Salomon, J., Sambado, S.B., Crews, A., Sidhu, S., Seredian, E., Almarinez, A., Grgich, R., Swei, A. 2023. International Journal for Parasitology: Parasites and Wildlife. Macroparasites and micro-parasites co-exist in wildlife communities but are influenced by different community-level parameters. 22, 51-59. Open access link


Schmeller, D.S., Cheng, T., Shelton, J. Lin, C.F., Alvarado, A.C., Bernardo-Cravo, A., Zoccarato, L. Ding, T.S., Yu, A., Lin, Y.P., Swei, A. Fisher, M, C., Vredenburg, V.T., Loyau, A. 2022. Environment is associated with chytrid infection and skin microbiome richness in an amphibian biodiversity hotspot. Scientific Reports, 12; 16456. Open Access link.

Paddock, C.D., Slater, K., Swei, A., Zambrano, M.L., Kleinjan, J.E., Padgett, K.A., Saunders, M.E.M., Andrews, E.S., Trent, E., Zhong, J., Sambado, S., Goldsmith, C.S., Pascoe, E.L., Foley, J., Lane, R.S., Karpathy, S.E. 2022 Detection and isolation of Rickettsia tillamookensis (Rickettsiales: Rickettsiaceae) from Ixodes pacificus (Acari: Ixodidae) from multiple regions of California. Journal of Medical Entomology, 59 (4): 1404-1412. PDF

Ring, K., Couper, L., Sapiro, A.L., Yarza, F. Yang, X.F., Clay, K., Mateusiak, C., Chou, S., Swei, A. 2022. Host blood meal identity modifies vector gene expression and competency. Molecular Ecology. 31, 9: 2698-2711. Open access link

Lilly, M.; Amaya-Mejia, W.; Pavan, L.; Peng, C.; Crews, A.; Tran, N.; Sehgal, R.; Swei, A. 2022. Local Community Composition Drives Avian Borrelia burgdorferi Infection and Tick Infestation. Vet. Sci. 9, 55.


Ring, K., Couper, L., Sapiro, A.L., Yarza, F. Yang, X.F., Clay, K., Mateusiak, C., Chou, S., Swei, A. 2021. Lizard feeding enhancing Ixodes pacificus vector competency. bioRxiv preprint. Posted 4/29/2021.

Swei, A. and Kwan, J. 2021. Response to Holmes: Practical considerations for vector microbiome studies. Molecular Ecology. 30 (10): 2214-2219. Online ahead 

Narasimhan, S., Swei, A., Abouneameh, S. Pal, U., Pedra, J.H.F., Fikrig, E. 2021. Grappling with the tick microbiome. Trends in Parasitology.   37 (8): P722-733. online access

Lilly, M. †, Crews, A. †, Cerna, L. †, and Swei, A. 2021. Community ecology in California is driving genetic variation and infectivity of the Lyme disease etiological agent. Proceedings and Papers of the Mosquito and Vector Control Association of California. 89(1): 89-90. PDF

Mai, V. †, Padgett, K., Paddock, C. Lane, R.S., Saunders, M., Billeter, S., Swei, A. 2021. Identifying potential mammalian reservoir hosts for Rickettsia 364D, an emerging tick-borne pathogen in California. Proceedings and Papers of the Mosquito and Vector Control Association of California. 89(1): 13-15. PDF 

Salomon, J., Crews, A., Lawrence, A., Swei, A. 2021 Host infection and community composition predict vector burden. Oecologia, I92 (2): 305-316. PDF


Salomon, J., Hamer, S.A., Swei, A. 2020.  A beginner's guide to collecting questing hard ticks (Acari: Ixodidae): A standardized tick dragging protocol. Journal of Insect Science, 20 (6); 1-8. PDF

Greer, J., Swei, A., Vredenburg, V., Zink, A. 2020Parental care alters the egg microbiome of the maritime earwig. Microbial Ecology. Microbial Ecology 80: 920-934.


Sambado, S., Salomon, J., Crews, A., Swei, A. 2020. Mixed transmission modes promote persistence of an emerging tick-borne pathogen. Ecosphere 11(6): e03171. Open Access PDF

MacDonald, A.J., Weinstein, S.B., O’Connor, K.E., Swei, A. 2020. Circulation of tick-borne spirochetes in tick and small mammal communities in Santa Barbara County, California, USA. Journal of Medical Entomology, tjz253. Open Access PDF doi: 10.1093/jme/tjz253

Couper, L.I., Yang, Y., Yang, X.F, Swei, A. 2020. Comparative vector competence of North American disease vectors. Parasites and Vectors, 13 (29). Open Access link:

Swei, A., Couper, L.I., Coffey, L.L., Kapan, D., Bennett, S. 2020. Patterns, drivers, and challenges of vector-borne zoonotic disease emergence. Vector Borne Zoonotic Diseases. 20 (3): 159-170. Open Access: DOI 10.1089/vbz.2018.2432 PDF

Swei, A. 2020. Vector Briefs: Of tick research and COVID-19 Pandemic. SOVE Newsletter 52(2): September 2020. PDF


Chicana, B.* †, Couper, L.I. †, Kwan, J.Y. †, Tahiraj, E.°, Swei, A. 2019. Microbiome profiles of sympatric tick species in the western United States. Insects-Special Issue on Vectors and Vector-borne Pathogens, 10(10):353;

Harrison, C. et al. 2019. Investigating instructor talk in novel contexts: Widespread use, unexpected categories, and an emergent sampling strategy. CBE Life, 18(3):ar47,1-23. PDF

Couper, L.I., Kwan, J.Y., Ma, J., Swei, A. 2019. Drivers and patterns of microbial community assembly in a Lyme disease vector. Ecology and Evolution, 9(2): 7768-7779.  DOI: 10.1002/ece3.5361 PDF

Emery, N., Hund, A., Burks, R., Duffy, M., Scoffoni, C., Swei, A. 2019. Students as ecologists: Strategies for successful mentorship of undergraduate researchers. Ecology and Evolution. Ecology and Evolution; 00;1-11. 

Virji, A.Z., Thekkiniath, J., Ma, W., Lawres, L., Knight, J., Swei, A., Le Roche, K., Ben Mamoun, C. 2019.  Insights into evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial apicoplast genomes, International Journal for Parasitology, 49 (2): 105-113. PDF

Swei, A., O'Connor, K.E.†, Couper, L. †, Conrad, P., Padgett, K., Burns, J., Yoshimizu, M.H., Ben Mamoun, C., Lane, R., Kjemtrup, A. 2019.  Evidence for transmission of the zoonotic apicomplexan parasite Babesia duncani, International Journal for Parasitology., 49 (9): 95-103. Online: PDF

Ellison, S., Sparagon, W., Knapp, R.A., Swei, A., Vredenburg, V.T. 2019. Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host. Molecular Ecology. 28 (1): 127-140. DOI: 10.1111/mec.14964 PDF


Couper, L.I. and Swei, A. 2018. Tick microbiome characterization by next-generation 16S rRNA amplicon sequencing. Journal of Visualized Experiments, 138: e58239. DOI: 10.3791/58239. PDF

MacDonald, A.J., Hyon, D.W., McDaniels, A., O'Connor, K.E., Swei, A., Briggs, C.J. 2018. Risk of vector tick exposure initially increases then declines through time in response to wildfire in California. Ecosphere, 9(5):e02227. Open Access Link: PDF

O'Connor, K.E., Kjemtrup, A., Conrad, P., Swei, A. 2018. A highly sensitive, diagnostic protocol to detect the blood-borne pathogen, Babesia duncani. Journal of Parasitology, 104 (4): 429-432.  PDF 

Lawrence, A.M., O'Connor, K.E., Swei, A. 2018. Patterns of diversity along a habitat size gradient in a biodiversity hotspot. Ecosphere 9 (4): e02183. Open Access Link;

Owens, M.T., G. Trujillo, S.B. Seidel, C.D. Harrison, K.M. Farrar, H.P. Benton, J.R. Blair, K.E. Boyer, J. Breckler, L.W. Burrus, D.T. Byrd, N. Caporale, E.J. Carpenter, Y.-H.M. Chan, J. Chen, L. Chen, L.H. Chen, D.S. Chu, W.P. Cochlan, R.J. Crook, K.D. Crow, J.R. de la Torre, W.F. Denetclaw, L.M. Dowdy, D. Franklin, M. Fuse, M.A. Goldman, B. Govindan, M. Green, H.E. Harris, Z.-H. He, S. Ingalls, P.D. Ingmire, A.R.B. Johnson, J.D. Knight, G. LeBuhn, T.L. Light, C. Low, L. Lund, L.M. Márquez-Magaña, V.C. Miller-Sims, C.A. Moffatt, H. Murdock, G.L. Nusse, V.T. Parker, S.G. Pasion, R. Patterson, P.S. Pennings, J.C. Ramirez, R.M. Ramirez, B. Riggs, R.V. Rohlfs, J.M. Romeo, B.S. Rothman, S.W. Roy, T. Russo-Tait, R.N.M Sehgal, K.A. Simonin, G.S. Spicer, J.H. Stillman, A. Swei, L.C. Tempe, V.T. Vredenburg, S.L. Weinstein, A.G. Zink, L.A. Kelley, C.R. Domingo, K.D. Tanner. Collectively Improving our Teaching: Attempting Biology Department-wide Professional Development in Scientific Teaching. CBE: Life Sciences Education. March 1; 17(1):ar2.


Kwan, J., Griggs, R., Chicana, B., Miller, C., Swei, A. 2017. Vertical versus horizontal transmission of the microbiome in a key disease vector. Molecular Ecology. 26 (23): 6599-6761. DOI: 10.1111/mec.14391 PDF

Bouquet, J., Melgar, M., Swei, A., Delwart, E., Lane, R.S. and Chiu, C.Y. 2017. Metagenomics of the Pacific Coast tick, Dermacentor occidentalis, in northwestern California, 2011-2014. Nature Scientific Reports. 7: 12234.  pdf

Catenazzi, A., A. Swei, J. Finkle, E. Foreyt, L. Wyman, V. Vredenburg. 2017. Epizootic to enzootic transition of a fungal disease in tropical Andean frogs: are surviving species still susceptible? PLoS ONE.  12(10):e0186478.

Swei, A. and J. Kwan. 2017. Tick microbiome and pathogen acquisition altered by host blood meal. The International Society for Microbial Ecology. 11: 813-816. Swei and Kwan 2017 PDF. 

Kilpatrick, A.M., Dobson, A.D.M., Levi, T., Salkeld, D.J., Swei, A. Ginsberg, H.S., Kjemptrup, A., Padgett, K.A., Jensen, P.M., Fish, D., Ogden, N.H., Diuk-Wasser, M. 2017. Lyme disease ecology in a changing world: consensus, uncertainty, and critical gaps for improving control. Philosophical Transactions of the Royal Society B. 322(1722): pii: 20160117. doi: 10.1098/rstb.2016.0117​ PDF

Owens, M.T., Seidel, S.S., Wong, M., Bejines, T., Lietz, S., Perez, J., Sit, S., Subedar, Z., Acker, G., Akana, S.F., Balukjian, B.J., Benton, H., Blair, J.R., Boaz, S., Boyer, K.E., Bram, J., Burrus, L.W., Byrd, D.T., Caporale, N., Carpenter, E.J., Chan, Y.M., Chen, L., Chovnick, A., Chu, D.S., Clarkson, B.K., Cooper, S. Creech, C., Crow, K.D., de la Torre, J.R., Denetclaw, W.F., Duncan, K., Edwards, A., Erickson, K., Fuse, M., Gorga, J., Govindan, B., Green, J.J, Hankamp, P., Harris, H.E., He, Z., Ingalls, S., Ingmire, P., Jacobs, J.B., Kamakea, M., Kimpo, R.R., Knight, J., Krause, S.K., Krueger, L., Light, T., Lund, L., Marquez-Magana, L.M., McCarthy, B., McPheron, L., Miller-Sims, V.C., Moffat, C., Muick, P.C., Nagami, P.H., Nusse, G.L., Okimura, K., Pasion, S.G., Patterson, R., Pennings, P.S., Riggs, B., Romeo, J., Roy, S.W., Russo-Tait, T., Schultheis, L., Sengupta, L., Small, R., Spicer, G.S., Stillman, J.H., Swei, A., Wade, J.M., Waters, S.B., Weinstein, S.L., Willsie, J., Wright, D., Harrison, C., Kelley, L., Trujillo, G., Domingo, C.R., Schinske, J.N., Tanner, K.D. 2017. Classroom sound can be used to classify teaching practices in college science courses. Proceedings of the National Academies of Sciences. 114 (12): 3085-3090. Owens et al. 2017 PDF

MacDonald, A.J., Hyon, D.W., Brewington, J.B., O'Connor, K.E, Swei, A., Briggs, C.J. 2017. Lyme disease risk in southern California: abiotic and environmental drivers of Ixodes pacificus (Acari: Ixodidae) density and infection prevalence with Borrelia burgdorferi. Parasites & Vectors. 10:7. MacDonald et al. 2017 PDF.


Bouquet, J., Soloski, M., Swei, A., Cheadle, C., Federman, S., Billaud, J., Rebman, A., Kabre, B., Halpert, R., Boorgula, M., Aucott, J., and Chiu, C.Y. 2016. Longitudinal transcriptome analysis reveals a sustained differential gene expression signature in patients treated for acute Lyme Disease. mBio. 7(1): e00100-16. Bouquet et al. 2016.

Springer, Y.P., Hoekman, D., Johnson, P.T.J., Duffy, P.A., Kao, R.H., Barnett, D.T., Allan, B.F., Amman, B.R., Barker, C.M., Barrera, R., Beard, C.B., Beati, L., Begon, M., Blackmore, M.S., Bradshaw, W.E., Brisson, D., Calisher, C.H., Childs, J.E., Diuk-Wasser, M.A., Douglass, R.J., Eisen, R.J., Foley, D.H., Foley, J.E., Gaff, H.D., Gardner, S.L., Ginsberg, H.S., Glass, G.E., Hamer, S.A., Hayden, M.H., Hjelle, B., Holzapfel, C.M., Juliano, S.A., Kramer, L.D., Kuenzi, A.J., LaDeau, S.L., Livdahl, T.P., Mills, J.N., Moore, C.G., Morand, S., Nasci, R.S., Ogden, N.H., Ostfeld, R.S., Parmenter, R.R., Piesman, J., Reisen, W.K., Savage, H.M., Sonenshine, D.E., Swei, A. and M.J. Yabsley. 2016. Continental-scale surveillance of infectious agents: tick-, mosquito-, and rodent-borne parasite sampling designs for NEON. Ecosphere. 7(5): e01271. Springer et al.pdf


Swei, A. Bowie, V., Bowie, R.C. 2015. Comparative genetic diversity of Lyme disease bacteria in Northern Californian ticks and their vertebrate hosts. Ticks and Tick-borne diseases. 6: 414-423. Swei et al. 2015


Swei, A., Russell, B.J., Naccache, S., Veeraraghaan, N., Pilgard, M., Johnson, B.J.B., Chiu, C.Y. 2013. The genome sequence of Lone Star virus, a novel bunyavirus found in the Amblyomma americanum tick. PlosOne 8(4): e62083. Lone_Star_Virus.pdf

Veeraraghavan, N., Russell, B.J., Naccache, S.N. , Kabre, B., Pilgard, M.A., Johnson, B.J.B., Swei, A., Chiu, C.Y. 2013 Deep sequencing reads matching to viral sequences. Figshare. DOI:


Swei, A., R.S. Ostfeld, R.S. Lane, C.J. Briggs. 2012. Impacts of an introduced forest pathogen on risk of Lyme disease in California. Vector borne zoonotic diseases, 12(8): 623-632. Swei 2012.pdf


Swei, A., J.J.L. Rowley, D. Rödder, M. L. L. Diesmos, A. C. Diesmos, C. J. Briggs, R. Brown, T. T. Cao, T. L. Cheng, R. A. Chong, B. Han, J.-M. Hero, H. D. Hoang, M. D. Kusrini, D. T. T. Le, J. A. McGuire, M. Meegaskumbura, M. S. Min, D. G. Mulcahy, T. Neang, S. Phimmachak, D.Q. Rao, N. M. Reeder, S. D. Schoville, N. Sivongxay, N. Srei, M. Stöck, B. L. Stuart, L. S. Torres, D. T. A. Tran, , T. S. Tunstall, D. Vieites, V. T. Vredenburg. Vredenburg. 2011. Is chytridiomycosis an emerging infectious disease in Asia? PLoS ONE 6(8): e23179. doi:10.1371/journal.pone.0023179 Swei_PlosOne2011_AsiaBd.pdf

Swei, A., C.J. Briggs, R.S. Lane, R.S. Ostfeld. 2011a. Impact of lizard removal on the abundance and infection prevalence of a Lyme disease vector. Proceedings of the Royal Society B, 278 (1720): 2970-2978. Proc. R. Soc. B-2011-Swei-rspb.2010.2402.pdf

Swei, A., R. Meentemeyer, C.J. Briggs. 2011b. Influence of abiotic and environmental factors on the density and infection prevalence of Ixodes pacificus (Acari:Ixodidae) with Borrelia burgdorferi. Journal of Medical Entomology, 48 (1): 20-28. JMedEnt2011.pdf

2010 and earlier

Swei, A., Ostfeld, R.S., Lane, R.S., Briggs, C.J. 2010. Effects of an invasive forest pathogen on abundance of vertebrate hosts in a California Lyme disease focus. Oecologia, 166 (1): 91-100. Oecologia_2010.pdf

Killilea, M. E., Swei, A., Lane, R.S., Briggs, C.J., and Ostfeld, R.S. 2008. Spatial dynamics of Lyme disease: A review. EcoHealth, 5(2): 167-195. EcoHealth2008.pdf

Lloyd-Smith, J.O., Cross, P.C., Briggs, C.J., Daugherty, M., Getz, W.M., Latto, J., Sanchez, M.S., Smith, A.B., Swei, A. 2005. Should we expect population thresholds in wildlife disease? Trends in Ecology and Evolution 20 (9); 511-519. Tree_thresholds_2005.pdf

Swei, A., Brylski, P.V., Spencer, W.D., Dodd, S.C., Patton, J.L. 2003. Hierarchical genetic structure in fragmented populations of the little pocket mouse (Perognathus longimembris) in Southern California. Conservation Genetics 4; 501-514.ConsGen_2003.pdf