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Katherine Atkins

Associate Professor / Chancellor's Fellow

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Prefer not to disclose

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Papers

Pujol-Hodge E, Salazar-Gonzalez JF, Ssemwanga D, Charlebois ED, Ayieko J, Grant HE, Liegler T, Atkins KE, Kaleebu P, Kamya MR, Petersen M, Havlir DV, Leigh Brown AJ. (2022). Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa. Viruses, 14(8)

Banks CJ, Colman E, Doherty T, Tearne O, Arnold M, Atkins KE, Balaz D, Beaunée G, Bessell PR, Enright J, Kleczkowski A, Rossi G, Ruget AS, Kao RR. (2022). SCoVMod - a spatially explicit mobility and deprivation adjusted model of first wave COVID-19 transmission dynamics. Wellcome open research, (7)

Lindsey BB, Villabona-Arenas CJ, Campbell F, Keeley AJ, Parker MD, Shah DR, Parsons H, Zhang P, Kakkar N, Gallis M, Foulkes BH, Wolverson P, Louka SF, Christou S, State A, Johnson K, Raza M, Hsu S, Jombart T, Cori A, , , , Evans CM, Partridge DG, Atkins KE, Hué S, de Silva TI. (2022). Publisher Correction: Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves. Nature communications, 13(1)

Villabona-Arenas CJ, Hué S, Baxter JAC, Hall M, Lythgoe KA, Bradley J, Atkins KE. (2022). Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs. Proceedings of the National Academy of Sciences of the United States of America, 119(38)

Endo 遠藤彰 A, , Uchida 内田満夫 M, Liu 刘扬 Y, Atkins KE, Kucharski AJ, Funk S. (2022). Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools. Proceedings of the National Academy of Sciences of the United States of America, 119(37)

Lindsey BB, Villabona-Arenas CJ, Campbell F, Keeley AJ, Parker MD, Shah DR, Parsons H, Zhang P, Kakkar N, Gallis M, Foulkes BH, Wolverson P, Louka SF, Christou S, State A, Johnson K, Raza M, Hsu S, Jombart T, Cori A, , , , Evans CM, Partridge DG, Atkins KE, Hué S, de Silva TI. (2022). Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves. Nature communications, 13(1)

Munday JD, Sherratt K, Meakin S, Endo A, Pearson CAB, Hellewell J, Abbott S, Bosse NI, , Atkins KE, Wallinga J, Edmunds WJ, van Hoek AJ, Funk S. (2021). Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England. Nature communications, 12(1)

Blassel L, Zhukova A, Villabona-Arenas CJ, Atkins KE, Hué S, Gascuel O. (2021). Drug resistance mutations in HIV: new bioinformatics approaches and challenges. Current opinion in virology, (51)

Endo A, Uchida M, Hayashi N, Liu Y, Atkins KE, Kucharski AJ, Funk S. (2021). Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan. Proceedings of the National Academy of Sciences of the United States of America, 118(46)

Davies NG, Flasche S, Jit M, Atkins KE. (2021). Modeling the effect of vaccination on selection for antibiotic resistance in Streptococcus pneumonia e. Science translational medicine, 13(606)

Munday JD, Pebody R, Atkins KE, van Hoek AJ. (2021). Changing socio-economic and ethnic disparities in influenza/A/H1N1 infection early in the 2009 UK epidemic: a descriptive analysis. BMC infectious diseases, 21(1)

Leclerc QJ, Fuller NM, Keogh RH, Diaz-Ordaz K, Sekula R, Semple MG, , , Atkins KE, Procter SR, Knight GM. (2021). Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England. BMC health services research, 21(1)

Li Y, Hodgson D, Wang X, Atkins KE, Feikin DR, Nair H. (2021). Respiratory syncytial virus seasonality and prevention strategy planning for passive immunisation of infants in low-income and middle-income countries: a modelling study. The Lancet. Infectious diseases

Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, Pearson CAB, Russell TW, Tully DC, Washburne AD, Wenseleers T, Gimma A, Waites W, Wong KLM, van Zandvoort K, Silverman JD, , , Diaz-Ordaz K, Keogh R, Eggo RM, Funk S, Jit M, Atkins KE, Edmunds WJ. (2021). Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science (New York, N.Y.)

Hodgson D, Pebody R, Panovska-Griffiths J, Baguelin M, Atkins KE. (2020). Evaluating the next generation of RSV intervention strategies: a mathematical modelling study and cost-effectiveness analysis. BMC medicine, 18(1)

Yang J, Atkins KE, Feng L, Baguelin M, Wu P, Yan H, Lau EHY, Wu JT, Liu Y, Cowling BJ, Jit M, Yu H. (2020). Cost-effectiveness of introducing national seasonal influenza vaccination for adults aged 60 years and above in mainland China: a modelling analysis. BMC medicine, 18(1)

Endo A, , Leclerc QJ, Knight GM, Medley GF, Atkins KE, Funk S, Kucharski AJ. (2020). Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks. Wellcome open research, (5)

Jit M, Ng DHL, Luangasanatip N, Sandmann F, Atkins KE, Robotham JV, Pouwels KB. (2020). Quantifying the economic cost of antibiotic resistance and the impact of related interventions: rapid methodological review, conceptual framework and recommendations for future studies. BMC medicine, 18(1)

Villabona-Arenas CJ, Hall M, Lythgoe KA, Gaffney SG, Regoes RR, Hué S, Atkins KE. (2020). Number of HIV-1 founder variants is determined by the recency of the source partner infection. Science (New York, N.Y.), 369(6499)

Wuerz TC, Kassim SS, Atkins KE. (2020). Acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) carriage after exposure to systemic antimicrobials during travel: Systematic review and meta-analysis. Travel medicine and infectious disease, (37)

Knight GM, Davies NG, Colijn C, Coll F, Donker T, Gifford DR, Glover RE, Jit M, Klemm E, Lehtinen S, Lindsay JA, Lipsitch M, Llewelyn MJ, Mateus ALP, Robotham JV, Sharland M, Stekel D, Yakob L, Atkins KE. (2019). Mathematical modelling for antibiotic resistance control policy: do we know enough?. BMC infectious diseases, 19(1)

Hodgson D, Atkins KE, Baguelin M, Panovska-Griffiths J, Thorrington D, van Hoek AJ, Zhao H, Fragaszy E, Hayward AC, Pebody R. (2020). Estimates for quality of life loss due to Respiratory Syncytial Virus. Influenza and other respiratory viruses, 14(1)

Davies NG, Flasche S, Jit M, Atkins KE. (2019). Within-host dynamics shape antibiotic resistance in commensal bacteria. Nature ecology & evolution, 3(3)

Munday JD, van Hoek AJ, Edmunds WJ, Atkins KE. (2018). Quantifying the impact of social groups and vaccination on inequalities in infectious diseases using a mathematical model. BMC medicine, 16(1)

Camacho A, Bouhenia M, Alyusfi R, Alkohlani A, Naji MAM, de Radiguès X, Abubakar AM, Almoalmi A, Seguin C, Sagrado MJ, Poncin M, McRae M, Musoke M, Rakesh A, Porten K, Haskew C, Atkins KE, Eggo RM, Azman AS, Broekhuijsen M, Saatcioglu MA, Pezzoli L, Quilici ML, Al-Mesbahy AR, Zagaria N, Luquero FJ. (2018). Cholera epidemic in Yemen, 2016-18: an analysis of surveillance data. The Lancet. Global health, 6(6)

Rock KS, Ndeffo-Mbah ML, Castaño S, Palmer C, Pandey A, Atkins KE, Ndung'u JM, Hollingsworth TD, Galvani A, Bever C, Chitnis N, Keeling MJ. (2018). Assessing Strategies Against Gambiense Sleeping Sickness Through Mathematical Modeling. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 66(suppl_4)

Atkins KE, Lafferty EI, Deeny SR, Davies NG, Robotham JV, Jit M. (2018). Use of mathematical modelling to assess the impact of vaccines on antibiotic resistance. The Lancet. Infectious diseases, 18(6)

Hodgson D, Baguelin M, van Leeuwen E, Panovska-Griffiths J, Ramsay M, Pebody R, Atkins KE. (2017). Effect of mass paediatric influenza vaccination on existing influenza vaccination programmes in England and Wales: a modelling and cost-effectiveness analysis. The Lancet. Public health, 2(2)

Atkins KE, Read AF, Walkden-Brown SW, Savill NJ, Woolhouse ME. (2013). The effectiveness of mass vaccination on Marek's disease virus (MDV) outbreaks and detection within a broiler barn: a modeling study. Epidemics, 5(4)

Atkins KE, Read AF, Savill NJ, Renz KG, Islam AF, Walkden-Brown SW, Woolhouse ME. (2013). Vaccination and reduced cohort duration can drive virulence evolution: Marek's disease virus and industrialized agriculture. Evolution; international journal of organic evolution, 67(3)

Atkins KE, Read AF, Savill NJ, Renz KG, Walkden-Brown SW, Woolhouse ME. (2011). Modelling Marek's disease virus (MDV) infection: parameter estimates for mortality rate and infectiousness. BMC veterinary research, (7)

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