Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States
Volume 184, Issue 19, 16 September 2021, Pages 4939-4952.e15
Emergence of an early SARS-CoV-2 epidemic in the United States
Volume 184, Issue 10, 13 May 2021, Pages 2587-2594.e7
Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic
Cell 2019 Volume 178, Issue 5, Pages 1057-1071.E11 (AUGUST 22, 2019)
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Genome Biology 2019 20:8
Systematic Analysis of Monoclonal Antibodies against Ebola Virus GP Defines Features that Contribute to Protection
Cell Volume 174, Issue 4, Pages 938-952.e13 (9 Aug 2018)
Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas.
PLoS Negl Trop Dis 12(1): e0006194
Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature 546, 401–405 (15 June 2017)
Zika virus evolution and spread in the Americas. Nature 546, 411–415 (15 June 2017)
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nature Protocols 12, 1261–1276 (2017)
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nature Genetics 49, 170–174 (2017).
Branch: an interactive, web-based tool for testing hypotheses and developing predictive models. Bioinformatics (2016) 32 (13): 2072-2074.
Author Details
*These authors contributed equally to this work
2020-2021
Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States
Volume 184, Issue 19, 16 September 2021, Pages 4939-4952.e15
Mark Zeller*, Karthik Gangavarapu*, Catelyn Anderson*, Allison R .Smither, John A. Vanchiere, Rebecca Rose, Daniel J. Snyder, Gytis Dudas, Alexander Watts, Nathaniel L. Matteson, Refugio Robles-Sikisaka, Maximilian Marshall, Amy K. Feehan, Gilberto Sabino-SantosJr., Antoinette R.Bell-Kareem, Laura D. Hughes, Manar Alkuzweny, Patricia Snarski, Julia Garcia-Diaz, Rona S. Scott, Lilia I. Melnik, Raphaëlle Klitting, Michelle McGraw, Pedro Belda-Ferre, Peter DeHoff, Shashank Sathe, Clarisse Marotz, Nathan D. Grubaugh, David J. Nolan, Arnaud C. Drouin, Kaylynn J. Genemaras, Karissa Chao, Sarah Topol, Emily Spencer, Laura Nicholson, Stefan Aigner, Gene W. Yeo, Lauge Farnaes, Charlotte A. Hobbs, Louise C. Laurent, Rob Knight, Emma B. Hodcroft, Kamran Khan, Dahlene N. Fusco, Vaughn S. Cooper, Phillipe Lemey, Lauren Gardner, Susanna L. Lamers, Jeremy P. Kamil, Robert F. Garry, Marc A. Suchard, Kristian G. Andersen
Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States
Volume 184, Issue 19, 16 September 2021, Pages 4939-4952.e15
Nicole L. Washington*, Karthik Gangavarapu*, Mark Zeller, Alexandre Bolze, Elizabeth T.Cirulli, Kelly M. Schiabor, Barrett Brendan B.Larsen, Catelyn Anderson, Simon White, Tyler Cassens, Sharoni Jacobs, Geraint Levan, Jason Nguyen, Jimmy M.Ramirez III, Charlotte Rivera-Garcia, Efren Sandoval, Xueqing Wang, David Wong, Emily Spencer, Refugio Robles-Sikisaka, Ezra Kurzban, Laura D.Hughes, Xianding Deng, Candace Wang, Venice Servellita, Holly Valentine, Peter De Hoff, Phoebe Seaver, Shashank Sathe, Kimberly Gietzen, Brad Sickler, Jay Antico, Kelly Hoon, Jingtao Liu, Aaron Harding, Omid Bakhtar, Tracy Basler, Brett Austin, Duncan MacCannell, Magnus Isaksson, Phillip G. Febbo, David Becker, Marc Laurent, Eric McDonald, Gene W.Yeo, Rob Knight, Louise C. Laurent, Eileende Feo, Michael Worobey, Charles Y. Chiu, Marc A.Suchard, James T.Lu, WilliamLee, Kristian G.Andersen
2019
Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic
Cell 2019 Volume 178, Issue 5, Pages 1057-1071.E11 (AUGUST 22, 2019)
Nathan D. Grubaugh*, Sharada Saraf*, Karthik Gangavarapu*, Alexander Watts, Amanda L. Tan, Rachel J. Oidtman, Jason T. Ladner, Glenn Oliveira, Nathaniel L. Matteson, Moritz U.G. Kraemer, Chantal B.F. Vogels, Aaron Hentoff, Deepit Bhatia, Danielle Stanek, Blake Scott, Vanessa Landis, Ian Stryker, Marshall R. Cone, Edgar W. Kopp IV, Andrew C. Cannons, Lea Heberlein-Larson, Stephen White, Leah D. Gillis, Michael J. Ricciardi, Jaclyn Kwal, Paola K. Lichtenberger, Diogo M. Magnani,, David I. Watkins, Gustavo Palacios, Davidson H. Hamer,, GeoSentinel Surveillance Network, Lauren M. Gardner, T. Alex Perkins,Guy Baele, Kamran Khan, Andrea Morrison, Sharon Isern, Scott F. Michael and Kristian G. Andersen
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Genome Biology 2019 20:8
Nathan D. Grubaugh*, Karthik Gangavarapu*, Joshua Quick, Nathaniel L. Matteson, Jaqueline Goes De Jesus, Bradley J. Main, Amanda L. Tan, Lauren M. Paul, Doug E. Brackney, Saran Grewal, Nikos Gurfield, Koen K. A. Van Rompay, Sharon Isern, Scott F. Michael, Lark L. Coffey, Nicholas J. Loman and Kristian G. Andersen
2018
Systematic Analysis of Monoclonal Antibodies against Ebola Virus GP Defines Features that Contribute to Protection
Cell Volume 174, Issue 4, Pages 938-952.e13 (9 Aug 2018)
Erica Ollmann Saphire, Sharon L.Schendel*, Marnie L.Fusco*, Karthik Gangavarapu*, Bronwyn M.Gunn*, Anna Z.Wec*, Peter J.Halfmann*, Jennifer M.Brannan*, Andrew S.Herbert*, Xiangguo Qiu*, Kshitij Wagh*, Shihua He, Elena E. Giorgi, James Theiler, Kathleen B.J.Pommert, Tyler B.Krause, Hannah L.Turner, Charles D.Murin, Jesper Pallesen, Edgar Davidson, Rafi Ahmed, M. Javad Aman, Alexander Bukreyev, Dennis R.Burton, James E.Crowe Jr., Carl W.Davis, George Georgiou, Florian Krammer, Christos A.Kyratsous, Jonathan R.Lai, Cory Nykiforuk, Michael H.Pauly, Pramila Rijal, Ayato Takada, Alain R.Townsend, Viktor Volchkov, Laura M.Walker, Cheng-I.Wang, Larry Zeitlin, Benjamin J.Doranz, Andrew B.Ward, Bette Korber, Gary P.Kobinger, Kristian G.Andersen, Yoshihiro Kawaoka, Galit Alter, Kartik Chandran, John M.Dyethe, Viral Hemorrhagic Fever Immunotherapeutic Consortium
Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas
Lauren M. Gardner , András Bóta, Karthik Gangavarapu, Moritz U. G. Kraemer, Nathan D. Grubaugh. PLoS Negl Trop Dis 12(1): e0006194.
2017
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Nathan D Grubaugh*, Jason T Ladner*, Moritz UG Kraemer*, Gytis Dudas*, Amanda L Tan*, Karthik Gangavarapu*, Michael R Wiley*, Stephen White*, Julien Thézé*, Diogo M Magnani, Karla Prieto, Daniel Reyes, Andrea Bingham, Lauren M Paul, Refugio Robles-Sikisaka, Glenn Oliveira, Darryl Pronty, Hayden C Metsky, Mary Lynn Baniecki, Kayla G Barnes, Bridget Chak, Catherine A Freije, Adrianne Gladden-Young, Andreas Gnirke, Cynthia Luo, Bronwyn MacInnis, Christian B Matranga, Daniel J Park, James Qu, Stephen F Schaffner, Christopher Tomkins-Tinch, Kendra L West, Sarah M Winnicki, Shirlee Wohl, Nathan L Yozwiak, Joshua Quick, Joseph R Fauver, Kamran Khan, Shannon E Brent, Robert CReiner Jr., Paola N Lichtenberger, Michael Ricciardi, Varian K Bailey, David I Watkins, Marshall R Cone, Edgar W Kopp IV, Kelly N Hogan, Andrew C Cannons, Reynald Jean, Robert F Garry, Nicholas J Loman, Nuno R Faria, Mario C Porcelli, Chalmers Vasquez, Elyse R Nagle, Derek AT Cummings, Danielle Stanek, Andrew Rambaut, Mariano Sanchez-Lockhart, Pardis C Sabeti, Leah D Gillis, ScottF Michael, Trevor Bedford, Oliver G Pybus, Sharon Isern, Gustavo Palacios, Kristian G Andersen. Nature 546, 401–405 (15 June 2017)
Zika virus evolution and spread in the Americas
Metsky, H.C., Matranga, C.B., Wohl, S., Schaffner, S.F., Freije, C.A., Winnicki, S.M., West, K., Qu, J., Baniecki, M.L., Gladden-Young, A., Lin, A.E., Tomkins-Tinch, C.H., Park, D.J., Luo, C.Y., Barnes, K.G., Chak, B., Barbosa-Lima, G., Delatorre, E., Vieira,Y.R., Paul, L.M., Tan, A.L., Porcelli, M.C., Vasquez, C., Cannons, A.C., Cone, M.R., Hogan, K.N., Kopp, E.W. IV, Anzinger, J.J., Garcia, K.F., Parham, L.A., Gélvez Ramírez, R.M., Miranda Montoya, M.C., Rojas, D.P., Brown, C.M., Hennigan, S., Sabina, B., Scotland, S., Gangavarapu, K., Grubaugh, N.D., Oliveira, G., Robles-Sikisaka, R., Rambaut, A., Gehrke, L., Smole, S., Halloran,M.E., Villar Centeno, L.A., Mattar, S., Lorenzana, I., Cerbino-Neto, J., Degrave,W., Bozza, P.T., Gnirke, A., Andersen, K.G., Isern, S., Michael, S., Bozza, F., Souza, T.M.L.,Bosch, Yozwiak, N.L., MacInnis, B.L., Sabeti,P.C. Nature 546, 411–415 (15 June 2017)
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Josh Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler, Dennis R Burton, Lia Laura Lewis-Ximenez, Jaqueline Goes de Jesus, Marta Giovanetti,Sarah Hill, Allison Black,Trevor Bedford, Miles W Carroll,Marcio Nunes, Luiz Carlos Jr. Alcantara, Ester C Sabino, Sally A Baylis, Nuno Faria, Matthew Loose, Jared T Simpson, Oliver G Pybus, Kristian G Andersen, Nicholas J Loman. Nature Protocols 12, 1261–1276 (2017)
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer
Malachi Griffith, Nicholas C Spies, Kilannin Krysiak, Joshua F McMichael, Adam C Coffman, Arpad M Danos, Benjamin J Ainscough, Cody A Ramirez, Damian T Rieke, Lynzey Kujan, Erica K Barnell, Alex H Wagner, Zachary L Skidmore, Amber Wollam, Connor J Liu, Martin R Jones, Rachel L Bilski, Robert Lesurf, Yan-Yang Feng, Nakul M Shah, Melika Bonakdar, Lee Trani, Matthew Matlock, Avinash Ramu, Katie M Campbell, Gregory C Spies, Aaron P Graubert, Karthik Gangavarapu, James M Eldred, David E Larson, Jason R Walker, Benjamin M Good, Chunlei Wu, Andrew I Su, Rodrigo Dienstmann, Adam A Margolin, David Tamborero, Nuria Lopez-Bigas, Steven J M Jones, Ron Bose, David H Spencer, Lukas D Wartman, Richard K Wilson, Elaine R Mardis & Obi L Griffith. Nature Genetics 49, 170–174 (2017).
2016
Branch: an interactive, web-based tool for testing hypotheses and developing predictive models
Karthik Gangavarapu, Vyshakh Babji, Tobias Meißner, Andrew I. Su, Benjamin M. Good. Bioinformatics (2016) 32 (13): 2072-2074.