Search Results - "Karthik Gangavarapu"

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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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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Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples by Quick, Joshua, Grubaugh, Nathan D, Pullan, Steven T, Claro, Ingra M, Smith, Andrew D, Gangavarapu, Karthik, Oliveira, Glenn, Robles-Sikisaka, Refugio, Rogers, Thomas F, Beutler, Nathan A, Burton, Dennis R, Lewis-Ximenez, Lia Laura, de Jesus, Jaqueline Goes, Giovanetti, Marta, Hill, Sarah C, Black, Allison, Bedford, Trevor, Carroll, Miles W, Nunes, Marcio, Alcantara, Luiz Carlos, Sabino, Ester C, Baylis, Sally A, Faria, Nuno R, Loose, Matthew, Simpson, Jared T, Pybus, Oliver G, Andersen, Kristian G, Loman, Nicholas J

“…This multiplex PCR enrichment protocol enables sequencing of Zika and other viral genomes of low abundance from clinical samples using the Illumina platform,…”
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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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A Role for Fc Function in Therapeutic Monoclonal Antibody-Mediated Protection against Ebola Virus by Gunn, Bronwyn M., Yu, Wen-Han, Karim, Marcus M., Brannan, Jennifer M., Herbert, Andrew S., Wec, Anna Z., Halfmann, Peter J., Fusco, Marnie L., Schendel, Sharon L., Gangavarapu, Karthik, Krause, Tyler, Qiu, Xiangguo, He, Shinhua, Das, Jishnu, Suscovich, Todd J., Lai, Jonathan, Chandran, Kartik, Zeitlin, Larry, Crowe, James E., Lauffenburger, Douglas, Kawaoka, Yoshihiro, Kobinger, Gary P., Andersen, Kristian G., Dye, John M., Saphire, Erica Ollmann, Alter, Galit

“…The recent Ebola virus (EBOV) epidemic highlighted the need for effective vaccines and therapeutics to limit and prevent outbreaks. Host antibodies against…”
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Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades by Klitting, Raphaëlle, Kafetzopoulou, Liana E., Thiery, Wim, Dudas, Gytis, Gryseels, Sophie, Kotamarthi, Anjali, Vrancken, Bram, Gangavarapu, Karthik, Momoh, Mambu, Sandi, John Demby, Goba, Augustine, Alhasan, Foday, Grant, Donald S., Okogbenin, Sylvanus, Ogbaini-Emovo, Ephraim, Garry, Robert F., Smither, Allison R., Zeller, Mark, Pauthner, Matthias G., McGraw, Michelle, Hughes, Laura D., Duraffour, Sophie, Günther, Stephan, Suchard, Marc A., Lemey, Philippe, Andersen, Kristian G., Dellicour, Simon

“…Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently…”
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Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas by Gardner, Lauren M, Bóta, András, Gangavarapu, Karthik, Kraemer, Moritz U G, Grubaugh, Nathan D

“…An unprecedented Zika virus epidemic occurred in the Americas during 2015-2016. The size of the epidemic in conjunction with newly recognized health risks…”
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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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High crossreactivity of human T cell responses between Lassa virus lineages by Sullivan, Brian M, Sakabe, Saori, Hartnett, Jessica N, Ngo, Nhi, Goba, Augustine, Momoh, Mambu, Demby Sandi, John, Kanneh, Lansana, Cubitt, Beatrice, Garcia, Selma D, Ware, Brian C, Kotliar, Dylan, Robles-Sikisaka, Refugio, Gangavarapu, Karthik, Branco, Luis, Eromon, Philomena, Odia, Ikponmwosa, Ogbaini-Emovon, Ephraim, Folarin, Onikepe, Okogbenin, Sylvanus, Okokhere, Peter O, Happi, Christian, de la Torre, Juan Carlos, Sabeti, Pardis C, Andersen, Kristian G, Garry, Robert F, Grant, Donald S, Schieffelin, John S, Oldstone, Michael B A

“…Lassa virus infects hundreds of thousands of people each year across rural West Africa, resulting in a high number of cases of Lassa fever (LF), a febrile…”
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Ontogeny of the B- and T-cell response in a primary Zika virus infection of a dengue-naïve individual during the 2016 outbreak in Miami, FL by Ricciardi, Michael J, Magnani, Diogo M, Grifoni, Alba, Kwon, Young-Chan, Gutman, Martin J, Grubaugh, Nathan D, Gangavarapu, Karthik, Sharkey, Mark, Silveira, Cassia G T, Bailey, Varian K, Pedreño-Lopez, Núria, Gonzalez-Nieto, Lucas, Maxwell, Helen S, Domingues, Aline, Martins, Mauricio A, Pham, John, Weiskopf, Daniela, Altman, John, Kallas, Esper G, Andersen, Kristian G, Stevenson, Mario, Lichtenberger, Paola, Choe, Hyeryun, Whitehead, Stephen S, Sette, Alessandro, Watkins, David I

“…Zika virus (ZIKV) is a mosquito-borne flavivirus of significant public health concern. In the summer of 2016, ZIKV was first detected in the contiguous United…”
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Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California by Deng, Xianding, Gu, Wei, Federman, Scot, du Plessis, Louis, Pybus, Oliver G, Faria, Nuno R, Wang, Candace, Yu, Guixia, Bushnell, Brian, Pan, Chao-Yang, Guevara, Hugo, Sotomayor-Gonzalez, Alicia, Zorn, Kelsey, Gopez, Allan, Servellita, Venice, Hsu, Elaine, Miller, Steve, Bedford, Trevor, Greninger, Alexander L, Roychoudhury, Pavitra, Starita, Lea M, Famulare, Michael, Chu, Helen Y, Shendure, Jay, Jerome, Keith R, Anderson, Catie, Gangavarapu, Karthik, Zeller, Mark, Spencer, Emily, Andersen, Kristian G, MacCannell, Duncan, Paden, Clinton R, Li, Yan, Zhang, Jing, Tong, Suxiang, Armstrong, Gregory, Morrow, Scott, Willis, Matthew, Matyas, Bela T, Mase, Sundari, Kasirye, Olivia, Park, Maggie, Masinde, Godfred, Chan, Curtis, Yu, Alexander T, Chai, Shua J, Villarino, Elsa, Bonin, Brandon, Wadford, Debra A, Chiu, Charles Y

“…The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000…”
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Many-core algorithms for high-dimensional gradients on phylogenetic trees by Gangavarapu, Karthik, Ji, Xiang, Baele, Guy, Fourment, Mathieu, Lemey, Philippe, Matsen, Frederick A, Suchard, Marc A

“…Abstract Motivation Advancements in high-throughput genomic sequencing are delivering genomic pathogen data at an unprecedented rate, positioning statistical…”
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Systematic Analysis of Monoclonal Antibodies against Ebola Virus GP Defines Features that Contribute to Protection by Saphire, Erica Ollmann, Schendel, Sharon L., Fusco, Marnie L., Gangavarapu, Karthik, Gunn, Bronwyn M., Wec, Anna Z., Halfmann, Peter J., Brannan, Jennifer M., Herbert, Andrew S., Qiu, Xiangguo, Wagh, Kshitij, He, Shihua, Giorgi, Elena E., Theiler, James, Pommert, Kathleen B.J., Krause, Tyler B., Turner, Hannah L., Murin, Charles D., Pallesen, Jesper, Davidson, Edgar, Ahmed, Rafi, Aman, M. Javad, Bukreyev, Alexander, Burton, Dennis R., Crowe, James E., Davis, Carl W., Georgiou, George, Krammer, Florian, Kyratsous, Christos A., Lai, Jonathan R., Nykiforuk, Cory, Pauly, Michael H., Rijal, Pramila, Takada, Ayato, Townsend, Alain R., Volchkov, Viktor, Walker, Laura M., Wang, Cheng-I., Zeitlin, Larry, Doranz, Benjamin J., Ward, Andrew B., Korber, Bette, Kobinger, Gary P., Andersen, Kristian G., Kawaoka, Yoshihiro, Alter, Galit, Chandran, Kartik, Dye, John M.

“…Antibodies are promising post-exposure therapies against emerging viruses, but which antibody features and in vitro assays best forecast protection are…”
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The Application of Genomic Epidemiology and the Development of Bioinformatics Tools to Support Viral Outbreak Investigation by Gangavarapu, Karthik

“…In its 2007 report, the World Health Organization (WHO) warned that new diseases are being identified at an unprecedented rate of one or more per year, with…”
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Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources by Tsueng, Ginger, Mullen, Julia L., Alkuzweny, Manar, Cano, Marco, Rush, Benjamin, Haag, Emily, Lin, Jason, Welzel, Dylan J., Zhou, Xinghua, Qian, Zhongchao, Latif, Alaa Abdel, Hufbauer, Emory, Zeller, Mark, Andersen, Kristian G., Wu, Chunlei, Su, Andrew I., Gangavarapu, Karthik, Hughes, Laura D.

“…Outbreak.info Research Library is a standardized, searchable interface of coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome coronavirus…”
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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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Analysis of CD8⁺ T cell response during the 2013–2016 Ebola epidemic in West Africa by Sakabe, Saori, Sullivan, Brian M., Hartnett, Jessica N., Robles-Sikisaka, Refugio, Gangavarapu, Karthik, Cubitt, Beatrice, Ware, Brian C., Kotliar, Dylan, Branco, Luis M., Goba, Augustine, Momoh, Mambu, Sandi, John Demby, Kanneh, Lansana, Grant, Donald S., Garry, Robert F., Andersen, Kristian G., de la Torre, Juan Carlos, Sabeti, Pardis C., Schieffelin, John S., Oldstone, Michael B. A.

“…The recent Ebola epidemic exemplified the importance of understanding and controlling emerging infections. Despite the importance of T cells in clearing virus…”
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Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic by Crits-Christoph, Alexander, Levy, Joshua I, Pekar, Jonathan E, Goldstein, Stephen A, Singh, Reema, Hensel, Zach, Gangavarapu, Karthik, Rogers, Matthew B, Moshiri, Niema, Garry, Robert F, Holmes, Edward C, Koopmans, Marion P G, Lemey, Philippe, Peacock, Thomas P, Popescu, Saskia, Rambaut, Andrew, Robertson, David L, Suchard, Marc A, Wertheim, Joel O, Rasmussen, Angela L, Andersen, Kristian G, Worobey, Michael, Débarre, Florence

“…Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan…”
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Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation by Fourment, Mathieu, Swanepoel, Christiaan J, Galloway, Jared G, Ji, Xiang, Gangavarapu, Karthik, Suchard, Marc A, Matsen IV, Frederick A

“…Abstract Gradients of probabilistic model likelihoods with respect to their parameters are essential for modern computational statistics and machine learning…”
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