Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
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 (05.02.2021)
Published in Science (05.02.2021)
Get full text
Journal Article
Web Resource
Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants
Welch, Nicole L, Zhu, Meilin, Hua, Catherine, Weller, Juliane, Mirhashemi, Marzieh Ezzaty, Nguyen, Tien G, Mantena, Sreekar, Bauer, Matthew R, Shaw, Bennett M, Ackerman, Cheri M, Thakku, Sri Gowtham, Tse, Megan W, Kehe, Jared, Uwera, Marie-Martine, Eversley, Jacqueline S, Bielwaski, Derek A, McGrath, Graham, Braidt, Joseph, Johnson, Jeremy, Cerrato, Felecia, Moreno, Gage K, Krasilnikova, Lydia A, Petros, Brittany A, Gionet, Gabrielle L, King, Ewa, Huard, Richard C, Jalbert, Samantha K, Cleary, Michael L, Fitzgerald, Nicholas A, Gabriel, Stacey B, Gallagher, Glen R, Smole, Sandra C, Madoff, Lawrence C, Brown, Catherine M, Keller, Matthew W, Wilson, Malania M, Kirby, Marie K, Barnes, John R, Park, Daniel J, Siddle, Katherine J, Happi, Christian T, Hung, Deborah T, Springer, Michael, MacInnis, Bronwyn L, Lemieux, Jacob E, Rosenberg, Eric, Branda, John A, Blainey, Paul C, Sabeti, Pardis C, Myhrvold, Cameron
Published in Nature medicine (01.05.2022)
Published in Nature medicine (01.05.2022)
Get full text
Journal Article
Combining genomics and epidemiology to track mumps virus transmission in the United States
Wohl, Shirlee, Metsky, Hayden C, Schaffner, Stephen F, Piantadosi, Anne, Burns, Meagan, Lewnard, Joseph A, Chak, Bridget, Krasilnikova, Lydia A, Siddle, Katherine J, Matranga, Christian B, Bankamp, Bettina, Hennigan, Scott, Sabina, Brandon, Byrne, Elizabeth H, McNall, Rebecca J, Shah, Rickey R, Qu, James, Park, Daniel J, Gharib, Soheyla, Fitzgerald, Susan, Barreira, Paul, Fleming, Stephen, Lett, Susan, Rota, Paul A, Madoff, Lawrence C, Yozwiak, Nathan L, MacInnis, Bronwyn L, Smole, Sandra, Grad, Yonatan H, Sabeti, Pardis C
Published in PLoS biology (11.02.2020)
Published in PLoS biology (11.02.2020)
Get full text
Journal Article
High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection
Normandin, Erica, Rudy, Melissa, Barkas, Nikolaos, Schaffner, Stephen F, Levine, Zoe, Padera, Jr, Robert F, Babadi, Mehrtash, Mukerji, Shibani S, Park, Daniel J, MacInnis, Bronwyn L, Siddle, Katherine J, Sabeti, Pardis C, Solomon, Isaac H
Published in Nature communications (02.02.2023)
Published in Nature communications (02.02.2023)
Get full text
Journal Article
Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing
Early, Angela M, Daniels, Rachel F, Farrell, Timothy M, Grimsby, Jonna, Volkman, Sarah K, Wirth, Dyann F, MacInnis, Bronwyn L, Neafsey, Daniel E
Published in Malaria journal (01.07.2019)
Published in Malaria journal (01.07.2019)
Get full text
Journal Article
Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing
Levine, Zoë C, Sene, Aita, Mkandawire, Winnie, Deme, Awa B, Ndiaye, Tolla, Sy, Mouhamad, Gaye, Amy, Diedhiou, Younouss, Mbaye, Amadou M, Ndiaye, Ibrahima M, Gomis, Jules, Ndiop, Médoune, Sene, Doudou, Faye Paye, Marietou, MacInnis, Bronwyn L, Schaffner, Stephen F, Park, Daniel J, Badiane, Aida S, Colubri, Andres, Ndiaye, Mouhamadou, Sy, Ngayo, Sabeti, Pardis C, Ndiaye, Daouda, Siddle, Katherine J
Published in Nature communications (25.01.2024)
Published in Nature communications (25.01.2024)
Get full text
Journal Article
Bidirectional thermotaxis in Caenorhabditis elegans is mediated by distinct sensorimotor strategies driven by the AFD thermosensory neurons
Luo, Linjiao, Cook, Nathan, Venkatachalam, Vivek, Martinez-Velazquez, Luis A., Zhang, Xiaodong, Calvo, Ana C., Hawk, Josh, MacInnis, Bronwyn L., Frank, Michelle, Ng, Jia Hong Ray, Klein, Mason, Gershow, Marc, Hammarlund, Marc, Goodman, Miriam B., Colón-Ramos, Daniel A., Zhang, Yun, Samuel, Aravinthan D. T.
Published in Proceedings of the National Academy of Sciences - PNAS (18.02.2014)
Published in Proceedings of the National Academy of Sciences - PNAS (18.02.2014)
Get full text
Journal Article
Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections
Early, Angela M, Lievens, Marc, MacInnis, Bronwyn L, Ockenhouse, Christian F, Volkman, Sarah K, Adjei, Samuel, Agbenyega, Tsiri, Ansong, Daniel, Gondi, Stacey, Greenwood, Brian, Hamel, Mary, Odero, Chris, Otieno, Kephas, Otieno, Walter, Owusu-Agyei, Seth, Asante, Kwaku Poku, Sorgho, Hermann, Tina, Lucas, Tinto, Halidou, Valea, Innocent, Wirth, Dyann F, Neafsey, Daniel E
Published in Nature communications (11.04.2018)
Published in Nature communications (11.04.2018)
Get full text
Journal Article
Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework
Petros, Brittany A., Paull, Jillian S., Tomkins-Tinch, Christopher H., Loftness, Bryn C., DeRuff, Katherine C., Nair, Parvathy, Gionet, Gabrielle L., Benz, Aaron, Brock-Fisher, Taylor, Hughes, Michael, Yurkovetskiy, Leonid, Mulaudzi, Shandukani, Leenerman, Emma, Nyalile, Thomas, Moreno, Gage K., Specht, Ivan, Sani, Kian, Adams, Gordon, Babet, Simone V., Baron, Emily, Blank, Jesse T., Boehm, Chloe, Botti-Lodovico, Yolanda, Brown, Jeremy, Buisker, Adam R., Burcham, Timothy, Chylek, Lily, Cronan, Paul, Dauphin, Ann, Desreumaux, Valentine, Doss, Megan, Flynn, Belinda, Gladden-Young, Adrianne, Glennon, Olivia, Harmon, Hunter D., Hook, Thomas V., Kary, Anton, King, Clay, Loreth, Christine, Marrs, Libby, McQuade, Kyle J., Milton, Thorsen T., Mulford, Jada M., Oba, Kyle, Pearlman, Leah, Schifferli, Mark, Schmidt, Madelyn J., Tandus, Grace M., Tyler, Andy, Vodzak, Megan E., Krohn Bevill, Kelly, Colubri, Andres, MacInnis, Bronwyn L., Ozsoy, A. Zeynep, Parrie, Eric, Sholtes, Kari, Siddle, Katherine J., Fry, Ben, Luban, Jeremy, Park, Daniel J., Marshall, John, Bronson, Amy, Schaffner, Stephen F., Sabeti, Pardis C.
Published in Med (New York, N.Y. : Online) (09.12.2022)
Published in Med (New York, N.Y. : Online) (09.12.2022)
Get full text
Journal Article
Advances and opportunities in malaria population genomics
Neafsey, Daniel E, Taylor, Aimee R, MacInnis, Bronwyn L
Published in Nature reviews. Genetics (01.08.2021)
Published in Nature reviews. Genetics (01.08.2021)
Get full text
Journal Article
A genome wide association study of Plasmodium falciparum susceptibility to 22 antimalarial drugs in Kenya
Wendler, Jason P, Okombo, John, Amato, Roberto, Miotto, Olivo, Kiara, Steven M, Mwai, Leah, Pole, Lewa, O'Brien, John, Manske, Magnus, Alcock, Dan, Drury, Eleanor, Sanders, Mandy, Oyola, Samuel O, Malangone, Cinzia, Jyothi, Dushyanth, Miles, Alistair, Rockett, Kirk A, MacInnis, Bronwyn L, Marsh, Kevin, Bejon, Philip, Nzila, Alexis, Kwiatkowski, Dominic P
Published in PloS one (08.05.2014)
Published in PloS one (08.05.2014)
Get full text
Journal Article
Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness
Obermeyer, Fritz, Jankowiak, Martin, Barkas, Nikolaos, Schaffner, Stephen F, Pyle, Jesse D, Yurkovetskiy, Leonid, Bosso, Matteo, Park, Daniel J, Babadi, Mehrtash, MacInnis, Bronwyn L, Luban, Jeremy, Sabeti, Pardis C, Lemieux, Jacob E
Published in Science (American Association for the Advancement of Science) (17.06.2022)
Published in Science (American Association for the Advancement of Science) (17.06.2022)
Get full text
Journal Article
Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2
Arizti-Sanz, Jon, Freije, Catherine A, Stanton, Alexandra C, Petros, Brittany A, Boehm, Chloe K, Siddiqui, Sameed, Shaw, Bennett M, Adams, Gordon, Kosoko-Thoroddsen, Tinna-Solveig F, Kemball, Molly E, Uwanibe, Jessica N, Ajogbasile, Fehintola V, Eromon, Philomena E, Gross, Robin, Wronka, Loni, Caviness, Katie, Hensley, Lisa E, Bergman, Nicholas H, MacInnis, Bronwyn L, Happi, Christian T, Lemieux, Jacob E, Sabeti, Pardis C, Myhrvold, Cameron
Published in Nature communications (20.11.2020)
Published in Nature communications (20.11.2020)
Get full text
Journal Article
Field-deployable viral diagnostics using CRISPR-Cas13
Myhrvold, Cameron, Freije, Catherine A, Gootenberg, Jonathan S, Abudayyeh, Omar O, Metsky, Hayden C, Durbin, Ann F, Kellner, Max J, Tan, Amanda L, Paul, Lauren M, Parham, Leda A, Garcia, Kimberly F, Barnes, Kayla G, Chak, Bridget, Mondini, Adriano, Nogueira, Mauricio L, Isern, Sharon, Michael, Scott F, Lorenzana, Ivette, Yozwiak, Nathan L, MacInnis, Bronwyn L, Bosch, Irene, Gehrke, Lee, Zhang, Feng, Sabeti, Pardis C
Published in Science (American Association for the Advancement of Science) (27.04.2018)
Published in Science (American Association for the Advancement of Science) (27.04.2018)
Get full text
Journal Article
Viral Lineages in the 2022 RSV Surge in the United States
Adams, Gordon, Moreno, Gage K., Petros, Brittany A., Uddin, Rockib, Levine, Zoe, Kotzen, Ben, Messer, Katelyn S., Dobbins, Sabrina T., DeRuff, Katherine C., Loreth, Christine M., Brock-Fisher, Taylor, Schaffner, Stephen F., Chaluvadi, Sushma, Kanjilal, Sanjat, Luban, Jeremy, Ozonoff, Al, Park, Daniel J., Turbett, Sarah E., Siddle, Katherine J., MacInnis, Bronwyn L., Sabeti, Pardis C., Lemieux, Jacob E.
Published in The New England journal of medicine (06.04.2023)
Published in The New England journal of medicine (06.04.2023)
Get full text
Journal Article
Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018
Siddle, Katherine J, Eromon, Philomena, Barnes, Kayla G, Mehta, Samar, Oguzie, Judith U, Odia, Ikponmwosa, Schaffner, Stephen F, Winnicki, Sarah M, Shah, Rickey R, Qu, James, Wohl, Shirlee, Brehio, Patrick, Iruolagbe, Christopher, Aiyepada, John, Uyigue, Eghosa, Akhilomen, Patience, Okonofua, Grace, Ye, Simon, Kayode, Tolulope, Ajogbasile, Fehintola, Uwanibe, Jessica, Gaye, Amy, Momoh, Mambu, Chak, Bridget, Kotliar, Dylan, Carter, Amber, Gladden-Young, Adrianne, Freije, Catherine A, Omoregie, Omigie, Osiemi, Blessing, Muoebonam, Ekene B, Airende, Michael, Enigbe, Rachael, Ebo, Benevolence, Nosamiefan, Iguosadolo, Oluniyi, Paul, Nekoui, Mahan, Ogbaini-Emovon, Ephraim, Garry, Robert F, Andersen, Kristian G, Park, Daniel J, Yozwiak, Nathan L, Akpede, George, Ihekweazu, Chikwe, Tomori, Oyewale, Okogbenin, Sylvanus, Folarin, Onikepe A, Okokhere, Peter O, MacInnis, Bronwyn L, Sabeti, Pardis C, Happi, Christian T
Published in The New England journal of medicine (01.11.2018)
Published in The New England journal of medicine (01.11.2018)
Get full text
Journal Article
Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak
Siddle, Katherine J., Krasilnikova, Lydia A., Moreno, Gage K., Schaffner, Stephen F., Vostok, Johanna, Fitzgerald, Nicholas A., Lemieux, Jacob E., Barkas, Nikolaos, Loreth, Christine, Specht, Ivan, Tomkins-Tinch, Christopher H., Paull, Jillian S., Schaeffer, Beau, Taylor, Bradford P., Loftness, Bryn, Johnson, Hillary, Schubert, Petra L., Shephard, Hanna M., Doucette, Matthew, Fink, Timelia, Lang, Andrew S., Baez, Stephanie, Beauchamp, John, Hennigan, Scott, Buzby, Erika, Ash, Stephanie, Brown, Jessica, Clancy, Selina, Cofsky, Seana, Gagne, Luc, Hall, Joshua, Harrington, Rachel, Gionet, Gabrielle L., DeRuff, Katherine C., Vodzak, Megan E., Adams, Gordon C., Dobbins, Sabrina T., Slack, Sarah D., Reilly, Steven K., Anderson, Lisa M., Cipicchio, Michelle C., DeFelice, Matthew T., Grimsby, Jonna L., Anderson, Scott E., Blumenstiel, Brendan S., Meldrim, James C., Rooke, Heather M., Vicente, Gina, Smith, Natasha L., Messer, Katelyn S., Reagan, Faye L., Mandese, Zoe M., Lee, Matthew D., Ray, Marianne C., Fisher, Marissa E., Ulcena, Maesha A., Nolet, Corey M., English, Sean E., Larkin, Katie L., Vernest, Kyle, Chaluvadi, Sushma, Arvidson, Deirdre, Melchiono, Maurice, Covell, Theresa, Harik, Vaira, Brock-Fisher, Taylor, Dunn, Molly, Kearns, Amanda, Hanage, William P., Bernard, Clare, Philippakis, Anthony, Lennon, Niall J., Gabriel, Stacey B., Gallagher, Glen R., Smole, Sandra, Madoff, Lawrence C., Brown, Catherine M., Park, Daniel J., MacInnis, Bronwyn L., Sabeti, Pardis C.
Published in Cell (03.02.2022)
Published in Cell (03.02.2022)
Get full text
Journal Article
Neuropathological features of SARS-CoV-2 delta and omicron variants
Normandin, Erica, Valizadeh, Navid, Rudmann, Emily A, Uddin, Rockib, Dobbins, Sabrina T, MacInnis, Bronwyn L, Padera, Robert F, Siddle, Katherine J, Lemieux, Jacob E, Sabeti, Pardis C, Mukerji, Shibani S, Solomon, Isaac H
Published in Journal of neuropathology and experimental neurology (01.04.2023)
Published in Journal of neuropathology and experimental neurology (01.04.2023)
Get full text
Journal Article