A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics

Cori, Anne, Ferguson, Neil M., Fraser, Christophe, Cauchemez, Simon·2013·American Journal of Epidemiology

Cited by (1,000)

Items 101–200 of 1,000

  1. Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland
    Joseph C. Lemaitre, Javier Perez‐Saez, Andrew S. Azman, Andrea Rinaldo, Jacques Fellay · 2020 · Swiss Medical Weekly
  2. Lessons from SARS-CoV-2 in India: A data-driven framework for pandemic resilience
    Maxwell Salvatore, Rupam Bhattacharyya, Soumik Purkayastha, Lauren Zimmermann, Debashree Ray, Aditi Hazra, Michael Kleinsasser, Thomas A. Mellan, C Whittaker, Seth R Flaxman et al. · 2022 · Science Advances
  3. A simple approach to measure transmissibility and forecast incidence
    Pierre Nouvellet, Anne Cori, Tini Garske, Isobel M. Blake, Ilaria Dorigatti, Wes R. Hinsley, Thibaut Jombart, Harriet L. Mills, Gemma L. Nedjati-Gilani, Maria D. Van Kerkhove et al. · 2017 · Epidemics
  4. The epidemiology of Mayaro virus in the Americas: A systematic review and key parameter estimates for outbreak modelling
    Edgar-Yaset Caicedo, Kelly Charniga, Amanecer Rueda-Monsalbe, Ilaria Dorigatti, Yardany Rafael Méndez, Arran Hamlet, Jean‐Paul Carrera, Zulma M. Cucunubá · 2021 · PLoS neglected tropical diseases
  5. Cholera outbreaks in sub-Saharan Africa during 2010-2019: a descriptive analysis
    Qulu Zheng, Francisco Javier Luquero, Iza Ciglenečki, Joseph Francis Wamala, Abdinasir Abubakar, Placide Okitayemba Welo, Mukemil Hussen, Mesfin Wossen, Sebastian Yennan, Alama Keita et al. · 2022 · International Journal of Infectious Diseases
  6. Impact of interventions and the incidence of ebola virus disease in Liberia—implications for future epidemics
    Thomas Dean Kirsch, Heidi Moseson, Moses B. F. Massaquoi, Tolbert Nyenswah, Rachel Goodermote, Isabel Rodríguez-Barraquer, Justin Lessler, Derek A T Cumings, David H. Peters · 2016 · Health Policy and Planning
  7. Testing and reopening in an SEIR model
    David Berger, Kyle Herkenhoff, Chengdai Huang, Simon Mongey · 2020 · Review of Economic Dynamics
  8. Data-driven methods for present and future pandemics: Monitoring, modelling and managing
    Teodoro Álamo, Daniel Gutiérrez Reina, Pablo Millán, Víctor M. Preciado, Giulia Giordano · 2021 · Annual Reviews in Control
  9. Urban dynamics through the lens of human mobility
    Yanyan Xu, Luis E. Olmos, David Mateo, Alberto Hernando, Xiaokang Yang, Marta C. González · 2023 · Nature Computational Science
  10. Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data
    Finlay Campbell, Anne Cori, Neil M. Ferguson, Thibaut Jombart · 2019 · PLoS Computational Biology
  11. What Explains Temporal and Geographic Variation in the Early US Coronavirus Pandemic?
    Hunt Allcott, Levi Boxell, Jacob Conway, Billy Ferguson, Matthew Aaron Gentzkow, Benjamin Goldman · 2020 · National Bureau of Economic Research
  12. Contact, travel, and transmission: The impact of winter holidays on influenza dynamics in the United States
    Anne Ewing, Elizabeth C. Lee, Cecile G. Viboud, Shweta Bansal · 2016 · The Journal of Infectious Diseases
  13. Comprehensive public health evaluation of lockdown as a non-pharmaceutical intervention on COVID-19 spread in India: national trends masking state-level variations
    Deepankar Basu, Maxwell Salvatore, Debashree Ray, Mike Kleinsasser, Soumik Purkayastha, Rupam Bhattacharyya, Bhramar Mukherjee · 2020 · BMJ Open
  14. Large-scale Lassa fever outbreaks in Nigeria: quantifying the association between disease reproduction number and local rainfall
    Shi Zhao, Salihu S. Musa, Hao Fu, Daihai He, Jing Qin · 2020 · Epidemiology and Infection
  15. The second and third waves in India: when will the pandemic be culminated?
    C. Kavitha, Arulprakash Gowrisankar, Santo Banerjee · 2021 · The European Physical Journal Plus
  16. Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo
    Xavier Didelot, Michelle Kendall, Yuanwei Xu, Peter J White, Noel Denis McCarthy · 2021 · Current Protocols
  17. College openings in the United States increase mobility and COVID-19 incidence
    Martin S. Andersen, Ana I. Bento, Anirban Basu, Christopher R. Marsicano, Kosali Ilayperuma Simon · 2022 · PLoS ONE
  18. Early epidemiological signatures of novel SARS-CoV-2 variants: establishment of B.1.617.2 in England
    Robert Challen, Louise Dyson, Christopher E. Overton, Laura M. Guzman-Rincon, Edward M. Hill, Helena B. Stage, Ellen Brooks‐Pollock, Lorenzo Pellis, Francesca Scarabel, David J. Pascall et al. · 2021 · medRxiv
  19. Comparison of control and transmission of COVID-19 across epidemic waves in Hong Kong: an observational study
    Bingyi Yang, Yun Lin, Weijia Xiong, Chang Liu, Huizhi Gao, Faith C. S. Ho, Jiayi Zhou, Ru Zhang, Jessica Y. Wong, Justin K. Cheung et al. · 2023 · The Lancet Regional Health - Western Pacific
  20. Real-time detection of COVID-19 epicenters within the United States using a network of smart thermometers
    Samuel D. Chamberlain, Inder Singh, C. Ariza, Amy L. Daitch, P. Philips, Benjamin D. Dalziel · 2020 · medRxiv
  21. Modelling insights into the COVID-19 pandemic
    Michael T. Meehan, Diana Patricia Rojas, Adeshina Israel Adekunle, Oyelola Abdulwasiu Adegboye, Jamie M. Caldwell, Evelyn M. Turek, Bridget M Williams, Ben J. Marais, James McCracken Trauer, Emma Sue McBryde · 2020 · Paediatric Respiratory Reviews
  22. Estimation of the basic reproduction number (R0) for the novel coronavirus disease in Sri Lanka
    Samath Dhamminda Dharmaratne, Supun Sudaraka Manathunga, Ishanya Ayeshini Abeyagunawardena, Kasun Manchanayake, Mahen Kothalawala, Wasantha Gunathunga · 2020 · Virology Journal
  23. Mathematical perspective of Covid-19 pandemic: Disease extinction criteria in deterministic and stochastic models
    Debadatta Adak, Abhijit Majumder, Nandadulal Bairagi · 2020 · Chaos Solitons & Fractals
  24. Are Epidemic Growth Rates More Informative than Reproduction Numbers?
    Kris Varun Parag, Robin N. Thompson, Christl Ann Donnelly · 2022 · Journal of the Royal Statistical Society Series A (Statistics in Society)
  25. COVID-19 outbreak reproduction number estimations and forecasting in Marche, Italy
    Nalini Chintalapudi, Gopi Battineni, Getu Gamo Sagaro, Francesco Amenta · 2020 · International Journal of Infectious Diseases
  26. COVID-19: Short term prediction model using daily incidence data
    Hongwei Zhao, Naveed Merchant, Alyssa McNulty, Tiffany A. Radcliff, Murray J. Côté, Rebecca S. B. Fischer, Huiyan Sang, Marcia G. Ory · 2021 · PLoS ONE
  27. Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models
    Bernard Cazelles, Clara Champagne, Joseph Dureau · 2018 · PLoS Computational Biology
  28. Effectiveness of Localized Lockdowns in the COVID-19 Pandemic
    Yige Li, Eduardo A. Undurraga, José R. Zubizarreta · 2022 · American Journal of Epidemiology
  29. COVID-19 non-pharmaceutical intervention portfolio effectiveness and risk communication predominance
    Louis Yat Hin Chan, Baoyin Yuan, Matteo Convertino · 2021 · Scientific Reports
  30. estimateR: an R package to estimate and monitor the effective reproductive number
    Jérémie Scire, Jana S. Huisman, Ana Grosu, Daniel C. Angst, Adrian Lison, Jinzhou Li, Marloes H. Maathuis, Sebastian Bonhoeffer, Tanja Stadler · 2023 · BMC Bioinformatics
  31. Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic
    Miguel I. Paredes, Nashwa Ahmed, Marlin D Figgins, Vittoria Colizza A, Philippe Lemey, John T. McCrone, Nicola Felix Müller, Cécile Tran Kiem, Trevor Bedford · 2024 · Cell
  32. Genomic Analysis and Comparison of Two Gonorrhea Outbreaks
    Xavier Didelot, Janina Dordel, Lilith K. Whittles, Caitlin Collins, Nicole Bilek, Cynthia Bishop, Peter J White, David M. Aanensen, Julian Parkhill, Stephen D. Bentley et al. · 2016 · mBio
  33. Estimating and Forecasting Disease Scenarios for COVID-19 with an SIR Model
    Andrew G. Atkeson, Karen Kopecky, Tao A. Zha · 2020 · National Bureau of Economic Research
  34. Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak
    Katherine J. Siddle, Lydia Andreyevna Krasilnikova, Gage K. Moreno, Stephen F. Schaffner, Johanna Vostok, Nicholas A. Fitzgerald, Jacob E. Lemieux, Nikolaos Barkas, Christine Loreth, Ivan Specht et al. · 2021 · Cell
  35. Estimating and explaining the spread of COVID-19 at the county level in the USA
    Anthony R. Ives, Claudio Bozzuto · 2021 · Communications Biology
  36. A Physics-Informed Neural Network approach for compartmental epidemiological models
    Caterina Millevoi, Damiano Pasetto, Massimiliano Ferronato · 2024 · PLoS Computational Biology
  37. Estimation of the serial interval and basic reproduction number of COVID‐19 in Qom, Iran, and three other countries: A data‐driven analysis in the early phase of the outbreak
    Mohammad Aghaali, Goodarz Kolifarhood, Roya Nikbakht, Hossein Mozafar Saadati, Seyed Saeed Hashemi Nazari · 2020 · Transboundary and Emerging Diseases
  38. BNT162b2 Vaccination Effectively Combats the Rapid Rise of SARS-CoV-2 Variant B.1.1.7 in High Risk Populations in Israel
    Ariel Munitz, Matan Yechezkel, Yoav Dickstein, Dan Yamin, Motti Gerlic · 2021 · Cell Reports Medicine
  39. Epidemic curves made easy using the R package incidence
    Zhian N. Kamvar, Jun Cai, Juliet R.C. Pulliam, Jakob Schumacher, Thibaut Jombart · 2019 · F1000Research
  40. Estimating effects of physical distancing on the COVID-19 pandemic using an urban mobility index
    Jean-Paul R. Soucy, Shelby L. Sturrock, Isha Berry, Duncan J. Westwood, Nick Daneman, Derek R. MacFadden, Kevin Antoine Brown · 2020 · medRxiv
  41. Factors Associated With Measles Transmission in the United States During the Postelimination Era
    Paul A. Gastañaduy, Sebastian Funk, Benjamin Alan Lopman, Paul A. Rota, Manoj Gambhir, Bryan Thomas Grenfell, Prabasaj Paul · 2019 · Archives of Pediatrics and Adolescent Medicine
  42. Effect of Nonpharmaceutical Interventions on Transmission of Severe Acute Respiratory Syndrome Coronavirus 2, South Korea, 2020
    Sukhyun Ryu, Seikh Taslim Ali, Cheolsun Jang, Baekjin Kim, Benjamin John Cowling · 2020 · Emerging infectious diseases
  43. Estimation of reproduction numbers of COVID-19 in typical countries and epidemic trends under different prevention and control scenarios
    Chen Xu, Yinqiao Dong, Xiaoyue Yu, Huwen Wang, Lhakpa Tsamlag, Ruijie Chang, Ruijie Chang, Zezhou Wang, Yuelin Yu, Rusi Long et al. · 2020 · Frontiers of Medicine
  44. Rapid review and meta-analysis of serial intervals for SARS-CoV-2 Delta and Omicron variants
    Zachary J. Madewell, Yang Yang, Ira M. Longini, M. Elizabeth Halloran, Alessandro Vespignani, Natalie E. Dean · 2023 · BMC Infectious Diseases
  45. Autochthonous dengue outbreak in Marche Region, Central Italy, August to October 2024
    Chiara Sacco, Augusto Liverani, Giulietta Venturi, Stefano Gavaudan, Flavia Riccardo, Giovanna Salvoni, Claudia Fortuna, Katia Marinelli, Giulia Marsili, Alessia Pesaresi et al. · 2024 · Eurosurveillance
  46. Epidemic trends, public health response and health system capacity: the Chilean experience in four months of the COVID-19 pandemic
    Mauricio Canals, Cristóbal Cuadrado, Andrea Canals, Karla Yohannessen V, Luis Álvaro Lefio, María Paz Bertoglia, Pamela Eguiguren, Izkia Siches, Verónica Iglesias, Óscar Arteaga · 2020 · Revista Panamericana de Salud Pública
  47. Transmission dynamics and control of COVID-19 in Chile, March-October, 2020
    Amna Tariq, Eduardo A. Undurraga, Carla Castillo-Laborde, Katia Vogt-Geisse, Ruiyan Luo, RICHARD B. ROTHENBERG, Gerardo Chowell · 2021 · PLoS neglected tropical diseases
  48. Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022
    Mircea T. Sofonea, Bénédicte Roquebert, Vincent Foulongne, David Morquin, Laura Verdurme, Sabine Trombert‐Paolantoni, Mathilde Roussel, Jean-Christophe Bonetti, Judith Zerah, Stéphanie Haïm‐Boukobza et al. · 2022 · Emerging infectious diseases
  49. Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges
    Rebecca K. Nash, Pierre Nouvellet, Anne Cori · 2022 · PLOS Digital Health
  50. Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years
    Amanda C. Perofsky, C. Hansen, Roy Burstein, Shanda Boyle, Robin A. Prentice, Cooper Marshall, David Reinhart, Ben Capodanno, Melissa Truong, Kristen Schwabe‐Fry et al. · 2024 · Nature Communications
  51. A new estimation method for COVID-19 time-varying reproduction number using active cases
    Agus Hasan, Hadi Susanto, Venansius Ryan Tjahjono, Rudy Kusdiantara, Endah R.M. Putri, Nuning Nuraini, Panji Fortuna Hadisoemarto · 2022 · Scientific Reports
  52. Estimating asymptomatic, undetected and total cases for the COVID-19 outbreak in Wuhan: a mathematical modeling study
    Xi Huo, Jing Chen, Shigui Ruan · 2021 · BMC Infectious Diseases
  53. A comparison of five epidemiological models for transmission of SARS-CoV-2 in India
    Soumik Purkayastha, Rupam Bhattacharyya, Ritwik Bhaduri, Ritoban Kundu, Xuelin Gu, Maxwell Salvatore, Debashree Ray, Swapnil Mishra, Bhramar Mukherjee · 2021 · BMC Infectious Diseases
  54. Containment efficiency and control strategies for the corona pandemic costs
    Claudius Gros, Roser Valenti, Lukas Stelz, Kilian Valenti, Daniel Gros · 2021 · Scientific Reports
  55. Commentary on the use of the reproduction number R during the COVID-19 pandemic
    Carolin Vegvari, Sam Abbott, Frank Ball, Ellen Brooks‐Pollock, Robert Challen, Benjamin S. Collyer, C. E. Dangerfield, Julia R. Gog, Katelyn M. Gostic, Jane Marie Heffernan et al. · 2021 · Statistical Methods in Medical Research
  56. Modelling the effective reproduction number of vector-borne diseases: the yellow fever outbreak in Luanda, Angola 2015–2016 as an example
    Shi Zhao, Salihu S. Musa, Jay Thomas Hebert, Peihua Cao, Jinjun Ran, Jiayi Meng, Daihai He, Jing Qin · 2020 · PeerJ
  57. Fundamental Identifiability Limits in Molecular Epidemiology
    Stilianos Louca, Angela McLaughlin, Ailene MacPherson, Jeffrey B. Joy, Matthew W. Pennell · 2021 · Molecular Biology and Evolution
  58. The Epidemiology of COVID-19 in Malaysia
    Vivek Jason Jayaraj, Sanjay Rampal, Chiu‐Wan Ng, Diane Woei-Quan Chong · 2021 · The Lancet Regional Health - Western Pacific
  59. Estimating relative generation times and reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta variant in Denmark
    Kimihito Ito, Chayada Piantham, Hiroshi Nishiura · 2022 · Mathematical Biosciences & Engineering
  60. Estimating the effective reproduction number of dengue considering temperature-dependent generation intervals
    Cláudia Torres Codeço, Daniel Antunes Maciel Villela, Flávio Codeço Coelho · 2018 · Epidemics
  61. Dynamics of conflict during the Ebola outbreak in the Democratic Republic of the Congo 2018–2019
    Moritz U. G. Kraemer, David M. Pigott, Sarah Catherine Hill, Samantha Vanderslott, Robert C. Reiner, Stephanie Stasse, John S. Brownstein, Bernardo Gutiérrez, Francis Dennig, Simon Iain Hay et al. · 2020 · BMC Medicine
  62. Using information theory to optimise epidemic models for real-time prediction and estimation
    Kris Varun Parag, Christl Ann Donnelly · 2020 · PLoS Computational Biology
  63. A Comparative Analysis of Statistical Methods to Estimate the Reproduction Number in Emerging Epidemics, With Implications for the Current Coronavirus Disease 2019 (COVID-19) Pandemic
    Megan O’Driscoll, Carole Harry, Christl Ann Donnelly, Anne Cori, Ilaria Dorigatti · 2020 · Clinical Infectious Diseases
  64. Nowcasting for Real-Time COVID-19 Tracking in New York City: An Evaluation Using Reportable Disease Data From Early in the Pandemic
    Sharon K. Greene, Sarah F. McGough, Gretchen M. Culp, Laura E. Graf, Marc Lipsitch, Nicolas A. Menzies, Rebecca J. Kahn · 2021 · JMIR Public Health and Surveillance
  65. Inferring time-varying generation time, serial interval, and incubation period distributions for COVID-19
    Dongxuan Chen, Yiu Chung Lau, Xiao-Ke Xu, Lin Wang, Zhanwei Du, Tim K. Tsang, Peng Wu, Eric H. Y. Lau, Jacco Wallinga, Benjamin John Cowling et al. · 2022 · Nature Communications
  66. Spatiotemporal Analysis of the 2014 Ebola Epidemic in West Africa
    Jantien A. Backer, Jacco Wallinga · 2016 · PLoS Computational Biology
  67. Development of a Critical Care Response - Experiences from Italy During the Coronavirus Disease 2019 Pandemic
    Emanuele Rezoagli, Aurora Magliocca, Giacomo Bellani, Antonio Pesenti, Giacomo Grasselli · 2021 · Anesthesiology Clinics
  68. Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England
    Perez-Guzman, Pablo N., Knock, Edward, Imai, Natsuko, Rawson, Thomas, Santoni, Cosmo Nazzareno, Alcada, Joana, Whittles, Lilith K., Thekke Kanapram, Divya, Sonabend, Raphael, Gaythorpe, Katy A. M. et al. · 2023 · Nature Communications
  69. OutbreakTools: A new platform for disease outbreak analysis using the R software
    Thibaut Jombart, David M. Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Caitlin Collins, Anne Cori, Xavier Didelot et al. · 2014 · Epidemics
  70. High Rate of Non-Human Feeding by Aedes aegypti Reduces Zika Virus Transmission in South Texas
    Mark F. Olson, Martial L. Ndeffo-Mbah, Jose Guillermo Juarez, Selene Garcia-Luna, Estelle M. Martin, Monica K. Borucki, Matthias A. Frank, José Guillermo Estrada-Franco, Mario Alberto Rodríguez-Pérez, Nadia A. Fernández‐Santos et al. · 2020 · Viruses
  71. Spatial variability in reproduction number and doubling time across two waves of the COVID-19 pandemic in South Korea, February to July, 2020
    Eunha Shim, Amna Tariq, Gerardo Chowell · 2020 · International Journal of Infectious Diseases
  72. EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves
    Anne Cori · 2012
  73. Transmission dynamics and control of two epidemic waves of SARS-CoV-2 in South Korea
    Sukhyun Ryu, Sheikh Taslim Ali, Eunbi Noh, Dasom Kim, Eric H. Y. Lau, Benjamin John Cowling · 2021 · BMC Infectious Diseases
  74. A critical evaluation of Nigeria’s response to the first wave of COVID-19
    Ezekiel Damilare Jacobs, Malachy Ifeanyi Okeke · 2022 · Bulletin of the National Research Centre/Bulletin of the National Research Center
  75. Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool
    Rebecca K. Nash, Samir Bhatt, Anne Cori, Pierre Nouvellet · 2023 · PLoS Computational Biology
  76. Forecasting hospital demand in metropolitan areas during the current COVID-19 pandemic and estimates of lockdown-induced 2nd waves
    Marcos A. Capistrán, Antonio Capella, J. Andrés Christen · 2021 · PLoS ONE
  77. The Effectiveness Of Government Masking Mandates On COVID-19 County-Level Case Incidence Across The United States, 2020
    Jing Yang Huang, Brian T. Fisher, Vicky W. Tam, Zi Wang, Lihai Song, Jiasheng Shi, Caroline La Rochelle, Xi Wang, Jeffrey S. Morris, Susan E Coffin et al. · 2022 · Health Affairs
  78. Monkeypox: Early estimation of basic reproduction number R 0 in Europe
    Francesco Branda, Massimo Pierini, Sandra Mazzoli · 2022 · Journal of Medical Virology
  79. Using digital traces to build prospective and real-time county-level early warning systems to anticipate COVID-19 outbreaks in the United States
    Lucas Martins Stolerman, Leonardo Clemente, Canelle Poirier, Kris V. Parag, Atreyee Majumder, Serge Masyn, Bernd Resch, Mauricio Santillana · 2023 · Science Advances
  80. A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies
    Anne Cori, Pierre Nouvellet, Tini Garske, Hervé Bourhy, Emmanuel Rivalyn Nakouné, Thibaut Jombart · 2018 · PLoS Computational Biology
  81. Rapid Changes in the Phytoplankton Community of a Subtropical, Shallow, Hypereutrophic Lake During the Rainy Season
    Osiris Díaz-Torres, José de Anda, Ofelia Yadira Lugo-Melchor, Adriana Pacheco, Danielle Annette Orozco-Nunnelly, Harvey Shear, Carolina Senés‐Guerrero, Misael Sebastian Gradilla Hernandez · 2021 · Frontiers in Microbiology
  82. Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of COVID-19 in England
    Katharine Sherratt, Sam Abbott, Sophie R. Meakin, Joel Hellewell, James D Munday, Nikos I Bosse, CMMID COVID-19 Working Group, Mark Jit, Sebastian Funk · 2021 · Philosophical Transactions of the Royal Society B Biological Sciences
  83. Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland
    Chaoran Chen, Sarah Nadeau, Ivan Topolsky, Marc Manceau, Jana S. Huisman, Kim Philipp Jablonski, Lara Fuhrmann, David Dreifuss, Katharina Jahn, Christiane Beckmann et al. · 2021 · Epidemics
  84. The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants
    Sang Woo Park, Benjamin M. Bolker, Sebastian Funk, Charlotte Jessica E. Metcalf, Joshua S. Weitz, Bryan Thomas Grenfell, Jonathan G. Dushoff · 2022 · Journal of The Royal Society Interface
  85. Economic and Health Impacts of Social Distancing Policies during the Coronavirus Pandemic
    Hunt Allcott, Levi Boxell, Jacob Conway, Billy Ferguson, Matthew Aaron Gentzkow, Benjamin Goldman · 2020 · SSRN Electronic Journal
  86. COVID-19 epidemic monitoring after non-pharmaceutical interventions: The use of time-varying reproduction number in a country with a large migrant population
    Adil Said Al Wahaibi, Abdullah Al Manji, Amal Saif Al-Maani, Bader Al Rawahi, Khalid Al Harthy, Fatma Alyaquobi, Amina Al‐Jardani, Eskild Petersen, Seif Al Abri · 2020 · International Journal of Infectious Diseases
  87. The methodologies to assess the effectiveness of non-pharmaceutical interventions during COVID-19: a systematic review
    Nicolas Banholzer, Adrian Lison, Dennis Özcelik, Tanja Stadler, Stefan Feuerriegel, Werner Vach · 2022 · European Journal of Epidemiology
  88. Estimating effective reproduction number using generation time versus serial interval, with application to covid-19 in the Greater Toronto Area, Canada
    Jesse Knight, Sharmistha Mishra · 2020 · Infectious Disease Modelling
  89. Successive epidemic waves of cholera in South Sudan between 2014 and 2017: a descriptive epidemiological study
    Forrest K. Jones, Joseph Francis Wamala, John Pasquale Rumunu, Pinyi Nyimol Mawien, Mathew Tut M. Kol, Shirlee Wohl, Lul Lojok Deng, Lorenzo Pezzoli, Linda Haj Omar, Justin Lessler et al. · 2020 · The Lancet Planetary Health
  90. Influenza Virus: Tracking, Predicting, and Forecasting
    Sheikh Taslim Ali, Benjamin John Cowling · 2020 · Annual Review of Public Health
  91. Epidemiological characteristics of the first 100 cases of coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region, China, a city with a stringent containment policy
    Christopher K.C. Lai, Rita W. Y. Ng, Martin C. S. Wong, Ka Chun Chong, Yun Kit Yeoh, Zigui Chen, Paul K.S. Chan · 2020 · International Journal of Epidemiology
  92. Meta-analysis of the severe acute respiratory syndrome coronavirus 2 serial intervals and the impact of parameter uncertainty on the coronavirus disease 2019 reproduction number
    Robert Challen, Ellen Brooks‐Pollock, Krasimira T. Tsaneva-Atanasova, León Danon · 2021 · Statistical Methods in Medical Research
  93. Mitigation of SARS-CoV-2 transmission at a large public university
    Diana Rose E. Rañoa, Robin L. Holland, Fadi G. Alnaji, Kelsie J. Green, Leyi Wang, Richard L. Fredrickson, Tong Wang, George N. Wong, Johnny A. Uelmen, Sergei Maslov et al. · 2022 · Nature Communications
  94. Transmission dynamics of the 2009 influenza A (H1N1) pandemic in India: The impact of holiday-related school closure
    Sheikh Taslim Ali, A. S. Kadi, Neil M. Ferguson · 2013 · Epidemics
  95. Reconstruction and prediction of viral disease epidemics
    Moritz U. G. Kraemer, Derek A. T. Cummings, Sebastian Funk, Robert C. Reiner, Nuno Rodrigues Faria, Oliver G. Pybus, Simon Cauchemez · 2018 · Epidemiology and Infection
  96. Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework
    George Nicholson, Brieuc Lehmann, Tullia Padellini, Koen Bernardus Pouwels, Radka Jersakova, James Lomax, Ruairidh King, Ann‐Marie Mallon, Peter John Diggle, Sylvia T. Richardson et al. · 2021 · Nature Microbiology
  97. COVID-19 monitoring with sparse sampling of sewered and non-sewered wastewater in urban and rural communities
    Dhammika Leshan Wannigama, Mohan Amarasiri, Parichart Hongsing, Cameron Paul Hurst, Charin Modchang, Sudarat Chadsuthi, Suparinthon Anupong, Phatthranit Phattharapornjaroen, Ali Hosseini Rad S.M., Stefan Fernandez et al. · 2023 · iScience
  98. Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction
    Mohamed Abbas, Tomás Robalo Nunes, Anne Cori, Samuel Cordey, Florian Laubscher, Stéphanie Baggio, Thibaut Jombart, Anne Iten, Laure Vieux, D. Teixeira et al. · 2021 · Journal of Hospital Infection
  99. EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number
    Oswaldo Gressani, Jacco Wallinga, Christian Lorenz Althaus, Niel Hens, Christel Faes · 2022 · PLoS Computational Biology
  100. Unreported cases in the 2014-2016 Ebola epidemic: Spatiotemporal variation, and implications for estimating transmission
    Benjamin D. Dalziel, Max S. Y. Lau, Amanda Tiffany, Amanda McClelland, Jon Zelner, Jessica Bliss, Bryan Thomas Grenfell · 2018 · PLoS neglected tropical diseases