2024

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

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