics in canopies, Annals of Botany, 122:2 291-302, doi:10.1093/aob/mcy067

Burgess A.J., Retkute R., Herman T., Murchie E.H. (2018) Exploring Relationships between Canopy Architecture, Light Distribution, and Photosynthesis in Contrasting Rice Genotypes Using 3D Canopy Reconstruction, Frontiers in Plant Science, 8:734 1-15, doi:10.3389/fpls.2017.00734
Burgess A.J., Retkute R., Pound M.P., Mayes S., Murchie E.H. (2017) Image-based 3D canopy reconstruction to determine potential productivity in complex multi-species crop systems, Annals of Botany, 119:4 517-532, doi:10.1093/aob/mcw242
Burgess A.J., Retkute R., Preston S.P., Jensen O.E., Pound M.P., Pridmore T.P., Murchie E.H. (2016) The 4-dimensional plant: effects of wind-induced canopy movement on light fluctuations and photosynthesis, Frontiers in Plant Science, 7:1392 1-12, doi:10.3389/fpls.2016.01392

Burgess A.J.∗, Retkute R.∗, Pound M.P., Foulkes J., Preston S.P., Jensen O.E., Pridmore T.T., Murchie E.H. (2015) High-resolution 3D structural data quantifies the impact of photoinhibition on long term carbon gain in wheat canopies in the field, Plant Physiology 169(2): 1192-1204, doi:10.1104/pp.15.00722

Retkute R., Smith-Unna S.E., Smith R.W., Burgess A,J., Jensen O.E., Johnson G.N. , Preston S.P., Murchie E.H. (2015) Exploiting heterogeneous environments: does photosynthetic acclimation optimise carbon gain in fluctuating light?, Journal of Experimental Botany 66 (9): 2437-2447, doi:10.1093/jxb/erv055

Genome Replication


Dimude J.U., Stein M., Andrzejewska E.E., Khalifa M.S., Retkute R., Skovgaard O., Rudolph C.J. (2018) Origins left, right and centre: increasing the number of initiation sites in the Escherichia coli chromosome, Genes 9(8), 376, doi:10.3390/genes9080376

Retkute R., Hawkins M., Rudolph C.J., Nieduszynski C.A. Modeling of DNA replication in rapidly growing bacteria with one and two replication origins, doi:10.1101/354654

Dimude J.U., Stockum A., Midgley-Smith S.L., Upton A.L., Foster H.A., Khan A., Saunders N.J., Retkute R., Rudolph C.J. (2015) The Consequences of Replicating in the Wrong Orientation: Bacterial Chromosome Duplication without an Active Replication Origin, MBIO 6(6): e01294-15, doi:10.1128/mBio.01294-15

Ivanova D., Taylor T., Smith S.L., Dimude J.U., Upton A.L., Mehrjouy M.M., Skovgaard O., Sherratt D.J., Retkute R., Rudolph C.J. (2015) Shaping the landscape of the Escherichia coli chromosome: replication- transcription encounters in cells with an ectopic replication origin, Nuclear Acids Research , 43(16): 7865- 7877, doi: 10.1093/nar/gkv704

Daigaku Y., Keszthelyi A., Muller C.A., Miyabe I., Brooks T., Retkute R., Hubank M., Nieduszyski C.A., Carr A.M. (2015) A global profile of replication polymerase usage. Nature Structural & Molecular Biology, 22(3): 192-8 doi:10.1038/nsmb.2962

Retkute R. (2014) Toward a General Model for the Evolution of DNA Replication in Three Domains of Life, Mathematical Modeling of Natural Phenomenon 9(3) 96-106,

Muller C.A., Hawkins M., Retkute R., Malla S., Wilson R., Blythe M.J., Nakato R., Komata M., Shirahige K., de Moura A.P.S. and Nieduszynski C.A. (2014) The dynamics of genome replication using deep sequencing, Nuclear Acids Research 42 (1): e3 1-11, doi:10.1093/nar/gkt878

Hawkins M ∗., Retkute R.∗, Muller C.A., Saner N., Tanaka T., de Moura A.P.S. and Nieduszynski C.A. (2013) High-resolution genome replication profiles, modeling and single-cell imaging define the stochastic nature of replication initiation and termination, Cell Reports 5 (4): 1132-1141, doi:10.1016/j.celrep.2013.10.014
Saner N., Karschau J., Natsume T., Gierlinski M., Retkute R., Hawkins M., Nieduszynski C., Blow J.J., de Moura A.P.S., Tanaka T.U. (2013) Stochastic association of neighboring replicons creates replication factories in budding yeast, The Journal of Cell Biology 202 (7): 1001-1012, doi:10.1083/jcb.201306143
Natsume T., Muller C.A., Katou Y., Retkute R., Gierlinski M., Araki H., Blow J.J., Shirahige K., Nieduszyn- ski C.A and Tanaka T.U. (2013) Kinetochores Coordinate Pericentromeric Cohesion and Early DNA Replica- tion by Cdc7-Dbf4 Kinase Recruitment, Molecular Cell 50 (5): 661-674, doi:10.1016/j.molcel.2013.05.011

Retkute R., Nieduszynski C.A., and de Moura A.P.S. (2012) Mathematical modeling of genome replication, Physical Review E 86 (3) 031916: 1-15, doi:10.1103/PhysRevE.86.031916
Retkute R., Nieduszynski C.A. and de Moura A.P.S. (2011) Dynamics of DNA replication in yeast, Physical Review Letters 107 (6) 068103: 1-4, doi:10.1103/PhysRevLett.107.068103
de Moura A.P.S., Retkute R., Hawkins M. and Nieduszynski C.A. (2010) Mathematical modelling of whole chromosome replication, Nuclear Acids Research 38 (17) pp.5623-5633,

Image Analysis & Machine Learning

Prusokas A., Prusokas A., Retkute R. (2019) Comparing AMR surveillance data and in silico MICs: case of Klebsiella pneumoniae. doi: 10.7303/syn17559498. Shiny app:

Prusokas A., Hawkins M., Nieduszynski C.A., Retkute R. The effectiveness of glass beads for plating cell cultures, doi:10.1101/241752

Abdel-Fahim R., Mistry N., Mougin O., Blazejewska A., Pitiot A., Retkute R., Gowland P., and Evangelou N. (2014) Improved detection of focal cortical lesions using 7 T magnetisation transfer imaging in patients with multiple sclerosis, Multiple Sclerosis and Related Disorders 3 (2): 258-265, doi:10.1016/j.msard.2013.10.004

Technology in the Mathematics Curriculum


Retkute R. (2009) Exploring Technology-Based Continuous Assessment via Electronic Voting Systems in Mathematics and Statistics, MSOR Connections 9 (1): 24-28. pdf

Other Interests

Science fiction, painting, playing harp and tap dancing.


Current address:

Department of Plant Sciences
University of Cambridge
Downing Street

Cambridge CB2 3EA

Office Phone: 01223 748957