Preprints/In Review
Markin, A., Anderson, T.K. Ordered Leaf Attachment (OLA) Vectors can Identify Reticulation Events even in Multifurcated Trees.
Wagle, S., Markin, A., Sherman, T.J., Mayo, C., Dunham, T.J., Brelsfoard, C., Cohnstaedt, L.W., Wilson, W.C., Anderson, T.K., Eulenstein, O. Objective tree measures for assessing coevolutionary dynamics.
Sarlo Davila, K.M., Wymore Brand, M., Putz, E.J., Boggiatto, P.M., Seger, H., Baker, A.L., Anderson, T.K.., Hutter, C., Buckley, A.C., Vander Plaats, A., Friedrich, R., Gordon, P., Arruda, B., Souza, C.K., Davidson, B.D., Palmer, M.V. Inoculation with highly pathogenic avian influenza H5N1 genotype D1.1 in naive dairy cows and dairy cows previously exposed to genotype B3.13.
Seger, H., Baker, A.L., Buckley, A.C., Anderson, T.K., Markin, A., Campos, A., Trinidad’s, B., Vincent, M.L., Ciacci Zanella, G., Torchetti, M., Lantz, K., Arruda, B.Systemic distribution and protracted detection of clade 2.3.4.4b highly pathogenic avian influenza A(H5N1) D1.2 in swine following experimental inoculation.
Cardenas, M.I., Chopra, P., Cowan, B., Caceres, C.J., Anderson, T.K., Baker, A.L., Perez, D.R., Boons, G-J., and Rajao, D.S. Evolution of a human H3N2 virus in pigs restricts receptor specificity for extended glycine and enhances a2,6-SA binding.
Goulart, D.B., Souza, C.K., Ciacci Zanella, G. Snyder, C., Ciacci Zanella, J., Markin, A., Arruda, B., Anderson, T.K., Baker, A.L. Pathogenesis and transmission of a reassorted H1 influenza A virus detected in North American swine.
Mollett, B.C., Byrne, A.M.P., Everett, H.E., Reid, S.M., Williamson, S., Anderson, T.K., James, J., Banyard, A.C., Brown, I.H., Lewis, N.S. Diverse genomic landscape of swine influenza A virus in England (2014-2021).
Ciacci Zanella, G., Cardenas, M.I., Hutter, C.R., Snyder, C.A., Wymore Brand, M., Arruda, B., Perez, D.R., Anderson, T.K., Rajao, D.S., Baker, A.L. Impact of maternal antibodies and weaning stress on the replication and transmission of human H3N2 influenza A in piglets.
Lopes, S., Anderson, T.K., Schaefer, R., Tochetto, C., Gava, D., Cantao, M.E., Ciacci-Zanella, J., Vincent Baker, A.L., and Lewis, N.S. Antigenic and genetic diversity of H1 and H3 influenza A viruses in swine in Brazil.
Vijendran, S., Arruda, B., Anderson, T.K., Eulenstein, O. An Active learning framework for Semantic segmentation of pulmonary histology sections using Bayesian deep learning.
2025
121. Wiarda, J.E., Arruda, B., Anderson, T.K., Anderson, S.J., Kim, H., Chang, T., Hanson, L.T., Zanella, E.L., Hau,S.J., Wymore Brand, M., Zhang, J., Buckley, A.C. (2025). Contemporary United States PRRSV 1-4-4 L1C.5 isolate causes sever disease comparable to historic highly pathogen PRRSV. Virology 615: 110748.
120. Dunham, T.J., Sherman, T.J., Reed, K.J., Brelsfoard, C., Anderson, T.K., Cohnstaedt, L.W., Stenglein, M.D., and Mayo, C.E. Optimized library preparation, sequencing, and data analysis protocols for multisegmented viruses. BMC Genomics XX:XX.
119. Chalkowski, K., Miller, R.S., Chandler, J.C., Campos, A., Arruda, B., Baker, A.L., Anderson, T.K., Klemm, J., Brown, V.R., VerCauteren, K.C., Snow, N.P., Pepin, K.M. Elevated exposure to influenza A viruses in wild pigs (Sus scrofa), Texas, USA. Journal of Wildlife Diseases XX:XX.
118. Thomas, M.N., Janzen, G.M., Markin, A., Sharma, A., Hewitt, K., Li, G., Baker, A.L., Gauger, P.C., and Anderson, T.K. (2025). Active surveillance for influenza A virus in swine reveals within-farm reassortment and cocirculation of distinct subtypes and genetic clades. Veterinary Microbiology 309: 110681.
117. Ciacci Zanella, G., Markin, A., Thomas, M., Snyder, C.A., Souza, C.K., Arruda, B., Anderson, T.K., Baker, A.L. (2025). Transmission and pathological findings of divergent human seasonal H1N1pdm09 influenza A viruses following spillover into pigs in the United States. Influenza and Other Respiratory Viruses 19: e70128.
116. Vijendran, S., Anderson, T.K., Markin, A., Eulenstein, O. (2025). Phylo-rs: an extensible phylogenetics library in Rust. BMC Bioinformatics 26: 197.
115. Janzen, G.M., Inderski, B.T., Chang, J., Arendsee, Z.W., Janas-Martindale, A., Torchetti, M.K., Baker, A.L., and Anderson, T.K. (2025). Sources and sinks of influenza A virus genomic diversity in swine from 2009 to 2022 in the United States. Journal of Virology 99: e00541-25.
114. Coggon, A., Lopes, S., Simon, G., Arendsee, Z., Chen, K-F., Chiapponi, C., Essen, S., Everett, H., Herve, S., Hufnagel, D., Mollett, B., Moreno, A., Pekosz, A., Richard, G., Rothman, R., Shaw-Saliba, K., Van Reeth, K., Venkatesh, D., Brown, I.H., Anderson, T.K., Baker, A.L., Lewis, N.S. (2025). Quantifying the zoonotic risk profile of European influenza A viruses in swine from 2010 to 2020 inclusive. Journal of Virology 99(7): e00306-25.
113. Markin, A., Macken, C.A., Baker, A.L., Anderson, T.K. (2025). Revealing reassortment in influenza A viruses with TreeSort. Molecular Biology and Evolution 42(8): msaf133
112. Anker, K.M., Ciucani, M., Nissen, J.N., Anderson, T.K., Pedersen, A.G., Trebbien, R. (2025). Exploring genetic signatures of zoonotic influenza A virus at the swine-human interface with phylogenetic and ancestral sequence reconstruction. Virus Evolution 2025: veaf028.
111. Le Sage, V., Souza, C.K., Rocket, N.C., Shepard, M., Zanella, G.C., Arruda, B., Wang, S., Drapeau, E.M., Doyle, J.D., Xu, L., Barbeau, D.J., Paulson, J.C., McElroy, A.K., Hensley, S.E., Anderson, T.K., Baker, A.L., Lakdawala, S.S. (2025). Eurasian 1C swine influenza A virus exhibits high pandemic risk traits. Emerging Microbes & Infections 14(1): 2492210.
110. Nguyen, T., Hutter, C., Markin, A., Thomas, M., Lantz, K., Killian, M.L., Janzen, G.M., Vijendran, S., Wagle, S., Inderksi, B., Magstadt, D.R., Li, G., Diel, D.G., Frye, E.A., Dimitrov, K.M., Swinford, A.K., Thompson, A.C., Snekvik, K.R., Suarez, D.L., Lakin, S.M., Schwabenlander, S. Ahola, S.C., Johnson, K.R., Baker, A.L., Robbe-Austerman, S., Torchetti, M.K., and Anderson, T.K. (2025). Emergence and spread of highly pathogenic avian influenza A(H5N1) in dairy cattle in the United States. Science 388(6745): eadq0900.
109. VanderWaal, K., Pamornchainavakul, N., Kikuti, M., Zhang, J., Zeller, M., Trevisan, G., Rossow, S., Schwartz, M., Linhares, D., Holtkamp, D., da Silva, J., Corzo, C., Baker, J., Anderson, T.K., Makau, D., Paploski, I. (2025). PRRSV-2 variant classification: a dynamic nomenclature for enhanced monitoring and surveillance. mSphere 10(2): e00709-24.
108. Wannarat Yim-im, Anderson, T.K., Bohmer, J., Balielles, J., Stadejek, T., Gauger, P.C., Kreuger, K.M., and Zhang, J. (2025). Refining genetic classification of global type 1 porcine reproductive and respiratory syndrome virus and characterization of geographic and dynamic distribution. Veterinary Microbiology 302: 110413.
2024
107. Moraes, D.C.A., Zeller, M.A., Thomas, M.N., Anderson, T.K., Linhares, D.C.L., Baker, A.L., Silva, G.S., Gauger, P.C. (2024). Influenza A Virus Detection at the Human–Swine Interface in US Midwest Swine Farms. Viruses 16: 1921.
106. Cardenas, M. Seibert, B., Cowan, B., Caceres, C.J., Gay, L.C., Faccin, F.C., Perez, D.R., Baker, A.L., Anderson, T.K., Rajao, D.S. (2024). Modulation of human-to-swine influenza A virus adaptation by the neuraminidase low-affinity calcium-binding pocket. Communications Biology 7(1): 1230.
105. Powell, J.D., Thomas M.N., Anderson T.K., Zeller M.A., Gauger P.C., Vincent Baker AL. (2024). 2018-2019 human seasonal H3N2 influenza A virus spillovers into swine with demonstrated virus transmission in pigs were not sustained in the pig population. Journal of Virology 98(12): e00087-24.
104. Baker, A.L., Arruda, B., Palmer, M.V., Boggiatto, P., Sarlo Davila, K., Buckley, A., Ciacci Zanella, G., Snyder, C.A., Anderson, T.K., Hutter, C., Nguyen, T-Q., MArkin, A., Lantz, K., Posey, E.A., Torchetti, M. Robbe-Austerman, S., Magstadt, D.R., Gorden, P.J. (2024). Dairy cows inoculated with highly pathogen avian influenza virus H5N1. Nature 637: 913-920.
103. VanderWaal, K., Pamornchainvakul, N., Kikuti, M., Linhares, D., Trevisan, G., Zhang, J., Anderson, T.K., Zeller, M.A., Rossow, S., Holtkamp, D.J., Makau, D.N., Corzo, C.A., Paploski, I.A.D. (2024). Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility. Frontiers in Virology 4: 2024.1433931.
102. Zeller, M.A., Moraes, D.C.A., Ciacci Zanella, G., Souza, C.K., Anderson, T.K., Baker, A.L., and Gauger, P.C. (2024). Reverse zoonosis of the 2022-2023 human seasonal H3N2 detected in swine. npj Viruses 2: 27.
101. Fausett, E., Kirstein, O.D., Bellman, S., Long, A., Roeske, I., Cheng, C., Piantadosi, A., Anderson, T.K., and Vazquez-Prokopec, G.M. (2024). Surveillance and detection of the Asian longhorned tick, Haemaphysalis longicornis (Ixodida: Ixodidae), in protected areas from Georgia, USA. Journal of Medical Entomology 61(4): 1071-1076.
100. Le Sage, V., Rocket, N.C., McCarthy, K.R., French, A.J., Shepard, M.J., McBride, R., Jones, J.E., Walter, S.G., Doyle, J.D., Xu, L., Barbeau, D,J., Wang, S., Frizzell, S.A., Rigatti, L.H., Myerburg, M.M., Paulson, J.C., McElroy, A.K., Anderson, T.K., Vincent Baker, A.L., Lakdawala, S.S. (2024). Potential pandemic risk of circulating swine H1N2 influenza viruses. Nature Communications 15(1): 5025.
99. Arruda, B., Vincent Baker, A.L., Buckley, A., Anderson, T.K., Torchetti, M., Hines Bergeson, N., Killian, M.L., Lantz, K. (2024). Divergent pathogenesis and transmission among avian and mammalian isolates of highly pathogenic avian influenza virus (H5N1) in swine. Emerging Infectious Diseases 30(4): 738.
98. Cardenas, M., Seibert, B., Cowan, B., Fraiha, A.L.S., Carnaccini, S., Gay, L.C., Faccin, F.C., Caceres, C.J., Anderson, T.K., Vincent Baker, A.L., Perez, D.R., and Rajao, D.S. (2024). Amino Acid 138 in the HA of a H3N2 subtype influenza A virus increases affinity for the lower respiratory tract and alveolar macrophages in pigs. PLOS Pathogens 20(2): e1012026.
97. Thomas, M.N., Ciacci Zanella, G., Cowan, B., Joaquin Caceres, C., Rajao, D.S., Perez, D.R., Gauger, P.C., Vincent Baker, A.L., and Anderson, T.K. (2024). Nucleoprotein reassortment enhanced transmissibility of H3 1990.4.a clade influenza A virus in swine. Journal of Virology 98(3): e01703-23.
96. Anderson, T.K., Medina, R., and Nelson, M.I. (2024). The evolution of SARS-CoV-2 and influenza A virus at the human-animal interface. In: Genetics and Evolution of Infectious Disease, 3rd edition (ed: Tibayrenc, M.). pp 549-572.
95. Wagle, S., Markin, A., Gorcki, P., Anderson, T.K., Eulenstein, O. (2024). Asymmetric Cluster-based Measures for Comparative Phylogenetics. Journal of Computational Biology 31(4): 312-327.
2023
94. Zeller, M.A., Arendsee, Z.W., Smith, G.J.D., and Anderson, T.K. (2023). classLog: Logistic regression for the classification of genetic sequences. Frontiers in Virology 3: 1215012. https://github.com/flu-crew/classLog
93. Yim-im, W. Anderson, T.K., Paploski, I.A.D., VanderWaal, K., Gauger, P.C., Krueger, K.M., Shi, M., Main, R., and Zhang, J. (2023). Refining PRRSV-2 genetic classification based on global ORF5 sequences and investigation of their geographic distributions and temporal changes. Microbiology Spectrum 11(6): e02916-23.
92. Junqueira, D.M., Tochetto, C., Anderson, T.K., Gava, D., Haach, V., Cantao, M.E., Vincent Baker, A.L., and Schaefer, R. (2023). Human-to-swine introductions and onward transmission of 2009 H1N1 pandemic influenza viruses in Brazil. Frontiers in Microbiology 14(2023): 1243567.
91. Markin, A., Zanella, G.C., Arendsee, Z.W., Zhang, J., Krueger, K.M., Gauger, P.C., Vincent Baker, A.L. and Anderson, T.K. (2023). Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential. PLOS Pathogens 19(7): e1011476.
90. Arruda, B.L., Kanefsky, R.A., Hau, S., Janzen, G.M., Anderson, T.K., Vincent Baker, A.L. (2023). Mucin 4 is a cellular biomarker of necrotizing bronchiolitis in influenza A virus infection. Microbes and Infection 25(2023): 105169.
89. Markin, A., Wagle, S., Grover, S., Vincent Baker, A.L., Eulenstein, O., and Anderson, T.K. (2023). PARNAS: Objectively selecting the most representative taxa on a phylogeny. Systematic Biology 72(5): 1052-1063. https://github.com/flu-crew/parnas
88. Grover, S., Markin, A., Anderson, T.K., and Eulenstein, O. (2023) Phylogenetic Diversity Statistics for All Clades in a Phylogeny. Bioinformatics 39(S1): i177-i184. (ISMB/ECCB 2023). https://github.com/flu-crew/PD_stats
87. Wagle, S., Markin, A., Gorecki, P. Anderson, T.K., Eulenstein, O. (2023). The asymmetric cluster affinity cost. Lecture Notes in Bioinformatics p.131-145. Special Issue for Research in Computational Molecular Biology Focused on Comparative Genomics (RECOMB-CG 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. (2023). Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in IAV from North American swine. Virus Evolution 9(1): vead015.
85. Tochetto, C., Junqueira, D.M., Anderson, T.K., Gava, D., Haach, V., Cantao, M.E., Vincent Baker, A.L., and Schaefer, R. (2023) Introductions of human-origin seasonal H3N2, H1N2, and pre-2009 H1N1 influenza viruses to swine in Brazil. Viruses 15(2): 576.
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. (2023) Live attenuated influenza A vaccine expressing an IgA-inducing protein proteins pigs against replication and transmission. Frontiers in Virology 3: 1042724
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Tavis Anderson 