Publications — Swapnil Mishra

2026

Wellcome Open Res.

A study protocol for a baseline community-based cross-sectional study to investigate malaria and dengue transmission dynamics in a development area of new capital city, Indonesia

A. Pradana, M. Oktaviani, H. Prameswari, D. Supriyanto, P. Waluyo, E. Ndoen, D. Rosadi, I. Lubis, S. Suwarti, D. Subekti, T. Kusumaningrum, M. Carroll et al.

Wellcome Open Research, 11 · Journal

DOI

Nature Health

Artificial intelligence for public health can harness data for healthier populations

M. Feng, S. Mishra, J. Ma, S. Flaxman, S. Bhatt, J. Car, L.Y. Hsu, T.Y. Wong

Nature Health, 1 (167--170) · Journal

DOI

PLOS Negl. Trop. Dis.

★ Dengue transmission heterogeneity across Indonesia’s archipelago: Climate-driven spatiotemporal patterns and policy implications

B.A. Djaafara, I.R.F. Elyazar, F.S.M. Silalahi, A. Surya, A. Handito, B. Thohir, D. Aryani, M. Kamal, A.L. Ramadona, D. Gunawan, Hipokrates, A.K. Nisa et al.

PLOS Neglected Tropical Diseases, 20 · Journal

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Epidemics

Evaluating age-dependent transmission and vaccination policy in Singapore's SARS-CoV-2 epidemic: A computational modelling approach

J. Huang, Z. Ling, M. Roy, S. Jin, J.W. Chan, K.B. Tan, S. Mishra, M.L.G.H. Network

Epidemics, 55 (100921) · Journal

DOI

Ecology Letters

★ Host-Pathogen Network and Eco-Evolutionary Drivers of Avian Influenza Transmission in Wild Birds

X. Wang, Z. Ling, X. Chen, S. Mishra, L. Dong

Ecology Letters, 29 (e70391) · Journal

DOI Read

Nature Communications

★ Uncovering latent urban mobility patterns via smart-card and survey data fusion

K.D. Vo, S.W. Ham, M. Roy, S. Mishra, P. Bansal

Nature Communications · Journal

DOI

2025

Sci. Reports

Addressing survey fatigue bias in longitudinal social contact studies to improve pandemic preparedness

S. Dan, Z. Ling, Y. Chen, J. Tegegne, V.K. Jaeger, A. Karch, S. Mishra, O. Ratmann, S. Vollmer, M. Kraemer, D.A. Duchene, N. Faria et al.

Scientific Reports, 15 · Journal

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Nature Communications

Differential gut transmission of IncP plasmid clades involving hypervirulent Klebsiella pneumoniae reveals plasmid-specific ecological adaptation

M. Yong, W.W. Low, S. Mishra, G. Williams, S. Mileto, C. Lim, C. Chwa, G. Oo, G. Cheam, Y. Chen, H. Chung The, T.D. Pham et al.

Nature Communications, 16 · Journal

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J. R. Soc. Interface

★ Estimating dengue force of infection from age-stratified surveillance data in Java, Indonesia

B. Djaafara, I.R.F. Elyazar, A. Surya, F.S.M. Silalahi, A. Handito, D. Aryani, M. Kamal, D. Gunawan, H. Hipokrates, A.K. Nisa, E. Prianto, I. Samad et al.

Journal of the Royal Society Interface, 22 · Journal

DOI

Int. J. Approx. Reason.

Evidential time-to-event prediction with calibrated uncertainty quantification

L. Huang, Y. Xing, S. Mishra, T. Denœux, M. Feng

International Journal of Approximate Reasoning, 181 · Journal

DOI

BMC Public Health

Exploring the potential and limitations of deep learning and explainable AI for longitudinal life course analysis

H. Coupland, N. Scheidwasser, A. Katsiferis, M. Davies, S. Flaxman, N. Hulvej Rod, S. Mishra, S. Bhatt, H.J.T. Unwin

BMC Public Health, 25 · Journal

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PLOS Comput. Biol.

★ Incorporating human mobility to enhance epidemic response and estimate real-time reproduction numbers

M. Roy, H.E. Clapham, S. Mishra

PLOS Computational Biology, 21 · Journal

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Cell Genomics

National investment case development for pathogen genomics

Y.K. Khoo, S. Wulandari, M. Getchell, L. Moe, S.S. Kumar, E.J. Liu, Y. Sun, J. Pang, S. Mishra, H. Clapham, B. Marais, V. Sintchenko et al.

Cell Genomics, 5 · Journal

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2024

Springer (Book Chapter)

Deep Learning and MCMC with aggVAE for Shifting Administrative Boundaries: Mapping Malaria Prevalence in Kenya

E. Semenova, S. Mishra, S. Bhatt, S. Flaxman, H.J.T. Unwin

Springer (Book Chapter), 14523 LNAI (13--27) · Chapter

DOI

Sci. Reports

Differential responses of SARS-CoV-2 variants to environmental drivers during their selective sweeps

T.P. Smith, S. Mishra, I. Dorigatti, M.K. Dixit, M. Tristem, W.D. Pearse

Scientific Reports, 14 · Journal

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PLOS Glob. Public Health

Ethnicity and anthropometric deficits in children: A cross-sectional analysis of national survey data from 18 countries in sub-Saharan Africa

L.S. Tusting, S. Mishra, H.S. Gibson, S.W. Lindsay, D.J. Weiss, S. Flaxman, S. Bhatt

PLOS Global Public Health, 4 · Journal

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Nature Communications

★ Mitigating risks of malaria and other vector-borne diseases in the new capital city of Indonesia

H. Surendra, B.A. Djaafara, H.D. Prameswari, D. Supriyanto, P. Waluyo, S.B. Basuki, H. Herdiana, E. Ndoen, S. Siswanto, I.N.D. Lubis, X. Liu, S. Mishra et al.

Nature Communications, 15 · Journal

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PLOS ONE

The interaction of disease transmission, mortality, and economic output over the first 2 years of the COVID-19 pandemic

C. Morgenstern, D.J. Laydon, C. Whittaker, S. Mishra, D. Haw, S. Bhatt, N.M. Ferguson

PLOS ONE, 19 · Journal

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2023

PLOS ONE

Application of referenced thermodynamic integration to Bayesian model selection

I. Hawryluk, S. Mishra, S. Flaxman, S. Bhatt, T.A. Mellan

PLOS ONE, 18 · Journal

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JAMA Network Open

Assessment of COVID-19 as the Underlying Cause of Death Among Children and Young People Aged 0 to 19 Years in the US

S. Flaxman, C. Whittaker, E. Semenova, T. Rashid, R.M. Parks, A. Blenkinsop, H.J.T. Unwin, S. Mishra, S. Bhatt, D. Gurdasani, O. Ratmann

JAMA Network Open, 6 (e2253590) · Journal

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PLOS Glob. Public Health

Comparative impact assessment of COVID-19 policy interventions in five South Asian countries using reported and estimated unreported death counts during 2020-2021

R. Kundu, J. Datta, D. Ray, S. Mishra, R. Bhattacharyya, L. Zimmermann, B. Mukherjee

PLOS Global Public Health, 3 · Journal

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Transactions on Machine Learning Research

Cox-Hawkes: doubly stochastic spatiotemporal Poisson processes

X. Miscouridou, S. Bhatt, G. Mohler, S. Flaxman, S. Mishra

Transactions on Machine Learning Research, 2023 · Journal

Scholar

Lancet Public Health

Effectiveness assessment of non-pharmaceutical interventions: lessons learned from the COVID-19 pandemic

A. Lison, N. Banholzer, M. Sharma, S. Mindermann, H.J.T. Unwin, S. Mishra, T. Stadler, S. Bhatt, N.M. Ferguson, J. Brauner, W. Vach

The Lancet Public Health, 8 (e311--e317) · Journal

DOI

Commun. Physics

Intrinsic randomness in epidemic modelling beyond statistical uncertainty

M.J. Penn, D.J. Laydon, J. Penn, C. Whittaker, C. Morgenstern, O. Ratmann, S. Mishra, M.S. Pakkanen, C.A. Donnelly, S. Bhatt

Communications Physics, 6 · Journal

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PLOS ONE

Machine learning models of healthcare expenditures predicting mortality: A cohort study of spousal bereaved Danish individuals

A. Katsiferis, S. Bhatt, L.H. Mortensen, S. Mishra, M.K. Jensen, R.G.J. Westendorp

PLOS ONE, 18 · Journal

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Age and Ageing

Predicting mortality risk after a fall in older adults using health care spending patterns: a population-based cohort study

A. Katsiferis, L.H. Mortensen, M.P. Khurana, S. Mishra, M.K. Jensen, S. Bhatt

Age and Ageing, 52 · Journal

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J. R. Stat. Soc. A

Semi-mechanistic Bayesian modelling of COVID-19 with renewal processes

S. Bhatt, N. Ferguson, S. Flaxman, A. Gandy, S. Mishra, J.A. Scott

Journal of the Royal Statistical Society: Series A, 186 · Journal

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PLOS ONE

Sex differences in health care expenditures and mortality after spousal bereavement: A register-based Danish cohort study

A. Katsiferis, S. Bhatt, L.H. Mortensen, S. Mishra, R.G.J. Westendorp

PLOS ONE, 18 · Journal

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J. Math. Biol.

Unifying incidence and prevalence under a time-varying general branching process

M.S. Pakkanen, X. Miscouridou, M.J. Penn, C. Whittaker, T. Berah, S. Mishra, T.A. Mellan, S. Bhatt

Journal of Mathematical Biology, 87 · Journal

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2022

J. R. Stat. Soc. A

A COVID-19 model for local authorities of the United Kingdom

S. Mishra, J.A. Scott, D.J. Laydon, H. Zhu, N.M. Ferguson, S. Bhatt, S. Flaxman, A. Gandy

Journal of the Royal Statistical Society: Series A, 185 (S86--S95) · Journal

DOI

Sci. Data

A dataset of non-pharmaceutical interventions on SARS-CoV-2 in Europe

G. Altman, J. Ahuja, J.T. Monrad, G. Dhaliwal, C. Rogers-Smith, G. Leech, B. Snodin, J.B. Sandbrink, L. Finnveden, A.J. Norman, S.B. Oehm, J.F. Sandkühler et al.

Scientific Data, 9 · Journal

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Commun. Medicine

Estimating the COVID-19 infection fatality ratio accounting for seroreversion using statistical modelling

N.F. Brazeau, R. Verity, S. Jenks, H. Fu, C. Whittaker, P. Winskill, I. Dorigatti, P.G.T. Walker, S. Riley, R.P. Schnekenberg, H. Hoeltgebaum, T.A. Mellan et al.

Communications Medicine, 2 · Journal

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J. R. Soc. Interface

PriorVAE: Encoding spatial priors with variational autoencoders for small-area estimation

E. Semenova, Y. Xu, A. Howes, T. Rashid, S. Bhatt, S. Mishra, S. Flaxman

Journal of the Royal Society Interface, 19 · Journal

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Nature Medicine

Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

A. Brizzi, C. Whittaker, L.M.S. Servo, I. Hawryluk, C.A. Prete, W.M. de Souza, R.S. Aguiar, L.J.T. Araujo, L.S. Bastos, A. Blenkinsop, L.F. Buss, D. Candido et al.

Nature Medicine, 28 (1476--1485) · Journal

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Stat. Comput.

★ πVAE: a stochastic process prior for Bayesian deep learning with MCMC

S. Mishra, S. Flaxman, T. Berah, H. Zhu, M. Pakkanen, S. Bhatt

Statistics and Computing, 32 · Journal

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2021

BMC Infect. Dis.

A comparison of five epidemiological models for transmission of SARS-CoV-2 in India

S. Purkayastha, R. Bhattacharyya, R. Bhaduri, R. Kundu, X. Gu, M. Salvatore, D. Ray, S. Mishra, B. Mukherjee

BMC Infectious Diseases, 21 · Journal

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J. R. Soc. Interface

A modified two-process Knox test for investigating the relationship between law enforcement opioid seizures and overdoses

G. Mohler, S. Mishra, B. Ray, L. Magee, P. Huynh, M. Canada, D. O'Donnell, S. Flaxman

Journal of the Royal Society Interface, 477 · Journal

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BMC Emerg. Med.

A unified machine learning approach to time series forecasting applied to demand at emergency departments

M.A.C. Vollmer, B. Glampson, T. Mellan, S. Mishra, L. Mercuri, C. Costello, R. Klaber, G. Cooke, S. Flaxman, S. Bhatt

BMC Emergency Medicine, 21 · Journal

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Science

Age groups that sustain resurging COVID-19 epidemics in the United States

M. Monod, A. Blenkinsop, X. Xi, D. Hebert, S. Bershan, S. Tietze, M. Baguelin, V.C. Bradley, Y. Chen, H. Coupland, S. Filippi, J. Ish-Horowicz et al.

Science, 371 · Journal

DOI

Nature

★ Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

E. Volz, S. Mishra, M. Chand, J.C. Barrett, R. Johnson, L. Geidelberg, W.R. Hinsley, D.J. Laydon, G. Dabrera, Á. O’Toole, R. Amato, M. Ragonnet-Cronin et al.

Nature, 593 (266--269) · Journal

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EClinicalMed.

Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

S. Mishra, S. Mindermann, M. Sharma, C. Whittaker, T.A. Mellan, T. Wilton, D. Klapsa, R. Mate, M. Fritzsche, M. Zambon, J. Ahuja, A. Howes et al.

EClinicalMedicine, 39 · Journal

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Sci. Reports

Comparing the responses of the UK, Sweden and Denmark to COVID-19 using counterfactual modelling

S. Mishra, J.A. Scott, D.J. Laydon, S. Flaxman, A. Gandy, T.A. Mellan, H.J.T. Unwin, M. Vollmer, H. Coupland, O. Ratmann, M. Monod, H.H. Zhu et al.

Scientific Reports, 11 · Journal

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Int. J. Infect. Dis.

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

H. Fu, H. Wang, X. Xi, A. Boonyasiri, Y. Wang, W. Hinsley, K.J. Fraser, R. McCabe, D. Olivera Mesa, J. Skarp, A. Ledda, T. Dewé et al.

International Journal of Infectious Diseases, 102 (463--471) · Journal

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Conf. on Uncertainty in AI (UAI)

Gaussian Process Nowcasting: Application to COVID-19 Mortality Reporting

I. Hawryluk, H. Hoeltgebaum, S. Mishra, X. Miscouridou, R.P. Schnekenberg, C. Whittaker, M. Vollmer, S. Flaxman, S. Bhatt, T.A. Mellan

Conf. on Uncertainty in AI (UAI), 161 (1258--1268) · Conference

Scholar

Nature Communications

Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions

M. Ragonnet-Cronin, O. Boyd, L. Geidelberg, D. Jorgensen, F.F. Nascimento, I. Siveroni, R.A. Johnson, M. Baguelin, Z.M. Cucunubá, E. Jauneikaite, S. Mishra, O.J. Watson et al.

Nature Communications, 12 · Journal

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Science

Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India

M.S. Dhar, R. Marwal, V.S. Radhakrishnan, K. Ponnusamy, B. Jolly, R.C. Bhoyar, V. Sardana, S. Naushin, M. Rophina, T.A. Mellan, S. Mishra, C. Whittaker et al.

Science, 374 (995--999) · Journal

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Science

★ Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

N.R. Faria, T.A. Mellan, C. Whittaker, I.M. Claro, D.D.S. Candido, S. Mishra, M.A.E. Crispim, F.C.S. Sales, I. Hawryluk, J.T. McCrone, R.J.G. Hulswit, L.A.M. Franco et al.

Science, 372 · Journal

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BMJ Global Health

Is the cure really worse than the disease? The health impacts of lockdowns during COVID-19

G. Meyerowitz-Katz, S. Bhatt, O. Ratmann, J.M. Brauner, S. Flaxman, S. Mishra, M. Sharma, S. Mindermann, V. Bradley, M. Vollmer, L. Merone, G. Yamey

BMJ Global Health, 6 · Journal

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Nature Communications

Leveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria

O.J. Watson, M. Alhaffar, Z. Mehchy, C. Whittaker, Z. Akil, N.F. Brazeau, G. Cuomo-Dannenburg, A. Hamlet, H.A. Thompson, M. Baguelin, R.G. FitzJohn, E. Knock et al.

Nature Communications, 12 · Journal

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Nature Communications

Maps and metrics of insecticide-treated net access, use, and nets-per-capita in Africa from 2000-2020

A. Bertozzi-Villa, C.A. Bever, H. Koenker, D.J. Weiss, C. Vargas-Ruiz, A.K. Nandi, H.S. Gibson, J. Harris, K.E. Battle, S.F. Rumisha, S. Keddie, P. Amratia et al.

Nature Communications, 12 · Journal

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BMJ Open

Modelling the impact of the tier system on SARS-CoV-2 transmission in the UK between the first and second national lockdowns

D.J. Laydon, S. Mishra, W.R. Hinsley, P. Samartsidis, S. Flaxman, A. Gandy, N.M. Ferguson, S. Bhatt

BMJ Open, 11 · Journal

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J. Med. Internet Res.

Quantifying online news media coverage of the COVID-19 pandemic: Text mining study and resource

K. Krawczyk, T. Chelkowski, D.J. Laydon, S. Mishra, D. Xifara, S. Flaxman, T. Mellan, V. Schwämmle, R. Röttger, J.T. Hadsund, S. Bhatt

Journal of Medical Internet Research, 23 · Journal

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Nature

SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

P. Mlcochova, S.A. Kemp, M.S. Dhar, G. Papa, B. Meng, I.A.T.M. Ferreira, R. Datir, D.A. Collier, A. Albecka, S. Singh, R. Pandey, J. Brown et al.

Nature, 599 (114--119) · Journal

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Nature Communications

Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe

M. Sharma, S. Mindermann, C. Rogers-Smith, G. Leech, B. Snodin, J. Ahuja, J.B. Sandbrink, J.T. Monrad, G. Altman, G. Dhaliwal, L. Finnveden, A.J. Norman et al.

Nature Communications, 12 · Journal

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PLOS Comput. Biol.

Using hawkes processes to model imported and local malaria cases in near-elimination settings

J.T.H. Unwin, I. Routledge, S. Flaxman, M.A. Rizoiu, S. Lai, J. Cohen, D.J. Weiss, S. Mishra, S. Bhatt

PLOS Computational Biology, 17 · Journal

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2020

Wellcome Open Res.

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

B. Jeffrey, C.E. Walters, K.E.C. Ainslie, O. Eales, C. Ciavarella, S. Bhatia, S. Hayes, M. Baguelin, A. Boonyasiri, N.F. Brazeau, G. Cuomo-Dannenburg, R.G. FitzJohn et al.

Wellcome Open Research, 5 (1--10) · Journal

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Lancet Infect. Dis.

Comparison of molecular testing strategies for COVID-19 control: a mathematical modelling study

N.C. Grassly, M. Pons-Salort, E.P.K. Parker, P.J. White, N.M. Ferguson, K. Ainslie, M. Baguelin, S. Bhatt, A. Boonyasiri, N. Brazeau, L. Cattarino, H. Coupland et al.

The Lancet Infectious Diseases, 20 (1381--1389) · Journal

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Nature

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

S. Flaxman, S. Mishra, A. Gandy, H.J.T. Unwin, T.A. Mellan, H. Coupland, C. Whittaker, H. Zhu, T. Berah, J.W. Eaton, M. Monod, P.N. Perez-Guzman et al.

Nature, 584 (257--261) · Journal

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Science

Evolution and epidemic spread of SARS-CoV-2 in Brazil

D.S. Candido, I.M. Claro, J.G. de Jesus, W.M. Souza, F.R.R. Moreira, S. Dellicour, T.A. Mellan, L. du Plessis, R.H.M. Pereira, F.C.S. Sales, E.R. Manuli, J. Thézé et al.

Science, 369 (1255--1260) · Journal

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The Lancet

Have deaths from COVID-19 in Europe plateaued due to herd immunity?

L.C. Okell, R. Verity, O.J. Watson, S. Mishra, P. Walker, C. Whittaker, A. Katzourakis, C.A. Donnelly, S. Riley, A.C. Ghani, A. Gandy, S. Flaxman et al.

The Lancet, 395 (e110--e111) · Journal

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J. R. Soc. Interface

Inference of COVID-19 epidemiological distributions from Brazilian hospital data: Inference of COVID-19 epidemiological distributions from Brazilian hospital data

I. Hawryluk, T.A. Mellan, H. Hoeltgebaum, S. Mishra, R.P. Schnekenberg, C. Whittaker, H. Zhu, A. Gandy, C.A. Donnelly, S. Flaxman, S. Bhatt

Journal of the Royal Society Interface, 17 · Journal

DOI

Lancet Glob. Health

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

A.B. Hogan, B.L. Jewell, E. Sherrard-Smith, J.F. Vesga, O.J. Watson, C. Whittaker, A. Hamlet, J.A. Smith, P. Winskill, R. Verity, M. Baguelin, J.A. Lees et al.

The Lancet Global Health, 8 (e1132--e1141) · Journal

DOI

BMC Medicine

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

A. Dighe, L. Cattarino, G. Cuomo-Dannenburg, J. Skarp, N. Imai, S. Bhatia, K.A.M. Gaythorpe, K.E.C. Ainslie, M. Baguelin, S. Bhatt, A. Boonyasiri, N.F. Brazeau et al.

BMC Medicine, 18 · Journal

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J. Travel Med.

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

H.A. Thompson, N. Imai, A. Dighe, K.E.C. Ainslie, M. Baguelin, S. Bhatia, S. Bhatt, A. Boonyasiri, O. Boyd, N.F. Brazeau, L. Cattarino, L.V. Cooper et al.

Journal of Travel Medicine, 27 · Journal

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Nature Communications

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

H.J.T. Unwin, S. Mishra, V.C. Bradley, A. Gandy, T.A. Mellan, H. Coupland, J. Ish-Horowicz, M.A.C. Vollmer, C. Whittaker, S.L. Filippi, X. Xi, M. Monod et al.

Nature Communications, 11 · Journal

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Nature

Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo’

E. Lavezzo, E. Franchin, C. Ciavarella, G. Cuomo-Dannenburg, L. Barzon, C. Del Vecchio, L. Rossi, R. Manganelli, A. Loregian, N. Navarin, D. Abate, M. Sciro et al.

Nature, 584 (425--429) · Journal

DOI

Science

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

P.G.T. Walker, C. Whittaker, O.J. Watson, M. Baguelin, P. Winskill, A. Hamlet, B.A. Djafaara, Z. Cucunubá, D.O. Mesa, W. Green, H. Thompson, S. Nayagam et al.

Science, 369 (413--422) · Journal

DOI

PLOS Comput. Biol.

Tracking progress towards malaria elimination in China: Individual-level estimates of transmission and its spatiotemporal variation using a diffusion network approach

I. Routledge, S. Lai, K.E. Battle, A.C. Ghani, M. Gomez-Rodriguez, K.B. Gustafson, S. Mishra, J. Unwin, J.L. Proctor, A.J. Tatem, Z. Li, S. Bhatt

PLOS Computational Biology, 16 · Journal

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