Dr Chris Illingworth
- Senior Lecturer (Virology)
https://orcid.org/0000-0002-0030-2784Publications
2024
Fozard, J. A., Thomson, E. C. and Illingworth, C. (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, (Accepted for Publication)
Sinclair, P., Zhao, L., Beggs, C. B. and Illingworth, C. J.R. (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, C. J.R. , Guerra-Assuncao, J. A., Gregg, S., Charles, O., Pang, J., Roy, S., Abdelnabi, R., Neyts, J. and Breuer, J. (2024) Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus Evolution, (doi: 10.1093/ve/veae001) (Early Online Publication)
2023
Flowers, P. , Leiser, R., Mapp, F., McLeod, J., Stirrup, O., Illingworth, C. J.R. , Blackstone, J. and Breuer, J. (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, (doi: 10.1111/bjhp.12666) (Early Online Publication)
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, R., Illingworth, C. J.R. , Geoghegan, J. L., Iranzo, J., Zwart, M. P., Ciota, A. T., Moratorio, G., Gago-Zachert, S., Duffy, S. and Vijaykrishna, D. (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, C. K., Zhao, L., Breuer, J. and Illingworth, C. J.R. (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, M., Lumby, C. K., Weissman, D. B. and Illingworth, C. J. R. (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, C. J.R. , Raghwani, J., Serwadda, D., Sewankambo, N. K., Robb, M. L., Eller, M. A., Redd, A. R., Quinn, T. C. and Lythgoe, K. 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, M., Mincheva, D., Grove, J. and Illingworth, C. J. R. (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, L., Abbasi, A. B. and Illingworth, C. J. R. (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, L. and Illingworth, C. J. R. (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, C. K., Nene, N. R. and Illingworth, C. J. R. (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, N. R., Dunham, A. S. and Illingworth, C. J. R. (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, A. J., Talman, A. M., Bennett, H. M., Gomes, A. R., Sanders, M. J., Illingworth, C. J. R. , Billker, O., Berriman, M. and Lawniczak, M. 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, N., Mustonen, V. and Illingworth, C. J.R. (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, C. J.R. , Roy, S., Beale, M. A., Tutill, H., Williams, R. and Breuer, J. (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. (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, J. , Cogni, R., Cao, C., Smith, S., Illingworth, C. J.R. and Jiggins, F. 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, J., Pybus, O. G. and Illingworth, C. J.R. (2016) Population genetic modeling of viruses. In: Weaver, S. C., Denison, M., Roossinck, M. and Vignuzzi, M. (eds.) Virus Evolution: Current Research and Future Directions. Caister Academic Press: Wymondham, pp. 293-327. ISBN 9781910190234
2015
Illingworth, C. J.R. (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, C. J. R. , Fischer, A. and Mustonen, V. (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, A., Vázquez-García, I., Illingworth, C. J.R. and Mustonen, V. (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, S. V., Illingworth, C. J.R. , Upton, G. J. G., Sacquin-Mora, S., Reeves, P. J., Mohammedali, H. S. and Reynolds, C. 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, A., Taddese, B., Vohra, S., Thimmaraju, P. K., Illingworth, C. J.R. , Simpson, L. M., Mukherjee, K., Reynolds, C. A. and Chintapalli, S. 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, M., Illingworth, C. J.R. , Parts, L., Bergström, A., Liti, G. and Mustonen, V. (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, A., Illingworth, C. J.R. , Campbell, P. J. and Mustonen, V. (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, C. J.R. and Mustonen, V. (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, C. J.R. and Mustonen, V. (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, R., Illingworth, C. J.R. and Mustonen, V. (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, C. J.R. , Chintipalli, S. V., Serapian, S. A., Miller, A. D., Veverka, V., Carr, M. D. and Reynolds, C. 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. , 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, C. and Illingworth, C. J.R. (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, E. R., Illingworth, C. J.R. , Coffin, J. M. and Stoye, J. 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, C. J.R. and Mustonen, V. (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, C. J.R. , Furini, S. and Domene, C. (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, S. V., Yew, B. K., Illingworth, C. J.R. , Upton, G. J.G., Reeves, P. J., Parkes, K. E. B., Snell, C. R. and Reynolds, C. 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, C. J.R. , Scott, P. D., Parkes, K. E. B., Snell, C. R., Campbell, M. P. and Reynolds, C. 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, C. J.R. , Loenarz, C., Schofield, C. J. and Domene, C. (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, C. J. and Domene, C. (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, C. J.R. , Morris, G. M., Parkes, K. E. B., Snell, C. R. and Reynolds, C. 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, C. J.R. , Parkes, K. E. B., Snell, C. R., Ferenczy, G. G. and Reynolds, C. 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, C. J.R. , Parkes, K. E., Snell, C. R., Mullineaux, P. M. and Reynolds, C. 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, C. J.R. , Parkes, K. E. B., Snell, C. R. and Reynolds, C. 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. , 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. , Winn, P.J., Ferenczy, G.G. and Reynolds, C. (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. , 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, C. J.R. , Gooding, S. R., Winn, P. J., Jones, G. A., Ferenczy, G. G. and Reynolds, C. 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)
Articles
Fozard, J. A., Thomson, E. C. and Illingworth, C. (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, (Accepted for Publication)
Sinclair, P., Zhao, L., Beggs, C. B. and Illingworth, C. J.R. (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, C. J.R. , Guerra-Assuncao, J. A., Gregg, S., Charles, O., Pang, J., Roy, S., Abdelnabi, R., Neyts, J. and Breuer, J. (2024) Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus Evolution, (doi: 10.1093/ve/veae001) (Early Online Publication)
Flowers, P. , Leiser, R., Mapp, F., McLeod, J., Stirrup, O., Illingworth, C. J.R. , Blackstone, J. and Breuer, J. (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, (doi: 10.1111/bjhp.12666) (Early Online Publication)
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, R., Illingworth, C. J.R. , Geoghegan, J. L., Iranzo, J., Zwart, M. P., Ciota, A. T., Moratorio, G., Gago-Zachert, S., Duffy, S. and Vijaykrishna, D. (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, C. K., Zhao, L., Breuer, J. and Illingworth, C. J.R. (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, M., Lumby, C. K., Weissman, D. B. and Illingworth, C. J. R. (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, C. J.R. , Raghwani, J., Serwadda, D., Sewankambo, N. K., Robb, M. L., Eller, M. A., Redd, A. R., Quinn, T. C. and Lythgoe, K. 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, M., Mincheva, D., Grove, J. and Illingworth, C. J. R. (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, L., Abbasi, A. B. and Illingworth, C. J. R. (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, L. and Illingworth, C. J. R. (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, C. K., Nene, N. R. and Illingworth, C. J. R. (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, N. R., Dunham, A. S. and Illingworth, C. J. R. (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, A. J., Talman, A. M., Bennett, H. M., Gomes, A. R., Sanders, M. J., Illingworth, C. J. R. , Billker, O., Berriman, M. and Lawniczak, M. 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, N., Mustonen, V. and Illingworth, C. J.R. (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, C. J.R. , Roy, S., Beale, M. A., Tutill, H., Williams, R. and Breuer, J. (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. (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, J. , Cogni, R., Cao, C., Smith, S., Illingworth, C. J.R. and Jiggins, F. 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, C. J.R. (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, C. J. R. , Fischer, A. and Mustonen, V. (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, A., Vázquez-García, I., Illingworth, C. J.R. and Mustonen, V. (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, S. V., Illingworth, C. J.R. , Upton, G. J. G., Sacquin-Mora, S., Reeves, P. J., Mohammedali, H. S. and Reynolds, C. 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, A., Taddese, B., Vohra, S., Thimmaraju, P. K., Illingworth, C. J.R. , Simpson, L. M., Mukherjee, K., Reynolds, C. A. and Chintapalli, S. 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, M., Illingworth, C. J.R. , Parts, L., Bergström, A., Liti, G. and Mustonen, V. (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, A., Illingworth, C. J.R. , Campbell, P. J. and Mustonen, V. (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, C. J.R. and Mustonen, V. (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, C. J.R. and Mustonen, V. (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, R., Illingworth, C. J.R. and Mustonen, V. (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, C. J.R. , Chintipalli, S. V., Serapian, S. A., Miller, A. D., Veverka, V., Carr, M. D. and Reynolds, C. 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. , 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, C. and Illingworth, C. J.R. (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, E. R., Illingworth, C. J.R. , Coffin, J. M. and Stoye, J. 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, C. J.R. and Mustonen, V. (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, C. J.R. , Furini, S. and Domene, C. (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, S. V., Yew, B. K., Illingworth, C. J.R. , Upton, G. J.G., Reeves, P. J., Parkes, K. E. B., Snell, C. R. and Reynolds, C. 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, C. J.R. , Scott, P. D., Parkes, K. E. B., Snell, C. R., Campbell, M. P. and Reynolds, C. 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, C. J.R. , Loenarz, C., Schofield, C. J. and Domene, C. (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, C. J. and Domene, C. (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, C. J.R. , Morris, G. M., Parkes, K. E. B., Snell, C. R. and Reynolds, C. 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, C. J.R. , Parkes, K. E. B., Snell, C. R., Ferenczy, G. G. and Reynolds, C. 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, C. J.R. , Parkes, K. E., Snell, C. R., Mullineaux, P. M. and Reynolds, C. 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, C. J.R. , Parkes, K. E. B., Snell, C. R. and Reynolds, C. 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. , 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. , Winn, P.J., Ferenczy, G.G. and Reynolds, C. (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. , 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, C. J.R. , Gooding, S. R., Winn, P. J., Jones, G. A., Ferenczy, G. G. and Reynolds, C. 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, J., Pybus, O. G. and Illingworth, C. J.R. (2016) Population genetic modeling of viruses. In: Weaver, S. C., Denison, M., Roossinck, M. and Vignuzzi, M. (eds.) Virus Evolution: Current Research and Future Directions. Caister Academic Press: Wymondham, pp. 293-327. ISBN 9781910190234
Grants
Grants and Awards listed are those received whilst working with the University of Glasgow.
- CVR Preparedness compute capacity
Medical Research Council
2023 - 2024
- Developing interventions to reduce 'missingness' in health care
UK Health Security Agency
2022 - 2023