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Postdoc fellowship in machine learning and pandemic preparedness

Postdoc fellowship in virology/influenza A virus (with Dr. Amy Vincent Baker)

Preprints/In Review

Kimble, J.B., Souza, C.K., Anderson, T.K., Arendsee, Z.W., Hufnagel, D.E., Young, K.M., Lewis, N.S., Davis, C.T., Vincent Baker, A.L.. Interspecies transmission from pigs to ferrets of antigenically distinct swine H1 influenza A viruses with loss in reactivity to human vaccine virus antisera as measures of relative zoonotic risk. bioRxiv 2022.09.12.507661; doi: https://doi.org/10.1101/2022.09.12.507661

Anderson, T.K. and Vincent, A.L. Swine influenza A viruses and pandemic preparedness.

Arendsee, Z.W., Vincent, A.L., and Anderson, T.K. smot: a python package and CLI tool for contextual phylogenetic subsampling. https://github.com/flu-crew/smot

Markin, A., Wagle, S., Grover, S., Vincent Baker, A.L., Eulenstein, O., and Anderson, T.K. PARNAS: Objectively selecting the most representative taxa on a phylogeny. https://github.com/flu-crew/parnas

Zeller, M.A., Arendsee, Z.W., Smith, G.J.D., and Anderson, T.K. classLog: Logistic regressions for the classification of genetic sequences. https://github.com/flu-crew/classLog

Venaktesh, D., Anderson, T.K., Kimble, J.B., Chang, J., Lopes, S., Souza, C.K., Pekosz, A., Shaw-Saliba, K., Rothman, R.E., Chen, K-F., Lewis, N.S., and Vincent, A.L. Antigenic characterization and pandemic risk assessment of North American H1 influenza A viruses circulating in swine.

Rajao, D.S., Zanella, G.C., Brand, M.W., Khan, S., Ferrari, L.M., Caceres, C.J., Cadernas-Garcia, S., Souza, C.K. Anderson, T.K., Gauger, P.C., Vincent Baker, A.L., Perez, D.R. Live attenuated influenza A vaccine expressing an IgA-inducing protein proteins pigs against replication and transmission.

2022

78. Rajao, D.S., Abente, E.J., Powell, J.D., Bolton, M.J., Gauger, P.C., Arruda, B., Anderson, T.K., Sutton, T.C., Perez, D.R., and Vincent Baker, A.L. (In press). Changes in the hemagglutinin and internal gene segments were needed for human seasonal H3 influenza A virus to efficiently infect and replicate in swine. Pathogens XX:XX.

77. Brand, M.W., Anderson, T.K., Kitikoon, P., Kimble, J.B., Otis, N., Gauger, P.C., Souza, C.K., Kaplan, B., Mogler, M., Strait, E., and Vincent Baker, A.L. (In press). Bivalent hemagglutinin and neuraminidase influenza replicon particle vaccines protect pigs against influenza A virus without causing vaccine associated enhanced respiratory disease. Vaccine XX:XX.

76. Hoffman, K.S., Humphrey, N.L., Korslund, J.A., Anderson, T.K., Faaberg, K.S., Lager, K.M., and Buckley, A.C. (In press). Characterization of Senecavirus A isolates collected from the environment of U.S. sow slaughter plants. Frontiers in Veterinary Science XX:XX.

75. Zeller, M.A., Saxena, A., Anderson, T.K., Vincent, A.L., and Gauger, P.C. (in press). Use of the ISU FLUture multisequence tool for rapid interpretation of swine influenza A virus sequences in the United States. Journal of Veterinary Diagnostic Investigation XX:XX.

74. Neveau, M.N., Zeller, M.A., Kaplan, B.S., Souza, C.K., Gauger, P.C., Vincent, A.L., and Anderson, T.K. (in press). Genetic and antigenic characterization of an expanding H3 influenza A virus clade in US swine visualized by Nextstrain. mSphere XX:XX. bioRxiv 2021.11.17.469008

73. Markin, A., Wagle, S., Anderson, T.K., and Eulenstein, O.E. (in press). RF-Net 2: Fast Inference of Virus Reassortment and Hybridization Networks. Bioinformatics XX:XX. bioRxiv 2021.05.05.442676.

72. Anderson, T.K., Inderski, B., Diel, D., Hause, B., Porter, E., Clement, T., Nelson, E., Bai, J., Christopher-Hennings, J., Gauger, P., Zhang, J., Harmon, K., Main, R., Lager, K., and Faaberg, K. (in press). The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine. Database XX:XX. bioRxiv 2021.04.16.439882.

71. Zeller, M.A., Chang, J., Vincent, A.L., Gauger, P.C., and Anderson, T.K. (in press). Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in United States swine. Virus Evolution XX: XX. bioRxiv 2020.05.29.123828.

70. Souza, C.K., Anderson, T.K., Chang, J., Venkatesh, D., Lewis, N.S., Pekosz, A., Shaw-Saliba, K., Rothman, R.E., Chen, K-F, Vincent, A.L. (2022). Antigenic distance between North American swine and human seasonal H3N2 influenza A viruses as an indication of zoonotic risk to humans. Journal of Virology 96(2): e01374-21.

69. Sharma, A., Zeller, M.A., Souza, C., Anderson, T.K., Vincent, A.L., Harmon, K., Li, G., Zhang, J., and Gauger, P.C. (2022). Characterization of a 2016-17 human-seasonal H3 influenza A virus spillover now endemic in United States swine. mSphere e00809-21.

2021

68. Arendsee, Z.W., Chang, J., Hufnagel, D.E., Markin, A., Janas-Martindale, A., Vincent, A.L., and Anderson, T.K. (2021). octoFLUshow: an interactive tool describing spatial and temporal trends in the genetic diversity of influenza A virus in U.S. swine. Microbiology Resource Announcements 10(5): e01081-21. octoFLUshow interactive tool available at https://flu-crew.org

67. Staton, M., Cannon, E., Sanderson, L., Wegrzyn, J., Anderson, T.K., Buehler, S., Cobo-Simon, I. Faaberg, K., Grau, E., Guignon, V., Gunoskey, J., Inderksi, B., Jung, S., Lager, K., Main, D., Poelchau,m M., Ramnath, R., Richter, P., West., J., and Ficklin, S. (2021). Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic, and breeding databases. Briefings in Bioinformatics 22(6): bbab238.

66. Kaplan, B.S., Anderson, T.K., Chang, J., Santos, J., Perez, D., Lewis, N.S., and Vincent, A.L. (2021). Evolution and antigenic advancement of N2 neuraminidase of swine influenza A viruses circulating in the United States following two separate introductions from humans seasonal viruses. Journal of Virology 95(2): e00632-21.

65. Zeller, M.A., Gauger, P.C., Arendsee, Z.W., Souza, C.K., Vincent, A.L., and Anderson, T.K. (2021). Machine learning prediction and experimental validation of antigenic drift in H3 influenza A viruses in swine. mSphere 6(2): e00920-20.  bioRxiv 2020.08.07.238279; https://doi.org/10.1101/2020.08.07.238279

64. Powell, J.D., Abente, E.J., Chang, J., Souza, C.K., Rajao, D.S., Anderson, T.K., Zeller, M.A., Gauger, P.G., Lewis, N.S., and Vincent, A.L. (2021). Characterization of contemporary 2010.1 H3N2 swine influenza A viruses circulating in United States pigs. Virology 553: 94-101.

63. Anderson, T.K., Chang, J., Arendsee, Z.W., Venkatesh, D., Souza, C.K., Kimble, J.B., Lewis, N.S., Davis, C.T., and Vincent, A.L. (2021). Swine influenza A viruses and the tangled relationship with humans. In: Influenza: The Cutting Edge (Eds. Y. Kawaoka and G. Neumann). Cold Spring Harbor Perspectives in Medicine, 11(3): a038737.

2020

62. Nicholson, T.L., Waack, U., Anderson, T.K., Bayles, D., Zaia, S.R., Goertz, I., Eppinger, M., Hau, S.J., Brockmeier, S.L., and Shore, S.M. (2020). Comparative virulence and genomic analysis of Streptococcus suis isolates. Frontiers in Microbiology 11: 620843.

61. Kaplan, B.S., Kimble, J.B., Chang, J., Anderson, T.K., Gauger, P.C., Janas-Martindale, A., Killian, M.L., Bowman, A.S., and Vincent, A.L. (2020). Aerosol transmission from infected swine to ferrets of a swine H3N2 virus collected from an agricultural fair and associated with human variant infections. Journal of Virology 94(16): e01009-20.

60. Sharma, A., Zeller, M.A., Li, G., Harmon, K.M., Zhang, J., Hoang, H., Anderson, T.K., Vincent, A.L., and Gauger, P.C. (2020). Diagnostic detection of live attenuated influenza vaccine virus and evidence of reassortment in United States swine. The Journal of Veterinary Diagnostic Investigation 32(2): 301-311.

59. Rambo-Martin, B.L.,  Keller, M.W.,  Wilson, M.M., Nolting, J.M., Anderson, T.K., Vincent, A.L., Bagal, U., Jang, Y., Neuhaus, E.B., Davis, C.T., Bowman, A.S., Wentworth, D.E., and Barnes, J.R. (2020). Influenza A virus field surveillance at a swine-human interface. mSphere 5(1): e00822-19. bioRxiv: 585588; bioRxiv Preprint.

58. Vincent, A.L., Anderson, T.K., and Lager, K.M. (2020). A brief introduction to influenza A virus in swine. In: Animal Influenza Virus (Methods in Molecular Biology 1161) (Ed. E. Spackman). pp. 249-271. Springer.

For full listing see: Google Scholar or My NCBI Collection