Open positions
Postdoc fellowship in machine learning and pandemic preparedness
Postdoc fellowship in virology/influenza A virus (with Dr. Amy Vincent Baker)
Preprints/In Review
Grover, S., Markin, A., Anderson, T.K., and Eulenstein, O. Phylogenetic Diversity Statistics for All Clades in a Phylogeny. https://github.com/flu-crew/PD_stats
Vijendran, S., Arruda, B., Anderson, T.K., Eulenstein, O. An Active learning framework for Semantic segmentation of pulmonary histology sections using Bayesian deep learning.
Markin, A., Zanella, G.C., Arendsee, Z.W., Zhang, J., Krueger, K.M., Gauger, P.C., Vincent Baker, A.L. and Anderson, T.K. Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential. bioRxiv 2022.12.15.520479. https://doi.org/10.1101/2022.12.15.520479
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 https://doi.org/10.1101/2022.09.12.507613
Zeller, M.A., Arendsee, Z.W., Smith, G.J.D., and Anderson, T.K. classLog: Logistic regression for the classification of genetic sequences. https://github.com/flu-crew/classLog https://doi.org/10.1101/2022.08.15.503907
Wagle, S., Markin, A., Gorecki, P. Anderson, T.K., Eulenstein, O. The asymmetric cluster affinity cost.
2023
86. Hufnagel, D.E. Young, K.M., Arendsee, Z.W., Gay, L.C., Caceres, C.J., Rajao, D.S., Perez, D.R., Vincent Baker, A.L., and Anderson, T.K. (In press). Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in IAV from North American swine. Virus Evolution XX:XX. bioRxiv 2022.11.18.517097.
85. Tochetto, C., Junqueira, D.M., Anderson, T.K., Gava, D., Haach, V., Cantao, M.E., Vincent Baker, A.L., and Schaefer, R. (in press) Introductions of human-origin seasonal H3N2, H1N2, and pre-2009 H1N1 influenza viruses to swine in Brazil. Viruses XX:XX.
84. Souza, C.K., Kimble, J.B., Anderson, T.K., Arendsee, Z.W., Hufnagel, D.E., Young, K.M., Gauger, P.C., Lewis, N.S., Davis, C.T., Thor, S., and Vincent Baker, A.L. (2023). Transmission from swine-to-ferret of antigenically drifted contemporary swine H3N2 influenza A virus as indications of zoonotic risk to humans. Viruses 15(2): 331.
83. 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. (In press) Live attenuated influenza A vaccine expressing an IgA-inducing protein proteins pigs against replication and transmission. Frontiers in Virology XX: xx.
2022
82. Arendsee, Z.W., Vincent, A.L., and Anderson, T.K. smot: a python package and CLI tool for contextual phylogenetic subsampling. Journal of Open Source Software 7(80), 4193. https://doi.org/10.21105/joss.04193. https://github.com/flu-crew/smot
81. 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.. (2022). 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. Viruses 14(11): 2398. Preprint at bioRxiv 2022.09.12.507661; doi: https://doi.org/10.1101/2022.09.12.507661
80. Anderson, T.K. and Vincent, A.L. Swine influenza A viruses and pandemic preparedness. (2022). In: Animal Agriculture and Zoonoses. A One Health Perspective (Council for Agricultural Science and Technology). pp.XX-XX.
79. 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. (2022). Antigenic characterization and pandemic risk assessment of North American H1 influenza A viruses circulating in swine. Microbiology Spectrum 10(6): e01781-22.
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. (2022). 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 11(9): 967.
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. (2022). Bivalent hemagglutinin and neuraminidase influenza replicon particle vaccines protect pigs against influenza A virus without causing vaccine associated enhanced respiratory disease. Vaccine 40(38): 5569-5578.
76. Hoffman, K.S., Humphrey, N.L., Korslund, J.A., Anderson, T.K., Faaberg, K.S., Lager, K.M., and Buckley, A.C. (2022). Characterization of Senecavirus A isolates collected from the environment of U.S. sow slaughter plants. Frontiers in Veterinary Science 9: 923878.
75. Zeller, M.A., Saxena, A., Anderson, T.K., Vincent, A.L., and Gauger, P.C. (2022). 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 34(5): 8764-878
74. Neveau, M.N., Zeller, M.A., Kaplan, B.S., Souza, C.K., Gauger, P.C., Vincent, A.L., and Anderson, T.K. (2022). Genetic and antigenic characterization of an expanding H3 influenza A virus clade in US swine visualized by Nextstrain. mSphere 7(3): e00994-21. bioRxiv 2021.11.17.469008
73. Markin, A., Wagle, S., Anderson, T.K., and Eulenstein, O.E. (2022). RF-Net 2: Fast Inference of Virus Reassortment and Hybridization Networks. Bioinformatics 38(8): 2144-2152. bioRxiv 2021.05.05.442676.
72. 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.
71. 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
70. 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. (2021). The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine. Database 2021: baab078. bioRxiv 2021.04.16.439882.
69. Zeller, M.A., Chang, J., Vincent, A.L., Gauger, P.C., and Anderson, T.K. (2021). Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in United States swine. Virus Evolution 7(2): veab090. bioRxiv 2020.05.29.123828.
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
Tavis Anderson 