Search Results - "Matteson, Nathaniel L"

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

“…How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon…”
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Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations by Gangavarapu, Karthik, Latif, Alaa Abdel, Mullen, Julia L., Alkuzweny, Manar, Hufbauer, Emory, Tsueng, Ginger, Haag, Emily, Zeller, Mark, Aceves, Christine M., Zaiets, Karina, Cano, Marco, Zhou, Xinghua, Qian, Zhongchao, Sattler, Rachel, Matteson, Nathaniel L., Levy, Joshua I., Lee, Raphael T. C., Freitas, Lucas, Maurer-Stroh, Sebastian, Suchard, Marc A., Wu, Chunlei, Su, Andrew I., Andersen, Kristian G., Hughes, Laura D.

“…In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11…”
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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

“…Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to…”
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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

“…Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory…”
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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.

“…The exterior minor protein IX of adenoviruses (AdVs) is a frequent target of attachment of antigens and the modified AdVs are being used as potent vaccine…”
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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.

“…The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the…”
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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

“…Regional connectivity and land travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is…”
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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

“…Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool…”
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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

“…Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool…”
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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

“…As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by…”
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The Use of Genomic Epidemiology in Viral Outbreak Monitoring and Intervention by Matteson, Nathaniel L

“…Viral infectious diseases are one of the greatest challenges public health faces. Since the beginning of the 21st century, a number of viruses have emerged…”
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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.

“…The Zika epidemic in the Americas has challenged surveillance and control. As the epidemic appears to be waning, it is unclear whether transmission is still…”
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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

“…Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network…”
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Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics by Matteson, Nathaniel L, Hassler, Gabriel W, Kurzban, Ezra, Schwab, Madison A, Perkins, Sarah A, Gangavarapu, Karthik, Levy, Joshua I, Parker, Edyth, Pride, David, Hakim, Abbas, De Hoff, Peter, Cheung, Willi, Castro-Martinez, Anelizze, Rivera, Andrea, Veder, Anthony, Rivera, Ariana, Wauer, Cassandra, Holmes, Jacqueline, Wilson, Jedediah, Ngo, Shayla N, Plascencia, Ashley, Lawrence, Elijah S, Smoot, Elizabeth W, Eisner, Emily R, Tsai, Rebecca, Chacón, Marisol, Baer, Nathan A, Seaver, Phoebe, Salido, Rodolfo A, Aigner, Stefan, Ngo, Toan T, Barber, Tom, Ostrander, Tyler, Fielding-Miller, Rebecca, Simmons, Elizabeth H, Zazueta, Oscar E, Serafin-Higuera, Idanya, Sanchez-Alavez, Manuel, Moreno-Camacho, Jose L, García-Gil, Abraham, Murphy Schafer, Ashleigh R, McDonald, Eric, Corrigan, Jeremy, Malone, John D, Stous, Sarah, Shah, Seema, Moshiri, Niema, Weiss, Alana, Anderson, Catelyn, Aceves, Christine M, Spencer, Emily G, Hufbauer, Emory C, Lee, Justin J, King, Alison J, Ramesh, Karthik S, Nguyen, Kelly N, Saucedo, Kieran, Robles-Sikisaka, Refugio, Fisch, Kathleen M, Gonias, Steven L, Birmingham, Amanda, McDonald, Daniel, Karthikeyan, Smruthi, Martin, Natasha K, Schooley, Robert T, Negrete, Agustin J, Reyna, Horacio J, Chavez, Jose R, Garcia, Maria L, Cornejo-Bravo, Jose M, Becker, David, Isaksson, Magnus, Washington, Nicole L, Lee, William, Garfein, Richard S, Luna-Ruiz Esparza, Marco A, Alcántar-Fernández, Jonathan, Henson, Benjamin, Jepsen, Kristen, Olivares-Flores, Beatriz, Barrera-Badillo, Gisela, Lopez-Martínez, Irma, Ramírez-González, José E, Flores-León, Rita, Kingsmore, Stephen F, Sanders, Alison, Pradenas, Allorah, White, Benjamin, Matthews, Gary, Hale, Matt, McLawhon, Ronald W, Reed, Sharon L, Winbush, Terri, McHardy, Ian H, Fielding, Russel A, Nicholson, Laura, Quigley, Michael M, Harding, Aaron, Mendoza, Art, Bakhtar, Omid

“…The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the…”
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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

“…Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests…”
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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

“…Background: Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous…”
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