recent publications
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academic article
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Deng, X. D., Gu, W., Federman, S., Du Plessis, L., Pybus, O. G., Faria, N. R., Wang, C., Yu, G. X., Bushnell, B., Pan, C. Y., Guevara, H., Sotomayor-Gonzalez, A., et al.
Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California
Science
2020
369:582-587
DOI:10.1126/science.abb9263
PMID:32513865
PMCID:PMC7286545
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Sullivan, B. M., Sakabe, S., Hartnett, J. N., Ngo, N., Goba, A., Momoh, M., Sandi, J. D., Kanneh, L., Cubitt, B., Garcia, S. D., Ware, B. C., Kotliar, D., et al.
High crossreactivity of human T cell responses between Lassa virus lineages
PLoS Pathogens
2020
16
DOI:10.1371/journal.ppat.1008352; 10.1371/journal.ppat.1008352.r001; 10.1371/journal.ppat.1008352.r002; 10.1371/journal.ppat.1008352.r003; 10.1371/journal.ppat.1008352.r004
PMID:32142546
PMCID:PMC7080273
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Dellicour, S., Lequime, S., Vrancken, B., Gill, M. S., Bastide, P., Gangavarapu, K., Matteson, N. L., Tan, Y., du Plessis, L., Fisher, A. A., Nelson, M. I., Gilbert, M., et al.
Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework
Nature Communications
2020
11
DOI:10.1038/s41467-020-19122-z
PMID:33159066
PMCID:PMC7648063
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Grubaugh, N. D., Saraf, S., Gangavarapu, K., Watts, A., Tan, A. L., Oidtman, R. J., Ladner, J. T., Oliveira, G., Matteson, N. L., Kraemer, M. U. G., Vogels, C. B. F., Hentoff, A., et al.
Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic
Cell
2019
178:1057-1071
DOI:10.1016/j.cell.2019.07.018
PMID:31442400
PMCID:PMC6716374
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Grubaugh, N. D., Gangavarapu, K., Quick, J., Matteson, N. L., De Jesus, J. G., Main, B. J., Tan, A. L., Paul, L. M., Brackney, D. E., Grewal, S., Gurfield, N., Van Rompay, K. K. A., et al.
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Genome Biology
2019
20
DOI:10.1186/s13059-018-1618-7
PMID:30621750
PMCID:PMC6325816
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Saphire, E. O., Schendel, S. L., Fusco, M. L., Gangavarapu, K., Gunn, B. M., Wec, A. Z., Halfmann, P. J., Brannan, J. M., Herbert, A. S., Qiu, X. G., Wagh, K., He, S., et al.
Systematic analysis of monoclonal antibodies against Ebola virus GP defines features that contribute to protection
Cell
2018
174:938-952
DOI:10.1016/j.cell.2018.07.033
PMID:30096313
PMCID:PMC6102396
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Gunn, B. M., Yu, W. H., Karim, M. M., Brannan, J. M., Herbert, A. S., Wec, A. Z., Halfmann, P. J., Fusco, M. L., Schendel, S. L., Gangavarapu, K., Krause, T., Qiu, X., et al.
A role for Fc function in therapeutic monoclonal antibody-mediated protection against Ebola virus
Cell Host & Microbe
2018
24:221-233
DOI:10.1016/j.chom.2018.07.009
PMID:30092199
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Sakabe, S., Sullivan, B. M., Hartnett, J. N., Robles-Sikisaka, R., Gangavarapu, K., Cubitt, B., Ware, B. C., Kotliar, D., Branco, L. M., Goba, A., Momoh, M., Sandi, J. D., et al.
Analysis of CD8(+) T cell response during the 2013-2016 Ebola epidemic in West Africa
Proceedings of the National Academy of Sciences of the United States of America
2018
115:E7578-E7586
DOI:10.1073/pnas.1806200115
PMID:30038008
PMCID:PMC6094108
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Gardner, L. M., Bota, A., Gangavarapu, K., Kraemer, M. U. G., Grubaugh, N. D.
Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas
PLoS Neglected Tropical Diseases
2018
12
DOI:10.1371/journal.pntd.0006194
PMID:29346387
PMCID:PMC5790294
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Grubaugh, N. D., Ladner, J. T., Kraemer, M. U. G., Dudas, G., Tan, A. L., Gangavarapu, K., Wiley, M. R., White, S., Theze, J., Magnani, D. M., Prieto, K., Reyes, D., et al.
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Nature
2017
546:401-405
DOI:10.1038/nature22400
PMID:28538723
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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., et al.
Zika virus evolution and spread in the Americas
Nature
2017
546:411-15
DOI:10.1038/nature22402
PMID:28538734
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Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., Oliveira, G., Robles-Sikisaka, R., Rogers, T. F., Beutler, N. A., Burton, D. R., Lewis-Ximenez, L. L., et al.
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Nature Protocols
2017
12:1261-1276
DOI:10.1038/nprot.2017.066
PMID:28538739
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Griffith, M., Spies, N. C., Krysiak, K., McMichael, J. F., Coffman, A. C., Danos, A. M., Ainscough, B. J., Ramirez, C. A., Rieke, D. T., Kujan, L., Barnell, E. K., Wagner, A. H., et al.
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer
Nature Genetics
2017
49:170-174
DOI:10.1038/ng.3774
PMID:28138153
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Ricciardi, M. J., Magnani, D. M., Grifoni, A., Kwon, Y. C., Gutman, M. J., Grubaugh, N. D., Gangavarapu, K., Sharkey, M., Silveira, C. G. T., Bailey, V. K., Pedreno-Lopez, N., Gonzalez-Nieto, L., et al.
Ontogeny of the B- and T-cell response in a primary Zika virus infection of a dengue-naive individual during the 2016 outbreak in Miami, FL
PLoS Neglected Tropical Diseases
2017
11
DOI:10.1371/journal.pntd.0006000
PMID:29267278
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Gangavarapu, K., Babji, V., Meissner, T., Su, A. I., Good, B. M.
Branch: an interactive, web-based tool for testing hypotheses and developing predictive models
Bioinformatics
2016
32:2072-2074
DOI:10.1093/bioinformatics/btw117
PMID:27153723
PMCID:PMC4920125
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