Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approachResearch in context 由 Hongru Du, Ensheng Dong, Hamada S. Badr, Mary E. Petrone, Nathan D. Grubaugh, Lauren M. Gardner

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Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic 由 Mary E. Petrone, Rebecca Earnest, José Lourenço, Moritz U. G. Kraemer, Robert Paulino-Ramirez, Nathan D. Grubaugh, Leandro Tapia

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Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics 由 Orchid M. Allicock, Mary E. Petrone, Devyn Yolda-Carr, Mallery Breban, Hannah Walsh, Anne E. Watkins, Jessica E. Rothman, Shelli F. Farhadian, Nathan D. Grubaugh, Anne L. Wyllie

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Real-time public health communication of local SARS-CoV-2 genomic epidemiology. 由 Chaney C Kalinich, Cole G Jensen, Peter Neugebauer, Mary E Petrone, Mario Peña-Hernández, Isabel M Ott, Anne L Wyllie, Tara Alpert, Chantal B F Vogels, Joseph R Fauver, Nathan D Grubaugh, Anderson F Brito

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Detection of SARS-CoV-2 RNA by multiplex RT-qPCR. 由 Eriko Kudo, Benjamin Israelow, Chantal B F Vogels, Peiwen Lu, Anne L Wyllie, Maria Tokuyama, Arvind Venkataraman, Doug E Brackney, Isabel M Ott, Mary E Petrone, Rebecca Earnest, Sarah Lapidus, M Catherine Muenker, Adam J Moore, Arnau Casanovas-Massana, Yale IMPACT Research Team, Saad B Omer, Charles S Dela Cruz, Shelli F Farhadian, Albert I Ko, Nathan D Grubaugh, Akiko Iwasaki

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DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus 由 Chantal B. F. Vogels, Verity Hill, Mallery I. Breban, Chrispin Chaguza, Lauren M. Paul, Afeez Sodeinde, Emma Taylor-Salmon, Isabel M. Ott, Mary E. Petrone, Dennis Dijk, Marcel Jonges, Matthijs R. A. Welkers, Timothy Locksmith, Yibo Dong, Namratha Tarigopula, Omer Tekin, Sarah Schmedes, Sylvia Bunch, Natalia Cano, Rayah Jaber, Charles Panzera, Ian Stryker, Julieta Vergara, Rebecca Zimler, Edgar Kopp, Lea Heberlein, Kaylee S. Herzog, Joseph R. Fauver, Andrea M. Morrison, Scott F. Michael, Nathan D. Grubaugh

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Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil 由 Anderson Fernandes Brito, Lais Ceschini Machado, Rachel J. Oidtman, Márcio Junio Lima Siconelli, Quan Minh Tran, Joseph R. Fauver, Rodrigo Dias de Oliveira Carvalho, Filipe Zimmer Dezordi, Mylena Ribeiro Pereira, Luiza Antunes de Castro-Jorge, Elaine Cristina Manini Minto, Luzia Márcia Romanholi Passos, Chaney C. Kalinich, Mary E. Petrone, Emma Allen, Guido Camargo España, Angkana T. Huang, Derek A. T. Cummings, Guy Baele, Rafael Freitas Oliveira Franca, Benedito Antônio Lopes da Fonseca, T. Alex Perkins, Gabriel Luz Wallau, Nathan D. Grubaugh

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Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques 由 Jasmijn A. Baaijens, Alessandro Zulli, Isabel M. Ott, Ioanna Nika, Mart J. van der Lugt, Mary E. Petrone, Tara Alpert, Joseph R. Fauver, Chaney C. Kalinich, Chantal B. F. Vogels, Mallery I. Breban, Claire Duvallet, Kyle A. McElroy, Newsha Ghaeli, Maxim Imakaev, Malaika F. Mckenzie-Bennett, Keith Robison, Alex Plocik, Rebecca Schilling, Martha Pierson, Rebecca Littlefield, Michelle L. Spencer, Birgitte B. Simen, Yale SARS-CoV-2 Genomic Surveillance Initiative, William P. Hanage, Nathan D. Grubaugh, Jordan Peccia, Michael Baym

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Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota 由 Mary E. Petrone, Jessica E. Rothman, Mallery I. Breban, Isabel M. Ott, Alexis Russell, Erica Lasek-Nesselquist, Hamada Badr, Kevin Kelly, Greg Omerza, Nicholas Renzette, Anne E. Watkins, Chaney C. Kalinich, Tara Alpert, Anderson F. Brito, Rebecca Earnest, Irina R. Tikhonova, Christopher Castaldi, John P. Kelly, Matthew Shudt, Jonathan Plitnick, Erasmus Schneider, Steven Murphy, Caleb Neal, Eva Laszlo, Ahmad Altajar, Claire Pearson, Anthony Muyombwe, Randy Downing, Jafar Razeq, Linda Niccolai, Madeline S. Wilson, Margaret L. Anderson, Jianhui Wang, Chen Liu, Pei Hui, Shrikant Mane, Bradford P. Taylor, William P. Hanage, Marie L. Landry, David R. Peaper, Kaya Bilguvar, Joseph R. Fauver, Chantal B. F. Vogels, Lauren M. Gardner, Virginia E. Pitzer, Kirsten St. George, Mark D. Adams, Nathan D. Grubaugh

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Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. 由 Chantal B F Vogels, Mallery I Breban, Isabel M Ott, Tara Alpert, Mary E Petrone, Anne E Watkins, Chaney C Kalinich, Rebecca Earnest, Jessica E Rothman, Jaqueline Goes de Jesus, Ingra Morales Claro, Giulia Magalhães Ferreira, Myuki A E Crispim, Brazil-UK CADDE Genomic Network, Lavanya Singh, Houriiyah Tegally, Ugochukwu J Anyaneji, Network for Genomic Surveillance in South Africa, Emma B Hodcroft, Christopher E Mason, Gaurav Khullar, Jessica Metti, Joel T Dudley, Matthew J MacKay, Megan Nash, Jianhui Wang, Chen Liu, Pei Hui, Steven Murphy, Caleb Neal, Eva Laszlo, Marie L Landry, Anthony Muyombwe, Randy Downing, Jafar Razeq, Tulio de Oliveira, Nuno R Faria, Ester C Sabino, Richard A Neher, Joseph R Fauver, Nathan D Grubaugh

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