Biography

I have an interdisciplinary research background, with a PhD in computational chemistry at the University of Essex following on from undergraduate training in mathematics.

After a first postdoctoral position in theoretical chemistry at the University of Oxford I pursued an interest in evolutionary biology via a second postdoc at what was the Wellcome Trust Sanger Institute, where I developed methods for analysing time-resolved genome sequence data from rapidly evolving populations. 

In 2013, I started a research group at the University of Cambridge supported by a Henry Dale Fellowship, working on rapid evolutionary processes in pathogens.

After brief spells at Queen Mary University of London and the MRC Biostatistics Unit in Cambridge, and after visiting positions in Computer Science at the University of Helsinki and in Physics at the University of Köln, I moved in 2021 to the MRC University of Glasgow Centre for Virus Research, where I set up my current group, studying virus infection, evolution, and transmission.

Research interests

My research interests span virus infection, virus evolution, and virus transmission, with a particular focus on respiratory viruses such as RSV, SARS-CoV-2, and influenza.

Concerning virus infection, we are building models to consider how different phenotypes, such as receptor binding during the process of virus entry into cells, impact upon the effectiveness of viruses in infecting cells.  Our key tool in this work is the development of mathematical models, using differential equations to describe the various stages of the viral life cycle.  Recent work in this area has also considered the effectiveness of different antiviral treatments, for example using genomic data to evaluate the role of nucleoside analogues in increasing viral mutation rates, and reducing the effectiveness of viruses causing infection.

In the area of virus evolution, we have pioneered the use of statistical methods for evaluating sequence data that describes changes in viral populations occurring during the infection of a single host.  An ongoing interest is the complexity of virus evolution within single cases of infection, in particular the phenomenon of compartmentalisation, whereby viruses infecting a host split into spatially distinct, independently evolving sub-populations.

A key theme in our work on virus transmission has been that of nosocomial transmission, studying new cases of infection that arise in hospitals.  Our work has built a better understanding of how transmission in hospitals occurs, how novel sources of data such as that from genome sequencing can best be used to inform hospital staff working to manage cases of infection, and of how different interventions could be used to prevent virus transmission.  Work in this area has involved the development of physics-based models to understand how the airborne spread of respiratory viruses shapes patterns of infection, and recently the integration of computational fluid dynamics into epidemiological models to track virus spread.

Work in my group is continually evolving, via new method development, the integration of new technologies, and collaborations with experts in different areas of virus research.  We welcome people from a variety of quantitative research backgrounds and regularly explore potential collaborations in a variety of new potential directions of study.

 

Publications

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Number of items: 74.

2025

Illingworth, C.J.R. et al. (2025) The role of spatial distance in SARS-CoV-2 nosocomial transmission. Journal of Hospital Infection, 166, pp. 71-81. (doi: 10.1016/j.jhin.2025.09.011)

Tate, M. et al. (2025) Clinical effectiveness, safety and viral mutagenicity of oral favipiravir for COVID-19: results from a community-based, open-label, randomised, phase III trial. Antimicrobial Agents and Chemotherapy, 69(8), e0005425. (doi: 10.1128/aac.00054-25) (PMID:40552814)

Stewart, Lauren, Evans, Stephanie, Brevini, Teresa, Sampaziotis, Fotios and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2025) Modelling the potential use of pre-exposure prophylaxis to reduce nosocomial SARS-CoV-2 transmission. PLoS Computational Biology, 21(8), e1013361. (doi: 10.1371/journal.pcbi.1013361) (PMID:40763307) (PMCID:PMC12370187)

Pascall, D. J. et al. (2025) The NOSTRA model: coherent estimation of infection sources in the case of possible nosocomial transmission. PLoS Computational Biology, 21(4), e1012949. (doi: 10.1371/journal.pcbi.1012949) (PMID:40258227) (PMCID:PMC12121921)

Leiser, R. et al. (2025) Insights into the implementation of a whole genome sequencing report form (SRF) to reduce nosocomial SARS-CoV-2 in UK hospitals within an unfolding pandemic: A qualitative process evaluation using normalisation process theory. PLoS ONE, 20(4), e0321534. (doi: 10.1371/journal.pone.0321534) (PMID:40245025) (PMCID:PMC12005541)

Smith, E. et al. (2025) Variable rates of SARS-CoV-2 evolution in chronic infections. PLoS Pathogens, 21(4), e1013109. (doi: 10.1371/journal.ppat.1013109) (PMID:40294077) (PMCID:PMC12061394)

Brock, Rebecca C., Goudie, Robert J.B., Peters, Christine, Thaxter, Rachel, Gouliouris, Theodore, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Morris, Andrew Conway, Beggs, Clive B., Butler, Matthew and Keevil, Victoria L. (2025) Efficacy of air cleaning units for preventing SARS-CoV-2 and other hospital-acquired infections on medicine for older people wards: a quasi-experimental controlled before-and-after study. Journal of Hospital Infection, 155, pp. 1-8. (doi: 10.1016/j.jhin.2024.09.017) (PMID:39374708)

2024

Fozard, John A., Thomson, Emma C. ORCID logoORCID: https://orcid.org/0000-0003-1482-0889 and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2024) Epidemiological inference at the threshold of data availability: an influenza A(H1N2)v spillover event in the United Kingdom. Journal of the Royal Society: Interface, 21(217), 20240168. (doi: 10.1098/rsif.2024.0168) (PMID:39109454) (PMCID:PMC11304334)

Sinclair, Patrick, Zhao, Lei, Beggs, Clive B. and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2024) The airborne transmission of viruses causes tight transmission bottlenecks. Nature Communications, 15(1), 3540. (doi: 10.1038/s41467-024-47923-z) (PMID:38670957) (PMCID:PMC11053022)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Guerra-Assuncao, Jose A., Gregg, Samuel, Charles, Oscar, Pang, Juanita, Roy, Sunando, Abdelnabi, Rana, Neyts, Johan and Breuer, Judith (2024) Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus Evolution, 10(1), veae001. (doi: 10.1093/ve/veae001) (PMID:38486802) (PMCID:PMC10939363)

2023

Flowers, Paul ORCID logoORCID: https://orcid.org/0000-0001-6239-5616, Leiser, Ruth, Mapp, Fiona, McLeod, Julie, Stirrup, Oliver, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Blackstone, James and Breuer, Judith (2023) A qualitative process evaluation using the behaviour change wheel approach: did a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 within UK hospitals operate as anticipated? British Journal of Health Psychology, 28(4), pp. 1011-1035. (doi: 10.1111/bjhp.12666) (PMID:37128667)

Brevini, T. et al. (2023) FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2. Nature, 615(7950), pp. 134-142. (doi: 10.1038/s41586-022-05594-0) (PMID:36470304) (PMCID:PMC9977684)

2022

Stejskal, L. et al. (2022) An entropic safety catch controls Hepatitis C virus entry and antibody resistance. eLife, 11, e71854. (doi: 10.7554/eLife.71854) (PMID:35796426) (PMCID:PMC9333995)

Nickbakhsh, S. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12, 11735. (doi: 10.1038/s41598-022-15661-1) (PMID:35853960) (PMCID:PMC9296497)

Kemp, S. A. et al. (2022) Transmission of B.1.617.2 Delta variant between vaccinated healthcare workers. Scientific Reports, 12, 10492. (doi: 10.1038/s41598-022-14411-7) (PMID:35729228) (PMCID:PMC9212198)

Illingworth, C. J.R. et al. (2022) A2B-COVID: a tool for rapidly evaluating potential SARS-CoV-2 transmission events. Molecular Biology and Evolution, 39(3), msac025. (doi: 10.1093/molbev/msac025) (PMID:35106603) (PMCID:PMC8892943)

Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z) (PMID:35197443) (PMCID:PMC8866425)

Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)

Twohig, K. A. et al. (2022) Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. Lancet Infectious Diseases, 22(1), pp. 35-42. (doi: 10.1016/S1473-3099(21)00475-8) (PMID:34461056) (PMCID:PMC8397301)

2021

Ferris, M. et al. (2021) Efficacy of FFP3 respirators for prevention of SARS-CoV-2 infection in healthcare workers. eLife, 10, e71131. (doi: 10.7554/elife.71131) (PMID:34783656)

Illingworth, C. J.R. et al. (2021) Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections. eLife, 10, e67308. (doi: 10.7554/eLife.67308)

Hamilton, W. L. et al. (2021) Applying prospective genomic surveillance to support investigation of hospital-onset COVID-19. Lancet Infectious Diseases, 21(7), pp. 916-917. (doi: 10.1016/S1473-3099(21)00251-6) (PMID:33984262) (PMCID:PMC8110208)

Graham, M. S. et al. (2021) Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. Lancet Public Health, 6(5), e335-e345. (doi: 10.1016/S2468-2667(21)00055-4)

Sanjuán, Rafael, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Geoghegan, Jemma L., Iranzo, Jaime, Zwart, Mark P., Ciota, Alexander T., Moratorio, Gonzalo, Gago-Zachert, Selma, Duffy, Siobain and Vijaykrishna, Dhanasekaran (2021) Five challenges in the field of viral diversity and evolution. Frontiers in Virology, 1, 684949. (doi: 10.3389/fviro.2021.684949)

Kemp, S. A. et al. (2021) SARS-CoV-2 evolution during treatment of chronic infection. Nature, 592(7853), pp. 277-282. (doi: 10.1038/s41586-021-03291-y) (PMID:33545711) (PMCID:PMC7610568)

2020

Lumby, C. K. et al. (2020) Favipiravir and zanamivir cleared infection with influenza B in a severely immunocompromised child. Clinical Infectious Diseases, 71(7), e191-e194. (doi: 10.1093/cid/ciaa023) (PMID:32124919)

Lumby, Casper K., Zhao, Lei, Breuer, Judith and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2020) A large effective population size for established within-host influenza virus infection. eLife, 9, e56915. (doi: 10.7554/eLife.56915) (PMID:32773034) (PMCID:PMC7431133)

Ghafari, Mahan, Lumby, Casper K., Weissman, Daniel B. and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2020) Inferring transmission bottleneck size from viral sequence data using a novel haplotype reconstruction method. Journal of Virology, 94(13), e00014-20. (doi: 10.1128/JVI.00014-20) (PMID:32295920) (PMCID:PMC7307158)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Raghwani, Jayna, Serwadda, David, Sewankambo, Nelson K., Robb, Merlin L., Eller, Michael A., Redd, Andrew R., Quinn, Thomas C. and Lythgoe, Katrina A. (2020) A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection. PLoS Pathogens, 16(6), e1008171. (doi: 10.1371/journal.ppat.1008171) (PMID:32492061) (PMCID:PMC7295245)

2019

Grech, L. et al. (2019) Fitness landscape of the fission yeast genome. Molecular Biology and Evolution, 36(8), pp. 1612-1623. (doi: 10.1093/molbev/msz113) (PMID:31077324) (PMCID:PMC6657727)

Doyle, S. R. et al. (2019) Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus. BMC Genomics, 20, p. 218. (doi: 10.1186/s12864-019-5592-6) (PMID:30876405) (PMCID:PMC6420744)

Kalemera, Mphatso, Mincheva, Dilyana, Grove, Joe and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2019) Building a mechanistic mathematical model of hepatitis C virus entry. PLoS Computational Biology, 15(3), e1006905. (doi: 10.1371/journal.pcbi.1006905) (PMID:30883541) (PMCID:PMC6445459)

Zhao, Lei, Abbasi, Ali B. and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2019) Mutational load causes stochastic evolutionary outcomes in acute RNA viral infection. Virus Evolution, 5(1), vez008. (doi: 10.1093/ve/vez008) (PMID:31024738) (PMCID:PMC6476161)

Zhao, Lei and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2019) Measurements of intrahost viral diversity require an unbiased diversity metric. Virus Evolution, 5(1), vey041. (doi: 10.1093/ve/vey041) (PMID:30723551) (PMCID:PMC6354029)

2018

Lumby, Casper K., Nene, Nuno R. and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2018) A novel framework for inferring parameters of transmission from viral sequence data. PLoS Genetics, 14(10), e1007718. (doi: 10.1371/journal.pgen.1007718) (PMID:30325921) (PMCID:PMC6203404)

Nené, Nuno R., Dunham, Alistair S. and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2018) Inferring fitness effects from time-resolved sequence data with a delay-deterministic model. Genetics, 209(1), pp. 255-264. (doi: 10.1534/genetics.118.300790) (PMID:29500183) (PMCID:PMC5937181)

Reid, Adam J., Talman, Arthur M., Bennett, Hayley M., Gomes, Ana R., Sanders, Mandy J., Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Billker, Oliver, Berriman, Matthew and Lawniczak, Mara K.N. (2018) Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites. eLife, 7, e33105. (doi: 10.7554/eLife.33105) (PMID:29580379) (PMCID:PMC5871331)

R. Nené, Nuno, Mustonen, Ville and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2018) Evaluating genetic drift in time-series evolutionary analysis. Journal of Theoretical Biology, 437, pp. 51-57. (doi: 10.1016/j.jtbi.2017.09.021) (PMID:28958783) (PMCID:PMC5703635)

2017

Anderson, T. J.C. et al. (2017) Rapid identification of genes controlling virulence and immunity in malaria parasites. PLoS Pathogens, 13(7), e1006447. (doi: 10.1371/journal.ppat.1006447) (PMID:28704525) (PMCID:PMC5507557)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Roy, Sunando, Beale, Mathew A., Tutill, Helena, Williams, Rachel and Breuer, Judith (2017) On the effective depth of viral sequence data. Virus Evolution, 3(2), vex030. (doi: 10.1093/ve/vex030) (PMID:29250429) (PMCID:PMC5724399)

Sobel Leonard, A. et al. (2017) The effective rate of influenza reassortment is limited during human infection. PLoS Pathogens, 13(2), e1006203. (doi: 10.1371/journal.ppat.1006203) (PMID:28170438) (PMCID:PMC5315410)

2016

Illingworth, C.J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2016) SAMFIRE: multi-locus variant calling for time-resolved sequence data. Bioinformatics, 32(14), pp. 2208-2209. (doi: 10.1093/bioinformatics/btw205) (PMID:27153641) (PMCID:PMC4937198)

Martinez, Julien ORCID logoORCID: https://orcid.org/0000-0001-8210-2921, Cogni, Rodrigo, Cao, Chuan, Smith, Sophie, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Jiggins, Francis M. (2016) Addicted? Reduced host resistance in populations with defensive symbionts. Proceedings of the Royal Society of London Series B: Biological Sciences, 283(1833), 20160778. (doi: 10.1098/rspb.2016.0778) (PMID:27335421) (PMCID:PMC4936038)

Shaw, C.D. et al. (2016) In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization. Molecular Microbiology, 99(6), pp. 1134-1148. (doi: 10.1111/mmi.13291) (PMID:26713880) (PMCID:PMC4832254)

Raghwani, Jayna, Pybus, Oliver G. and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2016) Population genetic modeling of viruses. In: Weaver, Scott C., Denison, Mark, Roossinck, Marilyn and Vignuzzi, Marco (eds.) Virus Evolution: Current Research and Future Directions. Caister Academic Press: Wymondham, pp. 293-327. ISBN 9781910190234

2015

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2015) Fitness inference from short-read data: within-host evolution of a reassortant H5N1 influenza virus. Molecular Biology and Evolution, 32(11), pp. 3012-3026. (doi: 10.1093/molbev/msv171) (PMID:26243288) (PMCID:PMC4651230)

2014

Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Fischer, Andrej and Mustonen, Ville (2014) Identifying selection in the within-host evolution of influenza using viral sequence data. PLoS Computational Biology, 10(7), e1003755. (doi: 10.1371/journal.pcbi.1003755) (PMID:25080215) (PMCID:PMC4117419)

Fischer, Andrej, Vázquez-García, Ignacio, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Mustonen, Ville (2014) High-definition reconstruction of clonal composition in cancer. Cell Reports, 7(5), pp. 1740-1752. (doi: 10.1016/j.celrep.2014.04.055) (PMID:24882004) (PMCID:PMC4062932)

Chintapalli, Sree V., Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Upton, Graham J. G., Sacquin-Mora, Sophie, Reeves, Philip J., Mohammedali, Hani S. and Reynolds, Christopher A. (2014) Assessing the effect of dynamics on the closed-loop protein-folding hypothesis. Journal of the Royal Society: Interface, 11(91), 20130935. (doi: 10.1098/rsif.2013.0935) (PMID:24258160) (PMCID:PMC3869168)

Roy, Aparna, Taddese, Bruck, Vohra, Shabana, Thimmaraju, Phani K., Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Simpson, Lisa M., Mukherjee, Keya, Reynolds, Christopher A. and Chintapalli, Sree V. (2014) Identifying subset errors in multiple sequence alignments. Journal of Biomolecular Structure and Dynamics, 32(3), pp. 364-371. (doi: 10.1080/07391102.2013.770371) (PMID:23527867)

2013

Cubillos, F. A. et al. (2013) High-resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics, 195(3), pp. 1141-1155. (doi: 10.1534/genetics.113.155515) (PMID:24037264) (PMCID:PMC3813843)

Lichten, Michael, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parts, Leopold, Bergström, Anders, Liti, Gianni and Mustonen, Ville (2013) Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses. PLoS ONE, 8(5), e62266. (doi: 10.1371/journal.pone.0062266) (PMID:23658715) (PMCID:PMC3642125)

Fischer, Andrej, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Campbell, Peter J. and Mustonen, Ville (2013) EMu: probabilistic inference of mutational processes and their localization in the cancer genome. Genome Biology, 14(4), R39. (doi: 10.1186/gb-2013-14-4-r39) (PMID:23628380) (PMCID:PMC3663107)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Mustonen, Ville (2013) Quantifying selection in evolving populations using time-resolved genetic data. Journal of Statistical Mechanics: Theory and Experiment, 2013(01), P01004. (doi: 10.1088/1742-5468/2013/01/P01004)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Mustonen, Ville (2013) A method to infer positive selection from marker dynamics in an asexual population. Bioinformatics, 28(6), pp. 831-837. (doi: 10.1093/bioinformatics/btr722) (PMID:22223745) (PMCID:PMC3307107)

2012

Andino, Raul, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Mustonen, Ville (2012) Components of selection in the evolution of the influenza virus: linkage effects beat inherent selection. PLoS Pathogens, 8(12), e1003091. (doi: 10.1371/journal.ppat.1003091) (PMID:23300444) (PMCID:PMC3531508)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Chintipalli, Sree V., Serapian, Stefano A., Miller, Andrew D., Veverka, Vaclav, Carr, Mark D. and Reynolds, Christopher A. (2012) The statistical significance of selected sense-antisense peptide interactions. Journal of Computational Chemistry, 33(16), pp. 1440-1447. (doi: 10.1002/jcc.22977) (PMID:22488506)

Illingworth, C.J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parts, L., Schiffels, S., Liti, G. and Mustonen, V. (2012) Quantifying selection acting on a complex trait using allele frequency time series data. Molecular Biology and Evolution, 29(4), pp. 1187-1197. (doi: 10.1093/molbev/msr289) (PMID:22114362) (PMCID:PMC3731369)

Domene, Carmen and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2012) Effects of point mutations in pVHL on the binding of HIF-1α. Proteins: Structure Function and Bioinformatics, 80(3), pp. 733-746. (doi: 10.1002/prot.23230) (PMID:22105711)

2011

Gray, Eleanor R., Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Coffin, John M. and Stoye, Jonathan P. (2011) Binding of more than one Tva800 molecule is required for ASLV-A entry. Retrovirology, 8(1), 96. (doi: 10.1186/1742-4690-8-96) (PMID:22099981) (PMCID:PMC3267798)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Mustonen, Ville (2011) Distinguishing driver and passenger mutations in an evolutionary history categorized by interference. Genetics, 189(3), pp. 989-1000. (doi: 10.1534/genetics.111.133975) (PMID:21900272) (PMCID:PMC3213378)

2010

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Furini, Simone and Domene, Carmen (2010) Computational studies on polarization effects and selectivity in K+ channels. Journal of Chemical Theory and Computation, 6(12), pp. 3780-3792. (doi: 10.1021/ct100276c)

Chintapalli, Sree V., Yew, Boon K., Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Upton, Graham J.G., Reeves, Philip J., Parkes, Kevin E. B., Snell, Christopher R. and Reynolds, Christopher A. (2010) Closed loop folding units from structural alignments: experimental foldons revisited. Journal of Computational Chemistry, 31(15), pp. 2689-2701. (doi: 10.1002/jcc.21562) (PMID:20839296)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Scott, Paul D., Parkes, Kevin E. B., Snell, Christopher R., Campbell, Matthew P. and Reynolds, Christopher A. (2010) Connectivity and binding-site recognition: applications relevant to drug design. Journal of Computational Chemistry, 31(15), pp. 2677-2688. (doi: 10.1002/jcc.21561) (PMID:20839295)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Loenarz, Christoph, Schofield, Christopher J. and Domene, Carmen (2010) Chemical basis for the selectivity of the von Hippel Lindau tumor suppressor pVHL for prolyl-hydroxylated HIF-1α. Biochemistry, 49(32), pp. 6936-6944. (doi: 10.1021/bi100358t) (PMID:20695530)

2009

Illingworth, Christopher J. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Domene, Carmen (2009) Many-body effects and simulations of potassium channels. Proceedings of the Royal Society of London Series A: Mathematical, Physical and Engineering Sciences, 465(2106), pp. 1701-1716. (doi: 10.1098/rspa.2009.0014)

2008

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Morris, Garrett M., Parkes, Kevin E. B., Snell, Christopher R. and Reynolds, Christopher A. (2008) Assessing the role of polarization in docking. Journal of Physical Chemistry A, 112(47), pp. 12157-12163. (doi: 10.1021/jp710169m) (PMID:18986122)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parkes, Kevin E. B., Snell, Christopher R., Ferenczy, György G. and Reynolds, Christopher A. (2008) Toward a consistent treatment of polarization in model QM/MM calculations. Journal of Physical Chemistry A, 112(47), pp. 12151-12156. (doi: 10.1021/jp710168q) (PMID:18986123)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parkes, Kevin E., Snell, Christopher R., Mullineaux, Philip M. and Reynolds, Christopher A. (2008) Criteria for confirming sequence periodicity identified by Fourier transform analysis: application to GCR2, a candidate plant GPCR? Biophysical Chemistry, 133(1-3), pp. 28-35. (doi: 10.1016/j.bpc.2007.11.004) (PMID:18086512)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parkes, Kevin E. B., Snell, Christopher R. and Reynolds, Christopher A. (2008) Quantitative measurement of protease ligand conformation. Journal of Computer-Aided Molecular Design, 22(2), pp. 105-109. (doi: 10.1007/s10822-008-9173-z) (PMID:18204905)

Illingworth, C.J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parkes, K.E., Snell, C.R., Marti, S., Moliner, V. and Reynolds, C.A. (2008) The effect of MM polarization on the QM/MM transition state stabilization: application to chorismate mutase. Molecular Physics, 106(12), pp. 1511-1515. (doi: 10.1080/00268970802077850)

Illingworth, C.J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Winn, P.J., Ferenczy, G.G. and Reynolds, Christopher (2008) Progress in modelling electrostatics and polarization through effective multipoles and induced charges. Studia Universitatis Babes-Bolyai Chemia, 2, pp. 21-28.

2007

Vohra, S., Chintapalli, S.V., Illingworth, C.J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Reeves, P.J., Mullineaux, P.M., Clark, H.S.X., Dean, M.K., Upton, G.J.G. and Reynolds, C.A. (2007) Computational studies of Family A and Family B GPCRs. Biochemical Society Transactions, 35(4), pp. 749-754. (doi: 10.1042/BST0350749) (PMID:17635140)

2006

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Gooding, Stuart R., Winn, Peter J., Jones, Garth A., Ferenczy, György G. and Reynolds, Christopher A. (2006) Classical polarization in hybrid QM/MM methods. Journal of Physical Chemistry A, 110(20), pp. 6487-6497. (doi: 10.1021/jp046944i) (PMID:16706406)

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Jump to: Articles | Book Sections
Number of items: 74.

Articles

Illingworth, C.J.R. et al. (2025) The role of spatial distance in SARS-CoV-2 nosocomial transmission. Journal of Hospital Infection, 166, pp. 71-81. (doi: 10.1016/j.jhin.2025.09.011)

Tate, M. et al. (2025) Clinical effectiveness, safety and viral mutagenicity of oral favipiravir for COVID-19: results from a community-based, open-label, randomised, phase III trial. Antimicrobial Agents and Chemotherapy, 69(8), e0005425. (doi: 10.1128/aac.00054-25) (PMID:40552814)

Stewart, Lauren, Evans, Stephanie, Brevini, Teresa, Sampaziotis, Fotios and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2025) Modelling the potential use of pre-exposure prophylaxis to reduce nosocomial SARS-CoV-2 transmission. PLoS Computational Biology, 21(8), e1013361. (doi: 10.1371/journal.pcbi.1013361) (PMID:40763307) (PMCID:PMC12370187)

Pascall, D. J. et al. (2025) The NOSTRA model: coherent estimation of infection sources in the case of possible nosocomial transmission. PLoS Computational Biology, 21(4), e1012949. (doi: 10.1371/journal.pcbi.1012949) (PMID:40258227) (PMCID:PMC12121921)

Leiser, R. et al. (2025) Insights into the implementation of a whole genome sequencing report form (SRF) to reduce nosocomial SARS-CoV-2 in UK hospitals within an unfolding pandemic: A qualitative process evaluation using normalisation process theory. PLoS ONE, 20(4), e0321534. (doi: 10.1371/journal.pone.0321534) (PMID:40245025) (PMCID:PMC12005541)

Smith, E. et al. (2025) Variable rates of SARS-CoV-2 evolution in chronic infections. PLoS Pathogens, 21(4), e1013109. (doi: 10.1371/journal.ppat.1013109) (PMID:40294077) (PMCID:PMC12061394)

Brock, Rebecca C., Goudie, Robert J.B., Peters, Christine, Thaxter, Rachel, Gouliouris, Theodore, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Morris, Andrew Conway, Beggs, Clive B., Butler, Matthew and Keevil, Victoria L. (2025) Efficacy of air cleaning units for preventing SARS-CoV-2 and other hospital-acquired infections on medicine for older people wards: a quasi-experimental controlled before-and-after study. Journal of Hospital Infection, 155, pp. 1-8. (doi: 10.1016/j.jhin.2024.09.017) (PMID:39374708)

Fozard, John A., Thomson, Emma C. ORCID logoORCID: https://orcid.org/0000-0003-1482-0889 and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2024) Epidemiological inference at the threshold of data availability: an influenza A(H1N2)v spillover event in the United Kingdom. Journal of the Royal Society: Interface, 21(217), 20240168. (doi: 10.1098/rsif.2024.0168) (PMID:39109454) (PMCID:PMC11304334)

Sinclair, Patrick, Zhao, Lei, Beggs, Clive B. and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2024) The airborne transmission of viruses causes tight transmission bottlenecks. Nature Communications, 15(1), 3540. (doi: 10.1038/s41467-024-47923-z) (PMID:38670957) (PMCID:PMC11053022)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Guerra-Assuncao, Jose A., Gregg, Samuel, Charles, Oscar, Pang, Juanita, Roy, Sunando, Abdelnabi, Rana, Neyts, Johan and Breuer, Judith (2024) Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus Evolution, 10(1), veae001. (doi: 10.1093/ve/veae001) (PMID:38486802) (PMCID:PMC10939363)

Flowers, Paul ORCID logoORCID: https://orcid.org/0000-0001-6239-5616, Leiser, Ruth, Mapp, Fiona, McLeod, Julie, Stirrup, Oliver, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Blackstone, James and Breuer, Judith (2023) A qualitative process evaluation using the behaviour change wheel approach: did a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 within UK hospitals operate as anticipated? British Journal of Health Psychology, 28(4), pp. 1011-1035. (doi: 10.1111/bjhp.12666) (PMID:37128667)

Brevini, T. et al. (2023) FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2. Nature, 615(7950), pp. 134-142. (doi: 10.1038/s41586-022-05594-0) (PMID:36470304) (PMCID:PMC9977684)

Stejskal, L. et al. (2022) An entropic safety catch controls Hepatitis C virus entry and antibody resistance. eLife, 11, e71854. (doi: 10.7554/eLife.71854) (PMID:35796426) (PMCID:PMC9333995)

Nickbakhsh, S. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12, 11735. (doi: 10.1038/s41598-022-15661-1) (PMID:35853960) (PMCID:PMC9296497)

Kemp, S. A. et al. (2022) Transmission of B.1.617.2 Delta variant between vaccinated healthcare workers. Scientific Reports, 12, 10492. (doi: 10.1038/s41598-022-14411-7) (PMID:35729228) (PMCID:PMC9212198)

Illingworth, C. J.R. et al. (2022) A2B-COVID: a tool for rapidly evaluating potential SARS-CoV-2 transmission events. Molecular Biology and Evolution, 39(3), msac025. (doi: 10.1093/molbev/msac025) (PMID:35106603) (PMCID:PMC8892943)

Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z) (PMID:35197443) (PMCID:PMC8866425)

Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)

Twohig, K. A. et al. (2022) Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. Lancet Infectious Diseases, 22(1), pp. 35-42. (doi: 10.1016/S1473-3099(21)00475-8) (PMID:34461056) (PMCID:PMC8397301)

Ferris, M. et al. (2021) Efficacy of FFP3 respirators for prevention of SARS-CoV-2 infection in healthcare workers. eLife, 10, e71131. (doi: 10.7554/elife.71131) (PMID:34783656)

Illingworth, C. J.R. et al. (2021) Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections. eLife, 10, e67308. (doi: 10.7554/eLife.67308)

Hamilton, W. L. et al. (2021) Applying prospective genomic surveillance to support investigation of hospital-onset COVID-19. Lancet Infectious Diseases, 21(7), pp. 916-917. (doi: 10.1016/S1473-3099(21)00251-6) (PMID:33984262) (PMCID:PMC8110208)

Graham, M. S. et al. (2021) Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. Lancet Public Health, 6(5), e335-e345. (doi: 10.1016/S2468-2667(21)00055-4)

Sanjuán, Rafael, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Geoghegan, Jemma L., Iranzo, Jaime, Zwart, Mark P., Ciota, Alexander T., Moratorio, Gonzalo, Gago-Zachert, Selma, Duffy, Siobain and Vijaykrishna, Dhanasekaran (2021) Five challenges in the field of viral diversity and evolution. Frontiers in Virology, 1, 684949. (doi: 10.3389/fviro.2021.684949)

Kemp, S. A. et al. (2021) SARS-CoV-2 evolution during treatment of chronic infection. Nature, 592(7853), pp. 277-282. (doi: 10.1038/s41586-021-03291-y) (PMID:33545711) (PMCID:PMC7610568)

Lumby, C. K. et al. (2020) Favipiravir and zanamivir cleared infection with influenza B in a severely immunocompromised child. Clinical Infectious Diseases, 71(7), e191-e194. (doi: 10.1093/cid/ciaa023) (PMID:32124919)

Lumby, Casper K., Zhao, Lei, Breuer, Judith and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2020) A large effective population size for established within-host influenza virus infection. eLife, 9, e56915. (doi: 10.7554/eLife.56915) (PMID:32773034) (PMCID:PMC7431133)

Ghafari, Mahan, Lumby, Casper K., Weissman, Daniel B. and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2020) Inferring transmission bottleneck size from viral sequence data using a novel haplotype reconstruction method. Journal of Virology, 94(13), e00014-20. (doi: 10.1128/JVI.00014-20) (PMID:32295920) (PMCID:PMC7307158)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Raghwani, Jayna, Serwadda, David, Sewankambo, Nelson K., Robb, Merlin L., Eller, Michael A., Redd, Andrew R., Quinn, Thomas C. and Lythgoe, Katrina A. (2020) A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection. PLoS Pathogens, 16(6), e1008171. (doi: 10.1371/journal.ppat.1008171) (PMID:32492061) (PMCID:PMC7295245)

Grech, L. et al. (2019) Fitness landscape of the fission yeast genome. Molecular Biology and Evolution, 36(8), pp. 1612-1623. (doi: 10.1093/molbev/msz113) (PMID:31077324) (PMCID:PMC6657727)

Doyle, S. R. et al. (2019) Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus. BMC Genomics, 20, p. 218. (doi: 10.1186/s12864-019-5592-6) (PMID:30876405) (PMCID:PMC6420744)

Kalemera, Mphatso, Mincheva, Dilyana, Grove, Joe and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2019) Building a mechanistic mathematical model of hepatitis C virus entry. PLoS Computational Biology, 15(3), e1006905. (doi: 10.1371/journal.pcbi.1006905) (PMID:30883541) (PMCID:PMC6445459)

Zhao, Lei, Abbasi, Ali B. and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2019) Mutational load causes stochastic evolutionary outcomes in acute RNA viral infection. Virus Evolution, 5(1), vez008. (doi: 10.1093/ve/vez008) (PMID:31024738) (PMCID:PMC6476161)

Zhao, Lei and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2019) Measurements of intrahost viral diversity require an unbiased diversity metric. Virus Evolution, 5(1), vey041. (doi: 10.1093/ve/vey041) (PMID:30723551) (PMCID:PMC6354029)

Lumby, Casper K., Nene, Nuno R. and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2018) A novel framework for inferring parameters of transmission from viral sequence data. PLoS Genetics, 14(10), e1007718. (doi: 10.1371/journal.pgen.1007718) (PMID:30325921) (PMCID:PMC6203404)

Nené, Nuno R., Dunham, Alistair S. and Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2018) Inferring fitness effects from time-resolved sequence data with a delay-deterministic model. Genetics, 209(1), pp. 255-264. (doi: 10.1534/genetics.118.300790) (PMID:29500183) (PMCID:PMC5937181)

Reid, Adam J., Talman, Arthur M., Bennett, Hayley M., Gomes, Ana R., Sanders, Mandy J., Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Billker, Oliver, Berriman, Matthew and Lawniczak, Mara K.N. (2018) Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites. eLife, 7, e33105. (doi: 10.7554/eLife.33105) (PMID:29580379) (PMCID:PMC5871331)

R. Nené, Nuno, Mustonen, Ville and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2018) Evaluating genetic drift in time-series evolutionary analysis. Journal of Theoretical Biology, 437, pp. 51-57. (doi: 10.1016/j.jtbi.2017.09.021) (PMID:28958783) (PMCID:PMC5703635)

Anderson, T. J.C. et al. (2017) Rapid identification of genes controlling virulence and immunity in malaria parasites. PLoS Pathogens, 13(7), e1006447. (doi: 10.1371/journal.ppat.1006447) (PMID:28704525) (PMCID:PMC5507557)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Roy, Sunando, Beale, Mathew A., Tutill, Helena, Williams, Rachel and Breuer, Judith (2017) On the effective depth of viral sequence data. Virus Evolution, 3(2), vex030. (doi: 10.1093/ve/vex030) (PMID:29250429) (PMCID:PMC5724399)

Sobel Leonard, A. et al. (2017) The effective rate of influenza reassortment is limited during human infection. PLoS Pathogens, 13(2), e1006203. (doi: 10.1371/journal.ppat.1006203) (PMID:28170438) (PMCID:PMC5315410)

Illingworth, C.J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2016) SAMFIRE: multi-locus variant calling for time-resolved sequence data. Bioinformatics, 32(14), pp. 2208-2209. (doi: 10.1093/bioinformatics/btw205) (PMID:27153641) (PMCID:PMC4937198)

Martinez, Julien ORCID logoORCID: https://orcid.org/0000-0001-8210-2921, Cogni, Rodrigo, Cao, Chuan, Smith, Sophie, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Jiggins, Francis M. (2016) Addicted? Reduced host resistance in populations with defensive symbionts. Proceedings of the Royal Society of London Series B: Biological Sciences, 283(1833), 20160778. (doi: 10.1098/rspb.2016.0778) (PMID:27335421) (PMCID:PMC4936038)

Shaw, C.D. et al. (2016) In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization. Molecular Microbiology, 99(6), pp. 1134-1148. (doi: 10.1111/mmi.13291) (PMID:26713880) (PMCID:PMC4832254)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2015) Fitness inference from short-read data: within-host evolution of a reassortant H5N1 influenza virus. Molecular Biology and Evolution, 32(11), pp. 3012-3026. (doi: 10.1093/molbev/msv171) (PMID:26243288) (PMCID:PMC4651230)

Illingworth, Christopher J. R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Fischer, Andrej and Mustonen, Ville (2014) Identifying selection in the within-host evolution of influenza using viral sequence data. PLoS Computational Biology, 10(7), e1003755. (doi: 10.1371/journal.pcbi.1003755) (PMID:25080215) (PMCID:PMC4117419)

Fischer, Andrej, Vázquez-García, Ignacio, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Mustonen, Ville (2014) High-definition reconstruction of clonal composition in cancer. Cell Reports, 7(5), pp. 1740-1752. (doi: 10.1016/j.celrep.2014.04.055) (PMID:24882004) (PMCID:PMC4062932)

Chintapalli, Sree V., Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Upton, Graham J. G., Sacquin-Mora, Sophie, Reeves, Philip J., Mohammedali, Hani S. and Reynolds, Christopher A. (2014) Assessing the effect of dynamics on the closed-loop protein-folding hypothesis. Journal of the Royal Society: Interface, 11(91), 20130935. (doi: 10.1098/rsif.2013.0935) (PMID:24258160) (PMCID:PMC3869168)

Roy, Aparna, Taddese, Bruck, Vohra, Shabana, Thimmaraju, Phani K., Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Simpson, Lisa M., Mukherjee, Keya, Reynolds, Christopher A. and Chintapalli, Sree V. (2014) Identifying subset errors in multiple sequence alignments. Journal of Biomolecular Structure and Dynamics, 32(3), pp. 364-371. (doi: 10.1080/07391102.2013.770371) (PMID:23527867)

Cubillos, F. A. et al. (2013) High-resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics, 195(3), pp. 1141-1155. (doi: 10.1534/genetics.113.155515) (PMID:24037264) (PMCID:PMC3813843)

Lichten, Michael, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parts, Leopold, Bergström, Anders, Liti, Gianni and Mustonen, Ville (2013) Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses. PLoS ONE, 8(5), e62266. (doi: 10.1371/journal.pone.0062266) (PMID:23658715) (PMCID:PMC3642125)

Fischer, Andrej, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Campbell, Peter J. and Mustonen, Ville (2013) EMu: probabilistic inference of mutational processes and their localization in the cancer genome. Genome Biology, 14(4), R39. (doi: 10.1186/gb-2013-14-4-r39) (PMID:23628380) (PMCID:PMC3663107)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Mustonen, Ville (2013) Quantifying selection in evolving populations using time-resolved genetic data. Journal of Statistical Mechanics: Theory and Experiment, 2013(01), P01004. (doi: 10.1088/1742-5468/2013/01/P01004)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Mustonen, Ville (2013) A method to infer positive selection from marker dynamics in an asexual population. Bioinformatics, 28(6), pp. 831-837. (doi: 10.1093/bioinformatics/btr722) (PMID:22223745) (PMCID:PMC3307107)

Andino, Raul, Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Mustonen, Ville (2012) Components of selection in the evolution of the influenza virus: linkage effects beat inherent selection. PLoS Pathogens, 8(12), e1003091. (doi: 10.1371/journal.ppat.1003091) (PMID:23300444) (PMCID:PMC3531508)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Chintipalli, Sree V., Serapian, Stefano A., Miller, Andrew D., Veverka, Vaclav, Carr, Mark D. and Reynolds, Christopher A. (2012) The statistical significance of selected sense-antisense peptide interactions. Journal of Computational Chemistry, 33(16), pp. 1440-1447. (doi: 10.1002/jcc.22977) (PMID:22488506)

Illingworth, C.J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parts, L., Schiffels, S., Liti, G. and Mustonen, V. (2012) Quantifying selection acting on a complex trait using allele frequency time series data. Molecular Biology and Evolution, 29(4), pp. 1187-1197. (doi: 10.1093/molbev/msr289) (PMID:22114362) (PMCID:PMC3731369)

Domene, Carmen and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2012) Effects of point mutations in pVHL on the binding of HIF-1α. Proteins: Structure Function and Bioinformatics, 80(3), pp. 733-746. (doi: 10.1002/prot.23230) (PMID:22105711)

Gray, Eleanor R., Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Coffin, John M. and Stoye, Jonathan P. (2011) Binding of more than one Tva800 molecule is required for ASLV-A entry. Retrovirology, 8(1), 96. (doi: 10.1186/1742-4690-8-96) (PMID:22099981) (PMCID:PMC3267798)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Mustonen, Ville (2011) Distinguishing driver and passenger mutations in an evolutionary history categorized by interference. Genetics, 189(3), pp. 989-1000. (doi: 10.1534/genetics.111.133975) (PMID:21900272) (PMCID:PMC3213378)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Furini, Simone and Domene, Carmen (2010) Computational studies on polarization effects and selectivity in K+ channels. Journal of Chemical Theory and Computation, 6(12), pp. 3780-3792. (doi: 10.1021/ct100276c)

Chintapalli, Sree V., Yew, Boon K., Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Upton, Graham J.G., Reeves, Philip J., Parkes, Kevin E. B., Snell, Christopher R. and Reynolds, Christopher A. (2010) Closed loop folding units from structural alignments: experimental foldons revisited. Journal of Computational Chemistry, 31(15), pp. 2689-2701. (doi: 10.1002/jcc.21562) (PMID:20839296)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Scott, Paul D., Parkes, Kevin E. B., Snell, Christopher R., Campbell, Matthew P. and Reynolds, Christopher A. (2010) Connectivity and binding-site recognition: applications relevant to drug design. Journal of Computational Chemistry, 31(15), pp. 2677-2688. (doi: 10.1002/jcc.21561) (PMID:20839295)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Loenarz, Christoph, Schofield, Christopher J. and Domene, Carmen (2010) Chemical basis for the selectivity of the von Hippel Lindau tumor suppressor pVHL for prolyl-hydroxylated HIF-1α. Biochemistry, 49(32), pp. 6936-6944. (doi: 10.1021/bi100358t) (PMID:20695530)

Illingworth, Christopher J. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 and Domene, Carmen (2009) Many-body effects and simulations of potassium channels. Proceedings of the Royal Society of London Series A: Mathematical, Physical and Engineering Sciences, 465(2106), pp. 1701-1716. (doi: 10.1098/rspa.2009.0014)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Morris, Garrett M., Parkes, Kevin E. B., Snell, Christopher R. and Reynolds, Christopher A. (2008) Assessing the role of polarization in docking. Journal of Physical Chemistry A, 112(47), pp. 12157-12163. (doi: 10.1021/jp710169m) (PMID:18986122)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parkes, Kevin E. B., Snell, Christopher R., Ferenczy, György G. and Reynolds, Christopher A. (2008) Toward a consistent treatment of polarization in model QM/MM calculations. Journal of Physical Chemistry A, 112(47), pp. 12151-12156. (doi: 10.1021/jp710168q) (PMID:18986123)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parkes, Kevin E., Snell, Christopher R., Mullineaux, Philip M. and Reynolds, Christopher A. (2008) Criteria for confirming sequence periodicity identified by Fourier transform analysis: application to GCR2, a candidate plant GPCR? Biophysical Chemistry, 133(1-3), pp. 28-35. (doi: 10.1016/j.bpc.2007.11.004) (PMID:18086512)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parkes, Kevin E. B., Snell, Christopher R. and Reynolds, Christopher A. (2008) Quantitative measurement of protease ligand conformation. Journal of Computer-Aided Molecular Design, 22(2), pp. 105-109. (doi: 10.1007/s10822-008-9173-z) (PMID:18204905)

Illingworth, C.J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Parkes, K.E., Snell, C.R., Marti, S., Moliner, V. and Reynolds, C.A. (2008) The effect of MM polarization on the QM/MM transition state stabilization: application to chorismate mutase. Molecular Physics, 106(12), pp. 1511-1515. (doi: 10.1080/00268970802077850)

Illingworth, C.J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Winn, P.J., Ferenczy, G.G. and Reynolds, Christopher (2008) Progress in modelling electrostatics and polarization through effective multipoles and induced charges. Studia Universitatis Babes-Bolyai Chemia, 2, pp. 21-28.

Vohra, S., Chintapalli, S.V., Illingworth, C.J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Reeves, P.J., Mullineaux, P.M., Clark, H.S.X., Dean, M.K., Upton, G.J.G. and Reynolds, C.A. (2007) Computational studies of Family A and Family B GPCRs. Biochemical Society Transactions, 35(4), pp. 749-754. (doi: 10.1042/BST0350749) (PMID:17635140)

Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784, Gooding, Stuart R., Winn, Peter J., Jones, Garth A., Ferenczy, György G. and Reynolds, Christopher A. (2006) Classical polarization in hybrid QM/MM methods. Journal of Physical Chemistry A, 110(20), pp. 6487-6497. (doi: 10.1021/jp046944i) (PMID:16706406)

Book Sections

Raghwani, Jayna, Pybus, Oliver G. and Illingworth, Christopher J.R. ORCID logoORCID: https://orcid.org/0000-0002-0030-2784 (2016) Population genetic modeling of viruses. In: Weaver, Scott C., Denison, Mark, Roossinck, Marilyn and Vignuzzi, Marco (eds.) Virus Evolution: Current Research and Future Directions. Caister Academic Press: Wymondham, pp. 293-327. ISBN 9781910190234

This list was generated on Sat Nov 15 09:14:09 2025 GMT.

Grants

Grants and Awards listed are those received whilst working with the University of Glasgow.

  • Economic analysis of real-time viral genomics as a tool for infection prevention and control
    Healthcare Infection Society
    2024 - 2027
     
  • CVR Preparedness compute capacity
    Medical Research Council
    2023 - 2024
     
  • Developing interventions to reduce 'missingness' in health care
    UK Health Security Agency
    2022 - 2023
     

Research datasets

Jump to: 2024
Number of items: 1.

2024

Stewart, L., Evans, S., Brevini, T., Sampaziotis, F. and Illingworth, C. J.R. (2024) Modelling the potential use of pre-exposure prophylaxis to reduce nosocomial SARS-CoV-2 transmission. [Data Collection]

This list was generated on Sat Nov 15 20:46:58 2025 GMT.

Dr Chris Illingworth on Bluesky