My NCBI Collection

Zeller, M.A., Chang, J., Vincent, A.L., Gauger, P.C., and Anderson, T.K. Coordinated evolution between N2 neuraminidase and H1 and H3 hemagglutinin genes increased influenza A virus genetic diversity in swine. bioRxiv ; bioRxiv Preprint.


In press and 2020

65. Zeller, M.A., Gauger, P.C., Arendsee, Z.W., Souza, C.K., Vincent, A.L., and Anderson, T.K. (in press). Machine learning prediction and experimental validation of antigenic drift in H3 influenza A viruses in swine. mSphere XX:XX.  bioRxiv 2020.08.07.238279;

64. 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. (in press). Comparative virulence and genomic analysis of Streptococcus suis isolates. Frontiers in Microbiology XX:XX.

63. 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. (in press). Characterization of contemporary 2010.1 H3N2 swine influenza A viruses circulating in United States pigs. Virology XX:XX.

62. 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. (in press). 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 XX:XX.

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

60. 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. (in press). Swine influenza A viruses and the tangled relationship with humans. In: Influenza: The Cutting Edge (Eds. Y. Kawaoka and G. Neumann). pp. XX-XX. Cold Spring Harbor Perspectives.

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. 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.. (in press). A Brief Introduction to Influenza A Virus in Swine. In: Animal Influenza Virus (Methods in Molecular Biology 1161) (Ed. E. Spackman). pp. XX-XX. Springer.




57. Alfieri, J.M. and Anderson, T.K. (2019). Local and regional urbanization: Correlates of parasite community composition and richness in the salt marsh fishFundulus heteroclitus. PLoS ONE 14(12): e0225896. bioRxiv: 404756; bioRxiv Preprint. Part of a special edition on Urban Ecosystems linked here: PLoS ONE Collection.

56. Tabaszewski, P., Gorecki, P., Markin, A., Anderson, T. and Eulenstein, O. (2019). Consensus of all Solutions for Intractable Phylogenetic Tree Inference. IEEE/ACM Transactions on Computational Biology and Bioinformatics XX:XX.

55. Chang, J.*, Anderson, T.K.*, Zeller, M.A.*, Gauger, P.C., and Vincent, A.L. (2019). octoFLU: Automated classification to evolutionary origin of influenza A virus gene sequences detected in U.S. swine. Microbiology Resource Announcements 8 (32), e00673-19. Github repo. *These authors contributed equally.

54. Register, K.B., Jelinski, M.D., Waldner, M., Boatwright, W.D., Anderson, T.K., Hunter, D.L., Hamilton, R.G., Burrage, P., Shury, T., Bildfell, R., Wolff, P.L., Miskimins, D., Derscheid, R.J., and Woodbury, M.R. (2019). Comparison of multilocus sequence types found among recent North American isolates of Mycoplasma bovis from cattle, bison and deer. The Journal of Veterinary Diagnostic Investigation 31 (6): 899-904.

53. Markin, A., Anderson, T.K., Vadali, V.S.K.T., Eulenstein, O. (2019). Robinson-Foulds Reticulation Networks. Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics pp77-86. Preprint available at bioRxiv: 642973; preprint.

52. Walia, R.R.*, Anderson, T.K.*, and Vincent, A.L. (2019). Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016. Influenza and Other Respiratory Viruses 2019(13): 262-273. *These authors contributed equally.

51. Bolton, M.J., Abente, E.A., Venkatesh, D., Stratton, J.A., Zeller, M., Anderson, T.K., Lewis, N.S., and Vincent, A.L. (2019). Antigenic evolution of H3N2 influenza A viruses in swine in the United States from 2012 to 2016. Influenza and Other Respiratory Viruses 13(1): 83-90.


50. Zeller, M.A., Li, G., Harmon, K., Zhang, J., Vincent, A.L., Anderson, T.K., and Gauger, P. C. (2018). Complete genome sequences of two novel human-like H3N2 influenza A viruses A/swine/Oklahoma/65980/2017(H3N2) and A/swine/Oklahoma/65260/2017(H3N2) detected in swine in the United States. Microbiology Resource Announcements 7(20): e01203-18.

49. Zeller, M.A., Anderson, T.K., Walia, R.W., Vincent, A.L., and Gauger, P.C., (2018). ISU FLUture: a veterinary diagnostic laboratory web-based platform to monitor the temporal genetic patterns of influenza A virus in swine. BMC Bioinformatics 19(1): 397.

48. Nelson, C.W., Sibley, S.D., Hamer, G.L., Newman, C.M., Anderson, T.K., Walker, E.D., Kitron, U.D., Brawn, J.D., Ruiz, M.O., and Goldberg, T.L. (2018). Selective constraint and adaptive potential of West Nile virus within and among naturally infected avian hosts and mosquito vectors. Virus Evolution 4(1): vey013.

47. Chen, Q., Wang, L., Yang, C., Zheng, Y., Gauger, P.C., Anderson, T.K., Harmon, K.M., Zhang, J., Yoon, K-J., Main, R.G., and Li, G. (2018). The emergence of novel sparrow deltacorornaviruses in the United States more closely related to porcine deltacoronaviruses than sparrow deltacoronavirus HKU17. Emerging Microbes and Infections 7(1): 1-4.

46. Rajao, D.S., Anderson, T.K., Kitikoon, P., Stratton, J., Lewis, N.S., and Vincent, A.L. (2018). Antigenic and genetic evolution of contemporary swine H1 influenza viruses in the United States. Virology 518: 45-54.

45. van Geelen, A.G., Anderson, T.K., Lager, K.M., Das, P.B., Otis, N.J., Montiel, N.A., Miller, L.C., Kulshreshtha, V., Buckley, A.C., Brockmeier, S.L., Zhang, J., Gauger, P.C., Harmon, K.M., and Faaberg, K.S. (2018). Porcine Reproductive and Respiratory Disease Virus: Evolution and Recombination Yields Distinct ORF5 RFLP 1-7-4 Viruses with Individual Pathogenicity. Virology 513: 168-179.


44. Vincent, A.L., Anderson, T.K., Macken, C.A., Zhang, Y., Lewis, N.S., and Scheuermann, R.H. (2017). OFFLU swine influenza experts develop global nomenclature system and automated annotation tool for H1 hemagglutinin genes of influenza A viruses. OIE-World Organization for Animal Health, Bulletin2017(3): 106-113.

43. Gao, S., Anderson, T.K., Walia, R.R., Dorman, K.S., Janas-Martindale, A., and Vincent, A.L. (2017). The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016. Journal of General Virology 98: 2001-2010.

42. Bowman, A.S., Walia, R.R., Nolting, J.M., Vincent, A.L., Killian, M.L., Zentkovich, M.M., Lorbach, J.N., Lauterbach, S.E., Anderson, T.K., Davis, C.T., Zanders, N., Jones, J., Jang, Y., Lynch, B., Rodriguez, M.R., Blanton, L., Lindstrom, S.E., Wentworth, D.E., Schiltz, J., Averill, J.J., Forshey, T. (2017). Emerging influenza A (H3N2) virus in swine responsible for zoonotic transmission at agricultural fairs, Michigan and Ohio, USA, 2016. Emerging Infectious Diseases 23: 1551-1555.

41. Newman, C.M., Krebs, B.L., Anderson, T.K., Hamer, G.L., Ruiz, M.O., Brawn, J.D., Brown, W.M., Kitron, U.D., and Goldberg, T.L. (2017). Culex flavivirus during West Nile virus epidemic and inter-epidemic years in Chicago, USA. Vector-Borne and Zoonotic Diseases 17: 567-575.

40. Abente, E.J. Kitikoon, P., Lager, K.M., Gauger, P.C., Anderson, T.K., and Vincent, A.L. (2017). A highly pathogenic avian influenza virus H5N1 with 2009 pandemic H1N1 internal genes demonstrates increased replication and transmission in pigs. Journal of General Virology 98: 18-30.

39. Vincent, A.L., Perez, D.R., Rajao, D.S., Anderson, T.K., Abente, E.J., Walia, R.R., and Lewis, N.S. (2017). Influenza A virus vaccines for swine. Veterinary Microbiology 206: 35-44.

38. Zhang, Y., Aevermann, B.D., Anderson, T.K., Burke, D.F., Dauphin, G., Gu, Z., He, S., Kumar, S., Larsen, C.N., Lee, A.J., Li, X., Macken, C.M., Mahaffey, C., Pickett, B.E., Reardon, B., Smith, T., Stewart, L., Suloway, C., Sun, G., Tong, L., Vincent, A.L., Walters, B., Zaremba, S., Zhao, H., Zhou, L., Zmasek, C., Klem, E.B., and Scheuermann, R.H. (2017). Influenza Research Database: An Integrated Bioinformatics Resource for Influenza Virus Research. Nucleic Acids Research 45: D466-D474.


37. Anderson, T.K., Macken, C.A., Lewis, N.S., Scheuermann, R.H., Van Reeth, K., Brown, I.H., Swenson, S.L., Simon, G., Saito, T., Berhane, Y., Ciacci-Zanella, J., Pereda, A., Davis, C.T., Donis, R.O., Webby, R.J., and Vincent, A.L. (2016). A phylogeny-based global nomenclature system and automated annotation tool for H1 hemagglutinin genes from swine influenza A viruses. mSphere 1(6): e00275-16.

36. Abente, E.J., Santos, J., Lewis, N.S., Gauger, P.C., Stratton, J., Skepner, E., Anderson, T.K., Rajao, D.S., Perez, D.R., and Vincent, A.L. (2016). The molecular determinants of antibody recognition and antigenic drift in the H3 hemagglutinin of swine influenza A virus. Journal of Virology 90: 8266 –8280.

35. Karki, S., Hamer, G.L., Anderson, T.K., Goldberg, T.L., Kitron, U.D., Krebs, B.L., Walker, E.D., and Ruiz, M.O. (2016). Effect of trapping methods, weather, and landscape on estimates of the Culex vector mosquito abundance. Environmental Health Insights 10: 93103.

34. Abente, E.J., Anderson, T.K., Rajao, D.S., Swenson, S.L., Gauger, P.C., and Vincent, A.L. (2016). The avian-origin H3N2 canine influenza virus that recently emerged in the United States has limited replication in swine. Influenza and Other Respiratory Viruses 10: 429432.

33. Lewis, N.S., Russell, C.A., Langat, P., Anderson, T.K., Berger, K., Bielejec, F., Burke, D.F., Dudas, G., Fonville, J.M., Fouchier, R.A.M., Kellam, P., Koel, B.F., Lemey, P., Nguyen, T., Nuansrichy, B., Peiris, J.S.M., Saito, T., Simon, G., Skepner, E., Takemae, N., ESNIP3 consortium, Webby, R., Van Reeth, K., Brookes, S.M., Larsen, L., Watson, S.J., Brown, I.H., and Vincent, A.L. (2016). The global antigenic diversity of swine influenza A viruses. eLife 5: e12217.

32. Anderson, T.K. and Sukhdeo, M.V.K. (2016). The worm’s eye view of community ecology. In: A Century of Parasitology: Discoveries, ideas, and lessons learned by scientists who published in The Journal of Parasitology 1914-2014 (Eds. John Janovy, Jr. and Gerald W. Esch). pp. 110-130. John Wiley and Sons.

31. Newman, C.M., Anderson, T.K., and Goldberg, T.L. (2016). Decreased flight activity in Culex pipiens (Diptera: Culicidae) naturally infected with Culex flavivirus. Journal of Medical Entomology 53: 233-236.


30. Rajão, D.S., Gauger, P.C., Anderson, T.K., Lewis, N.S., Abente, E.J., Killian, M.L., Perez, D.R., Sutton, T.C., Zhang, J., and Vincent A.L. (2015). Novel reassortant human-like H3N2 and H3N1 influenza A viruses detected in pigs are virulent and antigenically distinct from endemic viruses. Journal of Virology 89: 11213-11222.

29. McKee, E.M., Walker, E.D., Anderson, T.K., Kitron, U.D., Brawn, J.D., Krebs, B.L., Newman, C.M., Ruiz, M.O., Levine, R.S., Carrington, M.E., Goldberg, T.L., and Hamer, G.L. (2015). West Nile virus antibody decay rate in free-ranging birds. Journal of Wildlife Diseases 51: 601-608.

28. Anderson, T.K., Campbell, B.A., Nelson, M.I., Lewis, N.S., Janas-Martindale, A., Killian, M.L., and Vincent, A.L. (2015). Characterization of cocirculating swine influenza A viruses in North America and the identification of a novel H1 genetic clade with antigenic significance. Virus Research 201: 24-31.

27.  Henningson, J.N., Rajao, D.S., Kitikoon, P., Lorusso, A., Culhane, M.R., Lewis, N.S., Anderson, T.K., Vincent, A.L. (2015). Comparative virulence of wild-type H1N1pdm09 influenza A isolates in swine. Veterinary Microbiology 176: 40-49.


26. Krebs, B.L., Anderson, T.K., Goldberg, T.L., Hamer, G.L., Kitron, U.D., Newman, C.M., Ruiz, M.O., Walker, E.D., and Brawn, J.D. (2014). Host group formation decreases exposure to vector-borne disease: a field experiment in a “hotspot” of West Nile virus transmission. Proceedings of the Royal Society B: Biological Sciences 281: 20141586.

25. Vincent, A.L., Lager, K.M. and Anderson, T.K. (2014). A Brief Introduction to Influenza A Virus in Swine. In: Animal Influenza Virus (Methods in Molecular Biology 1161) (Ed. E. Spackman). pp. 243-258. Springer.

24. Kamlangdee, A., Kingstad-Bakke, B., Anderson, T.K., Goldberg, T.L., and Osorio, J.E. (2014). Broad Protection against Avian Influenza using a Modified Vaccinia Ankara Virus Expressing a Mosaic Hemagglutinin gene. Journal of Virology 88: 13300-13309.

23. Medeiros, M.C.I., Anderson, T.K., Higashiguchi, J.M., Kitron, U.D., Walker, E.D., Brawn, J.D., Krebs, B.L., Ruiz, M.O., Goldberg, T.L., Ricklefs, R.E., and Hamer, G.L. (2014). An inverse association between West Nile virus serostatus and avian malaria infection status. Parasites and Vectors 7: 415.

22. Rajao, D.S., Anderson, T.K., Gauger, P.C., and Vincent, A.L. (2014). Pathogenesis and vaccination of influenza A virus in swine. Current Topics in Microbiology and Immunology 385: 307-326.

21. Hamer, G.L., Anderson, T.K., Donovan, D.J., Brawn, J.D., Krebs, B.L., Gardner, A.M., Ruiz, M.O., Brown, W.M., Kitron, U.D., Newman, C.M., Goldberg, T.L., and Walker, E.D. (2014). Dispersal of Adult Culex Mosquitoes in an Urban West Nile Virus Hotspot: a Mark-Capture Study Incorporating Stable Isotope Enrichment of Natural Larval Habitats. PLoS Neglected Tropical Diseases 8(3): e2768.

20. Lewis, N.S., Anderson, T.K., Kitikoon, P., Skepner, E., Burke, D.F., and Vincent, A.L. (2014). Substitutions near the hemagglutinin receptor binding site determine the antigenic evolution of influenza A H3N2 viruses in U.S. swine. Journal of Virology 88: 4752-4763.


19. Kitikoon, P., Gauger, P.C., Anderson, T.K., Culhane, M.R., Swenson, S.L., Loving, C.L., Perez, D.R., and Vincent, A.L. (2013). Serological cross-reactivity of swine influenza virus vaccines to contemporary U.S. swine H3N2 viruses and vaccine efficacy in pigs infected with an H3N2 virus genetically similar to 2011-2012 H3N2v. Influenza and Other Respiratory Viruses 7(S4): 32-41.

18. Anderson, T.K., Nelson, M.I., Kitikoon, P., Swenson, S.L., Korslund, J.A., and Vincent, A.L. (2013). Population dynamics of co-circulating swine influenza A viruses in the United States from 2009-2012. Influenza and Other Respiratory Viruses 7(S4): 42-51.

17. Loving, C.L., Lager, K.M, Vincent, A.L., Brockmeier, S.L, Gauger, P.C., Anderson, T.K., Kitikoon, P., Perez, D.R., and Kehrli, Jr., M.E. (2013). Efficacy of inactivated and live-attenuated influenza virus vaccines in pigs against infection and transmission of emerging H3N2 similar to the 2011-2012 H3N2v. Journal of Virology 87: 9895-9903.

16. Anderson, T.K., and Sukhdeo, M.V.K. (2013). Qualitative community stability determines parasite establishment and richness in estuarine marshes. PeerJ 1: e92.

15. Peterson, N.A., Anderson, T.K., Jiao-Jun, W., and Yoshino, T.P. (2013). In silico analysis of the fucosylation-associated genome of the human blood fluke Schistosoma mansoni: cloning and characterization of the enzymes involved in GDP-L-fucose synthesis and Golgi import. Parasites and Vectors 6: 201.

14. Kitikoon, P., Nelson, M.I., Killian, M.L, Anderson, T.K., Koster, L., Culhane, M.R., and Vincent, A.L. (2013). Genotype patterns of contemporary reassorted H3N2 virus in U.S. swine. Journal of General Virology 94: 1236-1241.

13. Anderson, T.K., and Sukhdeo, M.V.K. (2013). The relationship between community species richness and the richness of the parasite community in Fundulus heteroclitusJournal of Parasitology 99: 391-396.

12. Peterson, N.A., Anderson, T.K. and Yoshino, T.P. (2013). In silico analysis of the fucosylation-associated genome of the human blood fluke Schistosoma mansoni: cloning and characterization of the fucosyltransferase multigene family. PLoS ONE 8(5): e63299.

11. Gardner, A.M., Anderson, T.K., Hamer, G.L., Johnson, D.E., Varela, K.E., Walker, E.D. and Ruiz, M.O. (2013). Terrestrial vegetation and aquatic chemistry influence larval mosquito abundance in catch basins, Chicago, USA. Parasites and Vectors 6: 9.

10. Hamer, G.L., Anderson, T.K., Berry, G.E., Makohon-Moore, A.P., Crafton, J.C., Brawn, J.D., Dolinski, A.C., Krebs, B.L., Ruiz, M.O., Muzzall, P.M., Goldberg, T.L., and Walker, E.D. (2013). Prevalence of filarioid nematodes and trypanosomes in American robins and house sparrows, Chicago, USA. International Journal for Parasitology: Parasites and Wildlife 2: 42-49.


9. Anderson, T.K., Laegreid, W.W., Cerutti, F., Osorio, F.A., Nelson, E.A., Christopher- Hennings, J. and Goldberg, T.L. (2012). Ranking viruses: measures of positional importance within networks define core viruses for rational polyvalent vaccine development. Bioinformatics 28(12): 1624-1632.

8. Hamer, S.A., Goldberg, T.L., Kitron, U.D., Brawn, J.D., Anderson, T.K., Loss, S.R., Walker, E.D. and Hamer, G.L. (2012). Wild birds and the urban ecology of ticks and tick-borne pathogens, Chicago, Illinois, USA, 2005-2010. Emerging Infectious Diseases 18(10): 1589-1595.


7. Anderson, T.K., and Sukhdeo, M.V.K. (2011). Host centrality in food web networks determines parasite diversity. PLoS ONE 6(10): e26798.

6. Newman, C.M., Cerutti, F., Anderson, T.K., Hamer, G.L., Walker, E.D., Kitron, U.D., Ruiz, M.O., Brawn, J.D. and Goldberg, T.L. (2011). Culex flavivirus and West Nile virus mosquito co-infection and positive association in Chicago, USA. Vector-Borne and Zoonotic Diseases 11: 1099-1105.

5. Hamer, G.L., Chaves, L.F., Anderson, T.K., Kitron, U.D., Brawn, J.D., Ruiz, M.O. Loss, S.R., Walker, E.D. and Goldberg, T.L. (2011). Spatial variation in Culex pipiens host selection and host community competence within an urban focus of West Nile virus transmission. PLoS ONE 6(8): e23767.

2010 and earlier

4. Goldberg, T.L., Anderson, T.K. and Hamer, G.L. (2010). West Nile virus may have hitched a ride across the Western United States on Culex tarsalis mosquitoes. Molecular Ecology 19: 1518- 1519.

3. Anderson, T.K., and Sukhdeo, M.V.K. (2010). Abiotic versus biotic hierarchies in the assembly of parasite populations. Parasitology 137: 743-754.

2. Raffel, T.R., and Anderson, T.K. (2009). A new species of Hysterothylacium (Nematoda: Anisakidae) from the stomach of the red-spotted newt, Notophthalmus viridescens, from Pennsylvania fishless ponds. Journal of Parasitology 95: 1503-1506.

1. Anderson, T.K. (2009). Food web networks and parasite diversity. Ph.D. Thesis. Rutgers University.