SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses von Banerjee, Abhik K., Blanco, Mario R., Bruce, Emily A., Honson, Drew D., Chen, Linlin M., Chow, Amy, Bhat, Prashant, Ollikainen, Noah, Quinodoz, Sofia A., Loney, Colin, Thai, Jasmine, Miller, Zachary D., Lin, Aaron E., Schmidt, Madaline M., Stewart, Douglas G., Goldfarb, Daniel, De Lorenzo, Giuditta, Rihn, Suzannah J., Voorhees, Rebecca M., Botten, Jason W., Majumdar, Devdoot, Guttman, Mitchell

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Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics von Kotliar, Dylan, Lin, Aaron E., Logue, James, Hughes, Travis K., Khoury, Nadine M., Raju, Siddharth S., Wadsworth, Marc H., Chen, Han, Kurtz, Jonathan R., Dighero-Kemp, Bonnie, Bjornson, Zach B., Mukherjee, Nilanjan, Sellers, Brian A., Tran, Nancy, Bauer, Matthew R., Adams, Gordon C., Adams, Ricky, Rinn, John L., Melé, Marta, Schaffner, Stephen F., Nolan, Garry P., Barnes, Kayla G., Hensley, Lisa E., McIlwain, David R., Shalek, Alex K., Sabeti, Pardis C., Bennett, Richard S.

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Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques von Santus, Luisa, Sopena-Rios, Maria, García-Pérez, Raquel, Lin, Aaron E., Adams, Gordon C., Barnes, Kayla G., Siddle, Katherine J., Wohl, Shirlee, Reverter, Ferran, Rinn, John L., Bennett, Richard S., Hensley, Lisa E., Sabeti, Pardis C., Melé, Marta

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A Proteomic Perspective of Inbuilt Viral Protein Regulation: pUL46 Tegument Protein is Targeted for Degradation by ICP0 during Herpes Simplex Virus Type 1 Infection von Lin, Aaron E., Greco, Todd M., Döhner, Katinka, Sodeik, Beate, Cristea, Ileana M.

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Evaluation of the potential impact of Ebola virus genomic drift on the efficacy of sequence-based candidate therapeutics von Kugelman, Jeffrey R, Sanchez-Lockhart, Mariano, Andersen, Kristian G, Gire, Stephen, Park, Daniel J, Sealfon, Rachel, Lin, Aaron E, Wohl, Shirlee, Sabeti, Pardis C, Kuhn, Jens H, Palacios, Gustavo F

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Programmable Inhibition and Detection of RNA Viruses Using Cas13 von Freije, Catherine A., Myhrvold, Cameron, Boehm, Chloe K., Lin, Aaron E., Welch, Nicole L., Carter, Amber, Metsky, Hayden C., Luo, Cynthia Y., Abudayyeh, Omar O., Gootenberg, Jonathan S., Yozwiak, Nathan L., Zhang, Feng, Sabeti, Pardis C.

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Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111 von Lin, Aaron E, Diehl, William E, Cai, Yingyun, Finch, Courtney L, Akusobi, Chidiebere, Kirchdoerfer, Robert N, Bollinger, Laura, Schaffner, Stephen F, Brown, Elizabeth A, Saphire, Erica Ollmann, Andersen, Kristian G, Kuhn, Jens H, Luban, Jeremy, Sabeti, Pardis C

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Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events von Lemieux, Jacob E, Siddle, Katherine J, Shaw, Bennett M, Loreth, Christine, Schaffner, Stephen F, Gladden-Young, Adrianne, Adams, Gordon, Fink, Timelia, Tomkins-Tinch, Christopher H, Krasilnikova, Lydia A, DeRuff, Katherine C, Rudy, Melissa, Bauer, Matthew R, Lagerborg, Kim A, Normandin, Erica, Chapman, Sinéad B, Reilly, Steven K, Anahtar, Melis N, Lin, Aaron E, Carter, Amber, Myhrvold, Cameron, Kemball, Molly E, Chaluvadi, Sushma, Cusick, Caroline, Flowers, Katelyn, Neumann, Anna, Cerrato, Felecia, Farhat, Maha, Slater, Damien, Harris, Jason B, Branda, John A, Hooper, David, Gaeta, Jessie M, Baggett, Travis P, O'Connell, James, Gnirke, Andreas, Lieberman, Tami D, Philippakis, Anthony, Burns, Meagan, Brown, Catherine M, Luban, Jeremy, Ryan, Edward T, Turbett, Sarah E, LaRocque, Regina C, Hanage, William P, Gallagher, Glen R, Madoff, Lawrence C, Smole, Sandra, Pierce, Virginia M, Rosenberg, Eric, Sabeti, Pardis C, Park, Daniel J, MacInnis, Bronwyn L

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Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013–2016 Epidemic von Diehl, William E., Lin, Aaron E., Grubaugh, Nathan D., Carvalho, Luiz Max, Kim, Kyusik, Kyawe, Pyae Phyo, McCauley, Sean M., Donnard, Elisa, Kucukural, Alper, McDonel, Patrick, Schaffner, Stephen F., Garber, Manuel, Rambaut, Andrew, Andersen, Kristian G., Sabeti, Pardis C., Luban, Jeremy

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Zika virus evolution and spread in the Americas von Metsky, Hayden C., Matranga, Christian B., Wohl, Shirlee, Schaffner, Stephen F., Freije, Catherine A., Winnicki, Sarah M., West, Kendra, Qu, James, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Tomkins-Tinch, Christopher H., Ye, Simon H., Park, Daniel J., Luo, Cynthia Y., Barnes, Kayla G., Shah, Rickey R., Chak, Bridget, Barbosa-Lima, Giselle, Delatorre, Edson, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Barcellona, Carolyn M., Porcelli, Mario C., Vasquez, Chalmers, Cannons, Andrew C., Cone, Marshall R., Hogan, Kelly N., Kopp, Edgar W., Anzinger, Joshua J., Garcia, Kimberly F., Parham, Leda A., Ramírez, Rosa M. Gélvez, Montoya, Maria C. Miranda, Rojas, Diana P., Brown, Catherine M., Hennigan, Scott, Sabina, Brandon, Scotland, Sarah, Gangavarapu, Karthik, Grubaugh, Nathan D., Oliveira, Glenn, Robles-Sikisaka, Refugio, Rambaut, Andrew, Gehrke, Lee, Smole, Sandra, Halloran, M. Elizabeth, Villar, Luis, Mattar, Salim, Lorenzana, Ivette, Cerbino-Neto, Jose, Valim, Clarissa, Degrave, Wim, Bozza, Patricia T., Gnirke, Andreas, Andersen, Kristian G., Isern, Sharon, Michael, Scott F., Bozza, Fernando A., Souza, Thiago M. L., Bosch, Irene, Yozwiak, Nathan L., MacInnis, Bronwyn L., Sabeti, Pardis C.

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Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time von Barnes, Kayla G., Lachenauer, Anna E., Nitido, Adam, Siddiqui, Sameed, Gross, Robin, Beitzel, Brett, Siddle, Katherine J., Freije, Catherine A., Dighero-Kemp, Bonnie, Mehta, Samar B., Carter, Amber, Uwanibe, Jessica, Ajogbasile, Fehintola, Olumade, Testimony, Odia, Ikponmwosa, Sandi, John Demby, Momoh, Mambu, Metsky, Hayden C., Boehm, Chloe K., Lin, Aaron E., Kemball, Molly, Park, Daniel J., Branco, Luis, Boisen, Matt, Sullivan, Brian, Amare, Mihret F., Tiamiyu, Abdulwasiu B., Parker, Zahra F., Iroezindu, Michael, Grant, Donald S., Modjarrad, Kayvon, Myhrvold, Cameron, Garry, Robert F., Palacios, Gustavo, Hensley, Lisa E., Schaffner, Stephen F., Happi, Christian T., Colubri, Andres, Sabeti, Pardis C.

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Capturing sequence diversity in metagenomes with comprehensive and scalable probe design von Metsky, Hayden C., Siddle, Katherine J., Gladden-Young, Adrianne, Qu, James, Yang, David K., Brehio, Patrick, Goldfarb, Andrew, Piantadosi, Anne, Wohl, Shirlee, Carter, Amber, Lin, Aaron E., Barnes, Kayla G., Tully, Damien C., Corleis, Bjӧrn, Hennigan, Scott, Barbosa-Lima, Giselle, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Garcia, Kimberly F., Parham, Leda A., Odia, Ikponmwosa, Eromon, Philomena, Folarin, Onikepe A., Goba, Augustine, Simon-Lorière, Etienne, Hensley, Lisa, Balmaseda, Angel, Harris, Eva, Kwon, Douglas S., Allen, Todd M., Runstadler, Jonathan A., Smole, Sandra, Bozza, Fernando A., Souza, Thiago M. L., Isern, Sharon, Michael, Scott F., Lorenzana, Ivette, Gehrke, Lee, Bosch, Irene, Ebel, Gregory, Grant, Donald S., Happi, Christian T., Park, Daniel J., Gnirke, Andreas, Sabeti, Pardis C., Matranga, Christian B.

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Membrane-proximal motifs encode differences in signaling strength between type I and III interferon receptors von Mesev, Emily V, Lin, Aaron E, Guare, Emma G, Heller, Brigitte L, Douam, Florian, Adamson, Britt, Toettcher, Jared E, Ploss, Alexander

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In vivo Ebola virus infection leads to a strong innate response in circulating immune cells von Caballero, Ignacio S, Honko, Anna N, Gire, Stephen K, Winnicki, Sarah M, Melé, Marta, Gerhardinger, Chiara, Lin, Aaron E, Rinn, John L, Sabeti, Pardis C, Hensley, Lisa E, Connor, John H

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Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection von Wang, Bruce, Lin, Aaron E., Yuan, Jiayi, Novak, Katherine E., Koch, Matthias D., Wingreen, Ned S., Adamson, Britt, Gitai, Zemer

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Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery von Barnes, Kayla G., Kindrachuk, Jason, Lin, Aaron E., Wohl, Shirlee, Qu, James, Tostenson, Samantha D., Dorman, William R., Busby, Michele, Siddle, Katherine J., Luo, Cynthia Y., Matranga, Christian B., Davey, Richard T., Sabeti, Pardis C., Chertow, Daniel S.

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DNA methyltransferase DNMT3A associates with viral proteins and impacts HSV-1 infection von Rowles, Daniell L., Tsai, Yuan-Chin, Greco, Todd M., Lin, Aaron E., Li, Minghao, Yeh, Justin, Cristea, Ileana M.

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Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus von Andersen, Kristian G., Shapiro, B. Jesse, Matranga, Christian B., Sealfon, Rachel, Lin, Aaron E., Moses, Lina M., Folarin, Onikepe A., Goba, Augustine, Odia, Ikponmwonsa, Ehiane, Philomena E., Momoh, Mambu, England, Eleina M., Winnicki, Sarah, Branco, Luis M., Gire, Stephen K., Phelan, Eric, Tariyal, Ridhi, Tewhey, Ryan, Omoniwa, Omowunmi, Fullah, Mohammed, Fonnie, Richard, Fonnie, Mbalu, Kanneh, Lansana, Jalloh, Simbirie, Gbakie, Michael, Saffa, Sidiki, Karbo, Kandeh, Gladden, Adrianne D., Qu, James, Stremlau, Matthew, Nekoui, Mahan, Finucane, Hilary K., Tabrizi, Shervin, Vitti, Joseph J., Birren, Bruce, Fitzgerald, Michael, McCowan, Caryn, Ireland, Andrea, Berlin, Aaron M., Bochicchio, James, Tazon-Vega, Barbara, Lennon, Niall J., Ryan, Elizabeth M., Bjornson, Zach, Milner, Danny A., Lukens, Amanda K., Broodie, Nisha, Rowland, Megan, Heinrich, Megan, Akdag, Marjan, Schieffelin, John S., Levy, Danielle, Akpan, Henry, Bausch, Daniel G., Rubins, Kathleen, McCormick, Joseph B., Lander, Eric S., Günther, Stephan, Hensley, Lisa, Okogbenin, Sylvanus, Schaffner, Stephen F., Okokhere, Peter O., Khan, S. Humarr, Grant, Donald S., Akpede, George O., Asogun, Danny A., Gnirke, Andreas, Levin, Joshua Z., Happi, Christian T., Garry, Robert F., Sabeti, Pardis C.

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Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k) von Newell, Evan W, Ely, Lauren K, Kruse, Andrew C, Reay, Philip A, Rodriguez, Stephanie N, Lin, Aaron E, Kuhns, Michael S, Garcia, K Christopher, Davis, Mark M

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Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses von Normandin, Erica, Triana, Sergio, Raju, Siddharth S., Lan, Tammy C.T., Lagerborg, Kim, Rudy, Melissa, Adams, Gordon C., DeRuff, Katherine C., Logue, James, Liu, David, Strebinger, Daniel, Rao, Arya, Messer, Katelyn S., Sacks, Molly, Adams, Ricky D., Janosko, Krisztina, Kotliar, Dylan, Shah, Rickey, Crozier, Ian, Rinn, John L., Melé, Marta, Honko, Anna N., Zhang, Feng, Babadi, Mehrtash, Luban, Jeremy, Bennett, Richard S., Shalek, Alex K., Barkas, Nikolaos, Lin, Aaron E., Hensley, Lisa E., Sabeti, Pardis C., Siddle, Katherine J.

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