Publications

Selected publications are listed below. An up-to-date list of all of my publications can always be found here. You can click on the entries below for more details.

Prior infections and effectiveness of SARS-CoV-2 vaccine in test-negative study: A systematic review and meta-analysis

American Journal of Epidemiology Jun 20:kwae142

Tim Tsang, Sheena G Sullivan, Xiaotong Huang, Can Wang, Yifan Wang, Joshua Nealon, Binjy Yang, Kylie E C Ainslie, Benjamin J Cowling

Association of COVID-19 vaccination with duration of hospitalization in older adults in Hong Kong

Vaccine 42(9):2385-2393

Dongxuan Chen, Benjamin J Cowling, Kylie E C Ainslie, Yun Lin, Jessica Y Wong, Eric H Y Lau, Peng Wu, Joshua Nealon

Characterising information gains and losses when collecting multiple epidemic model outputs

Epidemics 47:100765

Katharine Sherratt, Ajitesh Srivastava, Kylie E C Ainslie, David E Singh, Aymar Cublier, Maria Cristina Marinescu, Jesus Carretero, Alberto Cascajo Garcia, Nicolas Franco, Lander Willem, Steven Abrams, Christel Faes, Philippe Beutels, Niel Hens, Sebatian Müller, Billy Charlton, Ricardo Ewert, Sydney Paltra, Christian Rakow, Jakob Rehmann, Tim Conrad, Christof Schütte, Kai Nagel, Sam Abbott, Rok Grah, Rene Niehus, Bastian Prasse, Frank Sandmann, Sebastian Funk

Ethical frameworks should be applied to computational modelling of infectious disease interventions

PLoS Comput Biol 20(3):e1011933

Cameron Zachreson, Julian Savulescu, Freya M Shearer, Michael J Plank, Simon Coghlan, Joel C Miller, Kylie E C Ainslie, Nicholas Geard

Time scales of human monkeypox transmission in the Netherlands

Journal of Infectious Disease 229(3):800-804

Fuminari Miura, Jantien A Backer, Gini van Rijckevorsel, Roisin Bavalia, Stijn Raven, Mariska Petrignani, Kylie E C Ainslie, Jacco Wallinga; Dutch Mpox Response Team

Reflections On Epidemiological Modeling To Inform Policy During The COVID-19 Pandemic In Western Europe, 2020-23

Health Affairs (Millwood) 42(12):1630-1636

Mark Jit, Kylie Ainslie, Christian Althaus, Constantino Caetano, Vittoria Colizza, Daniela Paolotti, Philippe Beutels, Lander Willem, John Edmunds, Baltazar Nunes, Sónia Namorado, Christel Faes, Nicola Low, Jacco Wallinga, Niel Hens

The need for a clinical case definition in test-negative design studies estimating vaccine effectiveness

npj Vaccines 8, 118

Sheena G. Sullivan, Arseniy Khvorov, Xiaotong Huang, Can Wang, Kylie E. C. Ainslie, Joshua Nealon, Bingyi Yang, Benjamin J. Cowling, Tim K. Tsang

Trends in SARS-CoV-2 infection prevalence during England’s roadmap out of lockdown, January to July 2021

PLoS Computational Biology 18(11): e1010724

Oliver Eales, Haowei Wang, David Haw, et al.

A scenario modelling analysis to anticipate the impact of COVID-19 vaccination in adolescents and children on disease outcomes in the Netherlands, summer 2021

Eurosurveillance 27:2101090

Kylie Ainslie, Jantien A Backer, Pieter T de Boer, et al.

Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number

Epidemics 40:100604

Oliver Eales, Kylie EC Ainslie, Caroline E Walters, et al.

Is annual vaccination best? A modelling study of influenza vaccination strategies in children

Vaccine 40(21):2940-2948

Kylie E C Ainslie, Steven Riley

SARS-CoV-2 infection and vaccine effectiveness in England (REACT-1): a series of cross-sectional random community surveys

The Lancet Respiratory Medicine 10(4):355-366

Marc Chadeau-Hyam, Haowei Wang, Oliver Eales, et al.

Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2

Wellcome Open Research 7:102

Oliver Eales, Caroline E. Walters, Haowei Wang, et al.

Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Science, 375, 6587, (1406-1411)

Paul Elliott, David Haw, Haowei Wang, et al.

Optimal vaccine allocation for COVID-19 in the Netherlands: A data-driven prioritization

PLoS Computational Biology 17(12):e1009697

Fuminari Miura, Ka Yin Leung, Don Klinkenberg, et al.

State-level tracking of COVID-19 in the United States

Nature Communications 11(1): 1-9

H Juliette T Unwin, Swapnil Mishra, Valerie C Bradley, et al.

Response to COVID-19 in South Korea and implications for lifting stringent interventions

BMC Medicine 18(1): 1-11

Amy Dighe, Lorenzo Cattarino, Gina Cuomo-Dannenburg, et al.

Comparing statistical methods for detecting and estimating waning efficacy of rotavirus vaccines in developing countries

Human Vaccines & Immunotherapeutics 17(11):4632-4635

Michael Haber, Jacqueline E Tate, Benjamin A Lopman, et al.

SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China

Journal of travel medicine 27(8):taaa135

Hayley A Thompson, Natsuko Imai, Amy Dighe, et al.

Resurgence of SARS-CoV-2: detection by community viral surveillance

Science 372(6545): 990-995

Steven Riley, Kylie EC Ainslie, Oliver Eales, et al.

Prevalence of antibody positivity to SARS-CoV-2 following the first peak of infection in England: Serial cross-sectional studies of 365,000 adults

The Lancet Regional Health-Europe 4: 100098

Helen Ward, Graham S Cooke, Christina Atchison, et al.

Reduction in mobility and COVID-19 transmission

Nature Communications 12: 1090

Pierre Nouvellet, Sangeeta Bhatia, Anne Cori, et al.

SARS-CoV-2 antibody prevalence in England following the first peak of the pandemic

Nature Communications 12(1): 1-8

Helen Ward, Christina Atchison, Matthew Whitaker, et al.

Database of epidemic trends and control measures during the first wave of COVID-19 in mainland China

International Journal of Infectious Diseases 102:463-471

Han Fu, Haowei Wang, Xiaoyue Xi, et al.

Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment

Wellcome Open Research 5: 81

Kylie EC Ainslie, Caroline E Walters, Han Fu, et al.

Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries: a modelling study

Lancet Glob Health 8(9):e1132-e1141

Alexandra B Hogan, Britta L Jewell, Ellie Sherrard-Smith, Juan F Vesga, Oliver J Watson, Charles Whittaker, Arran Hamlet, Jennifer A Smith, Peter Winskill, Robert Verity, Marc Baguelin, John A Lees, Lilith K Whittles, Kylie E C Ainslie, Samir Bhatt, Adhiratha Boonyasiri, Nicholas F Brazeau, Lorenzo Cattarino, Laura V Cooper, Helen Coupland, Gina Cuomo-Dannenburg, Amy Dighe, Bimandra A Djaafara, Prof Christl A Donnelly, Jeff W Eaton, Sabine L van Elsland, Richard G FitzJohn, Han Fu, Katy A M Gaythorpe, William Green, David J Haw, Sarah Hayes, Wes Hinsley, Natsuko Imai, Daniel J Laydon, Tara D Mangal, Thomas A Mellan, Swapnil Mishra, Gemma Nedjati-Gilani, Kris V Parag, Hayley A Thompson, H Juliette T Unwin, Michaela A C Vollmer, Caroline E Walters, Haowei Wang, Yuanrong Wanga, Xiaoyue Xi, Prof Neil M Ferguson, Lucy C Okell, Thomas S Churcher, Nimalan Arinaminpathy, Prof Azra C Ghani, Patrick G T Walker, Prof Timothy B Hallett

The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries

Science 369(6502):413-422

Patrick G T Walker, Charles Whittaker, Oliver J Watson, Marc Baguelin, Peter Winskill, Arran Hamlet, Bimandra A Djafaara, Zulma Cucunubá, Daniela Olivera Mesa, Will Green, Hayley Thompson, Shevanthi Nayagam, Kylie E C Ainslie, Sangeeta Bhatia, Samir Bhatt, Adhiratha Boonyasiri, Olivia Boyd, Nicholas F Brazeau, Lorenzo Cattarino, Gina Cuomo-Dannenburg, Amy Dighe, Christl A Donnelly, Ilaria Dorigatti, Sabine L van Elsland, Rich FitzJohn, Han Fu, Katy A M Gaythorpe, Lily Geidelberg, Nicholas Grassly, David Haw, Sarah Hayes, Wes Hinsley, Natsuko Imai, David Jorgensen, Edward Knock, Daniel Laydon , Swapnil Mishra, Gemma Nedjati-Gilani, Lucy C Okell, H Juliette Unwin, Robert Verity, Michaela Vollmer, Caroline E Walters, Haowei Wang, Yuanrong Wang, Xiaoyue Xi, David G Lalloo, Neil M Ferguson, Azra C Ghani contributed equally

Anonymised and aggregated crowd level mobility data from mobile phones suggests that initial compliance with COVID-19 social distancing interventions was high and geographically consistent across the UK

Wellcome Open Research 27:2101090

Benjamin Jeffrey, Caroline E Walters, Kylie EC Ainslie, et al.

Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe

Nature 584:257–261

Seth Flaxman, Swapnil Mishra, Axel Gandy, H. Juliette T. Unwin, Thomas A. Mellan, Helen Coupland, Charles Whittaker, Harrison Zhu, Tresnia Berah, Jeffrey W. Eaton, Mélodie Monod, Imperial College COVID-19 Response Team, Azra C. Ghani, Christl A. Donnelly, Steven Riley, Michaela A. C. Vollmer, Neil M. Ferguson, Lucy C. Okell, Samir Bhatt

An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver

PLoS Comput Biol 16(5): e1007840

James A. Hay, Amanda Minter, Kylie E. C. Ainslie, Justin Lessler, Bingyi Yang, Derek A. T. Cummings,Adam J. Kucharski, Steven Riley

Challenges in estimating influenza vaccine effectiveness

Expert Rev Vaccines 18(6):615-628

Kylie E C Ainslie, Michael Haber, Walt A Orenstein

Bias of influenza vaccine effectiveness estimates from test-negative studies conducted during an influenza pandemic

Vaccine 37(14): 1987–1993.

Kylie E. C. Ainslie, Michael Haber, Walter A. Orenstein

A Dynamic Model for Evaluation of the Bias of Influenza Vaccine Effectiveness Estimates From Observational Studies

Am J Epidemiol 188(2):451-460.

Kylie E C Ainslie, Meng Shi, Michael Haber, Walter A Orenstein

Maximum likelihood estimation of influenza vaccine effectiveness against transmission from the household and from the community

Stat Med 37(6):970-982.

Kylie E C Ainslie, Michael J Haber, Ryan E Malosh, Joshua G Petrie, Arnold S Monto

On the bias of estimates of influenza vaccine effectiveness from the test-negative studies

Vaccine 35(52):7297-7301.

Kylie E C Ainslie, Meng Shi, Michael Haber, Walter A Orenstein

A comparison of the test-negative and the traditional case-control study designs for estimation of influenza vaccine effectiveness under nonrandom vaccination

BMC Infectious Diseases volume 17, 757 (2017)

Meng Shi, Qian An, Kylie E. C. Ainslie, Michael Haber, Walter A. Orenstein

Gene integrated set profile analysis: a context-based approach for inferring biological endpoints

Nucleic Acids Res 44(7):e69.

Jeanne Kowalski, Bhakti Dwivedi, Scott Newman, Jeffery M Switchenko, Rini Pauly, David A Gutman, Jyoti Arora, Khanjan Gandhi, Kylie Ainslie, Gregory Doho, Zhaohui Qin, Carlos S Moreno, Michael R Rossi, Paula M Vertino, Sagar Lonial, Leon Bernal-Mizrachi, Lawrence H Boise