An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar by Grubaugh, Nathan D, Gangavarapu, Karthik, Quick, Joshua, Matteson, Nathaniel L, De Jesus, Jaqueline Goes, Main, Bradley J, Tan, Amanda L, Paul, Lauren M, Brackney, Doug E, Grewal, Saran, Gurfield, Nikos, Van Rompay, Koen K A, Isern, Sharon, Michael, Scott F, Coffey, Lark L, Loman, Nicholas J, Andersen, Kristian G

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Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework by Dellicour, Simon, Lequime, Sebastian, Vrancken, Bram, Gill, Mandev S., Bastide, Paul, Gangavarapu, Karthik, Matteson, Nathaniel L., Tan, Yi, du Plessis, Louis, Fisher, Alexander A., Nelson, Martha I., Gilbert, Marius, Suchard, Marc A., Andersen, Kristian G., Grubaugh, Nathan D., Pybus, Oliver G., Lemey, Philippe

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The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2 by Pekar, Jonathan E, Magee, Andrew, Parker, Edyth, Moshiri, Niema, Izhikevich, Katherine, Havens, Jennifer L, Gangavarapu, Karthik, Malpica Serrano, Lorena Mariana, Crits-Christoph, Alexander, Matteson, Nathaniel L, Zeller, Mark, Levy, Joshua I, Wang, Jade C, Hughes, Scott, Lee, Jungmin, Park, Heedo, Park, Man-Seong, Ching Zi Yan, Katherine, Lin, Raymond Tzer Pin, Mat Isa, Mohd Noor, Noor, Yusuf Muhammad, Vasylyeva, Tetyana I, Garry, Robert F, Holmes, Edward C, Rambaut, Andrew, Suchard, Marc A, Andersen, Kristian G, Worobey, Michael, Wertheim, Joel O

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Structure-based assessment of protein-protein interactions and accessibility of protein IX in adenoviruses with implications for antigen display by Matteson, Nathaniel L., Barry, Michael A., Reddy, Vijay S.

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Emergence of an early SARS-CoV-2 epidemic in the United States by Zeller, Mark, Gangavarapu, Karthik, Anderson, Catelyn, Smither, Allison R., Vanchiere, John A., Rose, Rebecca, Snyder, Daniel J., Dudas, Gytis, Watts, Alexander, Matteson, Nathaniel L., Robles-Sikisaka, Refugio, Marshall, Maximilian, Feehan, Amy K., Sabino-Santos, Gilberto, Bell-Kareem, Antoinette R., Hughes, Laura D., Alkuzweny, Manar, Snarski, Patricia, Garcia-Diaz, Julia, Scott, Rona S., Melnik, Lilia I., Klitting, Raphaëlle, McGraw, Michelle, Belda-Ferre, Pedro, DeHoff, Peter, Sathe, Shashank, Marotz, Clarisse, Grubaugh, Nathan D., Nolan, David J., Drouin, Arnaud C., Genemaras, Kaylynn J., Chao, Karissa, Topol, Sarah, Spencer, Emily, Nicholson, Laura, Aigner, Stefan, Yeo, Gene W., Farnaes, Lauge, Hobbs, Charlotte A., Laurent, Louise C., Knight, Rob, Hodcroft, Emma B., Khan, Kamran, Fusco, Dahlene N., Cooper, Vaughn S., Lemey, Phillipe, Gardner, Lauren, Lamers, Susanna L., Kamil, Jeremy P., Garry, Robert F., Suchard, Marc A., Andersen, Kristian G.

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Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions by Parker, Edyth, Anderson, Catelyn, Zeller, Mark, Tibi, Ahmad, Havens, Jennifer L., Laroche, Geneviève, Benlarbi, Mehdi, Ariana, Ardeshir, Robles-Sikisaka, Refugio, Latif, Alaa Abdel, Watts, Alexander, Awidi, Abdalla, Jaradat, Saied A., Gangavarapu, Karthik, Ramesh, Karthik, Kurzban, Ezra, Matteson, Nathaniel L., Han, Alvin X., Hughes, Laura D., McGraw, Michelle, Spencer, Emily, Nicholson, Laura, Khan, Kamran, Suchard, Marc A., Wertheim, Joel O., Wohl, Shirlee, Côté, Marceline, Abdelnour, Amid, Andersen, Kristian G., Abu-Dayyeh, Issa

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets by Cantrell, Kalen, Fedarko, Marcus W, Rahman, Gibraan, McDonald, Daniel, Yang, Yimeng, Zaw, Thant, Gonzalez, Antonio, Janssen, Stefan, Estaki, Mehrbod, Haiminen, Niina, Beck, Kristen L, Zhu, Qiyun, Sayyari, Erfan, Morton, James T, Armstrong, George, Tripathi, Anupriya, Gauglitz, Julia M, Marotz, Clarisse, Matteson, Nathaniel L, Martino, Cameron, Sanders, Jon G, Carrieri, Anna Paola, Song, Se Jin, Swafford, Austin D, Dorrestein, Pieter C, Andersen, Kristian G, Parida, Laxmi, Kim, Ho-Cheol, Vázquez-Baeza, Yoshiki, Knight, Rob

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets by Cantrell, Kalen, Fedarko, Marcus W., Rahman, Gibraan, McDonald, Daniel, Yang, Yimeng, Zaw, Thant, Gonzalez, Antonio, Janssen, Stefan, Estaki, Mehrbod, Haiminen, Niina, Beck, Kristen L., Zhu, Qiyun, Sayyari, Erfan, Morton, James T., Armstrong, George, Tripathi, Anupriya, Gauglitz, Julia M., Marotz, Clarisse, Matteson, Nathaniel L., Martino, Cameron, Sanders, Jon G., Carrieri, Anna Paola, Song, Se Jin, Swafford, Austin D., Dorrestein, Pieter C., Andersen, Kristian G., Parida, Laxmi, Kim, Ho-Cheol, Vázquez-Baeza, Yoshiki, Knight, Rob

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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission by Karthikeyan, Smruthi, Levy, Joshua I., De Hoff, Peter, Humphrey, Greg, Birmingham, Amanda, Jepsen, Kristen, Farmer, Sawyer, Tubb, Helena M., Valles, Tommy, Tribelhorn, Caitlin E., Tsai, Rebecca, Aigner, Stefan, Moshiri, Niema, Henson, Benjamin, Mark, Adam M., Hakim, Abbas, Baer, Nathan A., Barber, Tom, Belda-Ferre, Pedro, Chacón, Marisol, Cresini, Evelyn S., Eisner, Emily R., Lastrella, Alma L., Lawrence, Elijah S., Marotz, Clarisse A., Ngo, Toan T., Ostrander, Tyler, Plascencia, Ashley, Salido, Rodolfo A., Seaver, Phoebe, Smoot, Elizabeth W., McDonald, Daniel, Neuhard, Robert M., Scioscia, Angela L., Satterlund, Alysson M., Simmons, Elizabeth H., Abelman, Dismas B., Brenner, David, Buckley, Anne, Gattas, Jeffrey, Gonias, Steven L., Hale, Matt, Ikeda, Lydia, Jhaveri, Hemlata, Kremer, Brendan, McLawhon, Ronald W., Ouillet, Pierre, Park, Daniel, Pradenas, Allorah, Riggs, Lindsay, Sanders, Alison, Sollenberger, Bradley, White, Benjamin, Winbush, Terri, Aceves, Christine M., Anderson, Catelyn, Gangavarapu, Karthik, Hufbauer, Emory, Kurzban, Ezra, Lee, Justin, Matteson, Nathaniel L., Parker, Edyth, Perkins, Sarah A., Ramesh, Karthik S., Schwab, Madison A., Wohl, Shirlee, Nicholson, Laura, McHardy, Ian H., Hobbs, Charlotte A., Bakhtar, Omid, Mendoza, Art, Becker, David, Cirulli, Elizabeth T., Isaksson, Magnus, Schiabor Barrett, Kelly M., Washington, Nicole L., Malone, John D., Schafer, Ashleigh Murphy, Fielding-Miller, Rebecca, Garfein, Richard S., Gaines, Tommi, Anderson, Cheryl, Martin, Natasha K., Schooley, Robert, Austin, Brett, Kingsmore, Stephen F., Lee, William, Shah, Seema, McDonald, Eric, Yu, Alexander T., Zeller, Mark, Fisch, Kathleen M., Longhurst, Christopher, Maysent, Patty, Pride, David, Khosla, Pradeep K., Laurent, Louise C., Yeo, Gene W., Andersen, Kristian G., Knight, Rob

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Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce by Keehner, Jocelyn, Horton, Lucy E, Binkin, Nancy J, Laurent, Louise C, Pride, David, Longhurst, Christopher A, Abeles, Shira R, Torriani, Francesca J

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Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic by Grubaugh, Nathan D., Saraf, Sharada, Gangavarapu, Karthik, Watts, Alexander, Tan, Amanda L., Oidtman, Rachel J., Ladner, Jason T., Oliveira, Glenn, Matteson, Nathaniel L., Kraemer, Moritz U.G., Vogels, Chantal B.F., Hentoff, Aaron, Bhatia, Deepit, Stanek, Danielle, Scott, Blake, Landis, Vanessa, Stryker, Ian, Cone, Marshall R., Kopp, Edgar W., Cannons, Andrew C., Heberlein-Larson, Lea, White, Stephen, Gillis, Leah D., Ricciardi, Michael J., Kwal, Jaclyn, Lichtenberger, Paola K., Magnani, Diogo M., Watkins, David I., Palacios, Gustavo, Hamer, Davidson H., Gardner, Lauren M., Perkins, T. Alex, Baele, Guy, Khan, Kamran, Morrison, Andrea, Isern, Sharon, Michael, Scott F., Andersen, Kristian G.

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Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting by Keehner, Jocelyn, Abeles, Shira R, Longhurst, Christopher A, Horton, Lucy E, Myers, Frank E, Riggs-Rodriguez, Lindsay, Ahmad, Mohammed, Baxter, Sally, Boussina, Aaron, Cantrell, Kalen, Cardenas, Priscilla, De Hoff, Peter, El-Kareh, Robert, Holland, Jennifer, Ikeda, Daryn, Kurashige, Kirk, Laurent, Louise C, Lucas, Andrew, Pride, David, Sathe, Shashank, Tran, Allen R, Vasylyeva, Tetyana I, Yeo, Gene, Knight, Rob, Wertheim, Joel O, Torriani, Francesca J

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Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools by Fielding-Miller, Rebecca, Karthikeyan, Smruthi, Gaines, Tommi, Garfein, Richard S., Salido, Rodolfo A., Cantu, Victor J., Kohn, Laura, Martin, Natasha K., Wynn, Adriane, Wijaya, Carrissa, Flores, Marlene, Omaleki, Vinton, Majnoonian, Araz, Gonzalez-Zuniga, Patricia, Nguyen, Megan, Vo, Anh V., Le, Tina, Duong, Dawn, Hassani, Ashkan, Tweeten, Samantha, Jepsen, Kristen, Henson, Benjamin, Hakim, Abbas, Birmingham, Amanda, De Hoff, Peter, Mark, Adam M., Nasamran, Chanond A., Rosenthal, Sara Brin, Moshiri, Niema, Fisch, Kathleen M., Humphrey, Greg, Farmer, Sawyer, Tubb, Helena M., Valles, Tommy, Morris, Justin, Kang, Jaeyoung, Khaleghi, Behnam, Young, Colin, Akel, Ameen D., Eilert, Sean, Eno, Justin, Curewitz, Ken, Laurent, Louise C., Rosing, Tajana, Knight, Rob, Baer, Nathan A., Barber, Tom, Castro-Martinez, Anelizze, Chacón, Marisol, Cheung, Willi, Crescini, Evelyn S., Eisner, Emily R., Franco Vargas, Lizbeth, Hakim, Abbas, Hobbs, Charlotte, Lastrella, Alma L., Lawrence, Elijah S., Matteson, Nathaniel L., Gangavarapu, Karthik, Ngo, Toan T., Seaver, Phoebe, Smoot, Elizabeth W., Tsai, Rebecca, Xia, Bing, Aigner, Stefan, Anderson, Catelyn, Belda-Ferre, Pedro, Sathe, Shashank, Zeller, Mark, Andersen, Kristian G., Yeo, Gene W., Kurzban, Ezra

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Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schoolsResearch in context by Rebecca Fielding-Miller, Smruthi Karthikeyan, Tommi Gaines, Richard S. Garfein, Rodolfo A. Salido, Victor J. Cantu, Laura Kohn, Natasha K. Martin, Adriane Wynn, Carrissa Wijaya, Marlene Flores, Vinton Omaleki, Araz Majnoonian, Patricia Gonzalez-Zuniga, Megan Nguyen, Anh V. Vo, Tina Le, Dawn Duong, Ashkan Hassani, Samantha Tweeten, Kristen Jepsen, Benjamin Henson, Abbas Hakim, Amanda Birmingham, Peter De Hoff, Adam M. Mark, Chanond A. Nasamran, Sara Brin Rosenthal, Niema Moshiri, Kathleen M. Fisch, Greg Humphrey, Sawyer Farmer, Helena M. Tubb, Tommy Valles, Justin Morris, Jaeyoung Kang, Behnam Khaleghi, Colin Young, Ameen D. Akel, Sean Eilert, Justin Eno, Ken Curewitz, Louise C. Laurent, Tajana Rosing, Rob Knight, Nathan A. Baer, Tom Barber, Anelizze Castro-Martinez, Marisol Chacón, Willi Cheung, Evelyn S. Crescini, Emily R. Eisner, Lizbeth Franco Vargas, Abbas Hakim, Charlotte Hobbs, Alma L. Lastrella, Elijah S. Lawrence, Nathaniel L. Matteson, Karthik Gangavarapu, Toan T. Ngo, Phoebe Seaver, Elizabeth W. Smoot, Rebecca Tsai, Bing Xia, Stefan Aigner, Catelyn Anderson, Pedro Belda-Ferre, Shashank Sathe, Mark Zeller, Kristian G. Andersen, Gene W. Yeo, Ezra Kurzban

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