A Proteomic Perspective of Inbuilt Viral Protein Regulation: pUL46 Tegument Protein is Targeted for Degradation by ICP0 during Herpes Simplex Virus Type 1 Infection

by Lin, Aaron E., Greco, Todd M., Döhner, Katinka, Sodeik, Beate, Cristea, Ileana M.
Published 2013

The DNA methyltransferase DNMT3A associates with viral proteins and impacts HSV-1 infection

by Rowles, Daniell L., Tsai, Yuan-Chin, Greco, Todd M., Lin, Aaron E., Li, Minghao, Yeh, Justin, Cristea, Ileana M.
Published in Proteomics (2015)

Structural Basis of Specificity and Cross-Reactivity in T Cell Receptors Specific for Cytochrome c–I-E(k)

by 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.
Published 2011

Innovative Technologies for Advancement of WHO Risk Group 4 Pathogens Research

by Logue, James, Solomon, Jeffrey, Niemeyer, Brian F., Benam, Kambez H., Lin, Aaron E., Bjornson, Zach, Jiang, Sizun, McIlwain, David R., Nolan, Garry P., Palacios, Gustavo, Kuhn, Jens H.
Published in Global Virology III: Virology in the 21st Century (2019)

Evaluation of the Potential Impact of Ebola Virus Genomic Drift on the Efficacy of Sequence-Based Candidate Therapeutics

by 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.
Published in mBio (2015)

In vivo Ebola virus infection leads to a strong innate response in circulating immune cells

by 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.
Published in BMC Genomics (2016)

Programmable inhibition and detection of RNA viruses using Cas13

by 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.
Published in Mol Cell (2019)

Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery

by 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
Published in Clin Infect Dis (2017)

Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111

by 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.
Published in Viruses (2020)

Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013–2016 Epidemic

by 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
Published in Cell (2016)

SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses

by 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
Published in Cell (2020)

Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

by 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.
Published in Cell (2020)

Field validation of recombinant antigen immunoassays for diagnosis of Lassa fever

by Boisen, Matthew L., Hartnett, Jessica N., Shaffer, Jeffrey G., Goba, Augustine, Momoh, Mambu, Sandi, John Demby, Fullah, Mohamed, Nelson, Diana K. S., Bush, Duane J., Rowland, Megan M., Heinrich, Megan L., Koval, Anatoliy P., Cross, Robert W., Barnes, Kayla G., Lachenauer, Anna E., Lin, Aaron E., Nekoui, Mahan, Kotliar, Dylan, Winnicki, Sarah M., Siddle, Katherine J., Gbakie, Michael, Fonnie, Mbalu, Koroma, Veronica J., Kanneh, Lansana, Kulakosky, Peter C., Hastie, Kathryn M., Wilson, Russell B., Andersen, Kristian G., Folarin, Onikepe O., Happi, Christian T., Sabeti, Pardis C., Geisbert, Thomas W., Saphire, Erica Ollmann, Khan, S. Humarr, Grant, Donald S., Schieffelin, John S., Branco, Luis M., Garry, Robert F.
Published in Sci Rep (2018)

Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time

by 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.
Published in Nat Commun (2020)

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

by 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.
Published in Nat Biotechnol (2019)

Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events.

by 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, Sinead 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, 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., Maclnnis, Bronwyn L.
Published in medRxiv (2020)

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

by 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.
Published in Science (2020)

Clinical sequencing uncovers origins and evolution of Lassa virus

by 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.
Published in Cell (2015)

Zika virus evolution and spread in the Americas

by 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., Gélvez Ramírez, Rosa M., Miranda Montoya, Maria C., 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.
Published in Nature (2017)

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

by Park, Daniel J., Dudas, Gytis, Wohl, Shirlee, Goba, Augustine, Whitmer, Shannon L.M., Andersen, Kristian G., Sealfon, Rachel S., Ladner, Jason T., Kugelman, Jeffrey R., Matranga, Christian B., Winnicki, Sarah M., Qu, James, Gire, Stephen K., Gladden-Young, Adrianne, Jalloh, Simbirie, Nosamiefan, Dolo, Yozwiak, Nathan L., Moses, Lina M., Jiang, Pan-Pan, Lin, Aaron E., Schaffner, Stephen F., Bird, Brian, Towner, Jonathan, Mamoh, Mambu, Gbakie, Michael, Kanneh, Lansana, Kargbo, David, Massally, James L.B., Kamara, Fatima K., Konuwa, Edwin, Sellu, Josephine, Jalloh, Abdul A., Mustapha, Ibrahim, Foday, Momoh, Yillah, Mohamed, Erickson, Bobbie R., Sealy, Tara, Blau, Dianna, Paddock, Christopher, Brault, Aaron, Amman, Brian, Basile, Jane, Bearden, Scott, Belser, Jessica, Bergeron, Eric, Campbell, Shelley, Chakrabarti, Ayan, Dodd, Kimberly, Flint, Mike, Gibbons, Aridth, Goodman, Christin, Klena, John, McMullan, Laura, Morgan, Laura, Russell, Brandy, Salzer, Johanna, Sanchez, Angela, Wang, David, Jungreis, Irwin, Tomkins-Tinch, Christopher, Kislyuk, Andrey, Lin, Michael F., Chapman, Sinead, MacInnis, Bronwyn, Matthews, Ashley, Bochicchio, James, Hensley, Lisa E., Kuhn, Jens H., Nusbaum, Chad, Schieffelin, John S., Birren, Bruce W., Forget, Marc, Nichol, Stuart T., Palacios, Gustavo F., Ndiaye, Daouda, Happi, Christian, Gevao, Sahr M., Vandi, Mohamed A., Kargbo, Brima, Holmes, Edward C., Bedford, Trevor, Gnirke, Andreas, Ströher, Ute, Rambaut, Andrew, Garry, Robert F., Sabeti, Pardis C.
Published in Cell (2015)