Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges. by Rebecca K Nash, Pierre Nouvellet, Anne Cori

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Sorting out assortativity: When can we assess the contributions of different population groups to epidemic transmission? by Cyril Geismar, Peter J White, Anne Cori, Thibaut Jombart

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Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool. by Rebecca K Nash, Samir Bhatt, Anne Cori, Pierre Nouvellet

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Sorting out assortativity: When can we assess the contributions of different population groups to epidemic transmission? by Cyril Geismar, Peter J. White, Anne Cori, Thibaut Jombart

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Advanced Analytics to Inform Policy Decision-Making in Public Health Emergencies: A Case Study of COVID-19 in Europe by Dr Paula Christen, Dr Anne Cori, Dr Sabine van Elsland

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Impact and Cost-Effectiveness of Point-Of-Care CD4 Testing on the HIV Epidemic in South Africa. by Alastair Heffernan, Ella Barber, Ranjeeta Thomas, Christophe Fraser, Michael Pickles, Anne Cori

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Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. by Thibaut Jombart, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser, Neil Ferguson

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Scoring epidemiological forecasts on transformed scales. by Nikos I Bosse, Sam Abbott, Anne Cori, Edwin van Leeuwen, Johannes Bracher, Sebastian Funk

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HIV treatment-as-prevention research: taking the right road at the crossroads. by Richard Hayes, Sarah Fidler, Anne Cori, Christophe Fraser, Sian Floyd, Helen Ayles, Nulda Beyers, Wafaa El-Sadr, HPTN 071 (PopART) Study Team

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Aetiology of vaginal discharge, urethral discharge, and genital ulcer in sub-Saharan Africa: A systematic review and meta-regression. by Julia Michalow, Magdalene K Walters, Olanrewaju Edun, Max Wybrant, Bethan Davies, Tendesayi Kufa, Thabitha Mathega, Sungai T Chabata, Frances M Cowan, Anne Cori, Marie-Claude Boily, Jeffrey W Imai-Eaton

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Comparing human and model-based forecasts of COVID-19 in Germany and Poland. by Nikos I Bosse, Sam Abbott, Johannes Bracher, Habakuk Hain, Billy J Quilty, Mark Jit, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Edwin van Leeuwen, Anne Cori, Sebastian Funk

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The Incidence Patterns Model to Estimate the Distribution of New HIV Infections in Sub-Saharan Africa: Development and Validation of a Mathematical Model. by Annick Bórquez, Anne Cori, Erica L Pufall, Jingo Kasule, Emma Slaymaker, Alison Price, Jocelyn Elmes, Basia Zaba, Amelia C Crampin, Joseph Kagaayi, Tom Lutalo, Mark Urassa, Simon Gregson, Timothy B Hallett

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Potential Biases in Estimating Absolute and Relative Case-Fatality Risks during Outbreaks. by Marc Lipsitch, Christl A Donnelly, Christophe Fraser, Isobel M Blake, Anne Cori, Ilaria Dorigatti, Neil M Ferguson, Tini Garske, Harriet L Mills, Steven Riley, Maria D Van Kerkhove, Miguel A Hernán

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Contrasting the impact and cost-effectiveness of successive intervention strategies in response to Ebola in the Democratic Republic of the Congo, 2018–2020 by Wu Zeng, Thomas Wilkinson, Mathias Mossoko, Michel Yao, Steve Ahuka-Mundeke, Thibaut Jombart, Hadia Samaha, Dominique Baabo, Jean-Pierre Lokonga, Sylvain Yuma, Anne Cori, Fatima El Kadiri El Yamini, Patrick Hoang-Vu Eozenou, Linda Mobula

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Best practices for estimating and reporting epidemiological delay distributions of infectious diseases. by Kelly Charniga, Sang Woo Park, Andrei R Akhmetzhanov, Anne Cori, Jonathan Dushoff, Sebastian Funk, Katelyn M Gostic, Natalie M Linton, Adrian Lison, Christopher E Overton, Juliet R C Pulliam, Thomas Ward, Simon Cauchemez, Sam Abbott

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Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis. by Daniela Bezemer, Anne Cori, Oliver Ratmann, Ard van Sighem, Hillegonda S Hermanides, Bas E Dutilh, Luuk Gras, Nuno Rodrigues Faria, Rob van den Hengel, Ashley J Duits, Peter Reiss, Frank de Wolf, Christophe Fraser, ATHENA observational cohort

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PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial. by Michael Pickles, Anne Cori, William J M Probert, Rafael Sauter, Robert Hinch, Sarah Fidler, Helen Ayles, Peter Bock, Deborah Donnell, Ethan Wilson, Estelle Piwowar-Manning, Sian Floyd, Richard J Hayes, Christophe Fraser, HPTN 071 (PopART) Study Team

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HPTN 071 (PopART): a cluster-randomized trial of the population impact of an HIV combination prevention intervention including universal testing and treatment: mathematical model. by Anne Cori, Helen Ayles, Nulda Beyers, Ab Schaap, Sian Floyd, Kalpana Sabapathy, Jeffrey W Eaton, Katharina Hauck, Peter Smith, Sam Griffith, Ayana Moore, Deborah Donnell, Sten H Vermund, Sarah Fidler, Richard Hayes, Christophe Fraser, HPTN 071 PopART Study Team

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Retrospective evaluation of real-time estimates of global COVID-19 transmission trends and mortality forecasts. by Sangeeta Bhatia, Kris V Parag, Jack Wardle, Rebecca K Nash, Natsuko Imai, Sabine L Van Elsland, Britta Lassmann, John S Brownstein, Angel Desai, Mark Herringer, Kara Sewalk, Sarah Claire Loeb, John Ramatowski, Gina Cuomo-Dannenburg, Elita Jauneikaite, H Juliette T Unwin, Steven Riley, Neil Ferguson, Christl A Donnelly, Anne Cori, Pierre Nouvellet

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Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study. by International Ebola Response Team, Junerlyn Agua-Agum, Archchun Ariyarajah, Bruce Aylward, Luke Bawo, Pepe Bilivogui, Isobel M Blake, Richard J Brennan, Amy Cawthorne, Eilish Cleary, Peter Clement, Roland Conteh, Anne Cori, Foday Dafae, Benjamin Dahl, Jean-Marie Dangou, Boubacar Diallo, Christl A Donnelly, Ilaria Dorigatti, Christopher Dye, Tim Eckmanns, Mosoka Fallah, Neil M Ferguson, Lena Fiebig, Christophe Fraser, Tini Garske, Lice Gonzalez, Esther Hamblion, Nuha Hamid, Sara Hersey, Wes Hinsley, Amara Jambei, Thibaut Jombart, David Kargbo, Sakoba Keita, Michael Kinzer, Fred Kuti George, Beatrice Godefroy, Giovanna Gutierrez, Niluka Kannangarage, Harriet L Mills, Thomas Moller, Sascha Meijers, Yasmine Mohamed, Oliver Morgan, Gemma Nedjati-Gilani, Emily Newton, Pierre Nouvellet, Tolbert Nyenswah, William Perea, Devin Perkins, Steven Riley, Guenael Rodier, Marc Rondy, Maria Sagrado, Camelia Savulescu, Ilana J Schafer, Dirk Schumacher, Thomas Seyler, Anita Shah, Maria D Van Kerkhove, C Samford Wesseh, Zabulon Yoti

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