Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data. by Finlay Campbell, Anne Cori, Neil Ferguson, Thibaut Jombart

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When are pathogen genome sequences informative of transmission events? by Finlay Campbell, Camilla Strang, Neil Ferguson, Anne Cori, Thibaut Jombart

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outbreaker2: a modular platform for outbreak reconstruction by Finlay Campbell, Xavier Didelot, Rich Fitzjohn, Neil Ferguson, Anne Cori, Thibaut Jombart

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epicontacts: Handling, visualisation and analysis of epidemiological contacts [version 2; peer review: 2 approved, 1 approved with reservations] by VP Nagraj, Nistara Randhawa, Finlay Campbell, Thomas Crellen, Bertrand Sudre, Thibaut Jombart

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Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves by Benjamin B. Lindsey, Ch. Julián Villabona-Arenas, Finlay Campbell, Alexander J. Keeley, Matthew D. 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, Sheffield COVID-19 Genomics Group, The COVID-19 Genomics UK (COG-UK) consortium, CMMID COVID-19 working group, Cariad M. Evans, David G. Partridge, Katherine E. Atkins, Stéphane Hué, Thushan I. de Silva

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WHO Global Situational Alert System: a mixed methods multistage approach to identify country-level COVID-19 alerts by Richard Pebody, Maria D Van Kerkhove, Mahmoud Hassan, Thierno Balde, Olivier Le Polain de Waroux, Sandra Adele, Kazuki Shimizu, Charlotte Christiane Hammer, Lisa Owen, Villyen Motaze, Michael Höhle, Piers Mook, Masaya Kato, Kathleen Ryan, Tanja Schmidt, Marjam Esmail, Jessica Lee Abbate, Opeayo Ogundiran, Sophie Maes, Victoria D Bélorgeot, Ana Riviere-Cinnamond, Martina McMenamin, Jessica Kolmer, Irena Djordjevic, Finlay Campbell, Henry Laurenson-Schafer, Basma Mostafa Abdelgawad, Amarnath Babu, Neale Batra, Hannah Brindle, Tshewang Dorji, Ingrid Hammermeister Nezu, Lucía Hernández-García, Friday Idoko, Sarah Karmin, Zyleen A Kassamali, Tamano Matsui, Mengjuan Duan, Boris I Pavlin, Tika Sedai, Teresa Zakaria, Abdi R Mahamud, Dominic Cocciolone, Christian Gapp, Kayla King, Aimee Latta, Sandra Lindmark, Ihor Perehinets, Amy Gimma, Jason McKnight, Margaux Mesle, Maarten Van Haverbeke, Tamar Amar, Ka Yeung Cheng, Silviu Ciobanu, Lauren E MacDonald, Jeff Pires, Jukka Pukkila, Celine Roman, Laila Skrowny, Ara Tadevosyan, Catherine Smallwood, Juniorcaius Ikejezie, Blanche Johanna Greene-Cramer, Adedoyin Abiola Awofisayo-Okuyelu, Bernadette Mirembe, Tondri Noe Guinko, Homa Attar-Cohen, Stephen Leshan Koyie, Samuel Mesfin, Veronica Cristea, Nikola Sklenovska, Mostafa Mahran, Emily Meyer, Grace Brough, Harsh Lata, Alessandro Miglietta, Sydel Parikh, Eri Togami, Yurie Izawa, Aura Rocio Escobar Corado Waeber, Anahi Rico Chinchilla, Yeo Won Jin, Raquel Medialdea Carrera, Amaia Artazcoz Glaria, Hyo Jeong Kim, Muhammed Tayyab

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