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240 results on '"Thackray, Larissa B."'

1. Computationally restoring the potency of a clinical antibody against Omicron

Author

Desautels, Thomas A., Arrildt, Kathryn T., Zemla, Adam T., Lau, Edmond Y., Zhu, Fangqiang, Ricci, Dante, Cronin, Stephanie, Zost, Seth J., Binshtein, Elad, Scheaffer, Suzanne M., Dadonaite, Bernadeta, Petersen, Brenden K., Engdahl, Taylor B., Chen, Elaine, Handal, Laura S., Hall, Lynn, Goforth, John W., Vashchenko, Denis, Nguyen, Sam, Weilhammer, Dina R., Lo, Jacky Kai-Yin, Rubinfeld, Bonnee, Saada, Edwin A., Weisenberger, Tracy, Lee, Tek-Hyung, Whitener, Bradley, Case, James B., Ladd, Alexander, Silva, Mary S., Haluska, Rebecca M., Grzesiak, Emilia A., Earnhart, Christopher G., Hopkins, Svetlana, Bates, Thomas W., Thackray, Larissa B., Segelke, Brent W., Lillo, Antonietta Maria, Sundaram, Shivshankar, Bloom, Jesse D., Diamond, Michael S., Crowe, Jr, James E., Carnahan, Robert H., and Faissol, Daniel M.

Published
2024
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2. A compendium of multi-omics data illuminating host responses to lethal human virus infections

Author

Eisfeld, Amie J., Anderson, Lindsey N., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff Smith, Danielle, Thackray, Larissa B., Tan, Qing, Sims, Amy C., Menachery, Vineet D., Schäfer, Alexandra, Sheahan, Timothy P., Cockrell, Adam S., Stratton, Kelly G., Webb-Robertson, Bobbie-Jo M., Kyle, Jennifer E., Burnum-Johnson, Kristin E., Kim, Young-Mo, Nicora, Carrie D., Peralta, Zuleyma, N’jai, Alhaji U., Sahr, Foday, van Bakel, Harm, Diamond, Michael S., Baric, Ralph S., Metz, Thomas O., Smith, Richard D., Kawaoka, Yoshihiro, and Waters, Katrina M.

Published
2024
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3. Defining the risk of SARS-CoV-2 variants on immune protection

Author

DeGrace, Marciela M, Ghedin, Elodie, Frieman, Matthew B, Krammer, Florian, Grifoni, Alba, Alisoltani, Arghavan, Alter, Galit, Amara, Rama R, Baric, Ralph S, Barouch, Dan H, Bloom, Jesse D, Bloyet, Louis-Marie, Bonenfant, Gaston, Boon, Adrianus CM, Boritz, Eli A, Bratt, Debbie L, Bricker, Traci L, Brown, Liliana, Buchser, William J, Carreño, Juan Manuel, Cohen-Lavi, Liel, Darling, Tamarand L, Davis-Gardner, Meredith E, Dearlove, Bethany L, Di, Han, Dittmann, Meike, Doria-Rose, Nicole A, Douek, Daniel C, Drosten, Christian, Edara, Venkata-Viswanadh, Ellebedy, Ali, Fabrizio, Thomas P, Ferrari, Guido, Fischer, Will M, Florence, William C, Fouchier, Ron AM, Franks, John, García-Sastre, Adolfo, Godzik, Adam, Gonzalez-Reiche, Ana Silvia, Gordon, Aubree, Haagmans, Bart L, Halfmann, Peter J, Ho, David D, Holbrook, Michael R, Huang, Yaoxing, James, Sarah L, Jaroszewski, Lukasz, Jeevan, Trushar, Johnson, Robert M, Jones, Terry C, Joshi, Astha, Kawaoka, Yoshihiro, Kercher, Lisa, Koopmans, Marion PG, Korber, Bette, Koren, Eilay, Koup, Richard A, LeGresley, Eric B, Lemieux, Jacob E, Liebeskind, Mariel J, Liu, Zhuoming, Livingston, Brandi, Logue, James P, Luo, Yang, McDermott, Adrian B, McElrath, Margaret J, Meliopoulos, Victoria A, Menachery, Vineet D, Montefiori, David C, Mühlemann, Barbara, Munster, Vincent J, Munt, Jenny E, Nair, Manoj S, Netzl, Antonia, Niewiadomska, Anna M, O’Dell, Sijy, Pekosz, Andrew, Perlman, Stanley, Pontelli, Marjorie C, Rockx, Barry, Rolland, Morgane, Rothlauf, Paul W, Sacharen, Sinai, Scheuermann, Richard H, Schmidt, Stephen D, Schotsaert, Michael, Schultz-Cherry, Stacey, Seder, Robert A, Sedova, Mayya, Sette, Alessandro, Shabman, Reed S, Shen, Xiaoying, Shi, Pei-Yong, Shukla, Maulik, Simon, Viviana, Stumpf, Spencer, Sullivan, Nancy J, Thackray, Larissa B, and Theiler, James

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Emerging Infectious Diseases, Pneumonia, Vaccine Related, Pneumonia & Influenza, Infectious Diseases, Biodefense, Immunization, Biotechnology, Prevention, Lung, Prevention of disease and conditions, and promotion of well-being, 2.1 Biological and endogenous factors, 3.4 Vaccines, Aetiology, Infection, Good Health and Well Being, Animals, Biological Evolution, COVID-19, COVID-19 Vaccines, Humans, National Institute of Allergy and Infectious Diseases (U.S.), Pandemics, Pharmacogenomic Variants, SARS-CoV-2, United States, Virulence, General Science & Technology
Abstract

The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced after infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants that could potentially affect the transmission, virulence, and resistance to infection- and vaccine-induced immunity. The SAVE programme is a critical data-generating component of the US Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines and therapeutics, and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models and notable findings facilitated by this collaborative approach and identify future challenges. This programme is a template for the response to rapidly evolving pathogens with pandemic potential by monitoring viral evolution in the human population to identify variants that could reduce the effectiveness of countermeasures.

Published
2022

4. Genetic loci regulate Sarbecovirus pathogenesis: A comparison across mice and humans

Author

Schäfer, Alexandra, Gralinski, Lisa E., Leist, Sarah R., Hampton, Brea K., Mooney, Michael A., Jensen, Kara L., Graham, Rachel L., Agnihothram, Sudhakar, Jeng, Sophia, Chamberlin, Steven, Bell, Timothy A., Scobey, D. Trevor, Linnertz, Colton L., VanBlargan, Laura A., Thackray, Larissa B., Hock, Pablo, Miller, Darla R., Shaw, Ginger D., Diamond, Michael S., de Villena, Fernando Pardo Manuel, McWeeney, Shannon K., Heise, Mark T., Menachery, Vineet D., Ferris, Martin T., and Baric, Ralph S.

Published
2024
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5. Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response

Author

Feng, Song, Heath, Emily, Jefferson, Brett, Joslyn, Cliff, Kvinge, Henry, Mitchell, Hugh D., Praggastis, Brenda, Eisfeld, Amie J., Sims, Amy C., Thackray, Larissa B., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff-Smith, Danielle, Tan, Qing, Menachery, Vineet D., Sheahan, Timothy P., Cockrell, Adam S., Kocher, Jacob F., Stratton, Kelly G., Heller, Natalie C., Bramer, Lisa M., Diamond, Michael S., Baric, Ralph S., Waters, Katrina M., Kawaoka, Yoshihiro, McDermott, Jason E., and Purvine, Emilie

Subjects
Quantitative Biology - Quantitative Methods, Mathematics - Combinatorics, 92C42, 92-08, 05C65
Abstract

Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges represent significantly perturbed genes, and vertices represent individual biological samples with specific experimental conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Conclusions: Our results demonstrate the utility of using hypergraphs to represent complex biological systems and highlight central important responses in common to a variety of highly pathogenic viruses.

Published
2020

6. Bivalent SARS-CoV-2 mRNA vaccines increase breadth of neutralization and protect against the BA.5 Omicron variant in mice

Author

Scheaffer, Suzanne M., Lee, Diana, Whitener, Bradley, Ying, Baoling, Wu, Kai, Liang, Chieh-Yu, Jani, Hardik, Martin, Philippa, Amato, Nicholas J., Avena, Laura E., Berrueta, Daniela Montes, Schmidt, Stephen D., O’Dell, Sijy, Nasir, Arshan, Chuang, Gwo-Yu, Stewart-Jones, Guillaume, Koup, Richard A., Doria-Rose, Nicole A., Carfi, Andrea, Elbashir, Sayda M., Thackray, Larissa B., Edwards, Darin K., and Diamond, Michael S.

Published
2023
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8. SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters

Author

Halfmann, Peter J., Iida, Shun, Iwatsuki-Horimoto, Kiyoko, Maemura, Tadashi, Kiso, Maki, Scheaffer, Suzanne M., Darling, Tamarand L., Joshi, Astha, Loeber, Samantha, Singh, Gagandeep, Foster, Stephanie L., Ying, Baoling, Case, James Brett, Chong, Zhenlu, Whitener, Bradley, Moliva, Juan, Floyd, Katharine, Ujie, Michiko, Nakajima, Noriko, Ito, Mutsumi, Wright, Ryan, Uraki, Ryuta, Warang, Prajakta, Gagne, Matthew, Li, Rong, Sakai-Tagawa, Yuko, Liu, Yanan, Larson, Deanna, Osorio, Jorge E., Hernandez-Ortiz, Juan P., Henry, Amy R., Ciuoderis, Karl, Florek, Kelsey R., Patel, Mit, Odle, Abby, Wong, Lok-Yin Roy, Bateman, Allen C., Wang, Zhongde, Edara, Venkata-Viswanadh, Chong, Zhenlu, Franks, John, Jeevan, Trushar, Fabrizio, Thomas, DeBeauchamp, Jennifer, Kercher, Lisa, Seiler, Patrick, Gonzalez-Reiche, Ana Silvia, Sordillo, Emilia Mia, Chang, Lauren A., van Bakel, Harm, Simon, Viviana, Douek, Daniel C., Sullivan, Nancy J., Thackray, Larissa B., Ueki, Hiroshi, Yamayoshi, Seiya, Imai, Masaki, Perlman, Stanley, Webby, Richard J., Seder, Robert A., Suthar, Mehul S., García-Sastre, Adolfo, Schotsaert, Michael, Suzuki, Tadaki, Boon, Adrianus C. M., Diamond, Michael S., and Kawaoka, Yoshihiro

Published
2022
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9. Intestinal helminth infection impairs vaccine-induced T cell responses and protection against SARS-CoV-2 in mice.

Author

Desai, Pritesh, Karl, Courtney E., Ying, Baoling, Liang, Chieh-Yu, Garcia-Salum, Tamara, Santana, Ana Carolina, ten-Caten, Felipe, Joseph F., Elbashir, Sayda M., Edwards, Darin K., Ribeiro, Susan P., Thackray, Larissa B., Sekaly, Rafick P., and Diamond, Michael S.

Subjects
SARS-CoV-2, SARS-CoV-2 Omicron variant, HELMINTHIASIS, COVID-19 vaccines, T cells
Abstract

Although vaccines have reduced the burden of COVID-19, their efficacy in helminth infection–endemic areas is not well characterized. We evaluated the impact of infection by Heligmosomoides polygyrus bakeri (Hpb), a murine intestinal roundworm, on the efficacy of an mRNA vaccine targeting the Wuhan-1 spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in mice. Although immunization generated similar B cell responses in Hpb-infected and uninfected mice, polyfunctional CD4+ and CD8+ T cell responses were markedly reduced in Hpb-infected mice. Hpb-infected and mRNA-vaccinated mice were protected against the ancestral SARS-CoV-2 strain WA1/2020, but control of lung infection was diminished against an Omicron variant compared with animals immunized without Hpb infection. Helminth-mediated suppression of spike protein–specific CD8+ T cell responses occurred independently of signal transducer and activator of transcription 6 (STAT6) signaling, whereas blockade of interleukin-10 (IL-10) rescued vaccine-induced CD8+ T cell responses. Together, these data show that, in mice, intestinal helminth infection impaired vaccine-induced T cell responses through an IL-10 pathway, which compromised protection against antigenically drifted SARS-CoV-2 variants. Editor's summary: Much of the global population lives in areas endemic to helminths, which are known to affect responses to vaccines. To discern how helminth infection affects responses to SARS-CoV-2 vaccines, Desai et al. infected mice with the hookworm Heligmosomoides polygyrus bakeri (Hpb) during the course of a primary SARS-CoV-2 vaccine series. The authors found that Hpb infection compromised T cell, but not antibody, responses to SARS-CoV-2 in an IL-10–dependent manner. Although Hpb-infected K18-hACE2 mice were protected from ancestral SARS-CoV-2 challenge through their antibody responses, they were more susceptible to challenge with an Omicron variant, which can evade antibodies but is still susceptible to T cell responses. Together, these data highlight the need to keep helminth infections in mind during vaccine development and deployment. —Courtney Malo [ABSTRACT FROM AUTHOR]

Published
2024
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10. Intestinal helminth infection impairs vaccine-induced T cell responses and protection against SARS-CoV-2

Author

Desai, Pritesh, primary, Karl, Courtney E., additional, Ying, Baoling, additional, Liang, Chieh-Yu, additional, Garcia-Salum, Tamara, additional, Santana, Ana Carolina, additional, Caten, Felipe Ten, additional, Urban, Joseph F., additional, Elbashir, Sayda M., additional, Edwards, Darin K., additional, Ribeiro, Susan P., additional, Thackray, Larissa B., additional, Sekaly, Rafick P., additional, and Diamond, Michael S., additional

Published
2024
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13. Integrated pipeline for the accelerated discovery of antiviral antibody therapeutics

Author

Gilchuk, Pavlo, Bombardi, Robin G., Erasmus, Jesse H., Tan, Qing, Nargi, Rachel, Soto, Cinque, Abbink, Peter, Suscovich, Todd J., Durnell, Lorellin A., Khandhar, Amit, Archer, Jacob, Liang, Jenny, Fouch, Mallorie E., Davidson, Edgar, Doranz, Benjamin J., Jones, Taylor, Larson, Elise, Ertel, Stacey, Granger, Brian, Fuerte-Stone, Jasmine, Roy, Vicky, Broge, Thomas, Linnekin, Thomas C., Linde, Caitlyn H., Gorman, Matthew J., Nkolola, Joseph, Alter, Galit, Reed, Steven G., Barouch, Dan H., Diamond, Michael S., Crowe, Jr, James E., Van Hoeven, Neal, Thackray, Larissa B., and Carnahan, Robert H.

Published
2020
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14. Hypergraph models of biological networks to identify genes critical to pathogenic viral response

Author

Feng, Song, Heath, Emily, Jefferson, Brett, Joslyn, Cliff, Kvinge, Henry, Mitchell, Hugh D., Praggastis, Brenda, Eisfeld, Amie J., Sims, Amy C., Thackray, Larissa B., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff-Smith, Danielle, Tan, Qing, Menachery, Vineet D., Sheahan, Timothy P., Cockrell, Adam S., Kocher, Jacob F., Stratton, Kelly G., Heller, Natalie C., Bramer, Lisa M., Diamond, Michael S., Baric, Ralph S., Waters, Katrina M., Kawaoka, Yoshihiro, McDermott, Jason E., and Purvine, Emilie

Published
2021
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15. Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein

Author

Zost, Seth J., Gilchuk, Pavlo, Chen, Rita E., Case, James Brett, Reidy, Joseph X., Trivette, Andrew, Nargi, Rachel S., Sutton, Rachel E., Suryadevara, Naveenchandra, Chen, Elaine C., Binshtein, Elad, Shrihari, Swathi, Chu, Helen Y., Ostrowski, Mario, Didier, Jonathan E., MacRenaris, Keith W., Jones, Taylor, Day, Samuel, Myers, Luke, Lee, F. Eun-Hyung, Nguyen, Doan C., Sanz, Ignacio, Martinez, David R., Rothlauf, Paul W., Bloyet, Louis-Marie, Whelan, Sean P.J., Baric, Ralph S., Thackray, Larissa B., Diamond, Michael S., Carnahan, Robert H., and Crowe, James E., Jr.

Subjects
Immunological research, Monoclonal antibodies -- Identification and classification, Viral proteins -- Research, Biological sciences, Health
Abstract

Antibodies are a principal determinant of immunity for most RNA viruses and have promise to reduce infection or disease during major epidemics. The novel coronavirus SARS-CoV-2 has caused a global pandemic with millions of infections and hundreds of thousands of deaths to date.sup.1,2. In response, we used a rapid antibody discovery platform to isolate hundreds of human monoclonal antibodies (mAbs) against the SARS-CoV-2 spike (S) protein. We stratify these mAbs into five major classes on the basis of their reactivity to subdomains of S protein as well as their cross-reactivity to SARS-CoV. Many of these mAbs inhibit infection of authentic SARS-CoV-2 virus, with most neutralizing mAbs recognizing the receptor-binding domain (RBD) of S. This work defines sites of vulnerability on SARS-CoV-2 S and demonstrates the speed and robustness of advanced antibody discovery platforms. A platform for rapid antibody discovery enabled the isolation of hundreds of human monoclonal antibodies against SARS-CoV-2 and the prioritization of potent antibody candidates for clinical trials in patients with COVID-19., Author(s): Seth J. Zost [sup.1] , Pavlo Gilchuk [sup.1] , Rita E. Chen [sup.2] [sup.3] , James Brett Case [sup.3] , Joseph X. Reidy [sup.1] , Andrew Trivette [sup.1] , [...]

Published
2020
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17. Potently neutralizing and protective human antibodies against SARS-CoV-2

Author

Zost, Seth J., Gilchuk, Pavlo, Case, James Brett, Binshtein, Elad, Chen, Rita E., Nkolola, Joseph P., Schäfer, Alexandra, Reidy, Joseph X., Trivette, Andrew, Nargi, Rachel S., Sutton, Rachel E., Suryadevara, Naveenchandra, Martinez, David R., Williamson, Lauren E., Chen, Elaine C., Jones, Taylor, Day, Samuel, Myers, Luke, Hassan, Ahmed O., Kafai, Natasha M., Winkler, Emma S., Fox, Julie M., Shrihari, Swathi, Mueller, Benjamin K., Meiler, Jens, Chandrashekar, Abishek, Mercado, Noe B., Steinhardt, James J., Ren, Kuishu, Loo, Yueh-Ming, Kallewaard, Nicole L., McCune, Broc T., Keeler, Shamus P., Holtzman, Michael J., Barouch, Dan H., Gralinski, Lisa E., Baric, Ralph S., Thackray, Larissa B., Diamond, Michael S., Carnahan, Robert H., and Crowe, Jr, James E.

Published
2020
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19. Domain-based mRNA vaccines encoding spike protein N-terminal and receptor binding domains confer protection against SARS-CoV-2

Author

Stewart-Jones, Guillaume B. E., primary, Elbashir, Sayda M., additional, Wu, Kai, additional, Lee, Diana, additional, Renzi, Isabella, additional, Ying, Baoling, additional, Koch, Matthew, additional, Sein, Caralyn E., additional, Choi, Angela, additional, Whitener, Bradley, additional, Garcia-Dominguez, Dario, additional, Henry, Carole, additional, Woods, Angela, additional, Ma, LingZhi, additional, Montes Berrueta, Daniela, additional, Avena, Laura E., additional, Quinones, Julian, additional, Falcone, Samantha, additional, Hsiao, Chiaowen J., additional, Scheaffer, Suzanne M., additional, Thackray, Larissa B., additional, White, Phil, additional, Diamond, Michael S., additional, Edwards, Darin K., additional, and Carfi, Andrea, additional

Published
2023
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21. CD209L (L-SIGN) Is a Receptor for Severe Acute Respiratory Syndrome Coronavirus

Author

Jeffers, Scott A., Tusell, Sonia M., Gillim-Ross, Laura, Hemmila, Erin M., Achenbach, Jenna E., Babcock, Gregory J., Thomas,, William D., Thackray, Larissa B., Young, Mark D., Mason, Robert J., Ambrosino, Donna M., Wentworth, David E., DeMartini, James C., Holmes, Kathryn V., and Palese, Peter

Published
2004

22. Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants

Author

Desautels, Thomas A., primary, Arrildt, Kathryn T., additional, Zemla, Adam T., additional, Lau, Edmond Y., additional, Zhu, Fangqiang, additional, Ricci, Dante, additional, Cronin, Stephanie, additional, Zost, Seth J., additional, Binshtein, Elad, additional, Scheaffer, Suzanne M., additional, Engdahl, Taylor B., additional, Chen, Elaine, additional, Goforth, John W., additional, Vashchenko, Denis, additional, Nguyen, Sam, additional, Weilhammer, Dina R., additional, Lo, Jacky Kai-Yin, additional, Rubinfeld, Bonnee, additional, Saada, Edwin A., additional, Weisenberger, Tracy, additional, Lee, Tek-Hyung, additional, Whitener, Bradley, additional, Case, James B., additional, Ladd, Alexander, additional, Silva, Mary S., additional, Haluska, Rebecca M., additional, Grzesiak, Emilia A., additional, Bates, Thomas W., additional, Petersen, Brenden K., additional, Thackray, Larissa B., additional, Segelke, Brent W., additional, Lillo, Antonietta Maria, additional, Sundaram, Shivshankar, additional, Diamond, Michael S., additional, Crowe, James E., additional, Carnahan, Robert H., additional, and Faissol, Daniel M., additional

Published
2022
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23. Bivalent SARS-CoV-2 mRNA vaccines increase breadth of neutralization and protect against the BA.5 Omicron variant in mice

Author

Scheaffer, Suzanne M., primary, Lee, Diana, additional, Whitener, Bradley, additional, Ying, Baoling, additional, Wu, Kai, additional, Liang, Chieh-Yu, additional, Jani, Hardik, additional, Martin, Philippa, additional, Amato, Nicholas J., additional, Avena, Laura E., additional, Berrueta, Daniela Montes, additional, Schmidt, Stephen D., additional, O’Dell, Sijy, additional, Nasir, Arshan, additional, Chuang, Gwo-Yu, additional, Stewart-Jones, Guillaume, additional, Koup, Richard A., additional, Doria-Rose, Nicole A., additional, Carfi, Andrea, additional, Elbashir, Sayda M., additional, Thackray, Larissa B., additional, Edwards, Darin K., additional, and Diamond, Michael S., additional

Published
2022
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24. Development of SARS-CoV-2 mRNA vaccines encoding spike N-terminal and receptor binding domains

Author

Stewart-Jones, Guillaume B.E., primary, Elbashir, Sayda M., additional, Wu, Kai, additional, Lee, Diana, additional, Renzi, Isabella, additional, Ying, Baoling, additional, Koch, Matthew, additional, Sein, Caralyn E., additional, Choi, Angela, additional, Whitener, Bradley, additional, Garcia-Dominguez, Dario, additional, Henry, Carole, additional, Woods, Angela, additional, Ma, LingZhi, additional, Montes Berrueta, Daniela, additional, Avena, Laura E., additional, Quinones, Julian, additional, Falcone, Samantha, additional, Hsiao, Chiaowen J., additional, Scheaffer, Suzanne M., additional, Thackray, Larissa B., additional, White, Phil, additional, Diamond, Michael S., additional, Edwards, Darin K., additional, and Carfi, Andrea, additional

Published
2022
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25. Bivalent SARS-CoV-2 mRNA vaccines increase breadth of neutralization and protect against the BA.5 Omicron variant

Author

Scheaffer, Suzanne M., primary, Lee, Diana, additional, Whitener, Bradley, additional, Ying, Baoling, additional, Wu, Kai, additional, Jani, Hardik, additional, Martin, Philippa, additional, Amato, Nicholas J., additional, Avena, Laura E., additional, Berrueta, Daniela Montes, additional, Schmidt, Stephen D., additional, O’Dell, Sijy, additional, Nasir, Arshan, additional, Chuang, Gwo-Yu, additional, Stewart-Jones, Guillaume, additional, Koup, Richard A., additional, Doria-Rose, Nicole A., additional, Carfi, Andrea, additional, Elbashir, Sayda M., additional, Thackray, Larissa B., additional, Edwards, Darin K., additional, and Diamond, Michael S., additional

Published
2022
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26. Host network-based discovery of critical regulators of innate immunity, virus growth, and pathogenesis in influenza virus infection

Author

Eisfeld, Amie J., primary, Fan, Shufang, additional, Rao, Hongyu, additional, Venkatachalam, Backiyalakshmi Ammayappan, additional, Smith, Danielle Westhoff, additional, Halfmann, Peter J., additional, Walters, Kevin B., additional, Nair, Sharmila, additional, Thackray, Larissa B., additional, Kocher, Jacob F., additional, Sims, Amy C., additional, Mitchell, Hugh D., additional, Neumann, Gabriele, additional, Blank, Volker, additional, Waters, Katrina M., additional, Baric, Ralph S., additional, Diamond, Michael S., additional, and Kawaoka, Yoshihiro, additional

Published
2022
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27. Kathryn V. Holmes: A Career of Contributions to the Coronavirus Field

Author

Bonavia, Aurelio, primary, Dominguez, Samuel R., additional, Dveksler, Gabriela, additional, Gagneten, Sara, additional, Howard, Megan, additional, Jeffers, Scott, additional, Qian, Zhaohui, additional, Smith, Mary Kathryn, additional, Thackray, Larissa B., additional, Tresnan, Dina B., additional, Wentworth, David E., additional, Wessner, David R., additional, Williams, Richard K., additional, and Miura, Tanya A., additional

Published
2022
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28. Boosting with variant-matched or historical mRNA vaccines protects against Omicron infection in mice

Author

Ying, Baoling, primary, Scheaffer, Suzanne M., additional, Whitener, Bradley, additional, Liang, Chieh-Yu, additional, Dmytrenko, Oleksandr, additional, Mackin, Samantha, additional, Wu, Kai, additional, Lee, Diana, additional, Avena, Laura E., additional, Chong, Zhenlu, additional, Case, James Brett, additional, Ma, LingZhi, additional, Kim, Thu T.M., additional, Sein, Caralyn E., additional, Woods, Angela, additional, Berrueta, Daniela Montes, additional, Chang, Gwo-Yu, additional, Stewart-Jones, Guillaume, additional, Renzi, Isabella, additional, Lai, Yen-Ting, additional, Malinowski, Agata, additional, Carfi, Andrea, additional, Elbashir, Sayda M., additional, Edwards, Darin K., additional, Thackray, Larissa B., additional, and Diamond, Michael S., additional

Published
2022
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29. Boosting with Omicron-matched or historical mRNA vaccines increases neutralizing antibody responses and protection against B.1.1.529 infection in mice

Author

Ying, Baoling, primary, Scheaffer, Suzanne M., additional, Whitener, Bradley, additional, Liang, Chieh-Yu, additional, Dmytrenko, Oleksandr, additional, Mackin, Samantha, additional, Wu, Kai, additional, Lee, Diana, additional, Avena, Laura E., additional, Chong, Zhenlu, additional, Case, James Brett, additional, Ma, LingZhi, additional, Kim, Thu, additional, Sein, Caralyn, additional, Woods, Angela, additional, Berrueta, Daniela Montes, additional, Carfi, Andrea, additional, Elbashir, Sayda M., additional, Edwards, Darin K., additional, Thackray, Larissa B., additional, and Diamond, Michael S., additional

Published
2022
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30. Protective activity of mRNA vaccines against ancestral and variant SARS-CoV-2 strains

Author

Ying, Baoling, primary, Whitener, Bradley, additional, VanBlargan, Laura A., additional, Hassan, Ahmed O., additional, Shrihari, Swathi, additional, Liang, Chieh-Yu, additional, Karl, Courtney E., additional, Mackin, Samantha, additional, Chen, Rita E., additional, Kafai, Natasha M., additional, Wilks, Samuel H., additional, Smith, Derek J., additional, Carreño, Juan Manuel, additional, Singh, Gagandeep, additional, Krammer, Florian, additional, Carfi, Andrea, additional, Elbashir, Sayda M., additional, Edwards, Darin K., additional, Thackray, Larissa B., additional, and Diamond, Michael S., additional

Published
2022
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33. Protective activity of mRNA vaccines against ancestral and variant SARS-CoV-2 strains

Author

Ying, Baoling, primary, Whitener, Bradley, additional, VanBlargan, Laura A., additional, Hassan, Ahmed O., additional, Shrihari, Swathi, additional, Liang, Chieh-Yu, additional, Karl, Courtney E., additional, Mackin, Samantha, additional, Chen, Rita E., additional, Kafai, Natasha M., additional, Wilks, Samuel H., additional, Smith, Derek J., additional, Carreño, Juan Manuel, additional, Singh, Gagandeep, additional, Krammer, Florian, additional, Carfi, Andrea, additional, Elbashir, Sayda, additional, Edwards, Darin K., additional, Thackray, Larissa B., additional, and Diamond, Michael S., additional

Published
2021
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34. Additional file 2 of Hypergraph models of biological networks to identify genes critical to pathogenic viral response

Author

Feng, Song, Heath, Emily, Jefferson, Brett, Joslyn, Cliff, Kvinge, Henry, Mitchell, Hugh D., Praggastis, Brenda, Eisfeld, Amie J., Sims, Amy C., Thackray, Larissa B., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff-Smith, Danielle, Tan, Qing, Menachery, Vineet D., Sheahan, Timothy P., Cockrell, Adam S., Kocher, Jacob F., Stratton, Kelly G., Heller, Natalie C., Bramer, Lisa M., Diamond, Michael S., Baric, Ralph S., Waters, Katrina M., Kawaoka, Yoshihiro, McDermott, Jason E., and Purvine, Emilie

Abstract

Additional file 2. These figure is analogous to Figure 4 for additional z-score threshold z.

Published
2021
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35. Hypergraph models of biological networks to identify genes critical to pathogenic viral response

Author

Kawaoka, Yoshihiro, Stratton, Kelly G., Purvine, Emilie, Cockrell, Adam S., Feng, Song, Bramer, Lisa M., Baric, Ralph S., Menachery, Vineet D., Praggastis, Brenda, Waters, Katrina M., Joslyn, Cliff, Sheahan, Timothy P., Kvinge, Henry, Tan, Qing, Diamond, Michael S., Fan, Shufang, Thackray, Larissa B., Heath, Emily, Walters, Kevin B., Eisfeld, Amie J., McDermott, Jason E., Heller, Natalie C., Jefferson, Brett, Mitchell, Hugh D., Kocher, Jacob F., Sims, Amy C., Halfmann, Peter J., and Westhoff‑Smith, Danielle

Abstract

Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges represent significantly perturbed genes, and vertices represent individual biological samples with specific experimental conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Conclusions: Our results demonstrate the utility of using hypergraphs to represent complex biological systems and highlight central important responses in common to a variety of highly pathogenic viruses.

Published
2021
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36. Additional file 4 of Hypergraph models of biological networks to identify genes critical to pathogenic viral response

Author

Feng, Song, Heath, Emily, Jefferson, Brett, Joslyn, Cliff, Kvinge, Henry, Mitchell, Hugh D., Praggastis, Brenda, Eisfeld, Amie J., Sims, Amy C., Thackray, Larissa B., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff-Smith, Danielle, Tan, Qing, Menachery, Vineet D., Sheahan, Timothy P., Cockrell, Adam S., Kocher, Jacob F., Stratton, Kelly G., Heller, Natalie C., Bramer, Lisa M., Diamond, Michael S., Baric, Ralph S., Waters, Katrina M., Kawaoka, Yoshihiro, McDermott, Jason E., and Purvine, Emilie

Abstract

Additional file 4. This figure is analogous to Figure 4 for additional z-score threshold z.

Published
2021
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37. Additional file 3 of Hypergraph models of biological networks to identify genes critical to pathogenic viral response

Author

Feng, Song, Heath, Emily, Jefferson, Brett, Joslyn, Cliff, Kvinge, Henry, Mitchell, Hugh D., Praggastis, Brenda, Eisfeld, Amie J., Sims, Amy C., Thackray, Larissa B., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff-Smith, Danielle, Tan, Qing, Menachery, Vineet D., Sheahan, Timothy P., Cockrell, Adam S., Kocher, Jacob F., Stratton, Kelly G., Heller, Natalie C., Bramer, Lisa M., Diamond, Michael S., Baric, Ralph S., Waters, Katrina M., Kawaoka, Yoshihiro, McDermott, Jason E., and Purvine, Emilie

Abstract

Additional file 3. These figure is analogous to Figure 4 for additional z-score threshold z.

Published
2021
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38. Common Mechanism of SARS-CoV and SARS-CoV-2 Pathogenesis across Species

Author

Schafer, Alexandra, primary, Gralinski, Lisa E., additional, Leist, Sarah R., additional, Winkler, Emma S., additional, Hampton, Brea K., additional, Mooney, Michael A., additional, Jensen, Kara L., additional, Graham, Rachel L., additional, Agnihothram, Sudhakar, additional, Jeng, Sophia, additional, Chamberlin, Steven, additional, Bell, Timothy A., additional, Scobey, D. Trevor, additional, VanBlargan, Laura A., additional, Thackray, Larissa B., additional, Hock, Pablo, additional, Miller, Darla R., additional, Shaw, Ginger D., additional, Pardo Manuel de Villena, Fernando, additional, McWeeney, Shannon K., additional, Montgomery, Stephanie A., additional, Diamond, Michael S., additional, Heise, Mark T., additional, Menachery, Vineet D., additional, Ferris, Martin T., additional, and Baric, Ralph S., additional

Published
2021
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39. Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein

Author

Suryadevara, Naveen Chandra, primary, Shrihari, Swathi, additional, Gilchuk, Pavlo, additional, VanBlargan, Laura A., additional, Binshtein, Elad, additional, Zost, Seth J., additional, Nargi, Rachel S., additional, Sutton, Rachel E., additional, Winkler, Emma S., additional, Chen, Elaine C., additional, Fouch, Mallorie E., additional, Davidson, Edgar, additional, Doranz, Benjamin J., additional, Carnahan, Robert H., additional, Thackray, Larissa B., additional, Diamond, Michael S, additional, and Crowe, James E., additional

Published
2021
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40. Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein

Author

Suryadevara, Naveenchandra, primary, Shrihari, Swathi, additional, Gilchuk, Pavlo, additional, VanBlargan, Laura A., additional, Binshtein, Elad, additional, Zost, Seth J., additional, Nargi, Rachel S., additional, Sutton, Rachel E., additional, Winkler, Emma S., additional, Chen, Elaine C., additional, Fouch, Mallorie E., additional, Davidson, Edgar, additional, Doranz, Benjamin J., additional, Chen, Rita E., additional, Shi, Pei-Yong, additional, Carnahan, Robert H., additional, Thackray, Larissa B., additional, Diamond, Michael S., additional, and Crowe, James E., additional

Published
2021
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41. Enteric helminth coinfection enhances host susceptibility to neurotropic flaviviruses via a tuft cell-IL-4 receptor signaling axis

Author

Desai, Pritesh, primary, Janova, Hana, additional, White, James P., additional, Reynoso, Glennys V., additional, Hickman, Heather D., additional, Baldridge, Megan T., additional, Urban, Joseph F., additional, Stappenbeck, Thaddeus S., additional, Thackray, Larissa B., additional, and Diamond, Michael S., additional

Published
2021
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43. Intramuscular Delivery of Replicon RNA Encoding ZIKV-117 Human Monoclonal Antibody Protects against Zika Virus Infection

Author

Erasmus, Jesse H., primary, Archer, Jacob, additional, Fuerte-Stone, Jasmine, additional, Khandhar, Amit P., additional, Voigt, Emily, additional, Granger, Brian, additional, Bombardi, Robin G., additional, Govero, Jennifer, additional, Tan, Qing, additional, Durnell, Lorellin A., additional, Coler, Rhea N., additional, Diamond, Michael S., additional, Crowe, James E., additional, Reed, Steven G., additional, Thackray, Larissa B., additional, Carnahan, Robert H., additional, and Van Hoeven, Neal, additional

Published
2020
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44. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection

Author

Alsoussi, Wafaa B., primary, Turner, Jackson S., additional, Case, James B., additional, Zhao, Haiyan, additional, Schmitz, Aaron J., additional, Zhou, Julian Q., additional, Chen, Rita E., additional, Lei, Tingting, additional, Rizk, Amena A., additional, McIntire, Katherine M., additional, Winkler, Emma S., additional, Fox, Julie M., additional, Kafai, Natasha M., additional, Thackray, Larissa B., additional, Hassan, Ahmed O., additional, Amanat, Fatima, additional, Krammer, Florian, additional, Watson, Corey T., additional, Kleinstein, Steven H., additional, Fremont, Daved H., additional, Diamond, Michael S., additional, and Ellebedy, Ali H., additional

Published
2020
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45. A SARS-CoV-2 Infection Model in Mice Demonstrates Protection by Neutralizing Antibodies

Author

Hassan, Ahmed O., primary, Case, James Brett, additional, Winkler, Emma S., additional, Thackray, Larissa B., additional, Kafai, Natasha M., additional, Bailey, Adam L., additional, McCune, Broc T., additional, Fox, Julie M., additional, Chen, Rita E., additional, Alsoussi, Wafaa B., additional, Turner, Jackson S., additional, Schmitz, Aaron J., additional, Lei, Tingting, additional, Shrihari, Swathi, additional, Keeler, Shamus P., additional, Fremont, Daved H., additional, Greco, Suellen, additional, McCray, Paul B., additional, Perlman, Stanley, additional, Holtzman, Michael J., additional, Ellebedy, Ali H., additional, and Diamond, Michael S., additional

Published
2020
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46. The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid-Type I IFN Signaling Axis

Author

Winkler, Emma S., primary, Shrihari, Swathi, additional, Hykes, Barry L., additional, Handley, Scott A., additional, Andhey, Prabhakar S., additional, Huang, Yan-Jang S., additional, Swain, Amanda, additional, Droit, Lindsay, additional, Chebrolu, Kranthi K., additional, Mack, Matthias, additional, Vanlandingham, Dana L., additional, Thackray, Larissa B., additional, Cella, Marina, additional, Colonna, Marco, additional, Artyomov, Maxim N., additional, Stappenbeck, Thaddeus S., additional, and Diamond, Michael S., additional

Published
2020
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47. Potently neutralizing human antibodies that block SARS-CoV-2 receptor binding and protect animals

Author

Zost, Seth J., primary, Gilchuk, Pavlo, additional, Case, James Brett, additional, Binshtein, Elad, additional, Chen, Rita E., additional, Reidy, Joseph X., additional, Trivette, Andrew, additional, Nargi, Rachel S., additional, Sutton, Rachel E., additional, Suryadevara, Naveenchandra, additional, Williamson, Lauren E., additional, Chen, Elaine C., additional, Jones, Taylor, additional, Day, Samuel, additional, Myers, Luke, additional, Hassan, Ahmed O., additional, Kafai, Natasha M., additional, Winkler, Emma S., additional, Fox, Julie M., additional, Steinhardt, James J., additional, Ren, Kuishu, additional, Loo, Yueh-Ming, additional, Kallewaard, Nicole L., additional, Martinez, David R., additional, Schäfer, Alexandra, additional, Gralinski, Lisa E., additional, Baric, Ralph S., additional, Thackray, Larissa B., additional, Diamond, Michael S., additional, Carnahan, Robert H., additional, and Crowe, James E., additional

Published
2020
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48. Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein

Author

Zost, Seth J., primary, Gilchuk, Pavlo, additional, Chen, Rita E., additional, Case, James Brett, additional, Reidy, Joseph X., additional, Trivette, Andrew, additional, Nargi, Rachel S., additional, Sutton, Rachel E., additional, Suryadevara, Naveenchandra, additional, Chen, Elaine C., additional, Binshtein, Elad, additional, Shrihari, Swathi, additional, Ostrowski, Mario, additional, Chu, Helen Y., additional, Didier, Jonathan E., additional, MacRenaris, Keith W., additional, Jones, Taylor, additional, Day, Samuel, additional, Myers, Luke, additional, Lee, F. Eun-Hyung, additional, Nguyen, Doan C., additional, Sanz, Ignacio, additional, Martinez, David R., additional, Baric, Ralph S., additional, Thackray, Larissa B., additional, Diamond, Michael S., additional, Carnahan, Robert H., additional, and Crowe, James E., additional

Published
2020
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49. A commensal Clostridium species restricts systemic alphavirus dissemination through a type I interferon signaling axis

Author

Winkler, Emma S, primary, Thackray, Larissa B, additional, Hykes, Barry L, additional, Handley, Scott A, additional, Droit, Lindsay, additional, Andhey, Prabhakar, additional, Mack, Matthias, additional, Shrihari, Swathi, additional, Swain, Amanda, additional, Cella, Marina, additional, Colonna, Marco, additional, Artyomov, Maxim, additional, Stappenbeck, Thaddeus S, additional, and Diamond, Michael S, additional

Published
2020
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50. Immune correlates of tuberculosis disease and risk translate across species

Author

Ahmed, Mushtaq, primary, Thirunavukkarasu, Shyamala, additional, Rosa, Bruce A., additional, Thomas, Kimberly A., additional, Das, Shibali, additional, Rangel-Moreno, Javier, additional, Lu, Lan, additional, Mehra, Smriti, additional, Mbandi, Stanley Kimbung, additional, Thackray, Larissa B., additional, Diamond, Michael S., additional, Murphy, Kenneth M., additional, Means, Terry, additional, Martin, John, additional, Kaushal, Deepak, additional, Scriba, Thomas J., additional, Mitreva, Makedonka, additional, and Khader, Shabaana A., additional

Published
2020
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