Publications

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
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. (Under Review at Nature)

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. (Under Review at Nature)

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. (Under review at Nature Protocols)

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.