In addition to the listed papers, I am also part of the Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group, whose publications are listed here.
2025
[77] Hannah C. Lepper, Emma Pujol-Hodge, Jada Hackman, Kevin Van Zandvoort, Kate Mellor-Wright, Oliver Lorenz, Stephanie Lo, Duc Anh Dang, Hung Thai Do, Gerry Tonkin-Hill, Stephen D. Bentley, Lay Myint Yoshida, Stefan Flasche, Nicholas G. Davies, Katherine E. Atkins (2025) Multiple mechanisms of strain competition are needed to explain pneumococcal serotype-specific antibiotic resistance patterns DOI: 10.1101/2025.05.16.25327750 Citations: 0 | Open Access
[76] Tomoka Nakamura, Ryo Kinoshita, Akira Endo, Katherine E. Atkins, Hitoshi Oshitani, Yoko Ibuka, Motoi Suzuki, Koya Ariyoshi, Kathleen M. O’Reilly (2025) Continuing to be cautious: Japanese contact patterns during the COVID-19 pandemic and their association with public health recommendations PLOS Global Public Health 5(9):e0004600 DOI: 10.1371/journal.pgph.0004600 Citations: 0 | Open Access
2024
[75] James D. Munday, Katherine E. Atkins, Don Klinkenberg, Marc Meurs, Erik Fleur, Susan Jm Hahné, Jacco Wallinga, Albert Jan Van Hoek (2024) Estimating the risk and spatial spread of measles in populations with high MMR uptake: Using school-household networks to understand the 2013 to 2014 outbreak in the Netherlands PLOS Medicine 21(10):e1004466 DOI: 10.1371/journal.pmed.1004466 Citations: 4 | Open Access
[74] David Hodgson, Neil Wilkins, Edwin Van Leeuwen, Conall H. Watson, Jonathan Crofts, Stefan Flasche, Mark Jit, Katherine E. Atkins (2024) Protecting infants against RSV disease: an impact and cost-effectiveness comparison of long-acting monoclonal antibodies and maternal vaccination The Lancet Regional Health - Europe 38:100829 DOI: 10.1016/j.lanepe.2023.100829 Citations: 57 | Open Access
[73] Luca Ferretti, Tanya Golubchik, Francesco Di Lauro, Mahan Ghafari, Julian Villabona-Arenas, Katherine E. Atkins, Christophe Fraser, Matthew Hall (2024) Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity DOI: 10.1101/2024.08.01.606208 Citations: 4 | Open Access
[72] James Baxter, Ch. Julián Villabona-Arenas, Robin N. Thompson, Stéphane Hué, Roland R. Regoes, Roger D. Kouyos, Huldrych F. Günthard, Jan Albert, Andrew Leigh Brown, Katherine E. Atkins (2024) Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4+ decline Journal of The Royal Society Interface 21(219):20240255 DOI: 10.1098/rsif.2024.0255 Citations: 0 | Open Access
2023
[71] Katherine E Atkins, David Hodgson (2023) Vaccination of Older Adults Against Respiratory Syncytial Virus: The Final Pieces of the Puzzle Clinical Infectious Diseases 77(3):490–491 DOI: 10.1093/cid/ciad162 Citations: 1 | Open Access
[69] Cinthy Jimenez-Silva, Ricardo Rivero, Jordan Douglas, Remco Bouckaert, Ch. Julian Villabona-Arenas, Katherine E. Atkins, Bertha Gastelbondo, Alfonso Calderon, Camilo Guzman, Daniel Echeverri-De La Hoz, Marina Muñoz, Nathalia Ballesteros, Sergio Castañeda, Luz H. Patiño, Angie Ramirez, Nicolas Luna, Alberto Paniz-Mondolfi, Hector Serrano-Coll, Juan David Ramirez, Salim Mattar, Alexei J. Drummond (2023) Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia Communications Medicine 3(1):97 DOI: 10.1038/s43856-023-00328-3 Citations: 20 | Open Access
2022
[70] David Hodgson, Mihály Koltai, Fabienne Krauer, Stefan Flasche, Mark Jit, Katherine E. Atkins (2022) Optimal Respiratory Syncytial Virus intervention programmes using Nirsevimab in England and Wales Vaccine 40(49):7151–7157 DOI: 10.1016/j.vaccine.2022.10.041 Citations: 29
[68] Katherine E. Atkins, David Hodgson, Mark Jit, Nicholas G. Davies (2022) Evaluating the impact of Respiratory Syncytial Virus immunisation strategies on antibiotic use and drug resistant bacterial infections in England Wellcome Open Research 7:286 DOI: 10.12688/wellcomeopenres.18183.1 Citations: 0 | Open Access
[66] Akira Endo, Mitsuo Uchida, Yang Liu, Katherine E. Atkins, Adam J. Kucharski, Sebastian Funk, Kaja Abbas, Kevin Zandvoort, Nikos I Bosse, Naomi R. Waterlow, Damien C. Tully, Sophie Meakin, Matthew Quaife, Timothy Russell, Mark Jit, Anna M. Foss, Alicia Roselló, Billy J. Quilty, Kiesha Prem, Gwenan M. Knight, Sam Abbott, Petra Klepac, Oliver J. Brady, Carl A. B. Pearson, Graham F. Medley, Samuel Clifford, Christopher I Jarvis, James D Munday, Frank Sandmann, Fiona Yueqian Sun, Thibaut Jombart, Joel Hellewell, Hamish Gibbs, Rosanna C. Barnard, Rosalind M. Eggo, Amy Gimma, Jack Williams, Nicholas G. Davies, Emily Nightingale, Simon R. Procter, W John Edmunds, Alicia Showering, Rachel Lowe, Katharine Sherratt, Christian Julián Villabona‐Arenas, David Simons, Y. Chan, Stefan Flasche (2022) Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools Proceedings of the National Academy of Sciences 119(37):e2203019119-e2203019119 DOI: 10.1073/pnas.2203019119 Citations: 11 | Open Access
[65] Christian Julián Villabona‐Arenas, Stéphane Hué, James Baxter, Matthew Hall, Katrina Lythgoe, John Bradley, Katherine E. Atkins (2022) Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs Proceedings of the National Academy of Sciences 119(38):e2210604119-e2210604119 DOI: 10.1073/pnas.2210604119 Citations: 8
[64] Emma Pujol-Hodge, Jesus F. Salazar-Gonzalez, Deogratius Ssemwanga, Edwin D. Charlebois, James Ayieko, Heather E. Grant, Teri Liegler, Katherine E. Atkins, Pontiano Kaleebu, Moses R. Kamya, Maya Petersen, Diane V. Havlir, Andrew Brown (2022) Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa Viruses 14(8):1673–1673 DOI: 10.3390/v14081673 Citations: 5 | Open Access
[63] Christopher J. Banks, Ewan Colman, Thomas Doherty, Oliver Tearne, Mark Arnold, Katherine E. Atkins, Daniel Balaz, Gaël Beaunée, Paul R. Bessell, Jessica Enright, Adam Kleczkowski, Gianluigi Rossi, Anne-Sophie Ruget, Rowland R. Kao (2022) SCoVMod – a spatially explicit mobility and deprivation adjusted model of first wave COVID-19 transmission dynamics Wellcome Open Research 7:161 DOI: 10.12688/wellcomeopenres.17716.1 Citations: 7 | Open Access
[62] Benjamin B. Lindsey, Christian Julián Villabona‐Arenas, Finlay Campbell, Alexander J. Keeley, Matthew Parker, Dhruv R. Shah, Helena Parsons, Peijun Zhang, Nishchay Kakkar, Marta Gallis, Benjamin H. Foulkes, Paige Wolverson, Stavroula F. Louka, Stella Christou, Amy State, Katie Johnson, Mohammad Raza, Sharon Hsu, Thibaut Jombart, Anne Cori, Dhruv R. Shah, Katie Johnson, Sharon Hsu, Thushan I. Silva, Alison Cope, Nasar Ali, Rasha Raghei, Joe Heffer, Darren Smith, Max Whiteley, Manoj Baliram Pohare, Samantha E. Hansford, Luke R. Green, Dennis Wang, Michael Anckorn, Adrienn Angyal, Rebecca E. Brown, Hailey Hornsby, Mehmet Yavuz, Danielle C. Groves, Paul J. Parsons, Rachel Tucker, Magdalena Dąbrowska, Thomas Saville, José Schutter, Matthew D. Wyles, Cariad Evans, Nicholas G. Davies, Carl A. B. Pearson, Matthew Quaife, Damien C. Tully, Sam Abbott, Cariad Evans, David G. Partridge, Katherine E. Atkins, Stéphane Hué, Thushan I. Silva (2022) Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves Nature Communications 13(1):671–671 DOI: 10.1038/s41467-022-28291-y Citations: 83 | Open Access
2021
[67] James Baxter, Sarah Langhorne, Ting Shi, Damien C. Tully, Christian Julián Villabona‐Arenas, Stéphane Hué, Jan Albert, Andrew Brown, Katherine E. Atkins (2021) Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis bioRxiv (Cold Spring Harbor Laboratory) DOI: 10.1101/2021.07.14.21259809 Citations: 1 | Open Access
[61] James D Munday, Richard Pebody, Katherine E. Atkins, Albert Jan Hoek (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):1243–1243 DOI: 10.1186/s12879-021-06936-5 Citations: 2 | Open Access
[60] Akira Endo, Mitsuo Uchida, Naoki Hayashi, Yang Liu, Katherine E. Atkins, Adam J. Kucharski, Sebastian Funk (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 118(46) DOI: 10.1073/pnas.2112605118 Citations: 26 | Open Access
[59] Luc Blassel, Anna Zhukova, Christian Julián Villabona‐Arenas, Katherine E. Atkins, Stéphane Hué, Olivier Gascuel (2021) Drug resistance mutations in HIV: new bioinformatics approaches and challenges Current Opinion in Virology 51:56–64 DOI: 10.1016/j.coviro.2021.09.009 Citations: 48
[58] Nicholas G. Davies, Stefan Flasche, Mark Jit, Katherine E. Atkins (2021) Modeling the effect of vaccination on selection for antibiotic resistance in Streptococcus pneumonia e Science Translational Medicine 13(606) DOI: 10.1126/scitranslmed.aaz8690 Citations: 18 | Open Access
[57] Quentin J. Leclerc, Naomi M. Fuller, Ruth H. Keogh, Karla Diaz-Ordaz, Richard Sekula, Malcolm G. Semple, ISARIC4C Investigators, J. Kenneth Baillie, Malcolm G. Semple, Peter J. M. Openshaw, Gail Carson, Beatrice Alex, Benjamin Bach, Wendy S. Barclay, Debby Bogaert, Meera Chand, Graham S. Cooke, Annemarie B. Docherty, Jake Dunning, Ana Da Silva Filipe, Tom Fletcher, Christopher A. Green, Ewen M. Harrison, Julian A. Hiscox, Antonia Ying Wai Ho, Peter W. Horby, Samreen Ijaz, Saye Khoo, Paul Klenerman, Andrew Law, Wei Shen Lim, Alexander J. Mentzer, Laura Merson, Alison M. Meynert, Mahdad Noursadeghi, Shona C. Moore, Massimo Palmarini, William A. Paxton, Georgios Pollakis, Nicholas Price, Andrew Rambaut, David L. Robertson, Clark D. Russell, Vanessa Sancho-Shimizu, Janet T. Scott, Thushan De Silva, Louise Sigfrid, Tom Solomon, Shiranee Sriskandan, David Stuart, Charlotte Summers, Richard S. Tedder, Emma C. Thomson, A. A. Roger Thompson, Ryan S. Thwaites, Lance C. W. Turtle, Maria Zambon, Hayley Hardwick, Chloe Donohue, Ruth Lyons, Fiona Griffiths, Wilna Oosthuyzen, Lisa Norman, Riinu Pius, Tom M. Drake, Cameron J. Fairfield, Stephen Knight, Kenneth A. Mclean, Derek Murphy, Catherine A. Shaw, Jo Dalton, James Lee, Daniel Plotkin, Michelle Girvan, Egle Saviciute, Stephanie Roberts, Janet Harrison, Laura Marsh, Marie Connor, Sophie Halpin, Clare Jackson, Carrol Gamble, Claire Petersen, Scott Mullaney, Gary Leeming, Murray Wham, Sara Clohisey, Ross Hendry, James Scott-Brown, William Greenhalf, Victoria Shaw, Sarah McDonald, Seán Keating, Katie A. Ahmed, Jane A. Armstrong, Milton Ashworth, Innocent G. Asiimwe, Siddharth Bakshi, Samantha L. Barlow, Laura Booth, Benjamin Brennan, Katie Bullock, Benjamin W. A. Catterall, Jordan J. Clark, Emily A. Clarke, Sarah Cole, Louise Cooper, Helen Cox, Christopher Davis, Oslem Dincarslan, Chris Dunn, Philip Dyer, Angela Elliott, Anthony Evans, Lorna Finch, Lewis W. S. Fisher, Terry Foster, Isabel Garcia-Dorival, Philip Gunning, Catherine Hartley, Antonia Ho, Rebecca L. Jensen, Christopher B. Jones, Trevor R. Jones, Shadia Khandaker, Katharine King, Robyn T. Kiy, Chrysa Koukorava, Annette Lake, Suzannah Lant, Diane Latawiec, L. Lavelle-Langham, Daniella Lefteri, Lauren Lett, Lucia A. Livoti, Maria Mancini, Sarah McDonald, Laurence McEvoy, John McLauchlan, Soeren Metelmann, Nahida S. Miah, Joanna Middleton, Joyce Mitchell, Ellen G. Murphy, Rebekah Penrice-Randal, Jack Pilgrim, Tessa Prince, Will Reynolds, P. Matthew Ridley, Debby Sales, Victoria E. Shaw, Rebecca K. Shears, Benjamin Small, Krishanthi S. Subramaniam, Agnieska Szemiel, Aislynn Taggart, Jolanta Tanianis-Hughes, Jordan Thomas, Erwan Trochu, Libby Van Tonder, Eve Wilcock, J. Eunice Zhang, Kayode Adeniji, Daniel Agranoff, Ken Agwuh, Dhiraj Ail, Ana Alegria, Brian Angus, Abdul Ashish, Dougal Atkinson, Shahedal Bari, Gavin Barlow, Stella Barnass, Nicholas Barrett, Christopher Bassford, David Baxter, Michael Beadsworth, Jolanta Bernatoniene, John Berridge, Nicola Best, Pieter Bothma, David Brealey, Robin Brittain-Long, Naomi Bulteel, Tom Burden, Andrew Burtenshaw, Vikki Caruth, David Chadwick, Duncan Chambler, Nigel Chee, Jenny Child, Srikanth Chukkambotla, Tom Clark, Paul Collini, Catherine Cosgrove, Jason Cupitt, Maria-Teresa Cutino-Moguel, Paul Dark, Chris Dawson, Samir Dervisevic, Phil Donnison, Sam Douthwaite, Ingrid DuRand, Ahilanadan Dushianthan, Tristan Dyer, Cariad Evans, Chi Eziefula, Chrisopher Fegan, Adam Finn, Duncan Fullerton, Sanjeev Garg, Sanjeev Garg, Atul Garg, Effrossyni Gkrania-Klotsas, Jo Godden, Arthur Goldsmith, Clive Graham, Elaine Hardy, Stuart Hartshorn, Daniel Harvey, Peter Havalda, Daniel B. Hawcutt, Maria Hobrok, Luke Hodgson, Anil Hormis, Michael Jacobs, Susan Jain, Paul Jennings, Agilan Kaliappan, Vidya Kasipandian, Stephen Kegg, Michael Kelsey, Jason Kendall, Caroline Kerrison, Ian Kerslake, Oliver Koch, Gouri Koduri, George Koshy, Shondipon Laha, Steven Laird, Susan Larkin, Tamas Leiner, Patrick Lillie, James Limb, Vanessa Linnett, Jeff Little, Michael MacMahon, Emily MacNaughton, Ravish Mankregod, Huw Masson, Elijah Matovu, Katherine McCullough, Ruth McEwen, Manjula Meda, Gary Mills, Jane Minton, Mariyam Mirfenderesky, Kavya Mohandas, Quen Mok, James Moon, Elinoor Moore, Patrick Morgan, Craig Morris, Katherine Mortimore, Samuel Moses, Mbiye Mpenge, Rohinton Mulla, Michael Murphy, Megan Nagel, Thapas Nagarajan, Mark Nelson, Igor Otahal, Mark Pais, Selva Panchatsharam, Hassan Paraiso, Brij Patel, Natalie Pattison, Justin Pepperell, Mark Peters, Mandeep Phull, Stefania Pintus, Jagtur Singh Pooni, Frank Post, David Price, Rachel Prout, Nikolas Rae, Henrik Reschreiter, Tim Reynolds, Neil Richardson, Mark Roberts, Devender Roberts, Alistair Rose, Guy Rousseau, Brendan Ryan, Taranprit Saluja, Aarti Shah, Prad Shanmuga, Anil Sharma, Anna Shawcross, Jeremy Sizer, Manu Shankar-Hari, Richard Smith, Catherine Snelson, Nick Spittle, Nikki Staines, Tom Stambach, Richard Stewart, Pradeep Subudhi, Tamas Szakmany, Kate Tatham, Jo Thomas, Chris Thompson, Robert Thompson, Ascanio Tridente, Darell Tupper-Carey, Mary Twagira, Andrew Ustianowski, Nick Vallotton, Lisa Vincent-Smith, Shico Visuvanathan, Alan Vuylsteke, Sam Waddy, Rachel Wake, Andrew Walden, Ingeborg Welters, Tony Whitehouse, Paul Whittaker, Ashley Whittington, Meme Wijesinghe, Martin Williams, Lawrence Wilson, Sarah Wilson, Stephen Winchester, Martin Wiselka, Adam Wolverson, Daniel G. Wooton, Andrew Workman, Bryan Yates, Peter Young, CMMID COVID-19 Working Group, Matthew Quaife, Christopher I. Jarvis, Sophie R. Meakin, Billy J. Quilty, Kiesha Prem, C. Julian Villabona-Arenas, Fiona Yueqian Sun, Kaja Abbas, Megan Auzenbergs, Amy Gimma, Damien C. Tully, Katharine Sherratt, Alicia Rosello, Nicholas G. Davies, Yang Liu, Rachel Lowe, Hamish P. Gibbs, Naomi R. Waterlow, W. John Edmunds, David Simons, Graham Medley, James D. Munday, Stefan Flasche, Frank G. Sandmann, Alicia Showering, Rosalind M. Eggo, Yung-Wai Desmond Chan, Carl A. B. Pearson, Adam J. Kucharski, Anna M. Foss, Timothy W. Russell, Nikos I. Bosse, Mark Jit, Sam Abbott, Jack Williams, Akira Endo, Samuel Clifford, Georgia R. Gore-Langton, Petra Klepac, Oliver Brady, Joel Hellewell, Sebastian Funk, Kevin Van Zandvoort, Rosanna C. Barnard, Emily S. Nightingale, Thibaut Jombart, Katherine E. Atkins, Simon R. Procter, Gwenan M. Knight (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):566 DOI: 10.1186/s12913-021-06509-x Open Access
[56] Nicholas G. Davies, Sam Abbott, Rosanna C. Barnard, Christopher I Jarvis, Adam J. Kucharski, James D Munday, Carl A. B. Pearson, Timothy Russell, Damien C. Tully, Alex Washburne, Tom Wenseleers, Amy Gimma, William Waites, Kerry LM Wong, Kevin Zandvoort, Justin D. Silverman, Karla Diaz‐Ordaz, Ruth H. Keogh, Rosalind M. Eggo, Sebastian Funk, Mark Jit, Katherine E. Atkins, W. John Edmunds (2021) Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England Science 372(6538) DOI: 10.1126/science.abg3055 Citations: 2557 | Open Access
[55] James D Munday, Katharine Sherratt, Sophie Meakin, Akira Endo, Carl A. B. Pearson, Joel Hellewell, Sam Abbott, Nikos I Bosse, Rosalind M. Eggo, David Simons, Kathleen O’Reilly, Timothy Russell, Rachel Lowe, Quentin J. Leclerc, Jon C. Emery, Petra Klepac, Emily Nightingale, Matthew Quaife, Kevin Zandvoort, Gwenan M. Knight, Thibaut Jombart, Christian Julián Villabona‐Arenas, Eleanor M. Rees, Charlie Diamond, Megan Auzenbergs, Graham F. Medley, Anna M. Foss, Georgia R. Gore‐Langton, Arminder Deol, Mark Jit, Hamish Gibbs, Simon R. Procter, Alicia Roselló, Christopher I Jarvis, Yang Liu, Rein M G J Houben, Stéphane Hué, Samuel Clifford, Billy J. Quilty, Amy Gimma, Damien C. Tully, Fiona Yueqian Sun, Kiesha Prem, Katherine E. Atkins, Jacco Wallinga, W. John Edmunds, Albert Jan Hoek, Sebastian Funk (2021) Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England Nature Communications 12(1):1942–1942 DOI: 10.1038/s41467-021-22213-0 Citations: 40 | Open Access
[53] Akira Endo, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Quentin J. Leclerc, Gwenan M. Knight, Graham F. Medley, Katherine E. Atkins, Sebastian Funk, Adam J. Kucharski (2021) Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks Wellcome Open Research 5:239 DOI: 10.12688/wellcomeopenres.16344.3 Citations: 91 | Open Access
[51] You Li, David Hodgson, Xin Wang, Katherine E Atkins, Daniel R Feikin, Harish Nair (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 21(9):1303–1312 DOI: 10.1016/S1473-3099(20)30703-9 Citations: 64 | Open Access
2020
[54] Natasha Wenzel, Katherine E. Atkins, Edwin Leeuwen, M. Elizabeth Halloran, Marc Baguelin (2020) Cost-effectiveness of live-attenuated influenza vaccination among school-age children Vaccine 39(2):447–456 DOI: 10.1016/j.vaccine.2020.10.007 Citations: 7
[52] David Hodgson, Richard Pebody, Jasmina Panovska‐Griffiths, Marc Baguelin, Katherine E. Atkins (2020) Evaluating the next generation of RSV intervention strategies: a mathematical modelling study and cost-effectiveness analysis BMC Medicine 18(1):348–348 DOI: 10.1186/s12916-020-01802-8 Citations: 76 | Open Access
[50] Terence Wuerz, Sameer S. Kassim, Katherine E. Atkins (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 37:101823–101823 DOI: 10.1016/j.tmaid.2020.101823 Citations: 25 | Open Access
[49] Christian Julián Villabona‐Arenas, Matthew Hall, Katrina Lythgoe, Stephen G. Gaffney, Roland R. Regoes, Stéphane Hué, Katherine E. Atkins (2020) Number of HIV-1 founder variants is determined by the recency of the source partner infection Science 369(6499):103–108 DOI: 10.1126/science.aba5443 Citations: 12 | Open Access
[48] Juan Yang, Katherine E. Atkins, Shuo Feng, Marc Baguelin, Peng Wu, Han Yan, Eric H. Y. Lau, Joseph T. Wu, Yang Liu, Benjamin J. Cowling, Mark Jit, Hongjie Yu (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):90–90 DOI: 10.1186/s12916-020-01545-6 Citations: 49 | Open Access
[47] Mark Jit, Dorothy Hui Lin Ng, Nantasit Luangasanatip, Frank Sandmann, Katherine E. Atkins, Julie V. Robotham, Koen B. Pouwels (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):38–38 DOI: 10.1186/s12916-020-1507-2 Citations: 92 | Open Access
2019
[46] Chungman Chae, Nicholas G. Davies, Mark Jit, Katherine E. Atkins (2019) Effect of Pediatric Influenza Vaccination on Antibiotic Resistance, England and Wales Emerging infectious diseases 26(1):138–142 DOI: 10.3201/eid2601.191110 Citations: 7 | Open Access
[45] Gwenan M. Knight, Nicholas G. Davies, Caroline Colijn, Francesc Coll, Tjibbe Donker, Danna R. Gifford, R. E. Glover, Mark Jit, Elizabeth J. Klemm, Sonja Lehtinen, Jodi A. Lindsay, Marc Lipsitch, Martin Llewelyn, Ana Mateus, Julie V. Robotham, Mike Sharland, Dov J. Stekel, Laith Yakob, Katherine E. Atkins (2019) Mathematical modelling for antibiotic resistance control policy: do we know enough? BMC Infectious Diseases 19(1):1011–1011 DOI: 10.1186/s12879-019-4630-y Citations: 59 | Open Access
[44] Martial L. Ndeffo-Mbah, Abhishek Pandey, Katherine E. Atkins, Serap Aksoy, Alison P. Galvani (2019) The impact of vector migration on the effectiveness of strategies to control gambiense human African trypanosomiasis PLoS neglected tropical diseases 13(12):e0007903-e0007903 DOI: 10.1371/journal.pntd.0007903 Citations: 12 | Open Access
[43] David Hodgson, Katherine E. Atkins, Marc Baguelin, Jasmina Panovska‐Griffiths, Dominic Thorrington, Albert Jan Hoek, Hongxin Zhao, Ellen Fragaszy, Andrew Hayward, Richard Pebody (2019) Estimates for quality of life loss due to Respiratory Syncytial Virus Influenza and Other Respiratory Viruses 14(1):19–27 DOI: 10.1111/irv.12686 Citations: 40 | Open Access
[42] Jeroen Luyten, Roselinde Kessels, Katherine E. Atkins, Mark Jit, Albert Jan Hoek (2019) Quantifying the public’s view on social value judgments in vaccine decision-making: A discrete choice experiment Social Science & Medicine 228:181–193 DOI: 10.1016/j.socscimed.2019.03.025 Citations: 32 | Open Access
[41] Paul Capewell, K. E. Atkins, William Weir, Vincent Jamonneau, Mamadou Camara, Caroline Clucas, Nono-Raymond Kuispond Swar, Dieudonné Mumba Ngoyi, Brice Rotureau, Paul Garside, Alison P. Galvani, Bruno Bucheton, Annette MacLeod (2019) Resolving the apparent transmission paradox of African sleeping sickness PLoS Biology 17(1):e3000105-e3000105 DOI: 10.1371/journal.pbio.3000105 Citations: 70 | Open Access
[40] Nicholas G. Davies, Stefan Flasche, Mark Jit, Katherine E. Atkins (2019) Within-host dynamics shape antibiotic resistance in commensal bacteria Nature Ecology & Evolution 3(3):440–449 DOI: 10.1038/s41559-018-0786-x Citations: 104
2018
[39] James D. Munday, Albert Jan Van Hoek, W. John Edmunds, Katherine E. Atkins (2018) Quantifying the impact of social groups and vaccination on inequalities in infectious diseases using a mathematical model BMC Medicine 16(1):162 DOI: 10.1186/s12916-018-1152-1 Citations: 35 | Open Access
[38] Katherine E Atkins, Marc Lipsitch (2018) Can antibiotic resistance be reduced by vaccinating against respiratory disease? The Lancet Respiratory Medicine 6(11):820–821 DOI: 10.1016/S2213-2600(18)30328-X Citations: 16 | Open Access
[37] Stefan Flasche, Katherine E. Atkins (2018) Balancing Benefits and Risks of Antibiotic Use The Journal of Infectious Diseases 218(9):1351–1353 DOI: 10.1093/infdis/jiy344 Citations: 22 | Open Access
[36] Anton Camacho, Malika Bouhenia, Reema Alyusfi, Abdulhakeem Alkohlani, Munna Abdulla Mohammed Naji, Xavier Radiguès, Abdinasir M Abubakar, Abdulkareem Almoalmi, Caroline Seguin, María José Sagrado, Marc Poncin, Melissa McRae, Mohammed Musoke, Ankur Rakesh, Klaudia Porten, Christopher Haskew, Katherine E. Atkins, Rosalind M. Eggo, Andrew S. Azman, Marije Broekhuijsen, Mehmet Akif Saatcioglu, Lorenzo Pezzoli, Marie-Laure Quilici, Abdul Rahman Al-Mesbahy, Nevio Zagaria, Francisco J. Luquero (2018) Cholera epidemic in Yemen, 2016–18: an analysis of surveillance data The Lancet Global Health 6(6):e680-e690 DOI: 10.1016/s2214-109x(18)30230-4 Citations: 246 | Open Access
[35] Jay R. McDonald, Stephen Y. Liang, Ping Li, Salwa Maalouf, Clinton K. Murray, Amy Weintrob, Elizabeth Schnaubelt, Janis Kuhn, Anuradha Ganesan, William P. Bradley, David R. Tribble (2018) Infectious Complications After Deployment Trauma: Following Wounded US Military Personnel Into Veterans Affairs Care Clinical Infectious Diseases 67(8):1205–1212 DOI: 10.1093/cid/ciy280 Citations: 20 | Open Access
[34] Katherine E. Atkins, Stefan Flasche (2018) Vaccination to reduce antimicrobial resistance The Lancet Global Health 6(3):e252-e252 DOI: 10.1016/s2214-109x(18)30043-3 Citations: 24 | Open Access
[33] Katherine E Atkins, Erin I Lafferty, Sarah R Deeny, Nicholas G Davies, Julie V Robotham, Mark Jit (2018) Use of mathematical modelling to assess the impact of vaccines on antibiotic resistance The Lancet Infectious Diseases 18(6):e204-e213 DOI: 10.1016/S1473-3099(17)30478-4 Citations: 79 | Open Access
2017
[32] Cordelia Coltart, W. John Edmunds, Katherine E. Atkins (2017) The 2013–2016 Ebola epidemic: multidisciplinary success conceals a missed opportunity Philosophical Transactions of the Royal Society B Biological Sciences 372(1721):20160292–20160292 DOI: 10.1098/rstb.2016.0292 Citations: 2 | Open Access
[31] Peter Piot, Cordelia Coltart, Katherine E. Atkins (2017) Preface: ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’ Philosophical Transactions of the Royal Society B Biological Sciences 372(1721):20170020–20170020 DOI: 10.1098/rstb.2017.0020 Citations: 11 | Open Access
[30] Kat S. Rock, Abhishek Pandey, Martial L. Ndeffo-Mbah, K. E. Atkins, Crispin Lumbala, Alison P. Galvani, Matt J. Keeling (2017) Data-driven models to predict the elimination of sleeping sickness in former Equateur province of DRC Epidemics 18:101–112 DOI: 10.1016/j.epidem.2017.01.006 Citations: 41
[29] David Hodgson, Marc Baguelin, Edwin Leeuwen, Jasmina Panovska‐Griffiths, Mary Ramsay, Richard Pebody, Katherine E. Atkins (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):e74-e81 DOI: 10.1016/s2468-2667(16)30044-5 Citations: 49 | Open Access
2016
[28] Sara L. Thomas, Jemma Walker, Justin Fenty, Katherine E. Atkins, Alex J. Elliot, Helen E. Hughes, Julia Stowe, Shamez Ladhani, Nick Andrews (2016) Impact of the national rotavirus vaccination programme on acute gastroenteritis in England and associated costs averted Vaccine 35(4):680–686 DOI: 10.1016/j.vaccine.2016.11.057 Citations: 59
[27] Juan Yang, Katherine E. Atkins, Shuo Feng, Mingfan Pang, Yaming Zheng, Xinxin Liu, Benjamin J. Cowling, Hongjie Yu (2016) Seasonal influenza vaccination in China: Landscape of diverse regional reimbursement policy, and budget impact analysis Vaccine 34(47):5724–5735 DOI: 10.1016/j.vaccine.2016.10.013 Citations: 201
[26] Meng Li, E. G. R. Taylor, Katherine E. Atkins, Gretchen B. Chapman, Alison P. Galvani (2016) Stimulating Influenza Vaccination via Prosocial Motives PLoS ONE 11(7):e0159780-e0159780 DOI: 10.1371/journal.pone.0159780 Citations: 90 | Open Access
[25] Dan Yamin, Katherine E Atkins, Vanessa Remy, Alison P Galvani (2016) Cost-Effectiveness of Rotavirus Vaccination in France—Accounting for Indirect Protection Value in Health 19(6):811–819 DOI: 10.1016/j.jval.2016.05.011 Citations: 13 | Open Access
[24] Meagan C. Fitzpatrick, Natasha Wenzel, Samuel V. Scarpino, Benjamin M. Althouse, Katherine E. Atkins, Alison P. Galvani, Jeffrey P. Townsend (2016) Cost-effectiveness of next-generation vaccines: The case of pertussis Vaccine 34(29):3405–3411 DOI: 10.1016/j.vaccine.2016.04.010 Citations: 4
[22] Katherine E. Atkins, Meagan C. Fitzpatrick, Alison P. Galvani, Jeffrey P. Townsend (2016) Cost-Effectiveness of Pertussis Vaccination During Pregnancy in the United States American Journal of Epidemiology 183(12):1159–1170 DOI: 10.1093/aje/kwv347 Citations: 46 | Open Access
[21] Katherine E. Atkins, Albert Jan Hoek, Conall Watson, Marc Baguelin, Lethiwe Choga, Anika Patel, Thara Raj, Mark Jit, Ulla Griffiths (2016) Seasonal influenza vaccination delivery through community pharmacists in England: evaluation of the London pilot BMJ Open 6(2):e009739-e009739 DOI: 10.1136/bmjopen-2015-009739 Citations: 50 | Open Access
2015
[23] Teruhisa Tanaka, Tetsuo Hirata, Gretchen Parrott, Miwa Higashiarakawa, Takeshi Kinjo, Tetsu Kinjo, Akira Hokama, Jiro Fujita (2015) Relationship Among Strongyloides stercoralis Infection, Human T-Cell Lymphotropic Virus Type 1 Infection, and Cancer: A 24-Year Cohort Inpatient Study in Okinawa, Japan American Journal of Tropical Medicine and Hygiene 94(2):365–370 DOI: 10.4269/ajtmh.15-0556 Citations: 46 | Open Access
[20] T. Déirdre Hollingsworth, Emily R. Adams, Roy M. Anderson, Katherine E. Atkins, Sarah M. Bartsch, María‐Gloria Basáñez, Matthew R. Behrend, David J. Blok, Lloyd A. C. Chapman, Luc E. Coffeng, Orin Courtenay, R. E. Crump, Sake J. Vlas, Andrew P. Dobson, Louise Dyson, Hajnal Farkas, Alison P. Galvani, Manoj Gambhir, David Gurarie, Michael A. Irvine, Sarah Jervis, Matt J. Keeling, Louise A. Kelly‐Hope, Charles H. King, Bruce Y. Lee, Epke A. Le Rutte, Thomas M. Lietman, Martial L. Ndeffo-Mbah, Graham F. Medley, Edwin Michael, Abhishek Pandey, Jennifer K. Peterson, Amy Pinsent, Travis C. Porco, Jan Hendrik Richardus, Lisa J. Reimer, Kat S. Rock, Brajendra K. Singh, Wilma A. Stolk, S. Subramanian, Stephen J. Torr, Jeffrey P. Townsend, James E. Truscott, Martin Walker, Alexandra Zoueva (2015) Quantitative analyses and modelling to support achievement of the 2020 goals for nine neglected tropical diseases Parasites & Vectors 8(1):630–630 DOI: 10.1186/s13071-015-1235-1 Citations: 90 | Open Access
[19] Abhishek Pandey, Katherine E. Atkins, Bruno Bucheton, Mamadou Camara, Serap Aksoy, Alison P. Galvani, Martial L. Ndeffo-Mbah (2015) Evaluating long-term effectiveness of sleeping sickness control measures in Guinea Parasites & Vectors 8(1):550–550 DOI: 10.1186/s13071-015-1121-x Citations: 51 | Open Access
[18] Yoko Ibuka, Yasushi Ohkusa, Tamie Sugawara, Gretchen B. Chapman, Dan Yamin, Katherine E. Atkins, Kiyosu Taniguchi, Nobuhiko Okabe, Alison P. Galvani (2015) Social contacts, vaccination decisions and influenza in Japan Journal of Epidemiology & Community Health 70(2):162–167 DOI: 10.1136/jech-2015-205777 Citations: 108 | Open Access
[17] Eric Taylor, Katherine E. Atkins, Jan Medlock, Meng Li, Gretchen B. Chapman, Alison P. Galvani (2015) Cross-Cultural Household Influence on Vaccination Decisions Medical Decision Making 36(7):844–853 DOI: 10.1177/0272989x15591007 Citations: 20
[16] Chad R. Wells, Dan Yamin, Martial L. Ndeffo-Mbah, Natasha Wenzel, Stephen G. Gaffney, Jeffrey P. Townsend, Lauren Ancel Meyers, Mosoka Fallah, Tolbert Nyenswah, Frederick L. Altice, Katherine E. Atkins, Alison P. Galvani (2015) Correction: Harnessing Case Isolation and Ring Vaccination to Control Ebola PLoS neglected tropical diseases 9(6):e0003888-e0003888 DOI: 10.1371/journal.pntd.0003888 Citations: 2 | Open Access
[15] K. E. Atkins, Natasha Wenzel, Martial L. Ndeffo-Mbah, Frederick L. Altice, Jeffrey P. Townsend, Alison P. Galvani (2015) Under-reporting and case fatality estimates for emerging epidemics BMJ 350(mar16 3):h1115-h1115 DOI: 10.1136/bmj.h1115 Citations: 41 | Open Access
2014
[14] Abhishek Pandey, Katherine E. Atkins, Jan Medlock, Natasha Wenzel, Jeffrey P. Townsend, James E. Childs, Tolbert Nyenswah, Martial L. Ndeffo-Mbah, Alison P. Galvani (2014) Strategies for containing Ebola in West Africa Science 346(6212):991–995 DOI: 10.1126/science.1260612 Citations: 309
[13] Kristina Talbert‐Slagle, Katherine E. Atkins, Koon‐Kiu Yan, Ekta Khurana, Mark Gerstein, Elizabeth H. Bradley, David N. Berg, Alison P. Galvani, Jeffrey P. Townsend (2014) Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body PLoS Pathogens 10(5):e1004092-e1004092 DOI: 10.1371/journal.ppat.1004092 Citations: 22 | Open Access
2013
[12] Katherine E. Atkins, Andrew F. Read, Stephen W. Walkden‐Brown, Nicholas J. Savill, Mark Woolhouse (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):208–217 DOI: 10.1016/j.epidem.2013.10.001 Citations: 27
[11] Jan Medlock, Katherine E. Atkins, David N. Thomas, Serap Aksoy, Alison P. Galvani (2013) Evaluating Paratransgenesis as a Potential Control Strategy for African Trypanosomiasis PLoS neglected tropical diseases 7(8):e2374-e2374 DOI: 10.1371/journal.pntd.0002374 Citations: 37 | Open Access
[10] Martial L. Ndeffo-Mbah, Eric M. Poolman, Katherine E. Atkins, Evan Orenstein, Lauren Ancel Meyers, Jeffrey P. Townsend, Alison P. Galvani (2013) Potential Cost-Effectiveness of Schistosomiasis Treatment for Reducing HIV Transmission in Africa – The Case of Zimbabwean Women PLoS neglected tropical diseases 7(8):e2346-e2346 DOI: 10.1371/journal.pntd.0002346 Citations: 35 | Open Access
[9] Greta Bocedi, Katherine E. Atkins, Jishan Liao, Roslyn Henry, Justin M. J. Travis, Jessica J. Hellmann (2013) Effects of local adaptation and interspecific competition on species’ responses to climate change Annals of the New York Academy of Sciences 1297(1):83–97 DOI: 10.1111/nyas.12211 Citations: 58 | Open Access
[8] Katherine E. Atkins, Jeffrey P. Townsend, Jan Medlock, Alison P. Galvani (2013) Epidemiological mechanisms of genetic resistance to kuru Journal of The Royal Society Interface 10(85):20130331–20130331 DOI: 10.1098/rsif.2013.0331 Citations: 4 | Open Access
[7] Martial L. Ndeffo-Mbah, Eyrun Floerecke Kjetland, Katherine E. Atkins, Eric M. Poolman, Evan Orenstein, Lauren Ancel Meyers, Jeffrey P. Townsend, Alison P. Galvani (2013) Cost-effectiveness of a community-based intervention for reducing the transmission ofSchistosoma haematobiumand HIV in Africa Proceedings of the National Academy of Sciences 110(19):7952–7957 DOI: 10.1073/pnas.1221396110 Citations: 37 | Open Access
2012
[6] Katherine E. Atkins, Andrew F. Read, Nicholas J. Savill, Katrin Renz, Afm Fakhrul Islam, Stephen W. Walkden‐Brown, Mark Woolhouse (2012) Vaccination and reduced cohort duration can drive virulence evolution: Marek’s disease virus and industrialized agriculture Evolution 67(3):851–860 DOI: 10.1111/j.1558-5646.2012.01803.x Citations: 110 | Open Access
[5] Katherine E. Atkins, Eunha Shim, Stuart Carroll, Sibilia Quilici, Alison P. Galvani (2012) The cost-effectiveness of pentavalent rotavirus vaccination in England and Wales Vaccine 30(48):6766–6776 DOI: 10.1016/j.vaccine.2012.09.025 Citations: 36
[4] Virginia E. Pitzer, Katherine E. Atkins, Birgitte Freiesleben Blasio, Thierry Van Effelterre, Christina Atchison, John Harris, Eunha Shim, Alison P. Galvani, W. John Edmunds, Cécile Viboud, Manish M. Patel, Bryan T. Grenfell, Umesh D. Parashar, Ben Lopman (2012) Direct and Indirect Effects of Rotavirus Vaccination: Comparing Predictions from Transmission Dynamic Models PLoS ONE 7(8):e42320-e42320 DOI: 10.1371/journal.pone.0042320 Citations: 74 | Open Access
2011
[3] Katherine E. Atkins, Eunha Shim, Virginia E. Pitzer, Alison P. Galvani (2011) Impact of rotavirus vaccination on epidemiological dynamics in England and Wales Vaccine 30(3):552–564 DOI: 10.1016/j.vaccine.2011.11.064 Citations: 59
[2] Katherine E. Atkins, Andrew F. Read, Nicholas J. Savill, Katrin Renz, Stephen W. Walkden‐Brown, Mark Woolhouse (2011) Modelling Marek’s Disease Virus (MDV) infection: parameter estimates for mortality rate and infectiousness BMC Veterinary Research 7(1):70–70 DOI: 10.1186/1746-6148-7-70 Citations: 30 | Open Access
2010
[1] Katherine E. Atkins, Justin M. J. Travis (2010) Local adaptation and the evolution of species’ ranges under climate change Journal of Theoretical Biology 266(3):449–457 DOI: 10.1016/j.jtbi.2010.07.014 Citations: 228 | Open Access