2021

Bertrand, I., Challant, J., Jeulin, H., Hartard, C., Mathieu, L., Lopez, S., Group Obépine, S.I., Schvoerer, E., Courtois, S., & Gantzer, C. (2021). Epidemiological surveillance of SARS-CoV-2 by genome quantification in wastewater applied to a city in the northeast of France: comparison of ultrafiltration- and protein precipitation-based methods. International Journal of Hygiene and Environmental Health doi:

Burgess, S.A., Aplin, J., Biggs, P.J., Breckell, G., Benschop, J., Fayaz, A., Toombs-Ruane, L.J., & Midwinter, A.C. (2021). Characterisation of AmpC and extended-spectrum beta-lactamase producing E. coli from New Zealand dairy farms. International Dairy Journal, 117 doi:

Crawshaw, T.R., Hunter, S., Wilkinson, D.A., Rogers, L.E., Christensen, N.H., & Midwinter, A.C. (2021). Isolation of Campylobacter hepaticus from free-range poultry with spotty liver disease in New Zealand. N Z Vet J, 69(1), 58-64. doi:

Donovan, G.H., Gatziolis, D., t Mannetje, A., Weinkove, R., Fyfe, C., & Douwes, J. (2021). An empirical test of the biodiversity hypothesis: Exposure to plant diversity is associated with a reduced risk of childhood acute lymphoblastic leukemia. Sci Total Environ, 768, 144627. doi:

Gates, M.C., Evans, C.A., Heuer, C., Voges, H., & Weston, J.F. (2021). Temporal trends in bulk tank milk antibody ELISA and PCR test results for bovine viral diarrhoea in New Zealand pastoral dairy herds. N Z Vet J, 69(2), 73-82. doi:

Gates, M.C., McLachlan, I., Butler, S., & Weston, J.F. (2021). Experiences of employers, work colleagues, and mentors with new veterinary graduates and preferences towards new graduate support programmes. N Z Vet J, 69(1), 38-50. doi:

Gates, M.C., McLachlan, I., Butler, S., & Weston, J.F. (2021). Practices, preferences, and opinions of New Zealand veterinarians towards continuing professional development. N Z Vet J, 69(1), 27-37. doi:

Gates, M.C., Palleson-Putt, P., & Sawicki, R.K. (2021). Veterinary technology graduates' perceptions of their education and subsequent employment experiences. N Z Vet J, 69(2), 93-103. doi:

Haase, C.G., Fuller, N.W., Dzal, Y.A., Hranac, C.R., Hayman, D.T.S., Lausen, C.L., Silas, K.A., Olson, S.H., & Plowright, R.K. (2021). Body mass and hibernation microclimate may predict bat susceptibility to white-nose syndrome. Ecol Evol, 11(1), 506-515. doi:

Hranac, C., Haase, C., Fuller, N., McClure, M., Marshall, J., Lausen, C., McGuire, L., Olson, S., & Hayman, D. (2021). doi:

Lake, R.J., Campbell, D.M., Hathaway, S.C., Ashmore, E., Cressey, P.J., Horn, B.J., Pirikahu, S., Sherwood, J.M., Baker, M.G., Shoemack, P., Benschop, J., Marshall, J.C., Midwinter, A.C., Wilkinson, D.A., & French, N.P. (2021). Source attributed case-control study of campylobacteriosis in New Zealand. Int J Infect Dis, 103, 268-277. doi:

Phiri, B.J., French, N.P., Biggs, P.J., Stevenson, M.A., Reynolds, A.D., Garcia, R.J., & Hayman, D.T.S. (2021). Microbial contamination in drinking water at public outdoor recreation facilities in New Zealand. J Appl Microbiol, 130(1), 302-312. doi:

Ranta, A., Thompson, S., Harwood, M.L.N., Cadilhac, D.A., Barber, P.A., Davis, A.J., Gommans, J.H., Fink, J.N., McNaughton, H.K., Denison, H., Corbin, M., Feigin, V., Abernethy, V., Levack, W., Douwes, J., Girvan, J., & Wilson, A. (2021). Reducing Ethnic and Geographic Inequities to Optimise New Zealand Stroke Care (REGIONS Care): Protocol for a Nationwide Observational Study. JMIR Res Protoc, 10(1), e25374. doi:

Riley, C.B., Pfeffer, H., MacLachlan, C., Wakeford, L., Gibson, I.R., Benschop, J., & Lawrence, K.E. (2021). Isolates, antimicrobial susceptibility profiles and multidrug resistance of bacteria cultured from samples collected from sheep in New Zealand (2003-2016). N Z Vet J, 69(1), 20-26. doi:

Swadi, T., Geoghegan, J.L., Devine, T., McElnay, C., Sherwood, J., Shoemack, P., Ren, X., Storey, M., Jefferies, S., Smit, E., Hadfield, J., Kenny, A., Jelley, L., Sporle, A., McNeill, A., Reynolds, G.E., Mouldey, K., Lowe, L., Sonder, G., Drummond, A.J., Huang, S., Welch, D., Holmes, E.C., French, N., Simpson, C.R., & de Ligt, J. (2021). Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing. Emerg Infect Dis, 27(3) doi:

Wilson, P.R., Mannewald, A., Collins-Emerson, J.M., Dreyfus, A., Sanhueza, J.M., Benschop, J., Verdugo, C., Emanuelson, U., Boqvist, S., & Heuer, C. (2021). Serological study of Leptospira interrogans serovar Copenhageni and L. borgpetersenii serovars Tarassovi and Ballum in beef cattle, sheep and deer in New Zealand. N Z Vet J, 69(2), 83-92. doi:

2020

Angelin-Bonnet, O., Biggs, P.J., Baldwin, S., Thomson, S., & Vignes, M. (2020). sismonr: simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R. Bioinformatics, 36(9), 2938-2940. doi:

Barnes, L.A., Eng, A., Corbin, M., Denison, H.J., t Mannetje, A., Haslett, S., McLean, D., Jackson, R., & Douwes, J. (2020). The Prevalence of Cardiovascular Risk Factors in Different Occupational Groups in New Zealand. Ann Work Expo Health, 64(6), 645-658. doi:

Bingham, P., Wada, M., van Andel, M., McFadden, A., Sanson, R., & Stevenson, M. (2020). Real-Time Standard Analysis of Disease Investigation (SADI)-A Toolbox Approach to Inform Disease Outbreak Response. Front Vet Sci, 7, 563140. doi:

Bloomfield, S., Wilkinson, D., Rogers, L., Biggs, P., French, N., Mohan, V., Savoian, M., Venter, P., & Midwinter, A. (2020). Campylobacter novaezeelandiae sp. nov., isolated from birds and water in New Zealand. Int J Syst Evol Microbiol, 70(6), 3775-3784. doi:

Bojanic, K., Acke, E., Roe, W.D., Marshall, J.C., Cornelius, A.J., Biggs, P.J., & Midwinter, A.C. (2020). Comparison of the Pathogenic Potential of Campylobacter jejuni, C. upsaliensis and C. helveticus and Limitations of Using Larvae of Galleria mellonella as an Infection Model. Pathogens, 9(9) doi:

Bojanic, K., Midwinter, A.C., Acke, E., Marshall, J.C., Cornelius, A.J., & Biggs, P.J. (2020). Draft Genome Sequences of Eight Strains of Campylobacter helveticus Isolated from Cats and a Dog in New Zealand. Microbiol Resour Announc, 9(5) doi:

Bolwell, C.F., Rogers, C.W., Benschop, J., Collins-Emerson, J.M., Adams, B., Scarfe, K.R., & Gee, E.K. (2020). Seroprevalence of Leptospira in Racehorses and Broodmares in New Zealand. Animals (Basel), 10(11) doi:

Boulton, A.C., Kells, N.J., Cogger, N., Johnson, C.B., O'Connor, C., Webster, J., Palmer, A., & Beausoleil, N.J. (2020). Risk factors for bobby calf mortality across the New Zealand dairy supply chain. Prev Vet Med, 174, 104836. doi:

Brooks, C., Slater, T., Corbin, M., McLean, D., Firestone, R.T., Zock, J.P., Pearce, N., & Douwes, J. (2020). Respiratory health in professional cleaners: Symptoms, lung function, and risk factors. Clin Exp Allergy, 50(5), 567-576. doi:

Chambers, G.P., O'Sullivan, M.L., & Gates, M.C. (2020). Evaluating the cost-effectiveness of diagnosing and treating phantom cows in seasonal-calving dairy herds. J Dairy Sci, 103(9), 8174-8188. doi:

Chen, G.X., Mannetje, A., Douwes, J., Berg, L.H., Pearce, N., Kromhout, H., Glass, B., Brewer, N., & McLean, D.J. (2020). Occupational Exposure to Electric Shocks and Extremely Low-Frequency Magnetic Fields and Motor Neurone Disease. Am J Epidemiol doi:

Collis, R.M., Biggs, P.J., Midwinter, A.C., Browne, A.S., Wilkinson, D.A., Irshad, H., French, N.P., Brightwell, G., & Cookson, A.L. (2020). Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies. PLoS One, 15(6), e0235066. doi:

Crump, J.A., Thomas, K.M., Benschop, J., Knox, M.A., Wilkinson, D.A., Midwinter, A.C., Munyua, P., Ochieng, J.B., Bigogo, G.M., Verani, J.R., Widdowson, M.A., Prinsen, G., Cleaveland, S., Karimuribo, E.D., Kazwala, R.R., Mmbaga, B.T., Swai, E.S., French, N.P., & Zadoks, R.N. (2020). Investigating the meat pathway as a source of human nontyphoidal Salmonella bloodstream infections and diarrhea in East Africa. Clin Infect Dis doi:

Davys, G., Marshall, J.C., Fayaz, A., Weir, R.P., & Benschop, J. (2020). Campylobacteriosis associated with the consumption of unpasteurised milk: findings from a sentinel surveillance site. Epidemiol Infect, 148, e16. doi:

Dittmer, K.E., Heathcott, R.W., Marshall, J.C., & Azarpeykan, S. (2020). Expression of Phosphatonin-Related Genes in Sheep, Dog and Horse Kidneys Using Quantitative Reverse Transcriptase PCR. Animals (Basel), 10(10) doi:

Eme, P.E., Burlingame, B., Kim, N.D., Foliaki, S., Wham, C., & Douwes, J. (2020). Obesity measures in the Kiribati population: a need to reclassify body mass index cut-points. BMC Public Health, 20(1), 1092. doi:

Eme, P.E., Kim, N.D., Douwes, J., Burlingame, B., Foliaki, S., & Wham, C. (2020). Are Households in Kiribati Nutrition Secure? A Case Study of South Tarawa and Butaritari. Food Nutr Bull, 41(1), 131-146. doi:

Evans, C.A., Han, J.H., Weston, J.F., Heuer, C., & Gates, M.C. (2020). Serological evidence for exposure to bovine viral diarrhoea virus in sheep co-grazed with beef cattle in New Zealand. N Z Vet J, 68(4), 238-241. doi:

Foliaki, S., Pulu, V., Denison, H., Weatherall, M., & Douwes, J. (2020). Pacific meets west in addressing palliative care for Pacific populations in Aotearoa/New Zealand: a qualitative study. BMC Palliat Care, 19(1), 100. doi:

Franz, E., Rotariu, O., Lopes, B.S., Bono, J.L., Laing, C., Gannon, V., Van Hoek, A., Friesema, I., French, N.P., George, T., Biggs, P.J., Jaros, P., Rivas, M., Chinen, I., Campos, J., Mellor, G.E., Chandry, P.S., Perez-Reche, F., Forbes, K.J., & Strachan, N.J. (2020). Reply to Baba and Kanamori. Clin Infect Dis, 71(5), 1353-1355. doi:

Fyfe, C., Telfar, L., Barnard, Howden-Chapman, P., & Douwes, J. (2020). Association between home insulation and hospital admission rates: retrospective cohort study using linked data from a national intervention programme. BMJ, 371, m4571. doi:

Garcia, R.J., Cox, M.P., & Hayman, D.T.S. (2020). Comparative genetic diversity of Cryptosporidium species causing human infections. Parasitology, 147(13), 1532-1537. doi:

Garcia-R, J.C., Lemmon, E.M., Lemmon, A.R., & French, N. (2020). Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution. Diversity-Basel, 12(2) doi:

Gates, M.C., Evans, C.A., Han, J.H., Heuer, C., & Weston, J.F. (2020). Practices and opinions of New Zealand beef cattle farmers towards bovine viral diarrhoea control in relation to real and perceived herd serological status. N Z Vet J, 68(2), 92-100. doi:

Gates, M.C., Littlewood, K.E., Kongara, K., Odom, T.F., & Sawicki, R.K. (2020). Cross-sectional survey of anaesthesia and analgesia protocols used to perform routine canine and feline ovariohysterectomies. Vet Anaesth Analg, 47(1), 38-46. doi:

Gates, M.C., Littlewood, K.E., Kongara, K., Odom, T.F., & Sawicki, R.K. (2020). Cross-sectional survey of surgical techniques used to perform dog and cat spays in New Zealand veterinary practice. N Z Vet J, 68(1), 46-53. doi:

Gates, M.C., Littlewood, K.E., Kongara, K., Odom, T.F., & Sawicki, R.K. (2020). Experience of Practicing Veterinarians with Supervising Final-Year Students and New Graduates in Performing Desexing Surgeries. J Vet Med Educ, 47(4), 465-474. doi:

Gates, M.C., Littlewood, K.E., Kongara, K., Odom, T.F., & Sawicki, R.K. (2020). Guidelines for Implementing a Low-Cost Volunteer Desexing Skills Training Program for Veterinary and Veterinary Technology Students. J Vet Med Educ, 47(1), 27-38. doi:

Gates, M.C., Mancera, K., Dale, A., & Zito, S. (2020). Preliminary analysis of post-adoption outcomes for kittens and adult cats rehomed through a New Zealand animal shelter. N Z Vet J, 68(1), 38-45. doi:

Gates, M.C., McLachlan, I., Butler, S., & Weston, J.F. (2020). Experiences of recent veterinary graduates in their first employment position and their preferences for new graduate support programmes. N Z Vet J, 68(4), 214-224. doi:

Geoghegan, J.L., Douglas, J., Ren, X., Storey, M., Hadfield, J., Silander, O.K., Freed, N.E., Jelley, L., Jefferies, S., Sherwood, J., Paine, S., Huang, S., Sporle, A., Baker, M.G., Murdoch, D.R., Drummond, A.J., Welch, D., Simpson, C.R., French, N., Holmes, E.C., & de Ligt, J. (2020). doi:

Geoghegan, J.L., Ren, X., Storey, M., Hadfield, J., Jelley, L., Jefferies, S., Sherwood, J., Paine, S., Huang, S., Douglas, J., Mendes, F.K., Sporle, A., Baker, M.G., Murdoch, D.R., French, N., Simpson, C.R., Welch, D., Drummond, A.J., Holmes, E.C., Duchene, S., & de Ligt, J. (2020). Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nat Commun, 11(1), 6351. doi:

Gilpin, B.J., Walker, T., Paine, S., Sherwood, J., Mackereth, G., Wood, T., Hambling, T., Hewison, C., Brounts, A., Wilson, M., Scholes, P., Robson, B., Lin, S., Cornelius, A., Rivas, L., Hayman, D.T.S., French, N.P., Zhang, J., Wilkinson, D.A., Midwinter, A.C., Biggs, P.J., Jagroop, A., Eyre, R., Baker, M.G., & Jones, N. (2020). A large scale waterborne Campylobacteriosis outbreak, Havelock North, New Zealand. J Infect, 81(3), 390-395. doi:

Glare, T., Campbell, M., Biggs, P., Winter, D., Durrant, A., McKinnon, A., & Cox, M. (2020). Mitochondrial evolution in the entomopathogenic fungal genus Beauveria. Arch Insect Biochem Physiol, 105(4), e21754. doi:

Gray, M.J., & Gates, M.C. (2020). A descriptive study of ciguatera fish poisoning in Cook Islands dogs and cats: Exposure history, clinical signs, and formulation of a case definition. Vet World, 13(2), 372-385. doi:

Gray, M.J., & Gates, M.C. (2020). A descriptive study of ciguatera fish poisoning in Cook Islands dogs and cats: Treatment and outcome. Vet World, 13(7), 1269-1279. doi:

Greening, S.S., Mulqueen, K., Rawdon, T.G., French, N.P., & Gates, M.C. (2020). Estimating the level of disease risk and biosecurity on commercial poultry farms in New Zealand. N Z Vet J, 68(5), 261-271. doi:

Grout, L., Baker, M.G., French, N., & Hales, S. (2020). A Review of Potential Public Health Impacts Associated With the Global Dairy Sector. Geohealth, 4(2), e2019GH000213. doi:

Han, J.H., Weston, J.F., Heuer, C., & Gates, M.C. (2020). Modelling the economics of bovine viral diarrhoea virus control in pastoral dairy and beef cattle herds. Prev Vet Med, 182, 105092. doi:

Harrison, S., Baker, M.G., Benschop, J., Death, R.G., French, N.P., Harmsworth, G., Lake, R.J., Lamont, I.L., Priest, P.C., Ussher, J.E., & Murdoch, D.R. (2020). One Health Aotearoa: a transdisciplinary initiative to improve human, animal and environmental health in New Zealand. One Health Outlook, 2(1), 4. doi:

Haviernik, J., Dawson, K., Anderson, T., Murdoch, D., Chambers, S., Biggs, P., Cree, S., & Slow, S. (2020). Complete Genome Sequence of a Legionella longbeachae Serogroup 2 Isolate Derived from a Patient with Legionnaires' Disease. Microbiol Resour Announc, 9(5) doi:

Hazelton, M.L., McVeagh, M.R., & van Brunt, B. (2020). Geometrically aware dynamic Markov bases for statistical linear inverse problems. Biometrika doi:

Hinz, R., Mannetje, A., Glass, B., McLean, D., Pearce, N., & Douwes, J. (2020). Exposures to Fumigants and Residual Chemicals in Workers Handling Cargo from Shipping Containers and Export Logs in New Zealand. Ann Work Expo Health, 64(8), 826-837. doi:

Isaksen, K.E., Linney, L., Williamson, H., Cave, N.J., Beausoleil, N.J., Norman, E.J., & Cogger, N. (2020). TeamMate: a longitudinal study of New Zealand working farm dogs. I. Methods, population characteristics and health on enrolment. BMC Vet Res, 16(1), 59. doi:

Isaksen, K.E., Linney, L., Williamson, H., Cave, N.J., Norman, E.J., & Cogger, N. (2020). TeamMate: A Longitudinal Study of New Zealand Working Farm Dogs. II. Occurrence of Musculoskeletal Abnormalities. Front Vet Sci, 7, 624. doi:

Jefferies, S., French, N., Gilkison, C., Graham, G., Hope, V., Marshall, J., McElnay, C., McNeill, A., Muellner, P., Paine, S., Prasad, N., Scott, J., Sherwood, J., Yang, L., & Priest, P. (2020). COVID-19 in New Zealand and the impact of the national response: a descriptive epidemiological study. Lancet Public Health, 5(11), e612-e623. doi:

Johnston, A.S., Riggs, C.M., Cogger, N., Benschop, J., Rogers, C.W., & Rosanowski, S.M. (2020). Using time-series analysis techniques to enhance the understanding of musculoskeletal injury in Thoroughbred racehorses. Equine Vet J, 52(5), 699-708. doi:

Juel Holst, G., Porneki, A., Lindgreen, J., Thuesen, B., Bonlokke, J., Hyvarinen, A., Elholm, G., Ostergaard, K., Loft, S., Brooks, C., Douwes, J., Linneberg, A., & Sigsgaard, T. (2020). Household dampness and microbial exposure related to allergy and respiratory health in Danish adults. Eur Clin Respir J, 7(1), 1706235. doi:

Kells, N.J., Beausoleil, N.J., Johnson, C.B., Chambers, J.P., O'Connor, C., Webster, J., Laven, R., & Cogger, N. (2020). Indicators of dehydration in healthy 4- to 5-day-old dairy calves deprived of feed and water for 24 hours. J Dairy Sci, 103(12), 11820-11832. doi:

Le, V.V.H., Biggs, P.J., Wheeler, D., Davies, I.G., & Rakonjac, J. (2020). Novel mechanisms of TolC-independent decreased bile-salt susceptibility in Escherichia coli. FEMS Microbiol Lett, 367(10) doi:

Li, Y., Gu, Y., Lv, J., Liang, H., Zhang, J., Zhang, S., He, M., Wang, Y., Ma, H., French, N., Zhang, J., & Zhang, M. (2020). Laboratory Study on the Gastroenteritis Outbreak Caused by a Multidrug-Resistant Campylobacter coli in China. Foodborne Pathog Dis, 17(3), 187-193. doi:

McClure, M.L., Crowley, D., Haase, C.G., McGuire, L.P., Fuller, N.W., Hayman, D.T.S., Lausen, C.L., Plowright, R.K., Dickson, B.G., & Olson, S.H. (2020). Linking surface and subterranean climate: implications for the study of hibernating bats and other cave dwellers. Ecosphere, 11(10) doi:

Murdoch, D., Addidle, M., Andersson, H.S., Arnold, B., Balm, M., Benschop, J., Betty, B., Birch, M., Bloomfield, M., Brunton, C., Burns, A., Chambers, S., Cook, L., Dalton, S., Duncan, H., Elvy, J., Everts, R., Freeman, J., French, N., Grimwade, K., Hammer, D., Hayman, D., Holland, D., Hudson, B., Huggan, P., Ikram, R., Jack, S., Kelly, M., Lamont, I., Maze, M., McAuliffe, G., McBride, S., Metcalf, S., Morpeth, S., Morris, A., Murton, S., Pink, R., Pithie, A., Pitout, M., Priest, P., Raymond, N., Read, K., Ritchie, S., Rogers, M., Schroeder, P., Taylor, S., Taylor, J., Thomas, M., Upton, A., Ussher, J., Werno, A., & Wiles, S. (2020). Politicians: please work together to minimise the spread of COVID-19. N Z Med J, 133(1511), 7-8.

Murdoch, D.R., & French, N.P. (2020). COVID-19: another infectious disease emerging at the animal-human interface. New Zealand Medical Journal, 133(1510), 12-15.

Nisa, S., Wilkinson, D.A., Angelin-Bonnet, O., Paine, S., Cullen, K., Wight, J., Baker, M.G., & Benschop, J. (2020). Diverse Epidemiology of Leptospira serovars Notified in New Zealand, 1999-2017. Pathogens, 9(10) doi:

Nohra, A., Grinberg, A., Marshall, J.C., Midwinter, A.C., Collins-Emerson, J.M., & French, N.P. (2020). Shifts in the Molecular Epidemiology of Campylobacter jejuni Infections in a Sentinel Region of New Zealand following Implementation of Food Safety Interventions by the Poultry Industry. Appl Environ Microbiol, 86(5) doi:

Notcovich, S., Williamson, N.B., Flint, S., Yapura, J., Schukken, Y.H., & Heuer, C. (2020). Effect of bismuth subnitrate on in vitro growth of major mastitis pathogens. J Dairy Sci, 103(8), 7249-7259. doi:

Notcovich, S., Williamson, N.B., Yapura, J., Schukken, Y., & Heuer, C. (2020). Cellular Response of Neutrophils to Bismuth Subnitrate and Micronized Keratin Products In Vitro. Vet Sci, 7(3) doi:

Ogbuigwe, P., Pita, A.B., Knox, M.A., Velathanthiri, N., & Hayman, D.T.S. (2020). High-Yield Purification of Giardia intestinalis Cysts from Fecal Samples. Curr Protoc Microbiol, 59(1), e117. doi:

Olival, K.J., Cryan, P.M., Amman, B.R., Baric, R.S., Blehert, D.S., Brook, C.E., Calisher, C.H., Castle, K.T., Coleman, J.T.H., Daszak, P., Epstein, J.H., Field, H., Frick, W.F., Gilbert, A.T., Hayman, D.T.S., Ip, H.S., Karesh, W.B., Johnson, C.K., Kading, R.C., Kingston, T., Lorch, J.M., Mendenhall, I.H., Peel, A.J., Phelps, K.L., Plowright, R.K., Reeder, D.M., Reichard, J.D., Sleeman, J.M., Streicker, D.G., Towner, J.S., & Wang, L.F. (2020). Possibility for reverse zoonotic transmission of SARS-CoV-2 to free-ranging wildlife: A case study of bats. PLoS Pathog, 16(9), e1008758. doi:

On, S.L.W., Miller, W.G., Biggs, P.J., Cornelius, A.J., & Vandamme, P. (2020). A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic, phylogenetic, and phenotypic criteria. Syst Appl Microbiol, 43(5), 126108. doi:

Parlane, N.A., Wedlock, D.N., Han, J.H., & Park, J.H. (2020). Heterologous peptide display on chromatin nanofibers: A new strategy for peptide vaccines. Biochem Biophys Res Commun, 524(4), 825-831. doi:

Pemberton, S., Odom, T.F., Dittmer, K.E., Kopke, M.A., Marshall, J.C., Poirier, V.J., & Owen, M.C. (2020). The hypoattenuating ocular lens on CT is not always due to cataract formation. Vet Radiol Ultrasound, 61(2), 147-156. doi:

Phiri, B.J., Hayman, D.T.S., Biggs, P.J., French, N.P., & Garcia, J.C. (2020). Microbial diversity in water and animal faeces: a metagenomic analysis to assess public health risk. New Zealand Journal of Zoology, 1-14. doi:

Phiri, B.J., Pita, A.B., Hayman, D.T.S., Biggs, P.J., Davis, M.T., Fayaz, A., Canning, A.D., French, N.P., & Death, R.G. (2020). Does land use affect pathogen presence in New Zealand drinking water supplies? Water Res, 185, 116229. doi:

Prinsen, G., Benschop, J., Cleaveland, S., Crump, J.A., French, N.P., Hrynick, T.A., Mariki, B., Mmbaga, B.T., Sharp, J.P., Swai, E.S., Thomas, K.M., Zadoks, R.N., & Waldman, L. (2020). Meat Safety in Tanzania's Value Chain: Experiences, Explanations and Expectations in Butcheries and Eateries. Int J Environ Res Public Health, 17(8) doi:

Roberts, M.G., & Heesterbeek, J.A.P. (2020). Characterizing reservoirs of infection and the maintenance of pathogens in ecosystems. J R Soc Interface, 17(162), 20190540. doi:

Rose, C.J., Hammerschmidt, K., Pichugin, Y., & Rainey, P.B. (2020). Meta-population structure and the evolutionary transition to multicellularity. Ecol Lett, 23(9), 1380-1390. doi:

Rulli, M.C., D’Odorico, P., Galli, N., & Hayman, D.T.S. (2020). doi:

Sanhueza, J.M., Baker, M.G., Benschop, J., Collins-Emerson, J.M., Wilson, P.R., & Heuer, C. (2020). Estimation of the burden of leptospirosis in New Zealand. Zoonoses Public Health, 67(2), 167-176. doi:

Slow, S., Anderson, T., Murdoch, D.R., Bloomfield, S., Winter, D., & Biggs, P.J. (2020). Characterising the methylome of Legionella longbeachae serogroup 1 clinical isolates and assessing geo-temporal genetic diversity. doi:

Straumfors, A., Corbin, M., McLean, D., t Mannetje, A., Olsen, R., Afanou, A., Daae, H.L., Skare, O., Ulvestad, B., Laier Johnsen, H., Eduard, W., & Douwes, J. (2020). Exposure Determinants of Wood Dust, Microbial Components, Resin Acids and Terpenes in the Saw- and Planer Mill Industry. Ann Work Expo Health, 64(3), 282-296. doi:

Taptiklis, P., Phipps, R., Jones, M., & Douwes, J. (2020). House characteristics and condition as determinants of visible mold and musty odor: Results from three New Zealand House Condition Surveys in 2005, 2010, and 2015. Indoor Air doi:

Thomas, K.M., de Glanville, W.A., Barker, G.C., Benschop, J., Buza, J.J., Cleaveland, S., Davis, M.A., French, N.P., Mmbaga, B.T., Prinsen, G., Swai, E.S., Zadoks, R.N., & Crump, J.A. (2020). Prevalence of Campylobacter and Salmonella in African food animals and meat: A systematic review and meta-analysis. Int J Food Microbiol, 315, 108382. doi:

Togami, E., Gyawali, N., Ong, O., Kama, M., Cao-Lormeau, V.M., Aubry, M., Ko, A.I., Nilles, E.J., Collins-Emerson, J.M., Devine, G.J., Weinstein, P., & Lau, C.L. (2020). First evidence of concurrent enzootic and endemic transmission of Ross River virus in the absence of marsupial reservoirs in Fiji. Int J Infect Dis, 96, 94-96. doi:

Toombs-Ruane, L.J., Benschop, J., French, N.P., Biggs, P.J., Midwinter, A.C., Marshall, J.C., Chan, M., Drinkovic, D., Fayaz, A., Baker, M.G., Douwes, J., Roberts, M.G., & Burgess, S.A. (2020). Carriage of Extended-Spectrum-Beta-Lactamase- and AmpC Beta-Lactamase-Producing Escherichia coli Strains from Humans and Pets in the Same Households. Appl Environ Microbiol, 86(24) doi:

Topham, I.A., Dittmer, K.E., Buckle, K.N., & Gates, M.C. (2020). An overview of dropped hock syndrome cases in New Zealand cattle. N Z Vet J, 68(4), 247-254. doi:

Touloupou, P., Finkenstädt, B., Besser, T.E., French, N.P., & Spencer, S.E.F. (2020). Bayesian inference for multistrain epidemics with application to ESCHERICHIA COLI O157:H7 in feedlot cattle. Annals of Applied Statistics, 14(4), 1925-1944. doi:

van Andel, M., Jones, G., Buckle, K., Phiri, B., McFadden, A., Dacre, I., Bingham, P., Heuer, C., Abila, R., Win, H.H., Lwin, K.O., Binney, B., Zaari, S., & Gates, M.C. (2020). Estimating foot-and-mouth disease (FMD) prevalence in central Myanmar: Comparison of village headman and farmer disease reports with serological findings. Transbound Emerg Dis, 67(2), 778-791. doi:

van Andel, M., Tildesley, M.J., & Gates, M.C. (2020). Challenges and opportunities for using national animal datasets to support foot-and-mouth disease control. Transbound Emerg Dis doi:

van Andel, M., Zaari, S., Bernard, P., McFadden, A., Dacre, I., Bingham, P., Heuer, C., Binney, B., Buckle, K., Abila, R., Win, H.H., Lwin, K.O., & Gates, M.C. (2020). Evaluating the utility of national-scale data to estimate the local risk of foot-and-mouth disease in endemic regions. Transbound Emerg Dis, 67(1), 108-120. doi:

Wada, M., Lam, C.T., Rosanowski, S., Patanasatienkul, T., Price, D., & St-Hilaire, S. (2020). Development of simulation models for transmission of Salmonid Rickettsial Septicaemia between salt water fish farms in Chile. Transbound Emerg Dis doi:

Waldman, L., Hrynick, T.A., Benschop, J., Cleaveland, S., Crump, J.A., Davis, M.A., Mariki, B., Mmbaga, B.T., Mtui-Malamsha, N., Prinsen, G., Sharp, J., Swai, E.S., Thomas, K.M., & Zadoks, R.N. (2020). Meat Safety in Northern Tanzania: Inspectors' and Slaughter Workers' Risk Perceptions and Management. Front Vet Sci, 7, 309. doi:

Webb, H.J., Weston, J.F., Norman, E.J., Cogger, N., Bolwell, C.F., & Rogers, C.W. (2020). A Descriptive Study of Training Methods for Federation Equestre Internationale Endurance Horses in New Zealand. J Equine Vet Sci, 92, 103155. doi:

Yang, D.A., Laven, R.A., Muller, K.R., & Gates, M.C. (2020). Modelling the transmission dynamics of bovine digital dermatitis in New Zealand pastoral dairy production systems. Vet Res, 51(1), 16. doi:

Ye, A., Wang, X., Lin, Q., Han, J., & Singh, H. (2020). Dynamic gastric stability and in vitro lipid digestion of whey-protein-stabilised emulsions: Effect of heat treatment. Food Chem, 318, 126463. doi:

Yupiana, Y., Vallee, E., Wilson, P., Weston, J.F., Benschop, J., Collins-Emerson, J., & Heuer, C. (2020). On-farm risk factors associated with Leptospira shedding in New Zealand dairy cattle. Epidemiol Infect, 148, e219. doi:

2019

Andrae, J.W., McInerney, F.A., Tibby, J., Henderson, A.C.G., Anthony Hall, P., Marshall, J.C., McGregor, G.B., Barr, C., Greenway, M. [2019] Variation in leaf wax n-alkane characteristics with climate in the broad-leaved paperbark (Melaleuca quinquenervia). Organic Geochemistry. doi 

Angelin-Bonnet, O., Biggs, P.J., Vignes, M. [2019] Gene Regulatory Networks: A Primer in Biological Processes and Statistical Modelling. Methods Mol Biol, 1883, 347-383. doi   

Bai, X., Zhang, J., Ambikan, A., Jernberg, C., Ehricht, R., Scheutz, F., Xiong, Y., & Matussek, A. (2019). Molecular Characterization and Comparative Genomics of Clinical Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains in Sweden. Sci Rep, 9(1), 5619. doi:

Barr, C., Tibby, J., Leng, M.J., Tyler, J.J., Henderson, A.C.G., Overpeck, J.T., Simpson, G.L., Cole, J.E., Phipps, S.J., Marshall, J.C., McGregor, G.B., Hua, Q., McRobie, F.H. [2019] Holocene El Nino-Southern Oscillation variability reflected in subtropical Australian precipitation. Sci Rep, 9(1), 1627. doi

Bayley, K.D., Read, R.A., & Gates, M.C. (2019). Superficial keratectomy as a treatment for non-healing corneal ulceration associated with primary corneal endothelial degeneration. Vet Ophthalmol, 22(4), 485-492. doi:

Bojanic, K., Midwinter, A.C., Marshall, J.C., Biggs, P.J., & Acke, E. (2019). Isolation of emerging Campylobacter species in working farm dogs and their frozen home-killed raw meat diets. J Vet Diagn Invest, 31(1), 23-32. doi:

Brauning, R., Plain, K., Gautam, M., Russell, T., Correa, C.C., Biggs, P., Whittington, R., Murray, A., & Price-Carter, M. (2019). Complete Genome Sequence of the Telford Type S Strain of Mycobacterium avium subsp. paratuberculosis. Microbiol Resour Announc, 8(11). doi:

Browne, A.S., Biggs, P.J., Wilkinson, D.A., Cookson, A.L., Midwinter, A.C., Bloomfield, S.J., Hranac, C.R., Rogers, L.E., Marshall, J.C., Benschop, J., Withers, H., Hathaway, S., George, T., Jaros, P., Irshad, H., Fong, Y., Dufour, M., Karki, N., Winkleman, T., & French, N.P. (2019). Use of Genomics to Investigate Historical Importation of Shiga Toxin-Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand. Emerg Infect Dis, 25(3), 489-500. doi:

Bruce, S.J., Zito, S., Gates, M.C., Aguilar, G., Walker, J.K., Goldwater, N., & Dale, A. (2019). Predation and Risk Behaviors of Free-Roaming Owned Cats in Auckland, New Zealand via the Use of Animal-Borne Cameras. Front Vet Sci, 6, 205. doi:

Collis, R.M., Burgess, S.A., Biggs, P.J., Midwinter, A.C., French, N.P., Toombs-Ruane, L., Cookson, A.L. [2019] Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Dairy Farm Environments: A New Zealand Perspective. Foodborne Pathog Dis, 16(1), 5-22. doi

Eme, P., Burlingame, B., Douwes, J., Kim, N., & Sunia, F. [2019]. Quantitative estimates of dietary intake in households of South Tarawa, Kiribati. Asia Pacific journal of clinical nutrition. 28(1)

Evans, C.A., Pinior, B., Larska, M., Graham, D., Schweizer, M., Guidarini, C., Decaro, N., Ridpath, J., & Gates, M.C. (2019). Global knowledge gaps in the prevention and control of bovine viral diarrhoea (BVD) virus. Transbound Emerg Dis, 66(2), 640-652. doi:

Garcia-R, J.C., Gonzalez-Orozco, C.E., & Trewick, S.A. (2019). Contrasting patterns of diversification in a bird family (Aves: Gruiformes: Rallidae) are revealed by analysis of geospatial distribution of species and phylogenetic diversity. Ecography, 42(3), 500-510. doi:

Gates, M.C., Evans, C.A., Weir, A.M., Heuer, C., & Weston, J.F. (2019). Recommendations for the testing and control of bovine viral diarrhoea in New Zealand pastoral cattle production systems. N Z Vet J, 67(5), 219-227. doi:

Gates, M.C., Han, J.H., Evans, C.A., Weston, J.F., & Heuer, C. (2019). Assessing the use of diagnostic laboratory accession data to support national bovine viral diarrhoea control in New Zealand. N Z Vet J, 67(4), 194-202. doi:

Gates, M.C., Walker, J., Zito, S., & Dale, A. (2019). Cross-sectional survey of pet ownership, veterinary service utilisation, and pet-related expenditures in New Zealand. N Z Vet J, 1-9. doi:

Gates, M.C., Walker, J., Zito, S., & Dale, A. (2019). A survey of opinions towards dog and cat management policy issues in New Zealand. N Z Vet J, 1-8. doi:

Gates, M.C., Zito, S., Harvey, L.C., Dale, A., & Walker, J.K. (2019). Assessing obesity in adult dogs and cats presenting for routine vaccination appointments in the North Island of New Zealand using electronic medical records data. N Z Vet J, 67(3), 126-133. doi:

Gates, M.C., Zito, S., Walker, J.K., & Dale, A.R. (2019). Owner perceptions and management of the adverse behavioural effects of fireworks on companion animals: an update. N Z Vet J, 1-6. doi:

Glennon, E.E., Becker, D.J., Peel, A.J., Garnier, R., Suu-Ire, R.D., Gibson, L., Hayman, D.T.S., Wood, J.L.N., Cunningham, A.A., Plowright, R.K., & Restif, O. (2019). What is stirring in the reservoir? Modelling mechanisms of henipavirus circulation in fruit bat hosts. Philos Trans R Soc Lond B Biol Sci, 374(1782), 20190021. doi:

Gordon, S., Gardner, D.H., Weston, J.F., Bolwell, C.F., Benschop, J., & Parkinson, T.J. (2019). Quantitative and thematic analysis of complaints by clients against clinical veterinary practitioners in New Zealand. N Z Vet J, 67(3), 117-125. doi:

Griffiths, K.J., Ridler, A.L., Compton, C., Corner-Thomas, R.A., & Kenyon, P.R. (2019). Associations between lamb growth to weaning and dam udder and teat scores. N Z Vet J, 67(4), 172-179. doi:

Griffiths, K.J., Ridler, A.L., Compton, C., Corner-Thomas, R.A., & Kenyon, P.R. (2019). Investigating associations between lamb survival to weaning and dam udder and teat scores. N Z Vet J, 67(4), 163-171. doi:

Haase, C.G., Fuller, N.W., Hayman, D.T.S., Hranac, C.R., Olson, S.H., Plowright, R.K., & McGuire, L.P. (2019). Bats Are Not Squirrels: Revisiting the Cost of Cooling in Hibernating Mammals. Integrative and Comparative Biology, 59, E91-E91.

Haase, C.G., Fuller, N.W., Hranac, C.R., Hayman, D.T.S., Olson, S.H., Plowright, R.K., & McGuire, L.P. (2019). Bats are not squirrels: Revisiting the cost of cooling in hibernating mammals. J Therm Biol, 81, 185-193. doi:

Hayman, D.T.S. (2019). Bat tolerance to viral infections. Nat Microbiol, 4(5), 728-729. doi:

Hayman, D.T.S. [2019] African primates: likely victims, not reservoirs, of ebolaviruses. J Infect Dis. doi

Hayman, D.T.S. (2019). Measles vaccination in an increasingly immunized and developed world. Hum Vaccin Immunother, 15(1), 28-33. doi:

Hayman, D.T.S., & Baker, M.G. (2019). Does scientific effort reflect global need? A review of infectious disease publications over 100 years. Epidemiol Infect, 147, e114. doi:

Hidano, A., & Gates, M.C. (2019). Why sold, not culled? Analysing farm and animal characteristics associated with livestock selling practices. Prev Vet Med, 166, 65-77. doi:

Hrynick, T.A., Barasa, V., Benschop, J., Cleaveland, S., Crump, J.A., Davis, M., Mariki, B., Mmbaga, B.T., Mtui-Malamsha, N., Prinsen, G., Sharp, J., Sindiyo, E., Swai, E.S., Thomas, K.M., Zadoks, R., & Waldman, L. (2019). Street-level diplomacy and local enforcement for meat safety in northern Tanzania: knowledge, pragmatism and trust. Bmc Public Health, 19(1), 863. doi:

Jamaludin, N., Gedye, K., Collins-Emerson, J., Benschop, J., & Nulsen, M. (2019). Phenotypic and Genotypic Characterization of Neisseria gonorrhoeae Isolates from New Zealand with Reduced Susceptibility to Ceftriaxone. Microb Drug Resist. doi:

Karkaba, A., Hill, K., Benschop, J., Pleydell, E., & Grinberg, A. (2019). Carriage and population genetics of extended spectrum beta-lactamase-producing Escherichia coli in cats and dogs in New Zealand. Vet Microbiol, 233, 61-67. doi:

Kock, R.,  Heuer, C. [2019]. Prevention and Control of Diseases at the Interface of Livestock, Wildlife and Humans. Vet Sci, 6(1). doi

Lawrence, K.E., Wakeford, L., Toombs-Ruane, L.J., MacLachlan, C., Pfeffer, H., Gibson, I.R., Benschop, J., & Riley, C.B. (2019). Bacterial isolates, antimicrobial susceptibility and multidrug resistance in cultures from samples collected from beef and pre-production dairy cattle in New Zealand (2003-2016). N Z Vet J, 67(4), 180-187. doi:

Le, V.V.H., Bruce, I., Biggs, P.J., & Rakonjac, J. (2019). Draft Genome Sequence of a Canine Uropathogenic Escherichia coli Strain Isolated in New Zealand. Microbiol Resour Announc, 8(10). doi:

Liao, S.J., Marshall, J., Hazelton, M.L., & French, N.P. (2019). Extending statistical models for source attribution of zoonotic diseases: a study of campylobacteriosis. J R Soc Interface, 16(150), 20180534. doi:

Lind, P.A., Libby, E., Herzog, J., Rainey, P.B. [2019] Predicting mutational routes to new adaptive phenotypes. Elife, 8. doi

Marquetoux, N., Ridler, A., Heuer, C., & Wilson, P. (2019). What counts? A review of in vitro methods for the enumeration of Mycobacterium avium subsp. paratuberculosis. Vet Microbiol, 230, 265-272. doi:

Nisa, S., Bercker, C., Midwinter, A.C., Bruce, I., Graham, C.F., Venter, P., Bell, A., French, N.P., Benschop, J., Bailey, K.M., Wilkinson, D.A. [2019] Combining MALDI-TOF and genomics in the study of methicillin resistant and multidrug resistant Staphylococcus pseudintermedius in New Zealand. Sci Rep. 2019 Feb 4;9(1):1271. doi

O'Connell, A., Scott, I., Cogger, N., Jones, B.R., & Hill, K.E. (2019). Parasitic Nematode and Protozoa Status of Working Sheepdogs on the North Island of New Zealand. Animals (Basel), 9(3). doi:

Patel, K.K., Burrows, E., Heuer, C., Asher, G.W., Wilson, P.R., & Howe, L. (2019). Investigation of Toxoplasma gondii and association with early pregnancy and abortion rates in New Zealand farmed red deer (Cervus elaphus). Parasitol Res, 118(7), 2065-2077. doi:

Patel, K.K., Stanislawek, W.L., Burrows, E., Heuer, C., Asher, G.W., Wilson, P.R., & Howe, L. (2019). Investigation of association between bovine viral diarrhoea virus and cervid herpesvirus type-1, and abortion in New Zealand farmed deer. Vet Microbiol, 228, 1-6. doi:

Penny, H., Hayman, D.T.S., Avci, E., 2019. Micromanipulation System for Isolating a Single Cryptosporidium Oocyst. Micromachines 11 (1). doi:

Rosanowski, S.M., Carpenter, T.E., Adamson, D., Rogers, C.W., Pearce, P., Burns, M., & Cogger, N. (2019). An economic analysis of a contingency model utilising vaccination for the control of equine influenza in a non-endemic country. PloS one, 14(1), e0210885. doi:

Shepherd, L.D., Frericks, J., Biggs, P.J., & de Lange, P.J. (2019). Phylogeography of the endemic New Zealand tree Entelea arborescens (whau; Malvaceae). New Zealand Journal of Botany, 57(3), 154-168. doi:

Sun, T.C., Riggs, C.M., Cogger, N., Wright, J., & Al-Alawneh, J.I. (2019). Noncatastrophic and catastrophic fractures in racing Thoroughbreds at the Hong Kong Jockey Club. Equine Vet J, 51(1), 77-82. doi:

Visnovska, T., Biggs, P.J., Schmeier, S., Frizelle, F.A., & Purcell, R.V. (2019). Metagenomics and transcriptomics data from human colorectal cancer. Sci Data, 6(1), 116. doi:

Webb, H.J., Weston, J.F., Norman, E.J., Cogger, N.D., & Rogers, C.W. (2019). Experience, riding practices and training methods of Federation Equestre Internationale (FEI: 80-160 km) level endurance horse rider-owner-trainers in New Zealand. Comparative Exercise Physiology, 15(2), 137-145. doi:

Wheeler, N.E., Blackmore, T., Reynolds, A.D., Midwinter, A.C., Marshall, J., French, N.P., Savoian, M.S., Gardner, P.P., & Biggs, P.J. (2019). Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni. Microb Genom, 5(2). doi:

Whittington, R., Donat, K., Weber, M.F., Kelton, D., Nielsen, S.S., Eisenberg, S., Arrigoni, N., Juste, R., Saez, J.L., Dhand, N., Santi, A., Michel, A., Barkema, H., Kralik, P., Kostoulas, P., Citer, L., Griffin, F., Barwell, R., Moreira, M.A.S., Slana, I., Koehler, H., Singh, S.V., Yoo, H.S., Chavez-Gris, G., Goodridge, A., Ocepek, M., Garrido, J., Stevenson, K., Collins, M., Alonso, B., Cirone, K., Paolicchi, F., Gavey, L., Rahman, M.T., de Marchin, E., Van Praet, W., Bauman, C., Fecteau, G., McKenna, S., Salgado, M., Fernandez-Silva, J., Dziedzinska, R., Echeverria, G., Seppanen, J., Thibault, V., Fridriksdottir, V., Derakhshandeh, A., Haghkhah, M., Ruocco, L., Kawaji, S., Momotani, E., Heuer, C., Norton, S., Cadmus, S., Agdestein, A., Kampen, A., Szteyn, J., Frossling, J., Schwan, E., Caldow, G., Strain, S., Carter, M., Wells, S., Munyeme, M., Wolf, R., Gurung, R., Verdugo, C., Fourichon, C., Yamamoto, T., Thapaliya, S., Di Labio, E., Ekgatat, M., Gil, A., Alesandre, A.N., Piaggio, J., Suanes, A., & de Waard, J.H. (2019). Control of paratuberculosis: who, why and how. A review of 48 countries. BMC Vet Res, 15(1), 198. doi:

Wild, R., McFadden, A., O'Connor, C., O'Grady, K., & Wada, M. (2019). Prevalence of lameness in sheep transported to meat processing plants in New Zealand and associated risk factors. N Z Vet J, 67(4), 188-193. doi:

Wilkinson, D.A., Midwinter, A.C., Kwan, E., Bloomfield, S.J., French, N.P., & Biggs, P.J. (2019). Draft Whole-Genome Sequences of Three Isolates of a Novel Strain of a Campylobacter sp. Isolated from New Zealand Birds and Water. Microbiol Resour Announc, 8(18). doi:

Yang, D.A., Gates, M.C., Muller, K.R., & Laven, R.A. (2019). Bayesian analysis of herd-level risk factors for bovine digital dermatitis in New Zealand dairy herds. BMC Vet Res, 15(1), 125. doi:

Yang, D.A., Johnson, W.O., Muller, K.R., Gates, M.C., & Laven, R.A. (2019). Estimating the herd and cow level prevalence of bovine digital dermatitis on New Zealand dairy farms: A Bayesian superpopulation approach. Prev Vet Med, 165, 76-84. doi:

Yang, D.A, Laven, R.A, [2019] Inter-observer agreement between two observers for bovine digital dermatitis identification in New Zealand using digital photographs. NZ Vet J. 2019 May;67(3):143-147. doi

Yang, D.A, Laven, R.A, [2019] Detecting bovine digital dermatitis in the milking parlour: To wash or not to wash, a Bayesian superpopulation approach. The Veterinary Journal 247:38-43. doi

Yang, D.A., Laven, R.A., Chesterton, R.N. [2019] Effects of climate and farm management practices on bovine digital dermatitis in spring-calving pasture-based dairy farms in Taranaki, New Zealand. The Veterinary Journal 247:75-80. doi

Yupiana, Y., Wilson, P.R., Weston, J.F., Vallee, E., Collins-Emerson, J.M., Benschop, J., Scotland, T., & Heuer, C. (2019). Epidemiological investigation of Leptospira spp. in a dairy farming enterprise after the occurrence of three human leptospirosis cases. Zoonoses Public Health, 66(5), 470-479. doi:

Zhang, D., Palmer, J., Teh, K.H., Biggs, P., & Flint, S. (2019). 16S rDNA high-throughput sequencing and MALDI-TOF MS are complementary when studying psychrotrophic bacterial diversity of raw cows' milk. International Dairy Journal, 97, 86-91. doi:

Zito, S., Walker, J., Gates, M.C., & Dale, A. (2019). A Preliminary Description of Companion Cat, Managed Stray Cat, and Unmanaged Stray Cat Welfare in Auckland, New Zealand Using a 5-Component Assessment Scale. Front Vet Sci, 6, 40. doi:

2018

Babylon, A.M., Roberts, M.G., Wake, G.C. [2018] Modelling leptospirosis in livestock. Theor Popul Biol 121:26-32. doi

Barkema, H.W., Orsel, K., Nielsen, S.S., Koets, A.P., Rutten, V.P.M.G., Bannantine, J.P. Kelton, D.F., Wells, S.J., Whittington, R.J., Mackintosh, C.G., Manning, E.J., Weber, M.F., Heuer,C., Forde, T.L., Ritter, C., Roche, S., Corbett, C.S., Wolf, R., Griebel, P.J., Kastelic, J.P., De Buck ,J.[2018] Knowledge gaps that hamper prevention and control of Mycobacterium avium subspecies paratuberculosis infection.. Transbound Emerg Dis.doi

Bayley, K.D., Read, R.A., Gates, M.C. [2018] Superficial keratectomy as a treatment for non-healing corneal ulceration associated with primary corneal endothelial degeneration. Vet Ophthalmol. doi

Betz-Stablein, B., Hazelton, M. L., Morgan, W. H. [2018] Modelling retinal pulsatile blood flow from video data. Statistical Methods in Medical Research 27[5]:1575-1584. doi

Bloomfield, S.J., Midwinter, A.C., Biggs, P.J., French, N.P., Marshall, J.C., Hayman, D.T.S., Carter, P.E., Thornley, C., Yap, R., Benschop, J. [2018] Long-term Colonization by Campylobacter jejuni Within a Human Host: Evolution, Antimicrobial Resistance, and Adaptation, The Journal of Infectious Diseases, v217:1 p103–111 doi

Bojanic, K., Midwinter, A.C., Marshall, J.C., Biggs, P.J., Acke, E. [2018] Isolation of emerging Campylobacter species in working farm dogs and their frozen home-killed raw meat diets. J Vet Diagn Invest, 1040638718820082. doi

Browne, A.S., Midwinter,A.C., Withers, H., Cookson, A.L., Biggs, P.J., Marshall, J.C. Benschop, J.,Hathaway, S., Haack, N.A., Akhter, R.N., French, N.P. [2018] Molecular Epidemiology of Shiga Toxin-Producing Escherichia Coli (Stec) on New Zealand Dairy Farms: Application of a Culture-Independent Assay and Whole Genome Sequencing. Appl Environ Microbiol. doi

Browne, A.S., Biggs, P.J., Elliott, A., Jaros, P., French, N.P., Midwinter, A.C. [2018] Draft Whole-Genome Sequences of Three Diarrheagenic Escherichia coli Strains Isolated from Farmed Deer in New Zealand. Genome Announc 6[16]. doi:10.1128/genomeA.00300-18

Coakley, J., Bridgen, P., Bates, M.N., Douwes, J., t Mannetje, A. [2018] Chlorinated persistent organic pollutants in serum of New Zealand adults, 2011-2013. Sci Total Environ ,615:624-631. doi:10.1016/j.scitotenv.2017.09.331

Coakley, J., Bridgen, P., Mueller, J., Douwes, J., 't Mannetje, A. 2018]. Polybrominated diphenyl ethers and perfluorinated alkyl substances in blood serum of New Zealand adults, 2011-2013. Chemosphere. 208, 382-389. doi 

Coupe, A., Howe, L., Burrows, E., Sine, A., Pita, A., Velathanthiri, N., Vallee, E., Hayman, D.T.S., Shapiro, K., Roe, W.D. [2018] First report of Toxoplasma gondii sporulated oocysts and Giardia duodenalis in commercial green-lipped mussels (Perna canaliculus) in New Zealand. Parasitol Res 117[5]:1453-1463. doi:10.1007/s00436-018-5832-8

Davies, T.M., Flynn, C.R., Hazelton, M.L. [2018] On the utility of asymptotic bandwidth selectors for spatially adaptive kernel density estimation. Statistics & Probability Letters 138:75-81. doi:10.1016/j.spl.2018.02.067

Davies, T.M., Marshall, J.C., Hazelton, M.L. [2018] Tutorial on kernel estimation of continuous spatial and spatiotemporal relative risk. Statistics in medicine 37[7]:1191-1221. doi:10.1002/sim.7577

Denison, HJ., Eng, A., Barnes, LA., Cheng, S., T'Mannetje, A., Haddock, K., Douwes, J., Pearce, N., Ellison-Loschmann, L. [2018] Inequities in exposure to occupational risk factors between Māori and non-Māori workers in Aotearoa New Zealand. Journal of Epidemiology and Community Health. doi  

Donovan, GH., Gatziolis, D., Longley, I.,  Douwes, J. [2018] Vegetation diversity protects against childhood asthma: Results from a large New Zealand birth cohort. Nature Plants. 4(6), 358-364. doi 

Douwes, J., 't Mannetje, A., McLean, D., Pearce, N., Woodward, A., Potter, J.[2018] Carcinogenicity of glyphosate: why is New Zealand’s EPA lost in the weeds? NZ Med J, 2018; 131: 1472.

Douwes, J., Slater, T., Shanthakumar, M., McLean, D., Firestone, R.T., Judd, L., Pearce, N. [2018] Determinants of hand dermatitis, urticaria and loss of skin barrier function in professional cleaners in New Zealand. Int J Occup Environ Health 23[2]:110-119. doi:10.1080/10773525.2018.1427307

Dreyfus, A., Wilson, P., Benschop, J., Collins-Emerson, J., Verdugo, C., Heuer, C. [2018] Seroprevalence and Herd-Level Risk Factors for Seroprevalence of Leptospira Spp. In Sheep, Beef Cattle and Deer in New Zealand. N Z Vet J (Aug 19 2018): 1-27. doi

Ekong, P.S., Cardona, C.J., Bryssinckx, W., Ikechukwu-Eneh, C., Lombin, L.H., Carpenter, T.E. [2018] Spatial clustering of pathology submissions during the initial introduction and spread of avian influenza H5N1 in poultry in Nigeria in 2006-2007. Vet Ital54[1]:13-20. doi:10.12834/VetIt.870.4301.3

Evans, C.A., Pinior, B., Larska, M., Graham, D., Schweizer, M., Guidarini, C., Decaro, N., Ridpath, J., Gates, M.C. [2018]. Global knowledge gaps in the prevention and control of bovine viral diarrhoea (BVD) virus. Transbound Emerg Dis. doi

Franz, E., Rotariu, O., Lopes, B.S., MacRae, M., Bono, J.L., Laing, C., Gannon, V., Soderlund, R., van Hoek, A.H.A.M, Friesema, I., French, N.P., George, T., Biggs, P.J., Jaros, P., Rivas, M., Chinen, I., Campos, J., Jernberg, C., Gobius, K., Mellor, G.E., Chandry, P.S., Perez-Reche, F., Forbes, K.J., Strachan, N.J.C. [2018] Phylogeographic analysis reveals multiple international transmission events have driven the global emergence of Escherichia coli O157:H7. Clinical Infectious Diseases. doi

Frei, R., Ferstl, R., Roduit, C., Ziegler, M., Schiavi, E., Barcik, W., Rodriguez-Perez, N., Wirz, O.F., Wawrzyniak, M., Pugin, B., Nehrbass, D., Jutel, M., Smolinska, S., Konieczna, P., Bieli, C., Loeliger, S., Waser, M., Pershagen, G., Riedler, J., Depner, M., Schaub, B., Genuneit, J., Renz, H., Pekkanen, J., Karvonen, A.M., Dalphin, J.C., van Hage, M., Doekes, G., Akdis, M., Braun-Fahrlander, C., Akdis, C.A., von Mutius, E., O'Mahony, L., Lauener, R. P. Prevention of Allergy Risk factors for Sensitization in Children Related to, Farming anthroposophic Lifestyle study, group protection Against Allergy Study in Rural Environments /Mechanisms of Early Protective Exposures on Allergy Development study, group[2018]. Exposure to nonmicrobial N-glycolylneuraminic acid protects farmers' children against airway inflammation and colitis. Journal of Allergy and Clinical Immunology. 141(1), 382-390.e7. doi 

Froud, K.J., Beresford, R.M., Cogger, N. [2018] Impact of kiwifruit bacterial canker on productivity of cv. Hayward kiwifruit using observational data and multivariable analysis. Plant Pathology 67(3):671-681 . doi:10.1111/ppa.12764 

Gal, A., Burchell, R.K., Worth, A.J., Lopez-Villallobos, N., Marshall, J.C., MacNeill, A.L. [2018] The Site of Bone Marrow Acquisition Affects the Myeloid to Erythroid Ratio in Apparently Healthy Dogs. Vet Pathol 55(6):853-860 doi

Gates, M.C., Odom, T.F., Sawicki, R.K. [2018] Experience and confidence of final year veterinary students in performing desexing surgeries, New Zealand Veterinary Journal, 66:4, 10-21. doi  

Gates, M.C., Zito, S., Thomas, J.,  Dale, A. (2018). Post-adoption problem behaviours in adolescent and adult dogs rehomed through a New Zealand animal shelter. Animals 8(6). doi 

Gautam, M., Anderson, P., Ridler, A., Wilson, P.,  Heuer, C. [2018] Economic Cost of Ovine Johne's Disease in Clinically Affected New Zealand Flocks and Benefit-Cost of Vaccination.. Vet Sci. 5(1) doi:10.3390/vetsci5010016

Gautam, M., Ridler, A., Wilson, P.R.,  Heuer, C. [2018] Control of clinical paratuberculosis in New Zealand pastoral livestock. New Zealand Veterinary Journal. 66(1), 1-8 doi:10.1080/00480169.2017.1379914

Giles, JC., Johnson, W., Jones, G., Heuer, C.,  Dunowska, M. [2018]. Development of an indirect ELISA for detection of antibody to wobbly possum disease virus in archival sera of Australian brushtail possums (Trichosurus vulpecula) in New Zealand. New Zealand Veterinary Journal. 66(4), 186-193. doi

Griffiths, K.J., Ridler, A.L., Heuer, C., Corner-Thomas, R.A., Kenyon,P.R. [2018] Associations between liveweight, body condition score and previous reproductive outcomes, and the risk of ewes bred at 18-months of age being dry at docking, New Zealand Veterinary Journal. doi

Grout, L., Hales, S., French, N.P., Baker. M.G. [2018] A Review of Methods for Assessing the Environmental Health Impacts of an Agricultural System. Int J Environ Res Public Health 15, no. 7. doi 

Guernier, V., Goarant, C., Benschop, J., Lau, C.L. [2018] A systematic review of human and animal leptospirosis in the Pacific Islands reveals pathogen and reservoir diversity. PLoS Negl Trop Dis 12[5].doi 10.1371/journal.pntd.0006503 

Han, J.H., Holter, J., Moffat, J., Weston, J. F., Heuer, C., Gates, M. C. [2018]. Using Bayesian network modelling to untangle farm management risk factors for bovine viral diarrhoea virus infection. Preventive veterinary medicine, 161, 75-82. doi

Han, J.H., Weir, A.M., Weston, J.F., Heuer, C., Gates, M.C. [2018] Elimination of Bovine Viral Diarrhoea Virus in New Zealand: A Review of Research Progress and Future Directions. N Z Vet J (Aug 28 2018): 1-8.  doi

Hayman, D.T.S. [2018] Measles vaccination in an increasingly immunized and developed world. Hum Vaccin Immunother 1-6. doi   

Hayman, D.T.S, Luis, A.D, Restif, O., Baker, K.S., Fooks, A.R., Leach, C., Horton, D.L., Suu-Ire, R., Cunningham, A.A, Wood, J.L.N., Webb, C.T. (2018) Maternal antibody and the maintenance of a lyssavirus in populations of seasonally breeding African bats. PLoS ONE 13(6): e0198563. doi

Hidano, A., Enticott, G., Christley, R.M., Gates, M.C. [2018] Modeling Dynamic Human Behavioral Changes in Animal Disease Models: Challenges and Opportunities for Addressing Bias. Front Vet Sci 5:137. doi 

Hunt, H., Cave, N.J., Gartrell, B.D., Cogger, N., Petersen, J.A., Roe, W.D. [2018] An epidemiological investigation of an idiopathic myopathy in hunting dogs in New Zealand New Zealand Veterinary Journal 66(4):199-204 04 Jul 2018. doi 

Jaros, P., Cookson, A.L., Reynolds, A., Withers, H., Clemens, R., Brightwell, G., Mills, J., Marshall, J., Prattley, D.J., Campbell, D.M., Hathaway, S., French, N.P. [2018] The effect of transportation and lairage on faecal shedding and carcass contamination with Escherichia coli O157 and O26 in very young calves in New Zealand. Epidemiology & Infection 146:1089-1100. doi

Keer, S., McLean, D., Glass, B., Douwes, J. [2018] Effects of Personal Protective Equipment Use and Good Workplace Hygiene on Symptoms of Neurotoxicity in Solvent-Exposed Vehicle Spray Painters. Ann Work Expo Health 62[3]:307-320. doi:10.1093/annweh/wxx100

Keer, S., Taptiklis, P., Glass, B., McLean, D., McGlothlin, JD., Douwes, J. [2018] Determinants of Airborne Solvent Exposure in the Collision Repair Industry. Ann Work Expo Health. doi

Lal, A.,Marshall, J.,Benschop, J.,Brock, A.,Hales, S.,Baker, M.G.,French, N.P. [2018] A Bayesian spatio-temporal framework to identify outbreaks and examine environmental and social risk factors for infectious diseases monitored by routine surveillance. Spatial and Spatio-temporal Epidemiology, 25: 39-48 doi:10.1016/j.sste.2017.10.004

Lind, P.A., Libby, E., Herzog, J., Rainey, P.B. [2018] Disentangling the effects of genetic architecture, mutational bias and selection on evolutionary forecasting.bioRxiv, 335711. doi 

Matthews, Z.M., Edwards, P.J.B., Kahnt, A., Collett, M.G., Marshall, J.C., Partridge, A.C., Harrison, S.J., Fraser, K., Cao, M., Derrick, P.J. [2018] Serum metabolomics using ultra performance liquid chromatography coupled to mass spectrometry in lactating dairy cows following a single dose of sporidesmin. Metabolomics (2018) 14: 61 doi 

Matthews, Z.M., Collett, M.G., Marshall, J.C., Partridge, A.C., Derrick P.J., Edwards, P.J.B. [2018] Effect of a one-off sporidesmin challenge on the milk production of dairy cows, New Zealand Veterinary Journal, 66:5, 261-266, doi

Marquetoux, N., Mitchell, R., Ridler, A., Heuer, C., Wilson, P. [2018] A synthesis of the patho-physiology of Mycobacterium avium subspecies paratuberculosis infection in sheep to inform mathematical modelling of ovine paratuberculosis. Vet Res 49[1]:27. doi:10.1186/s13567-018-0522-1

McGuigan, R., Bolwell, C., Rogers, C., Benschop, J., Collins-Emerson, J., Wilkinson, D., . . . Gee, E. [2018]. Leptospirosis - an unknown problem in horses. New Zealand Thoroughbred Racing. (March 2018), 32-32

Muellner, P., Hodges, D., Ahlstrom, C., Newman, M., Davidson, R., Pfeiffer, D., Marshall, J., Morley, C. [2018] Creating a framework for the prioritization of biosecurity risks to the New Zealand dairy industry.Transbound Emerg Dis. 2018 Aug;65(4):1067-1077. doi

Nohra, A., Grinberg, A., Midwinter, A.C., Marshall, J.C., Collins-Emerson, J.M., French, N.P. [2018] Exposure to Whole Chicken Carcasses May Present a Greater Risk of Campylobacteriosis Compared to Exposure to Chicken Drumsticks. Zoonoses Public Health (Jul 11 2018). doi  

Patel, K.K., Howe, L., Haack, N., Heuer, C., Asher, G.W., Wilson, P.R. [2018] Lack of association between Leptospira spp. serovars Hardjobovis and Pomona and pregnancy and mid-term abortion in New Zealand farmed red deer. Vet Microbiol 215:83-89. doi:10.1016/j.vetmic.2018.01.008

Patel, KK., Howe, L., Heuer, C., Asher, GW.,  Wilson, PR. [2018]. Pregnancy and mid-term abortion rates in farmed red deer in New Zealand. Animal Reproduction Science. 193, 140-152. doi 

Peel, A.J., Baker, K.S., Hayman, D.T.S., Broder, C.C., Cunningham, A.A., Fooks, A.R., Garnier, R., Wood, J.L.N., Restif, O. [2018] Support for viral persistence in bats from age-specific serology and models of maternal immunity. Sci Rep 8[1]:3859 . doi:10.1038/s41598-018-22236-6

Pembrey, L., Barreto, M.L., Douwes, J., Cooper, P., Henderson, J., Mpairwe, H., Ardura-Garcia, C., Chico, M., Brooks, C., Cruz, A.A., Elliott, A.M., Figueiredo, C.A., Langan, S.M., Nassanga, B., Ring, S., Rodrigues, L., Pearce, N. [2018] Understanding asthma phenotypes: the World Asthma Phenotypes (WASP) international collaboration. ERJ Open Res 4[3] doi

Remigi, P., Ferguson, G.C., De Monte, S., Rainey, P.B. [2018] Pyrimidine starvation activates a bistable phenotypic switch leading to ribosome provisioning and rapid exit from stationary phase. bioRxiv, 244129 .doi: 10.1101/244129

Pinpimai, K., Roe, W.D., Biggs, P.J., & Dittmer, K.E. [2018] Draft Whole-Genome Sequences of Seven Isolates of Klebsiella pneumoniae from New Zealand Sea Lions. Microbiol Resour Announc, 7(20). doi

Roberts, M.G., Hickson, R.I., McCaw, J.M., Talarmain, L. [2018] A simple influenza model with complicated dynamics. J Math Biol. doi  

Roberts, M.G., Heesterbeek, J.A.P. [2018] Quantifying the dilution effect for models in ecological epidemiology. J R Soc Interface 15[140]. doi:10.1098/rsif.2017.0791

Rouco, C., Jewell, C., Richardson, K.S., French, N.P., Buddle, B.M.,  Tompkins, D.M. [2018]. Brushtail possum (Trichosurus vulpecula) social interactions and their implications for bovine tuberculosis epidemiology. Behaviour. doi

Sanhueza, J.M., Wilson, P.R., Benschop, J., Collins-Emerson, J.M., Heuer, C. [2018] Meta-analysis of the efficacy of Leptospira serovar Hardjo vaccines to prevent urinary shedding in cattle. Prev Vet Med. 153:71-75. doi:10.1016/j.prevetmed.2018.02.015

Sariningsih, S.M., Shadbolt, T., McKenzie, J., Collins-Emerson, J., Benschop, J. [2018] Institutional gastroenteritis outbreaks and time to notify public health services. N Z Med J. 2018 Jul 13;131(1478):39-49.

Sherman, S.M., Bartholomew, K., Denison, H.J., Patel, H., Moss, E.L., Douwes, J.,  Bromhead, C. [2018] Knowledge, attitudes and awareness of the human papillomavirus among health professionals in New Zealand. PLoS One, 13(12), e0197648. doi

Shorter, C., Crane, J., Pierse, N., Barnes, P., Kang, J., Wickens, K., Douwes, J., Stanley, T., Taubel, M., Hyvarinen, A., Howden-Chapman, P., Wellington Region General Practitioner Research, Network [2018] Indoor visible mold and mold odor are associated with new-onset childhood wheeze in a dose-dependent manner. Indoor Air 28(1):6-15. doi:10.1111/ina.12413

Shrestha, R., McKenzie, J.S., Gautam, M., Adhikary, R., Pandey, K., Koirala, P., Bc, G.B., Miller, L.C., Collins-Emerson, J., Craig, S.B., Shrestha, S., Heuer, C. [2018]. Determinants of clinical leptospirosis in Nepal.. Zoonoses Public Health. doi

Slow, S., Anderson, T., Biggs, P.J., Kennedy, M., Murdoch, D., Cree, S. [2018] Complete Genome Sequence of Legionella sainthelensi Isolated from a Patient with Legionnaires' Disease. Genome Announc 6[5]. doi:10.1128/genomeA.01588-17

Straub, C., Colombi, E., Li, L., Huang, H., Templeton, M.D., McCann, H.C., Rainey, P.B. [2018] The ecological genetics of Pseudomonas syringae from kiwifruit leaves. Environ Microbiol. doi:10.1111/1462-2920.14092

Straumfors, A., Olsen, R., Daae, HL., Afanou, A., McLean, D., Corbin, M., Mannetje, A., Ulvestad, B., Bakke, B., Johnsen, H.L., Douwes, J., Eduard, W. [2018] Exposure to Wood Dust, Microbial Components, and Terpenes in the Norwegian Sawmill Industry.. Ann Work Expo Health. 62(6), 674-688. doi 

Sun, T.C, Riggs, C.M, Cogger N, Wright, J, Al-Alawneh, J.I.[2018] Noncatastrophic and catastrophic fractures in racing Thoroughbreds at the Hong Kong Jockey Club Equine Veterinary Journal 01 Jan 2018.  doi

t Mannetje, A., Eng, A., Walls, C., Dryson, E., Douwes, J., Bertazzi, P., Ryder-Lewis, S., Scott, D., Brooks, C., McLean, D., Cheng, S., Pearce, N. [2018] Morbidity in New Zealand pesticide producers exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Environ Int,110:22-31. doi:10.1016/j.envint.2017.09.018

Vallee, E., Heuer, C., Collins-Emerson, J.M., Benschop, J., Ridler, A.L., Wilson, P.R. [2018] Effects of natural infection by L. borgpetersenii serovar Hardjo type Hardjo-bovis, L. interrogans serovar Pomona and leptospiral vaccination on sheep reproduction. Theriogenology ,114:126:135. doi:10.1016/j.theriogenology.2018.03.022

Vallee, E., Heuer, C., Collins-Emerson, J.M., Benschop, J., Ridler, A.L., Wilson, P.R. [2018] Effects of natural infection by L. borgpetersenii serovar Hardjo type Hardjo-bovis, L. interrogans serovar Pomona, and leptospiral vaccination, on sheep growth. Prev Vet Med 159:196-202. doi

Van Andel, M., Hollings, T., Bradhurst, R., Robinson, A., Burgman, M., Gates, MC., Bingham, P,  Carpenter, T. (2018). Does size matter to models? Exploring the effect of herd size on outputs of a herd-level disease spread simulator. Frontiers in Veterinary Science. 5:78  doi

Varrone, L., Stafford, R.J., Lilly, K., Selvey, L., Glass, K., Ford, L., Bulach, D., Kirk, M.D. CampySource Project, T. [2018] Investigating locally relevant risk factors for Campylobacter infection in Australia: protocol for a case-control study and genomic analysis. BMJ Open, 8(12), e026630. doi 

Watling, D.P., Hazelton, M.L. [2018] Asymptotic approximations of transient behaviour for day-to-day traffic models. Transportation Research Part B: Methodological 118:90-105 doi

Wilkinson, D.A., Marshall, J.C., French, N.P., Hayman, D.T.S. [2018]. Habitat fragmentation, biodiversity loss and the risk of novel infectious disease emergence. J R Soc Interface, 15(149). doi

Wilkinson, D.A., O'Donnell, A.J., Akhter, R.N., Fayaz, A., Mack, H.J., Rogers, L.E., Biggs, P.J., French, N.P., Midwinter, A.C. [2018] Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis. Sci Rep 8[1]:2393. doi:10.1038/s41598-018-20889-x

Yang, D.A., Laven, R.A., Heuer, C., Vink, W.D., Chesterton, R.N. [2018] Farm level risk factors for bovine digital dermatitis in Taranaki, New Zealand: An analysis using a Bayesian hurdle model. Vet J 234:91-95. doi:10.1016/j.tvjl.2018.02.012

Yildirim, Y., Anderson, M.J., Hansson, B., Patel, S., Millar, C.D., Rainey, P.B. [2018] Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand. PLoS One. 13(8):e0202197. doi

Yulo, P.R., Desprat, N., Gerth, M.L., Liu, Y., Zhang, X.X., Rainey, P.B., Hendrickson, H.L. [2018] Experimental Evolution of Cell Shape in Bacteria. bioRxiv, 263681 doi  

Zhang, D.F., Yang, X.Y., Zhang, J., Qin, X., Huang, X., Cui, Y., Zhou, M., Shi, C., French, N.P., Shi, X. [2018] Identification and characterization of two novel superantigens among Staphylococcus aureus complex. Int J Med Microbiol. doi:10.1016/j.ijmm.2018.03.002 

Zhang, J., Xiong, Y., Rogers, L., Carter, G.P., French, N.P. [2018] Genome-by-genome approach for fast bacterial genealogical relationship evaluation. Bioinformatics. doi:10.1093/bioinformatics/bty195

2017

Benschop, J., Booker, C., Shadbolt, T., Weston, J. [2017] A Retrospective Cohort Study of an Outbreak of Cryptosporidiosis among Veterinary Students. Veterinary Sciences 4, no. 2:29. doi:10.3390/vetsci4020029

Benschop, J., Collins-Emerson, J., Maskill, A., O'Connor, P., Tunbridge, M., Yupiana, Y., Weston, J. [2017] Leptospirosis in three workers on a dairy farm with unvaccinated cattle. N Z Med J v130(1462).

Bertels, F., Gallie, J., Rainey, P.B. [2017] Identification and Characterization of Domesticated Bacterial Transposases. bioRxiv (2017). 

Bloomfield, S.J., Benschop, J., Biggs, P.J., Marshall, J.C., Hayman, D.T.S, Carter, P. E., Midwinter, A.C., Mather, A. E., French, N.P. [2017]. Genomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998-2012. Emerging Infectious Diseases, 23(6), 906-913. doi:10.3201/eid2306.161934

Brooks, C.R., Van Dalen, C.J., Harding, E., Hermans, I.F., Douwes, J. [2017] Effects of treatment changes on asthma phenotype prevalence and airway neutrophil function. BMC Pulm Med, 17(1). doi:10.1186/s12890-017-0511-6

Brooks, C.R., van Dalen, C.J., Hermans, I.F., Gibson, P.G., Simpson, J.L., Douwes, J. [2017] Sputum Basophils Are Increased in Eosinophilic Asthma Compared with Non-Eosinophilic Asthma Phenotypes. Allergy . doi:10.1111/all.13185 

Burgess, S.A., Flint, S.H., Lindsay, D, Cox, M.P., Biggs, P.J. [2017] Insights into the Geobacillus Stearothermophilus Species Based on Phylogenomic Principles. BMC Microbiol 17, no. 1 (Jun 26 2017): 140. doi:10.1186/s12866-017-1047-x 

Cogger, N., Sheard, H. [2017] Working farm dogs. In Livestock Production in New Zealand. Massey University Press, pp.280-297  

Colombi, E., Straub, C., Kunzel, S., Templeton, M.D., McCann, H.C., Rainey, P.B. [2017] Evolution of copper resistance in the kiwifruit pathogen Pseudomonas syringae pv. actinidiae through acquisition of integrative conjugative elements and plasmids. bioRxiv. 070391. doi:10.1101/070391

Compton, C.W.R., Heuer, C., Thomsen, P.T, Carpenter, T.E., Phyn, C.V.C., McDougall, S.[2017] A systematic literature review and meta-analysis of mortality and culling in dairy cattle. J. Dairy Sci. 100(1):1-16. doi:10.3168/jds.2016-11302

Cookson, A.L., Biggs, P.J., Marshall, J.C., Reynolds, A., Collis, R.M., French, N.P., Brightwell, G.[2017] Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure. Sci Rep, 7(1): 814. doi: 10.1038/s41598-017-00890-6

Cornelius, A.J., Miller, W.G.,Lastovica, A.J., On, S.L.W., French, N.P., Vandenberg, O., Biggs, P.J. [2017] Complete Genome Sequence of Campylobacter concisus ATCC 33237(T) and Draft Genome Sequences for an Additional Eight Well-Characterized C.concisus Strains. Genome Announc v5:29. doi:10.1128/genomeA.00711-17

Da Silva, A.G., Baines, S., Carter, G., Heffernan, H., French, N.P., Ren, U.,Stinear, T., Howden, B., Williamson, D. [2017] A phylogenomic framework for assessing the global emergence and evolution of clonal complex 398 methicillin-resistant Staphylococcus aureus. Microbial Genomics 3, no. 1.doi:10.1099/mgen.0.000105

Dixon, M, Flint, S, Palmer, J, Love, R, Biggs,P.J, Beuger, A. [2017] Analysis of Culturable and Non-Culturable Bacteria and Their Potential to Form Biofilms in a Primary Treated Dairy Wastewater System. Environ Technol (Jul 18 2017): 1-8. doi: 10.1080/09593330.2017.1352034

Douwes, J., Cheung, K., Prezant, B., Sharp, M., Corbin, M., McLean, D., t Mannetje, A., Schlunssen, V., Sigsgaard, T., Kromhout, H., LaMontagne, A.D., Pearce, N., McGlothlin, J.D. [2017] Wood Dust in Joineries and Furniture Manufacturing: An Exposure Determinant and Intervention Study. Ann Work Expo Health, 61(4) . doi:10.1093/annweh/wxx020

Farr, A.D., Remigi, P., Rainey, P.B. [2017] Adaptive evolution by spontaneous domain fusion and protein relocalization. Nat Ecol Evol 1[10]:1562-1568. doi:10.1038/s41559-017-0283-7

French, N.P. [2017] Impacts of non-native species on livestock. Impact of biological invasions on ecosystem services pp 139–154.

Froud, K.J., Beresford, R.M., Cogger, N. [2017] Risk factors for kiwifruit bacterial canker disease development in 'Hayward' kiwifruit blocks. Australasian Plant Pathology, 45(5):421-431. doi:10.1007/s13313-017-0504-1

Gates, M.C., Cave, N., Luckman, C. [2017] Feline leukaemia virus in New Zealand. Vetscript, Volume 30(3):48-50.

Gates, M.C., Hinds, H.J., Dale, A. [2017] Preliminary description of aging cats and dogs presented to a New Zealand first-opinion veterinary clinic at end-of-life. N Z Vet J, 65(6):313-317.doi:10.1080/00480169.2017.1360161 

Gates, M.C., Vigeant, S., Dale, A. [2017] Prevalence and risk factors for cats testing positive for feline immunodeficiency virus and feline leukaemia virus infection in cats entering an animal shelter in New Zealand. N Z Vet J 65(6):285-291. doi:10.1080/00480169.2017.1348266

Garcia, R.J.C., Hayman, D.T.S.[2017] Evolutionary Processes in Populations of Cryptosporidium Inferred from Gp60 Sequence Data. Parasitol Res . doi:10.1007/s00436-017-5459-1 

Garcia, R.J.C., French, N.P., Pita, A., Velathanthiri, N., Shrestha, R., Hayman, D.T.S. [2017] Local and global genetic diversity of protozoan parasites: Spatial distribution of Cryptosporidium and Giardia genotypes. PLoS Negl Trop Dis 11(7): e0005736. doi:10.1371/journal.pntd.0005736

Gartrell, B., Agnew, D., Alley, M., Carpenter, T., Ha, H.J., Howe, L., Hunter, S., McInnes, K., Munday, R., Roe, W., Young, M. [2017] Investigation of a Mortality Cluster in Wild Adult Yellow-Eyed Penguins (Megadyptes Antipodes) at Otago Peninsula, New Zealand." Avian Pathol 46, no. 3: 278-88. doi:10.1080/03079457.2016.1264568 

Gerth, M.L., Liu, Y., Jiao, W., Zhang, X.X., Baker, E.N., Lott, J.S., Rainey, P.B., Johnston, J.M. [2017] Crystal Structure of a Bicupin Protein Hutd Involved in Histidine Utilization in Pseudomonas. Proteins 85, no. 8 (Aug 2017): 1580-88. doi: 10.1002/prot.25303 

Grange, Z.L., Biggs, P J., Rose, S.P., Gartrell, B.D., Nelson, N.J., French, N.P. [2017]  Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation. Microb Ecol (2017). doi:10.1007/s00248-017-0959-1

Hayman, D.T.S., Cryan, P.M., Fricker, P.D., Dannemiller, N.G., Freckleton, R. [2017] Long-term video surveillance and automated analyses reveal arousal patterns in groups of hibernating bats. Methods in Ecology and Evolution 8(12) doi:10.1111/2041-210x.12823

Hayman, D.T.S., Marshall, J.C, French, N.P., Carpenter, T.E., Roberts, M.G., Kiedrzynski, T.[2017] Global Importation and Population Risk Factors for Measles in New Zealand: A Case Study for Highly Immunized Populations. Epidemiol Infect 145, no. 9 (Jul 2017): 1875-85. doi:10.1017/S0950268817000723

Hayman, D.T.S., Marshall, J.C., French, N.P., Carpenter, T.E., Roberts, M.G., Kiedrzynski, T. [2017] Cost-benefit analyses of supplementary measles immunisation in the highly immunized population of New Zealand. Vaccine v35:37-p4913-4922. doi:10.1016/j.vaccine.2017.07.077

Hazelton, M.L.,  Bilton, T.P. [2017] Polytope samplers for network tomography. Australian and New Zealand Journal of Statistics. doi:10.1111/anzs.12216

Hazelton, M.L. (2017) Testing for changes in spatial relative risk. Statist. Med., doi:10.1002/sim.7306

Heuer, C., Yuplana, Y., Collins-Emerson, J., Benschop, J., Weston, J., Wilkinson, D., Vallee, E., Wilson, P. [2017] Leptospira shedding in dairy herds: New findings. VetScript 45-46.

Hidano, A., Sharma, B., Rinzin, K., Dahal, N., Dukpa, K., Stevenson, M.A., [2017] Revisiting an old disease? Risk factors for bovine enzootic haematuria in the Kingdom of Bhutan. Preventive Veterinary Medicine 140, 10–18.doi:10.1016/j.prevetmed.2017.02.011 

Howe, L. J., Patel, K., Asher, G., Heuer, C., & Wilson, P. [2017]. Investigation of association between toxoplasma gondii and early pregnancy and abortion rates in New Zealand farmed red deer. In New Zeland society for parasitology (pp. 16). Palmerston North, New Zealand.

Iraola, G., Forster, S.C., Kumar, N., Lehours, P., Bekal, S., Garcia-Pena, F.J., Paolicchi, F., Morsella, C., Hotzel, H., Hsueh, P.R., Vidal, A., Levesque, S., Yamazaki, W., Balzan, C., Vargas, A., Piccirillo, A., Chaban, B., Hill, J.E., Betancor, L., Collado, L., Truyers, I., Midwinter, A.C., Dagi, H.T., Megraud, F., Calleros, L., Perez, R., Naya, H., Lawley, T.D. [2017] Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota. Nat Commun 8(1):1367. doi:10.1038/s41467-017-01449-9

Irshad, H., Cookson, A.L., Prattley, D.J., Marshall, J., French, N.P. [2017] Epidemiology of Escherichia coli serogroups O26, O103, O111 and O145 in very young ('bobby') calves in the North Island, New Zealand.Epidemiol Infect. 2017 Mar 7:1-11. doi: 10.1017/S0950268817000401

Jay, S.M., Gander, P.H., Eng, A., Cheng, S., Douwes, J., Ellison-Loschmann, L,. McLean, D., Pearce, N., 'tMannetje, A. [2017] New Zealanders Working Non-Standard Hours Also Have Greater Exposure to Other Workplace Hazards. Chronobiology International 34, no. 4 (May 2017): 519-26. doi: 10.1080/07420528.2017.1307850 

Karkaba, A., Benschop, J., Hill, K. E., Grinberg, A. [2017]  Characterisation of methicillin-resistant Staphylococcus aureus clinical isolates from animals in New Zealand, 2012–2013, and subclinical colonisation in dogs and cats in Auckland. N Z Vet J 65, no.2:78-83 . doi: 10.1080/00480169.2016.1222919

Keer, S., Glass, B., McLean, D., Harding, E., Babbage, D., Leathem, J., Brinkmann, Y., Prezant, B., Pearce, N., Douwes, J. [2017] Neuropsychological performance in solvent-exposed vehicle collision repair workers in New Zealand. PLoS One, 12(12):e0189108. doi:10.1371/journal.pone.0189108

Kim, E., Carpenter, T., Rowanowski, S., Cogger, N. [2017] Criteria and indicators for foot and mouth disease control strategy decision-making in Asia-Oceania countries. OIE Revue Scientifique et Technique 36(3):867-878 

Lind, P.A., Farr, A.D., Rainey, P.B. [2017] Evolutionary Convergence in Experimental Pseudomonas Populations. ISME J 11, no. 3 (Mar 2017): 589-600. doi:10.1038/ismej.2016.157 doi:10.1038/ismej.2016.157

Lucas-Roxburgh, R., Benschop, J., Lockett, B., van den Heever, U., Williams, R., Howe, L. [2017] The prevalence of human papillomavirus in oropharyngeal cancer in a New Zealand population. PLoS ONE 12(10): e0186424. doi:10.1371/journal.pone.0186424

Luckman, C., Gates, M.C. [2017] Epidemiology and clinical outcomes of feline immunodeficiency virus and feline leukaemia virus in client-owned cats in New Zealand. Journal of Feline Medicine and Surgery Open Reports, 3(2):205511691772931. doi:10.1177/2055116917729311

McCann, H.C., Li, L., Liu, Y., Li, D., Pan, H., Zhong, C., Rikkerink, E.H.A., Templeton, M.D., Straub, C., Colombi, E., Rainey, P.B., Huang, H. [2017] Origin and Evolution of the Kiwifruit Canker Pandemic. Genome Biol Evol 2017; 9 (4): 932-944. doi:10.1093/gbe/evx055 

McLean, D., Glass, B., 't Mannetje, A., Douwes, J. [2017] Exposure to respirable crystalline silica in the construction industry-do we have a problem? N Z Med J. 2017 Dec 1;130(1466):78-82.

McMeekin, C. H., Hill, K. E., Gibson, I. R., Bridges, J. P., Benschop, J. [2017] Antimicrobial Resistance Patterns of Bacteria Isolated from Canine Urinary Samples Submitted to a New Zealand Veterinary Diagnostic Laboratory between 2005-2012. N Z Vet J 65, no. 2: 99-104. doi:10.1080/00480169.2016.1259594 

Miller, P., Marshall, J.C., French, N.P., Jewell, C. [2017] sourceR: Classification and Source Attribution of Infectious Agents among Heterogeneous Populations. arXiv preprint arXiv:1702.07422

Mohan, V, Stevenson, M.A., Marshall, J.C,  French, N.P [2017] Characterisation by multilocus sequence and porA and flaA typing of Campylobacter jejuni isolated from samples of dog faeces collected in one city in New Zealand. NZVJ  65(4)L:209-213. doi:10.1080/00480169.2017.1311810

Moloney, B.J., Heuer, C., Kirkland, P.D. [2017] Neospora caninum in beef herds in New South Wales, Australia. 2: analysis of risk factors. Aust Vet J, 95: 101-109. doi:10.1111/avj.12563 

Moloney, B.J., Kirkland, P.D., Heuer, C. [2017] Neospora caninum in beef herds in New South Wales, Australia. 1: seroprevalence study. Aust Vet J 95(3):72-79, 2017, doi:10.1111/avj.12561

Patel, K.K., Howe, L., Heuer, C., Asher, G.W.,  Wilson, P.R. (2017). Evaluation of Western blot, ELISA and latex agglutination tests to detect Toxoplasma gondii serum antibodies in farmed red deer. Veterinary Parasitology. 244, 154-159 doi: 10.1016/j.vetpar.2017.08.003

Peel, A.J., Wood, J.L.N., Baker, K.S., Breed, A.C., Carvalho, A.D., Fernández-Loras, A., Gabrieli, H.S., Gembu, G.C., Kakengi, V.A., Kaliba, P.M., Kityo, R.M., Lembo, T., Mba, F.E., Ramos, D., Rodriguez-Prieto, I., Suu-Ire, R., Cunningham, A.A., Hayman, D.T.S. [2017] How Does Africa's Most Hunted Bat Vary across the Continent? Population Traits of the Straw-Coloured Fruit Bat (Eidolon Helvum) and Its Interactions with Humans. Acta Chiropterologica 19, no. 1:77-92. doi:10.3161/15081109acc2017.19.1.006 

Pereira, M.M., Schneider, M.C., Munoz-Zanzi, C., Costa, F.,Benschop, J.,Hartskeerl, R., Martinez, J., Jancloes, M., Bertherat, E. [2017] A road map for leptospirosis research and health policies based on country needs in Latin America. Revista Panamericana de Salud Publica. doi:10.26633/rpsp.2017.131

Pichugin, Y., Pena, J., Rainey, P.B., Traulse, A. [2017] Fragmentation modes and the evolution of life cycles. bioRxiv [preprint] 

Pittavino, M., Dreyfus, A., Heuer, C., Benschop, J., Wilson, P.R., Collins-Emerson, J.M., Torgerson, P.R, Furrer. R. [2017] Comparison between Generalized Linear Modelling and Additive Bayesian Network; Identification of Factors Associated with the Incidence of Antibodies against Leptospira Interrogans sv Pomona in Meat Workers in New Zealand. Acta Trop . doi:10.1016/j.actatropica.2017.04.034 

Pittavino, M., Dreyfus, A., Heuer, C., Benschop, J., Wilson, P.R., Collins-Emerson, J.M., Torgerson, P.R., Furrer, R. [2017] Data on Leptospira Interrogans sv Pomona Infection in Meat Workers in New Zealand. Data in Brief . doi:10.1016/j.dib.2017.05.053

Pomeroy, L. W., Bansal, S., Tildesley, M., Moreno-Torres, K. I., Moritz, M., Xiao, N., Carpenter, T. E., Garabed, R. B. (2017) Data-Driven Models of Foot-and-Mouth Disease Dynamics: A Review. Transbound Emerg Dis 64, no. 3. doi: 10.1111/tbed.12437

Priest, P., Toombs-Ruane, L., Benschop, J., Burgess, S., French, N., Murdoch, D., [2017]. A One Health future to meet the AMR challenge? N Z Vet J 65, 60-61.doi:10.1080/00480169.2016.1270651

Purcell, R., Visnovska, M., Biggs, P.J, Schmeier, S., Frizelle, F. [2017] Consensus Molecular Classification of Colorectal Cancer and Association with the Colonic Microbiome. Diseases of the Colon & Rectum, v60-i60: e90-e91. 

Rainey, P.B., Remigi, P., Farr, A.D., Lind, P.A. [2017] Darwin was right: where now for experimental evolution? Curr Opin Genet Dev, v47. doi:10.1016/j.gde.2017.09.003

Richardson, K.S., Rouco, C., Jewell, C., French, N.P., Buddle, B.M., Tompkins, D.M. [2017] Investigating brushtail possum (Trichosurus vulpecula) home-range size determinants in a New Zealand native fores. Wildlife Research v44:4-p316. doi:10.1071/wr16215

Roberts, M.G. [2017] An Epidemic Model with Noisy Parameters. Math Biosci 287: 36-41. doi: 10.1016/j.mbs.2016.08.002 

Rulli, M.C., Santini, M., Hayman, D.T.S., D'Odorico, P. [2017] The Nexus between Forest Fragmentation in Africa and Ebola Virus Disease Outbreaks. Sci Rep 7:41613. doi:10.1038/srep41613 

Sanhueza, J.M., Heuer, C., Wilson, P. R., Benschop, J., Collins-Emerson, J.M. [2017] Seroprevalence and Risk Factors for Leptospira Seropositivity in Beef Cattle, Sheep and Deer Farmers in New Zealand. Zoonoses Public Health . doi:10.1111/zph.12317

Slow, S., Anderson, T., Miller, J., Singh, S., Murdoch, D., Biggs, P.J. [2017] Complete Genome Sequence of a Legionella Longbeachae Serogroup 1 Strain Isolated from a Patient with Legionnaires' Disease. Genome Announc 5, no. 24. doi: 10.1128/genomeA.00564-17 

Shewaramani, S., Finn, T.J., Leahy, S.C., Kassen, R., Rainey, P.B., Moon, C.D. [2017] Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra. PLoS Genet 13(1): e1006570. doi:10.1371/journal.pgen.1006570

Swinburn, B., Vandevijvere, S., Woodward, A., Hornblow, A., Richardson, A., Burlingame, B., Borman, B., Taylor, B., Breier, B., Arroll, B., Drummond, B., Grant, C., Bullen, C., Wall, C., Mhurchu, C. N., Cameron-Smith, D., Menkes, D., Murdoch, D., Mangin, D., Lennon, D., Sarfati, D., Sellman, D., Rush, E., Sopoaga, F., Thomson, G., Devlin, G., Abel, G., White, H., Coad, J. ,Hoek, J., Connor, J., Krebs, J., Douwes, J., Mann, J., McCall, J., Broughton, J., Potter, J. D., Toop, L., McCowan, L., Signal, L., Beckert, L., Elwood, M., Kruger, M., Farella, M., Baker, M., Keall, M., Skeaff, M., Thomson, M., Wilson, N., Chandler, N., Reid, P., Priest, P., Brunton, P., Crampton, P., Davis, P., Gendall, P., Howden-Chapman, P., Taylor, R., Edwards, R., Beaglehole, R., Doughty, R., Scragg, R., Gauld, R., McGee, R., Jackson, R., Hughes, R., Mulder, R., Bonita, R., Kruger, R., Casswell, S., Derrett, S., Ameratunga, S., Denny, S., Hales, S., Pullon, S., Wells, S., Cundy, T., Blakely, T. [2017] Proposed new industry code on unhealthy food marketing to children and young people: will it make a difference? N Z Med J ,130(1450):94-101.

Toombs-Ruane, L.J., Benschop, J., Burgess, S., Priest, P., Murdoch, D.R., French, N.P., [2017]. Multidrug resistant Enterobacteriaceae in New Zealand: a current perspective. N Z Vet J 65, 62-70.doi:10.1080/00480169.2016.1269621

Vallee, E., Ridler, A.L., Heuer, C., Collins-Emerson, J.M., Benschop, J., Wilson, P.R. [2017] Effectiveness of a commercial leptospiral vaccine on urinary shedding in naturally exposed sheep in New Zealand. Vaccine 35, no. 9:1362-68. doi:10.1016/j.vaccine.2016.04.037

van Andel, M., Jewell, C., McKenzie, J., Hollings, T., Robinson, A., Burgman, M., Bingham, P., Carpenter, T. [2017] Predicting Farm-Level Animal Populations Using Environmental and Socioeconomic Variables. Preventive Veterinary Medicine 145 (2017): 121-32. doi:10.1016/j.prevetmed.2017.07.005

Vaughan, T.G., Welch, D., Drummond, A.J., Biggs, P.J., George, T., French, N.P., [2017]. Inferring Ancestral Recombination Graphs from Bacterial Genomic Data. Genetics 205, 857-870.

Wada, M., Stevenson, M., Cogger, N., Carpenter, T. (2017) Evaluation of the control strategy for the 2010 foot-and-mouth disease outbreak in Japan using disease simulation, Transboundary and Emerging Diseases,64, no.3:978-89. doi:10.1111/tbed.12467

Webb, C.T., Ferrari, M., Lindstrom, T., Carpenter, T., Durr, S., Garner, G., Jewell, C., Stevenson, M., Ward, M.P., Werkman, M., Backer, J.,Tildesley, M. [2017] Ensemble Modelling and Structured Decision-Making to Support Emergency Disease Management. Prev Vet Med 138 (Mar 01 2017): 124-33. doi:10.1016/j.prevetmed.2017.01.003

White, J.D., Cave, N.J., Grinberg, A., Thomas, D.G., Heuer, C. [2017], Subclinical Bacteriuria in Older Cats and its Association with Survival. J Vet Intern Med, 30: 1824-1829. doi:10.1111/jvim.14598 

Wilkinson, D.A., Hayman, D.T.S. [2017] Bat and virus ecology in a dynamic world. Microbiology Australia v38(1):33-35.  

Williamson, D.A., Baines, S.L., Carter, G.,Gonçalves da Silva, A.,Ren, X., Sherwood, J., Dufour, M., Schultz, M.B., French, N.P.,Seemann, T., Stinear, Timothy P.,Howden, B.P.[2017] Genomic Insights into a Sustained National Outbreak of Yersinia pseudotuberculosis. Genome Biol Evol (2016) 8 (12): 3806-3814. doi:10.1093/gbe/evw285

Yan, J., Blair, H.T., Liu, M.,Li, W.,He, S.,Chen, L., Dittmer, K.E., Garrick, D.J. ,Biggs, P.J., Dukkipati, V.S.R. [2017] Genome-wide detection of autosomal copy number variants in several sheep breeds using Illumina OvineSNP50 BeadChips. Small Ruminant Research 155:24-32. doi:10.1016/j.smallrumres.2017.08.022

Yang, D.A., Heuer, C., Laven, R., Vink, W.D., & Chesterton, R.N. [2017] Estimating the true prevalence of bovine digital dermatitis in taranaki, New Zealand using a bayesian latent class model. PREVENTIVE VETERINARY MEDICINE. 147, 158-162 doi: 10.1016/j.prevetmed.2017.09.008

Yang, D.A., Heuer, C., Laven, R., Vink, W.D., & Chesterton, R.N. [2017] Farm and cow-level prevalence of bovine digital dermatitis on dairy farms in Taranaki, New Zealand. New Zealand Veterinary Journal. 65(5), 252-256 doi: 10.1080/00480169.2017.1344587

2016

Azarpeykan, S., Dittmer, K.E., Gee, E.K., Marshall, J.C., Elder, P., Acke, E., Thompson, K.G. [2016] Circadian rhythm of calciotropic hormones, serum calcium, phosphorus and magnesium during the shortest and longest days of the year in horses in New Zealand. Journal of Animal Physiology and Animal Nutrition. doi:10.1111/jpn.12477

Azarpeykan, S., Dittmer, K.E., Gee, E.K., Marshall, J.C., Wallace, J., Elder, P., Acke, E., Thompson, K.G. [2016] Influence of blanketing and season on vitamin D and parathyroid hormone, calcium, phosphorus, and magnesium concentrations in horses in New Zealand. Domestic Animal Endocrinology 56:75–84. doi:10.1016/j.domaniend.2016.03.003

Barrett, L. A., Beausoleil, N. J., Benschop, J., Stafford, K. J. [2016] Pain-related behavior was not observed in dairy cattle in the days after liver biopsy, regardless of whether NSAIDs were administered.Research in Veterinary Science  104:195-199. doi:10.1016/j.rvsc.2015.12.020

Bogers, S.H.,Rogers, C.W.,Bolwell, C.,Roe, W.,Gee, E.,McIlwraith, C.W.(2016) Quantitative comparison of bone mineral density characteristics of the distal epiphysis of third metacarpal bones from Thoroughbred racehorses with or without condylar fracture. American Journal of Veterinary Research  77(1):32-38. doi:10.2460/ajvr.77.1.32 

Bojanic, K., Midwinter, A. C., Marshall, J. C., Rogers, L. E., Biggs, P. J., Acke, E. [2016] Variation in the limit-of-detection of the ProSpecT Campylobacter microplate enzyme immunoassay in stools spiked with emerging Campylobacter species. Journal of Microbiological Methods. v127,p236-241. doi:10.1016/j.mimet.2016.06.016 

Bojanić, K., Midwinter, A. C., Marshall, J. C., Rogers, L. E., Biggs, P. J., Acke, E. [2016] Isolation of Campylobacter spp. from Client-Owned Dogs and Cats, and Retail Raw Meat Pet Food in the Manawatu, New Zealand. Zoonoses Public Health. doi:10.1111/zph.12323

Bolwell C.F., Rogers C.W., Gee E.K., Rosanowski S.M. (2016) Descriptive statistics and the pattern of horse racing in New Zealand. 1. Thoroughbred racing. Animal Production Science 56, 77–81. doi:10.1071/AN13442

Brooks, C., van Dalen, C., Zacharasiewicz, A., Simpson, J., Harper, J., Le Gros, G., Gibson, P., Pearce, N., Douwes, J. [2016]Absence of airway inflammation in a large proportion of adolescents with asthma. Respirology, 2016; 21(3): 460-466. doi:10.1111/resp.12701

Cottinet, D., Condamine, F., Bremond, N., Griffiths, A.D., Rainey, P.B., de Visser, J.A., Baudry, J., Bibette, J. [2016] Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution. PLoS One 11(4): e0152395. doi:10.1371/journal.pone.0152395 

Davies, T.M., Jones, K., Hazelton, M.L. [2016] Symmetric adaptive smoothing regimens for estimation of the spatial relative risk function. Computational Statistics & Data Analysis v101 p12-28. doi:10.1016/j.csda.2016.02.008 

Friedrich, A., Marshall, J.C., Biggs, P.J., Midwinter, A.C., French, N.P. [2016]. Seasonality of Campylobacter jejuni isolates associated with human campylobacteriosis in the Manawatu region, New Zealand. Epidemiology and Infection 144, 820-828.doi: 10.1017/S0950268815002009

Froud, K.J., Cogger, N., Beresford, R.M. [2016]. Kiwifruit bacterial canker in 'Hayward' kiwifruit: Design of a quantitative questionnaire for kiwifruit growers. New Zealand Plant Protection. 69, 30-38

Garcia, J., Hayman, D.[2016]. Origin of a major infectious disease in vertebrates: The timing of Cryptosporidium evolution and its hosts. Parisitology. doi:10.1017/S0031182016001323

Grange, Z.L., Gartrell, B.D., Biggs, P.J., Nelson, N.J., Anderson, M., French, N.P. [2016]. Microbial genomics of a host-associated commensal bacterium in fragmented populations of endangered takahe. Microbial Ecology 71, 1020-1029. doi: 10.1007/s00248-015-0721-5

Han, B.A., Schmidt, J.P., Alexander, L.W., Bowden, S.E., Hayman, D.T.S, Drake, J.M. [2016] Undiscovered Bat Hosts of Filoviruses. PLoS Negl Trop Dis 10(7): e0004815. doi:10.1371/journal.pntd.0004815 

Hayman, D.T.S. (2016) Conservation as vaccination: Integrated approaches to public health and environmental protection could prevent future disease outbreaks. EMBO reports(2016). doi:10.15252/embr.201541675

Hayman, D.T.S. (2016) Bats as Viral Reservoirs. Annual Review of Virology. Vol. 3. doi:10.1146/annurev-virology-110615-042203

Hayman, D.T.S. [2016] As the Bat Flies. Science 354, no. 6316:1099-100. doi:10.1126/science.aaj1818

Hayman, D.T.S, Fooks, A.R., Marston, D.A., Garcia, J.C. [2016] The Global Phylogeography of Lyssaviruses - Challenging the 'out of Africa' Hypothesis. PLoS Negl Trop Dis 10, no. 12:e0005266.doi:10.1371/journal.pntd.0005266

Hayman, D.T.S., Peel, A.J. (2016) Can survival analyses detect hunting pressure in a highly connected species? Lessons from straw-coloured fruit bats. Biological Conservation v200:131-139. doi:10.1016/j.biocon.2016.06.003

Hayman, D.T.S., Pulliam, J.R.C., Marshall, J.C., Cryan, P.M., Webb, C.T. (2016) Environment, host, and fungal traits predict continental-scale white-nose syndrome in bats. Science Advances v2-1. doi:10.1126/sciadv.1500831

Hazelton, M.L., Cox, M.P. [2016] Bandwidth selection for kernel log-density estimation. Computational Statistics & Data Analysis v103 p56-57. doi:10.1016/j.csda.2016.05.003

Hidano, A., Carpenter, T.E., Stevenson, M.A., Gates, M.C. [2016] Evaluating the efficacy of regionalisation in limiting high-risk livestock trade movements. Preventive Veterinary Medicine 133(1):31–41 doi:10.1016/j.prevetmed.2016.09.015

Hidano, A., Dukpa, K., Rinzin, K., Sharma, B., Dahal, N., Stevenson, M.A. [2016] A cross-sectional survey of population demographics, the prevalence of major disease conditions and reason-specific proportional mortality of domestic cattle in the Kingdom of Bhutan. Preventive Veterinary Medicine 130(1):1-9 doi:10.1016/j.prevetmed.2016.05.012 

Hill, A.E., Gardner, I.A., Carpenter, T.E., Lee, C.M., Hitchens, P.L. and Stover, S.M. (2016) Prevalence, location and symmetry of noncatastrophic ligamentous suspensory apparatus lesions in California Thoroughbred racehorses, and association of these lesions with catastrophic injuries. Equine Veterinary Journal, 48: 27–32. doi:10.1111/evj.12367

Hurley, M.J., Riggs, C.M., Cogger, N., Rosanowski, S.M. [2016] The incidence and risk factors for shipping fever in horses transported by air to Hong Kong: Results from a 2-year prospective study. The Veterinary Journal 214:34–39. doi:10.1016/j.tvjl.2016.01.006

Irshad, H., Cookson, A.L., Ross, C.M., Jaros, P., Prattley, D.J., Donnison, A., Mc, B.G., Marshall, J., French, N.P. [2016] Diversity and relatedness of Shiga toxin-producing Escherichia coli and Campylobacter jejuni between farms in a dairy catchment. Epidemiology and Infection 144, 1406-1417. doi: 10.1017/S0950268815002782

Jaros, P., Cookson, A.L., Reynolds, A., Prattley, D.J., Campbell, D.M., Hathaway, S., French, N.P. (2016) Nationwide prevalence and risk factors for faecal carriage of Escherichia coli O157 and O26 in very young calves and adult cattle at slaughter in New Zealand. Epidemiology and Infection 144, 1736-1747. doi:10.1017/S0950268815003209

Karkaba, A., Benschop, J., Hill, K. E., Grinberg, A. [2016]  Characterisation of methicillin-resistant Staphylococcus aureus clinical isolates from animals in New Zealand, 2012–2013, and subclinical colonisation in dogs and cats in Auckland. New Zealand Veterinary Journal 1-6 10 Aug 2016. doi: 10.1080/00480169.2016.1222919

Karkaba, A., Grinberg, A., Benschop, J., Pleydell, E. (2016). Characterisation of extended spectrum β-lactamase and AmpC β-lactamase-producing Enterobacteriaceae isolated from companion animals in New Zealand. New Zealand Veterinary Journal 65:2, 105-112, doi:10.1080/00480169.2016.1271730

Keer, S., Glass, B., Prezant, B., McLean, D., Pearce, N., Harding, E., Echeverria, D., McGlothlin, J., Babbage, D.R., Douwes, J. [2016] Solvent Neurotoxicity in Vehicle Collision Repair Workers in New Zealand. Neurotoxicology 57 (Dec 2016): 223-29. doi:10.1016/j.neuro.2016.10.005 

Lal, A., Dobbins, T., Bagheri, N., Baker, M.G., French, N.P., Hales, S., 2016. Cryptosporidiosis Risk in New Zealand Children Under 5 Years Old is Greatest in Areas with High Dairy Cattle Densities. EcoHealth.

Lam, J., Chan, G., Morgan, W.H., Hazelton, M.L., Betz-Stablein, B., Cringle, S. J., Yu, D. Y. [2016] Structural characteristics of the optic nerve head influencing human retinal venous pulsations. Experimental Eye Research v145 p341–346. doi:10.1016/j.exer.2016.02.003

Marquetoux, N., Heuer, C., Wilson, P., Ridler, A., Stevenson, M. [2016] Merging DNA typing and network analysis to assess the transmission of paratuberculosis between farms.Preventive Veterinary Medicine. 134:113-221. doi:10.1016/j.prevetmed.2016.09.014

Marshall, J.C., Soboleva, T.K., Jamieson, P., French, N.P. [2016] Estimating Bacterial Pathogen Levels in New Zealand Bulk Tank Milk. Journal of Food Protection 79, 771-780. doi:10.4315/0362-028X.JFP-15-230

McCulloch, K., Roberts, M.G., Laing, C.R., [2016] Exact analytical expressions for the final epidemic size of an SIR model on small networks. ANZIAM Journal 57, 429-444, doi:10.1017/S1446181116000043

McKee, C.D., Hayman, D.T.S., Kosoy, M.Y., Webb, C.T. [2016] Phylogenetic and geographic patterns of bartonella host shifts among bat species. Infection, Genetics and Evolution 44:382–394. doi:10.1016/j.meegid.2016.07.033

Morgan-Richards, M., Hills, S.F.K, Biggs, P.J., Trewick, S.A. [2016] Sticky Genomes: Using NGS Evidence to Test Hybrid Speciation Hypotheses. PLoS ONE 11(5): e0154911. doi:10.1371/journal.pone.0154911

Morgan, W.H., Hazelton, M.L., Yu, D.Y. [2016] Retinal venous pulsation: Expanding our understanding and use of this enigmatic phenomenon. Progress in Retinal and Eye Research (July). doi:10.1016/j.preteyeres.2016.06.003

Morgan, W.H., House, P.H., Hazelton, M.L., Betz-Stablein, B.D., Chauhan, B.C., Viswanathan, A., Yu, D.Y. [2016] Intraocular Pressure Reduction Is Associated with Reduced Venous Pulsation Pressure. PLoS One. 2016 Jan 29;11(1). doi: 10.1371/journal.pone.0147915

Muellner, P., Muellner, U., Gates, M.C., Pearce, T., Ahlstrom, C., O’Neill, D., Brodbelt, D. and Cave, N.J., [2016] Evidence in Practice–A Pilot study leveraging companion animal and equine health Data from Primary care Veterinary clinics in new Zealand. Front Vet Sci, 3. doi:10.3389/fvets.2016.00116

Nohra, A., Grinberg, A., Midwinter, A. C., Marshall, J. C., Collins-Emerson, J. M., French, N. P. [2016] Molecular Epidemiology of Campylobacter coli Strains Isolated from Different Sources in New Zealand between 2005 and 2014. Applied and Environmental Microbiology 82(14):4363-4370 01  doi:10.1128/AEM.00934-16

O'Shea, T.J., Cryan, P.M., Hayman, D.T.S., Plowright, R.K., Streicker, D.G. (2016) Multiple mortality events in bats: a global review. Mammal Review. doi:10.1111/mam.12064

Parry, K., Watling, D.P., Hazelton, M.L. [2016] A new class of doubly stochastic day-to-day dynamic traffic assignment models. EURO Journal on Transportation and Logistics  v5:p5-23. doi:10.1007/s13676-013-0037-x

Peel, A. J., Baker, K. S., Hayman, D. T. S., Suu-Ire, R., Breed, A. C., Gembu, G., Lembo, T., Fernández-Loras, A., Sargan, D. R.,Fooks, A. R., Cunningham, A.A., Wood, J. L. N. (2016). Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum. Scientific Data. doi:10.17863/CAM.325

Peel, A. J., Field, H. E., Reid, P. A., Plowright, R. K., Broder, C. C., Skerratt, L. F., Hayman, D. T. S., Restif, O., Taylor, M., Martin, G., Crameri, G., Smith, I., Baker, M., Marsh, G. A., Barr, J., Breed, A. C., Wood, J. L., Dhand, N., Toribio, J. A., Cunningham, A. A., Fulton, I., Bryden, W. L., Secombe, C., Wang, L. F.(2016) The equine Hendra virus vaccine remains a highly effective preventative measure against infection in horses and humans: 'The imperative to develop a human vaccine for the Hendra virus in Australia'. Infection Ecology and Epidemiology 2016, 6: 31658 - doi:10.3402/iee.v6.31658

Pirikahu, S., Jones, G., Hazelton, M.L., and Heuer, C. (2016) Bayesian methods of confidence interval construction for the population attributable risk from cross-sectional studies. Statist. Med., doi:10.1002/sim.6870

Probert, W.J., Shea, K., Fonnesbeck, C.J., Runge, M.C., Carpenter, T.E., Durr, S., Garner, M.G., Harvey, N., Stevenson, M.A., Webb, C.T., Werkman, M., Tildesley, M.J., Ferrari, M.J. [2016] Decision-making for foot-and-mouth disease control: Objectives matter. Epidemics 15:10–19. doi:10.1016/j.epidem.2015.11.002

Ritchie, S.R., Isdale, E., Priest, P., Rainey, P.B., Thomas, M.G. (2016) The turnover of strains in intermittent and persistent nasal carriers of Staphylococcus aureus. Journal of Infection 72(3) : 295-301 doi:10.1016/j.jinf.2015.12.010 

Roberts, M.G. [2016] An epidemic model with noisy parameters. Mathematical Biosciences, published online, doi:10.1016/j.mbs.2016.08.002

Rouco, C., Richardson, K.S., Buddle, B.M., French, N.P., Tompkins, D.M. [2016] Sex difference in the survival rate of wild brushtail possums (Trichosurus vulpecula) experimentally challenged with bovine tuberculosis. Research in Veterinary Science v107:p102-105. doi:10.1016/j.rvsc.2016.05.008

Tanner, J., Rogers, C., Bolwell, C., Cogger, N., Gee, E., McLlwraith, W. [2016] Analysis of Failure to Finish a Race in a Cohort of Thoroughbred Racehorses in New Zealand. Animals (Basel) 6(6). doi:10.3390/ani6060036

Van Andel, M., McInnes, K., Tana, T. & French, N.P. (2016) Network analysis of wildlife translocations in New Zealand, New Zealand Veterinary Journal 64, 169-173, doi:10.1080/00480169.2015.1110065  

VanWormer, E., Carpenter, T.E., Singh, P., Shapiro, K., Wallender, W.W., Conrad, P.A., Largier, J.L., Maneta, M.P., Mazet, J.A. [2016] Coastal development and precipitation drive pathogen flow from land to sea: evidence from a Toxoplasma gondii and felid host system. Scientific Reports 6:29252 doi:10.1038/srep29252

Vaughan, T.G.,Welch, D.,Drummond, A.J.,Biggs, P.J.,George, T., French, N.P. [2016] Bayesian inference of ancestral recombination graphs for bacterial populations. bioRxiv, 059105. doi:10.1101/059105(submitted) 

Widder, S., Allen, R.J., Pfeiffer, T.,Curtis, T.P., Wiuf, C., Sloan, W.T., Cordero, O.X., Brown, S.P., Momeni, B., Shou, W., Kettle, H., Flint, H.J., Haas, A.F., Laroche, B., Kreft, J.U., Rainey, P.B., Freilich, S., Schuster, S., Milferstedt, K., van der Meer, J.R., Groszkopf, T., Huisman, J., Free, A., Picioreanu, C., Quince, C., Klapper, I., Labarthe, S., Smets, B.F., Wang, H., Isaac Newton Institute, Fellows, Soyer, O.S. [2016] Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME Journal . doi:10.1038/ismej.2016.45

Williamson, D.A., Baines, S.L., Carter, G.P., da Silva, A.G., Ren, X., Sherwood, J., Dufour, M., Schultz, M.B., French, N.P., Seemann, T., Stinear, T.P., Howden, B.P., 2016. Genomic Insights into a Sustained National Outbreak of Yersinia pseudotuberculosis. Genome Biol. Evol. 8, 3806-3814.

Williamson, D., Baker, M., French, N.P., Thomas, M. [2016] Missing in action: an antimicrobial resistance strategy for New Zealand. New Zealand Medical Journal 128(128):65-67.  

2015

Acke, E.,Midwinter, A.C., Lawrence, K., Gordon, S.J.G., Moore, S., Rasiah, I., Steward, K., French, N., & Waller, A. (2015) Prevalence of Streptococcus dysgalactiae subsp. equisimilis and S. equi subsp. zooepidemicus in a sample of healthy dogs, cats and horses., New Zealand Veterinary Journal, doi: 10.1080/00480169.2015.1016133

Al Mawly, J., Grinberg, A., Prattley, D., Moffat, J., Marshall, J., & French, N. (2015) Risk factors for neonatal calf diarrhoea and enteropathogen shedding in New Zealand dairy farms. The Veterinary Journal. doi: 10.1016/j.tvjl.2015.01.010

Al Mawly, J., Grinberg, A., Prattley, D., Moffat, J., and French, N. (2015) Prevalence of endemic enteropathogens of calves in New Zealand dairy farms. New Zealand Veterinary Journal, 1-18. doi: 10.1080/00480169.2014.966168 

Al Mawly, J., Grinberg, A., Velathanthiri, N., & French, N. (2015). Cross sectional study of prevalence, genetic diversity and zoonotic potential of Cryptosporidium parvum cycling in New Zealand dairy farms. Parasites & Vectors, 8, 240. doi:10.1186/s13071-015-0855-9

Bai, Y., Hayman, D. T., McKee, C. D., Kosoy, M. Y., & Walker, D. H. (2015) Classification of Bartonella Strains Associated with Straw-Colored Fruit Bats (Eidolon helvum) across Africa Using a Multi-locus Sequence Typing Platform. PLOS Neglected Tropical Diseases, 9(1). 

Bolwell C. F.,  Gilpin B. J.,  Campbell D.,  French, N. P. (2015) Evaluation of the representativeness of a sentinel surveillance site for campylobacteriosis. Epidemiology and Infection / Volume 143 / Issue 09. doi: 10.1017/S0950268814003173  

Bolwell C. F., Rogers C. W., Gee E. K., Rosanowski S. M. (2015) Descriptive statistics and the pattern of horse racing in New Zealand. 2. Harness racing. Animal Production Science 56, 82–86.doi:10.1071/AN13443

Bolwell, C. F.,Rogers, C. W.,Rosanowski, S. M., Weston, J. F., Gee, E. K., Gordon, S. J. G. (2015) Cross-sectional survey of the management and training practices of endurance horses in New Zealand: a pilot study. Journal of Equine Veterinary Science. doi: 10.1016/j.jevs.2015.07.019

Bolwell, C. F., Rosanowski, S. M., Scott, I., Sells, P. D., Rogers, C. W. (2015) Questionnaire study on parasite control practices on Thoroughbred and Standardbred breeding farms in New Zealand.Veterinary parasitology. doi : 10.1016/j.vetpar.2015.02.011

Brownlie T.S,, Morton J.M,, Heuer C,, McDougall S. (2015) A  randomised controlled study to assess the effects of an extension programme on the 6 week in-calf rate of seasonal calving, pasture-based dairy herds in New Zealand. The Veterinary Journal 203(2):169-176 doi: 10.1016/j.tvjl.2014.11.014

Brownlie T,S,, Morton J.M., Heuer C,, McDougall S. (2015) Effects of a group-based reproductive management extension programme on key management outcomes affecting reproductive performance. The Veterinary Journal 203(2):177-186 doi:10.1016/j.tvjl.2014.11.016 

Burgess, S.A., Cox, M.P., Flint, S.H., Lindsay, D., Biggs, P.J. [2015] Draft genome sequences of three strains of Geobacillus stearothermophilus isolated from a milk powder manufacturing plant. Genome Announc 3(5):e00939-15. doi:10.1128/genomeA.00939-15

Buhnerkempe, M., Roberts, M.G., Dobson, A.P., Heesterbeek, J.A.P., Hudson, P., Lloyd-Smith, J., (2015)  Eight challenges in modelling disease ecology in multi-host, multi-agent systems. Epidemics 10, 26-30. . doi: 10.1016/j.epidem.2014.10.001  

Dreyfus, A, Wilson, P, Collins-Emerson, J, Benschop, J, Moore, S, & Heuer, C. (2015)  Risk factors for new infection with Leptospira in meat workers in New Zealand. Occupational and Environmental Medicine. doi: 10.1136/oemed-2014-102457

Fang, F., Collins-Emerson, J.M., Cullum, A., Heuer, C., Wilson, P.R., & Benschop. J. (2015)  Shedding and seroprevalence of pathogenic Leptospira spp. in sheep and cattle at a New Zealand abattoir. Zoonoses and Public Health. doi: 10.1111/zph.12146

Fearnhead, P., Yu, S., Biggs, P., Holland, B., & French, N. (2015) Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods. Annals of Applied Statistics arXiv preprint arXiv:1411.1200.

Firestone R., Cheng S., Pearce N., Douwes J., Merletti F., Pizzi C., Pivetta E., Rusconi F., Richiardi L. (2015) Internet-Based Birth-Cohort Studies: Is This the Future for Epidemiology? JMIR Res Protoc 2015;4(2):e71 doi: 10.2196/resprot.3873 

Froud, K.J., Everett, K.R., Tyson, J.L., Beresford, R.M., Cogger, N. [2015]. Review of the risk factors associated with kiwifruit bacterial canker caused by Pseudomonas syringae pv. Actinidiae. New Zealand Plant Protection. 68, 313-327

Gallie, J. ,Libby, E., Bertels, F., Remigi, P., Jendresen, C.B., Ferguson, G. C., Desprat, N., Buffing, M. F., Sauer, U., Beaumont, H. J. E., Martinussen, J., Kilstrup, M., Rainey, P.B.  (2015)  Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens. PLoS Biol 13(3): e1002109. doi: 10.1371/journal.pbio.1002109 

Gates, M.C., Holmstrom, L.K., Biggers, K.E.,  Beckham, T.R. (2015) Integrating novel data streams to support biosurveillance in commercial livestock production systems in developed countries: challenges and opportunities. Frontiers in Public Health, 3, 74. doi: 10.3389/fpubh.2015.00074

Gordon S. J. G., Bolwell C., Rogers C., Musuka G., Kelly P.,  Labuschagne K.,Guthrie A. J.,Denison E., Mellor P. S.,Hamblin C. (2015) The occurrence of Culicoides species, the vectors of arboviruses, at selected trap sites in Zimbabwe. Onderstepoort J Vet Res; Vol 82, No 1. doi: 10.4102/ojvr.v82i1.900 

Grange, Z., Gartrell, B. D., Biggs, P. J.,Nelson, N. J., Marshall,  J. C.Howe, L., Balm, M. G., French, N. P. (2015) Using a common commensal bacterium in endangered Takahe as a model to explore pathogen dynamics in isolated wildlife populations. Conserv Biol. doi : 10.1111/cobi.12521

Gregory S. J.,  Anderson C. W. N., Camps-Arbestain M., Biggs P. J., Ganley A. R. D., O'Sullivan J. M., McManus M. T. (2015) Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation. PLoS ONE 10(4): e0125393. doi: 10.1371/journal.pone.0125393 

Guillot E. G., Hazelton M. L., Karafet T. M., Lansing  J. S., Sudoyo  H., Cox M. P. (2015) Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity. Mol Biol Evol-32:9 2254-62 doi: 10.1093/molbev/msv102

Hayman D. T. S. (2015) Biannual birth pulses allow filoviruses to persist in bat populations. Proc. R. Soc. B 282: 20142591. doi: 10.1098/rspb.2014.2591

Hazelton M. L. (2015) Network Tomography for Integer-Valued Traffic. arXiv:1501.02514 Ann. Appl. Stat. 9 (2015), no. 1, 474--506. doi:10.1214/15-AOAS805.

Hazelton M. L., Parry  K. (2015) Statistical methods for comparison of day-to-day traffic models, Transportation Research Part B: Methodological, ISSN 0191-2615, doi: 10.1016/j.trb.2015.08.005

Heesterbeek, J.A.P., Anderson, R.M., Andreasen, V., Bansal, S., de Angelis, D., Dye, C., Eames, K.T.D., Edmunds, J., Frost, S.D.W., Funk, S., Hollingsworth, T.D., House, T., Isham, V.S., Klepac, P., Lessler, J., Lloyd-Smith, J.O., Metcalf, C.J.E., Mollison, D., Pellis, L., Pulliam, J.R.C., Roberts, M.G., Viboud, C., Isaac Newton Institute IDD Collaboration (2015) Modelling infectious disease dynamics in the complex landscape of global health. Science 347 (6227), aaa4339 [DOI:10.1126/science.aaa4339], aaa4339. 

Heesterbeek, J.A.P., Roberts, M.G. (2015) How mathematical epidemiology became a field of biology: a commentary on Anderson and May (1981) 'The population dynamics of microparasites and their invertebrate hosts'. Philosophical Transactions of the Royal Society of London B 370, 20140307.  doi: 10.1098/rstb.2014.0307

Heuer, C., Yupiana, Y., Wilson, P., Benschop, J., Collins-Emerson, J., Vallée, E., Weston, J. (2015) Are vaccinated dairy cows shedding leptospires? VetScript XXXVIII 7-34.

Hill, K. E., Chambers, J. P., Jones, B. R., Bolwell, C. F., Aberdein, D,. Mills, P. C. (2015) Regional variations in percutaneous absorption of methimazole: an in vitro study on cat skin. doi: 10.1111/jvp.12220 

Hill, K. E., Chambers, J. P., Jones, B. R., Bolwell, C. F., Aberdein, D,. Mills, P. C. (2015) Trans-pinnal movement of methimazole: an in vitro study showing that methimazole can cross from the inner to outer pinna of cats. Journal of feline medicine and surgery. doi: 10.1177/1098612X14567548 

Hill, K. E., Mills, P. C, Jones, B. R, Bolwell, C. F., Aberdein, D. Chambers, J. P. (2015) Percutaneous absorption of methimazole: an in vitro study of the absorption pharmacokinetics for two different vehicles. Journal of veterinary pharmacology and therapeutics. doi: 10.1111/jvp.12213 

Howe L. D., Ellison-Loschmann L., Pearce N., Douwes J., Jeffreys M., Firestone R. (2015) Ethnic differences in risk factors for obesity in New Zealand infants. Journal of Epidemiology and Community Health. doi: 10.1136/jech-2014-204464 

Jaros, P. Dufour, M. Gilpin, B. Freeman, M. M. Ribot, E. M. (2015) PFGE for Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) and non-O157 STEC. Pulse Field Gel Electrophoresis: Methods and Protocols, Methods in Molecular Biology, vol. 1301, doi:10.1007/978-1-4939-2599-5_15. 

Lal, A, Lill, A, Mcintyre, M, Baker, M, Hales, S, and French, N. (2015) Environmental change and enteric zoonoses in New Zealand: A systematic review of the evidence. Australian and New Zealand Journal of Public Health. .doi:  10.1111/1753-6405.12274

Lal, A., Hales, S., Kirk, M., Baker, M. G. and French, N. P. (2015) Spatial and temporal variation in the association between temperature and salmonellosis in NZ. Australian and New Zealand Journal of Public Health. doi: 10.1111/1753-6405.12413

Lind P. A., Farr A. D., Rainey P. B. (2015) Experimental evolution reveals hidden diversity in evolutionary pathways. eLife 4, e07074. doi: 10.7554/eLife.07074 

Liu, Y., Rainey, P. B. and Zhang, X.-X. (2015) Molecular mechanisms of xylose utilization by Pseudomonas fluorescens: overlapping genetic responses to xylose, xylulose, ribose and mannitol. Molecular Microbiology. doi: 10.1111/mmi.13142

Lubaba, C. H., Hidano, A., Welburn, S. C., Revie, C. W., Eisler, M. C. (2015) Movement Behaviour of Traditionally Managed Cattle in the Eastern Province of Zambia Captured Using Two-Dimensional Motion Sensors  PLoS One 10(9): e0138125 doi: 10.1371/journal.pone.0138125

Lucas-Roxburgh, R., Benschop, J., Dunowska, M., Perrott, M. (2015) Prevalence of Human Papilloma Viruses in the mouths of New Zealand women. Accepted New Zealand Medical Journal

Luis, A. D., O'Shea, T. J., Hayman, D. T. S., Wood, J. L. N., Cunningham, A. A., Gilbert, A. T., Mills, J. N., Webb, C. T. (2015),  Network analysis of host-virus communities in bats and rodents reveals determinants of cross-species transmission. Ecology Letters. doi: 10.1111/ele.12491

Mardones, F.O., Valdes-Donoso, P., Pérez, A.M., and Carpenter, T.E. (2015) Lecciones aprendidas a través de la epidemiología veterinaria: El virus ISA, siete años después, Salmon Expert, April 2015, pp. 48-52.

Mather, A. E., Vaughan, T. G., French, N. P. [2015] Molecular Approaches to Understanding Transmission and Source Attribution in Nontyphoidal Salmonella and Their Application in Africa. Clin Infect Dis.(2015)61(suppl 4): S259-S265. doi:10.1093/cid/civ727

Morgan W. H., Abdul-Rahman A., Yu D., Hazelton M. L., Betz-Stablein B., Lind C. R. P. (2015) Objective Detection of Retinal Vessel Pulsation. PLoS ONE 10(2): e0116475. doi:10.1371/journal.pone.0116475 

Pearce N, Blair A, Vineis P, Ahrens W, Andersen A, Anto JM, Armstrong BK, Baccarelli AA, Beland FA, Berrington A, Bertazzi PA, Birnbaum LS, Brownson RC, Bucher JR, Cantor KP, Cardis E, Cherrie JW, Christiani DC, Cocco P, Coggon D, Comba P, Demers PA, Dement JM, Douwes J, Eisen EA, Engel LS, Fenske RA, Fleming LE, Fletcher T, Fontham E, Forastiere F, Frentzel-Beyme R, Fritschi L, Gerin M, Goldberg M, Grandjean P, Grimsrud TK, Gustavsson P, Haines A, Hartge P, Hansen J, Hauptmann M, Heederik D, Hemminki K, Hemon D, Hertz-Picciotto I, Hoppin JA, Huff J, Jarvholm B, Kang D, Karagas MR, Kjaerheim K, Kjuus H, Kogevinas M, Kriebel D, Kristensen P, Kromhout H, Laden F, Lebailly P, LeMasters G, Lubin JH, Lynch CF, Lynge E, ‘t Mannetje A, McMichael AJ, McLaughlin JR, Marrett L, Martuzzi M, Merchant JA, Merler E, Merletti F, Miller A, Mirer FE, Monson R, Nordby KC, Olshan AF, Parent ME, Perera FP, Perry MJ, Pesatori AC, Pirastu R, Porta M, Pukkala E, Rice C, Richardson DB, Ritter L, Ritz B, Ronckers CM, Rushton L, Rusiecki JA, Rusyn I, Samet JM, Sandler DP, de Sanjose S, Schernhammer E, Seniori Costantini A, Seixas N, Shy C, Siemiatycki J, Silverman DT, Simonato L, Smith AH, Smith MT, Spinelli JJ, Spitz MR, Stallones L, Stayner LT, Steenland K, Stenzel M, Stewart BW, Stewart PA, Symanski E, Terracini B, Tolbert PE, Vainio H, Vena J, Vermeulen R, Victora CG, Ward EM, Weinberg CR, Weisenburger D, Wesseling C, Weiderpass E, Zahm SH. (2015) IARC Monographs: 40 years of evaluating carcinogenic hazards to humans. Environ Health Perspect 123:507-514; doi: 10.1289/ehp.1409149 

Pepin K.M., Leach C. B., Marques-ToledoC., LaassK. H., Paixao K. S., LuisA. D., Hayman D. T. S., Johnson N. G., Buhnerkempe M. G., Carver S., Grear D. A., Tsao K., Eiras A. E. and Webb C. T. (2015) Utility of mosquito surveillance data for spatial prioritization of vector control against dengue viruses in three Brazilian cities. Pepin et al. Parasites & Vectors (2015) 8:98 doi: 10.1186/s13071-015-0659-y

Pichugin, Y., Gokhale, C. S., Garcia, J., Traulsen, A. , Rainey, P. B. [2015] Modes of migration and multilevel selection in evolutionary multiplayer games. J Theor Biol v387, p144-153 . doi:10.1016/j.jtbi.2015.09.027 

Rainey, P. B. (2015) Precarious development: The uncertain social life of cellular slime molds. PNAS 2015 112 (9), 2639-2640. doi:10.1073/pnas.1500708112

Ridler, A. L. Vallee, E. Corner, R. A. Kenyon, P. R. Heuer, C. (2015) Factors associated with fetal losses in ewe lambs on a New Zealand sheep farm. doi: 10.1080/00480169.2015.1037813 

Roberts, M., Andreasen, V., Lloyd, A., & Pellis, L. (2015) Nine challenges for deterministic epidemic models. Epidemics. doi: 10.1016/j.epidem.2014.09.006

Rosanowski, S.M.,Rogers, C.W.,Bolwell, C.F., Cogger, N. [2015] The movement pattern of horses around race meetings in New Zealand. Animal Production Science 55(8) 1075-1080 doi:10.1071/AN13345

Rosanowski, S.M., Scott, I., Sells, P.D., Rogers, C.W. and Bolwell, C.F. (2015), Cross-sectional survey of parasite control practices on Thoroughbred and Standardbred training yards in New Zealand. Equine Veterinary Journal. doi: 10.1111/evj.12558   doi:10.1111/evj.12558

Sanhueza J.M., Heuer C., Wilson P.R., Benschop J., Collins-Emerson J.M. (2015)  Prevalence and risk factors for Leptospira exposure in New Zealand veterinarians.. Epidemiology and infection doi: 10.1017/S0950268815000515

Shao, H.,Lam, W.H.K., Sumalee, A. and Hazelton, M.L. [2015] Estimation of mean and covariance of stochastic multi-class OD demands from classified traffic counts. Transportation Research Part C: Emerging Technologies 59:92-110 doi:10.1016/j.trc.2015.05.017

Spencer, S. E., Besser, T. E., Cobbold, R. N., French, N. P. (2015) 'Super' or just 'above average'? Supershedders and the transmission of Escherichia coli O157:H7 among feedlot cattle.J R Soc Interfac: 12-110. doi:10.1098/rsif.2015.0446

Strachan, N. J., Rotariu, O., Lopes, B., MacRae, M., Fairley, S., Laing, C., Gannon, V., Allison, L. J., Hanson, M. F., Dallman, T., Ashton, P., Franz, E., van Hoek, A. H., French, N. P., George, T., Biggs, P. J., Forbes, K. J. (2015) Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli  O157 Genotypes Dominates Host Association. Sci Rep. 2015 Oct 7;5:14145. doi: 10.1038/srep14145

Toombs-Ruane, L.J., Riley, C.B., Kendall, A.T., Bolwell, C.F., Benschop, J. and Rosanowski, S.M. (2015), Antimicrobial Susceptibilities of Aerobic Isolates from Respiratory Samples of Young New Zealand Horses. Journal of Veterinary Internal Medicine. doi: 10.1111/jvim.13600 

Toombs-Ruane, L. J., Riley, C. B., Kendall, A. T., Hill, K. E., Benschop, J., Rosanowski, S. M. (2015) Antimicrobial susceptibility of bacteria isolated from neonatal foal samples submitted to a New Zealand veterinary pathology laboratory (2004 to 2013). N Z Vet J. 2015 Nov 23:1-5. doi:10.1080/00480169.2015.1109006

Toombs-Ruane, L.J., Riley, C.B., Rosanowski, S.M., Kendall, A.T. , Benschop, J. (2015), Antimicrobial Resistance of Aerobic Respiratory Isolates From Young New Zealand Horses. Equine Veterinary Journal, 47: 20. doi: 10.1111/evj.12486_45 

Toombs-Ruane, L., Rosanowski, S., Riley, C., Kendall, A., Bolwell, C., Benschop, J. (2015) Antimicrobial sensitivities of aerobic isolates from respiratory samples of young New Zealand horses submitted to a commercial laboratory. Accepted Journal of Veterinary Internal Medicine

Theoret, C. L., Bolwell, C. F., Riley, C. B. (2015) A cross-sectional survey on wounds in horses in New Zealand. N Z Vet J 1-16 doi: 10.1080/00480169.2015.1091396

Vallée E., Heuer C., Collins-Emerson J.M., Benschop J., Wilson P.R. (2015) Serological patterns, antibody half-life and shedding in urine of Leptospira spp. in naturally exposed sheep. New Zealand Veterinary Journal: 1-32. doi: 10.1080/00480169.2015.1049668

Van Andel, M., Jackson, B., Midwinter, A., Alley, M., Ewen, J., McInnes, K., Jakob Hoff, R., Reynolds, A., and French, N. (2015) Investigation of mortalities associated with Salmonella spp. infection in wildlife on Tiritiri Matangi Island in the Hauraki Gulf of New Zealand. New Zealand Veterinary Journal, 1-12. doi: 10.1080/00480169.2014.990065

Zhang, X. X., Gauntlett, J. C., Oldenburg, D. G., Cook, G. M., Rainey, P. B. (2015) Role of the Transporter-Like Sensor Kinase CbrA in Histidine Uptake and Signal Transduction. J Bacteriol 197-17 2867-78. doi: 10.1128/JB.00361-15

2014 

Abdul-Rahman, A., Morgan, W., Hazelton, M., Betz-Stablein, B., Yu, D. Y., Chan, G., & Lam, J. 2014. A novel method of non-invasive retinal vascular pulse waveform assessment using fourier analysis. Clinical and experimental ophthalmology Vol. 42, pp. 99-99

Alsohim, A.S., Taylor, T.B., Barrett, G.A., Gallie, J., Zhang, X.X., AltamiranoÂ?]Junqueira, A.E., Johnson, L.J., Rainey, P. B., & Jackson, R.W. 2014. The biosurfactant viscosin produced by Pseudomonas fluorescens SBW25 aids spreading motility and plant growth promotion. Environmental microbiology. 16(7), 2267-2281. doi: 10.1111/1462-2920.12469

Bajardi P., Paolotti D., Vespignani A., Eames K., Funk S., Edmunds W. J., Turbelin C., Debin M., Colizza V., Smallenburg R., Koppeschaar C., Franco A. O., Faustino V., Carnahan A., Rehn M., Merletti F., Douwes J., Firestone R.,Richiardi L. 2014. Association between Recruitment Methods and Attrition in Internet-Based Studies. PLoS ONE 9(12): e114925. doi: 10.1371/journal.pone.0114925 

Baker, K.S., Suu-Ire, R., Barr, J., Hayman, D.T.S., Broder, C.C., Horton, D.L., Durrant, C., Murcia, P.R., Cunningham, A.A., & Wood, J.L.N. 2014. Viral antibody dynamics in a chiropteran host. Journal of Animal Ecology. 83(2), 415–428. doi: 10.1111/1365-2656.12153

Bertels, F., Silander, O.K., Pachkov, M., Rainey, P.B., & van Nimwegen, E. 2014. Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular biology and evolution. doi: 10.1093/molbev/msu088

Binney, B.M., Biggs, P.J., Carter P.E., Holland, B.R. & French, N.P. 2014. Quantification of historical livestock importation into New Zealand. New Zealand Veterinary Journal, 62(6). pp 309-314 doi: 10.1080/00480169.2014.914861

Bolwell, C. F., Rogers, C. W. , Gee, E. K., Rosanowski, S. M. 2014. Descriptive statistics and the pattern of horse racing in New Zealand: Part One Thoroughbred racing. Animal Production Science. doi : dx.doi.org/10.1071/AN13442 

Bolwell, C. F., Rogers, C. W. , Gee, E. K., Rosanowski, S. M. 2014. Descriptive statistics and the pattern of horse racing in New Zealand: Part Two Harness racing. Animal Production Science. doi : dx.doi.org/10.1071/AN13443

Carpenter, T.E., Coggins, V.L., McCarthy, C., O'Brien, C.S., O'Brien, J.M., & Schommer, T.J. 2014. A spatial risk assessment of bighorn sheep extirpation by grazing domestic sheep on public lands. Preventive Veterinary Medicine. 114(1), 3-10 DOI: 10.1016/j.prevetmed.2014.01.008

De Monte, S., & Rainey, P.B. 2014. Nascent multicellular life and the emergence of individuality. Journal of Biosciences. 39(2), 237-48. doi: 10.1007/s12038-014-9420-5

Dervan, E., Morgan, W.,Abdul-Rahman, A., Yu, D. Y., Hazelton, M., Betz-Stablein, B.,Lind C., Chan G. Lam, J. 2014. Tissue small vessel pulse amplitude differentiates between the cup, neuroretinal rim and retina in normal eyes. Clinical and experimental ophthalmology Vol.42, pp. 22-22.

Douwes J., & Pearce, N . 2014 Epidemiology of respiratory allergies and athma. In Ahrens,W. & Pigeot, I (Eds.), Handbook of Epidemiology (2nd ed). Heidelberg: Springer-Verlag. pp 2263-2319

Dreyfus, A, Heuer, C., Wilson, P., Collins-Emerson, J., Baker, M., & Benschop, J. 2014. Risk of infection and associated flu-like disease among abattoir workers due to two Leptospira species. Epidemiology and Infection. doi:10.1017/S0950268814002477

Dreyfus, A, Benschop, J., Collins-Emerson, J., Wilson, P., Baker, M. & Heuer, C. 2014. Sero-prevalence and Risk Factors for Leptospirosis in Abattoir Workers in New Zealand. International Journal of Environmental Research and Public Health. 11(2), 1756-1775. doi:10.3390/ijerph110201756

Duncan, J. S., Leatherbarrow, A. J., French, N.P., & Grove-White, D. H. 2014. Temporal and farm-management-associated variation in faecal-pat prevalence of Campylobacter fetus in sheep and cattle. Epidemiology and Infection. 142(6), 1196-1204. doi:http://dx.doi.org/10.1017/S0950268813002379

Dürr, S., Fasel-Clemenz, C., Thür, B., Schwermer, H., Doherr, M.G., Dohna, H.Z., Carpenter, T.E., Perler, L., & Hadorn, D.C. 2014. Evaluation of the benefit of emergency vaccination in a foot-and-mouth disease free country with low livestock density. Preventive Veterinary Medicine. 113(1), 34-46 http://dx.doi.org/10.1016/j.prevetmed.2013.10.015

Fang, F., Benschop, J., Wilson, P., Collins-Emerson, J., Heuer, C., & Prattley, D. 2014. Sero-prevalence and exposure to risk factors for leptospirosis among veterinary students at Massey University. New  Zealand  Veterinary Journal 62(3), 130-135. doi: 10.1080/00480169.2013.862161.  

Fang, F., Collins-Emerson, J.M., Heuer, C., Hill, F.J., Tisdall, D. J., Wilson, P.R., & Benschop, J. 2014. Inter-laboratory and between-specimen comparisons of diagnostic tests for leptospirosis in sheep and cattle. Journal of Veterinary Diagnostic Investigation. doi: 10.1177/1040638714548476

Fearnhead, P., Biggs, P., & French, N. 2014. Learning about recombination in Campylobacter. In: Sheppard, S., & Méric, G. (Eds.), Campylobacter Ecology and Evolution. Horizon Scientific Press, 9-22  http://www.horizonpress.com/campy2

Fernando, S. W. T. P., & Hazelton, M. 2014. Generalizing the Spatial Relative Risk Function. Spatial and Spatio-temporal Epidemiology. 8, 1-10. doi: http://dx.doi.org/10.1016/j.sste.2013.12.002  

Fernando, W.T.P.S., Ganesalingam, S., & Hazelton, M.L. 2014. A comparison of estimators of the geographical relative risk function. Journal of Statistical Computation and Simulation. 84(7), 1471-1485 doi:10.1080/00949655.2012.748055

French, N., Yu, S., Biggs, P., Holland, B., Fearnhead, P., Binney, B., Fox, A., Grove-White, D.H., Leigh, J., Miller, W., Muellner, P., & Carter, P. 2014. Evolution of Campylobacter species in New Zealand. In: Sheppard, S., & Méric, G. (Eds.), Campylobacter Ecology and Evolution. Horizon Scientific Press, 221-240 http://www.horizonpress.com/campy2

Franz, E., Delaquis, P., Morabito, S., Beutin, L., Gobius, K., Rasko, D. A., Bono, J., French, N., Osek, J., Lindstedt, B.-A., Muniesa, M., Manning, S., LeJeune, J., Callaway, T., Beatson, S., Eppinger, M., Dallman, T., Forbes, K. J., Aarts, H., Pearl, D. L., Gannon, V. P. J., Laing, C. R., & Strachan, N. J. C. 2014. Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems. International Journal of Food Microbiology, 187(0), 57-72. doi: http://dx.doi.org/10.1016/j.ijfoodmicro.2014.07.002

Froud,K.J., Cogger, N., Beresford, R.M. 2014. Relationships between kiwifruit bacterial canker disease and kiwifruit productivity. New Zealand Plant Protection 67: 34-40 

Grange, Z., van Andel, M., French, N.P., & Gartrell, B. 2014. Social networking of an endangered flightless bird and its use in targeting disease surveillance. Conservation Biology. 28(2), 518-528. doi: 10.1111/cobi.12178

Grove-White, D.H., Leatherbarrow, A.J., Cripps, P.J., & French, N.P. 2014. Temporal and farm-management-associated variation in faecal pat prevalence of Arcobacter spp. in ruminants. Epidemiology and Infection. 142(4), 861-870. http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8951596&fulltextType=RA&fileId=S095026881300160X

Hammerschmidt, K., Rose, C. J., Kerr, B. & Rainey, P. B. 2014. Life cycles, fitness decoupling and the evolution of multicellularity.  Nature xx 2014 doi:10.1038/nature13884 

Hamoonga, R., Stevenson, M.A., Allepuz, A., Carpenter, T.E., & Sinkala, Y. 2014. Risk factors for foot-and-mouth disease in Zambia, 1981-2012. Preventive Veterinary Medicine. 114(1), 64-71. http://dx.doi.org/10.1016/j.prevetmed.2014.01.014  

Hickson, R.I., & Roberts, M.G. 2014. How population heterogeneity in susceptibility and infectivity influences epidemic dynamics. Journal of Theoretical Biology. 350(7), 70-80. doi: http://dx.doi.org/10.1016/j.jtbi.2014.01.014

Hill, A. E., Gardner, I. A., Carpenter, T. E., Lee, C. M., Hitchens, P. L. and Stover, S. M. 2014. Prevalence, location and symmetry of noncatastrophic ligamentous suspensory apparatus lesions in California Thoroughbred racehorses, and association of these lesions with catastrophic injuries. Equine Veterinary Journal. doi: 10.1111/evj.12367

Holden, N. J., Wright, F., Mackenzie, K., Marshall, J., Mitchell, S., Mahajan, A., Wheatley, R., & Daniell, T. J. 2014. Prevalence and diversity of Escherichia coli isolated from a barley trial supplemented with bulky organic soil amendments: Green compost and bovine slurry. Letters in Applied Microbiology, 58(3), 205-212. doi: 10.1111/lam.12180

Holland, K.; Jones, G.; & Benschop, J. 2014. Spatio-temporal modeling of disease incidence with missing covariate values. Epidemiology and Infection. doi: http://dx.doi.org/10.1017/S0950268814002854

Irshad, H., Cookson, A.,  Prattley, D.J., Dufour, M., & French, N.P. 2014. Distribution of Escherichia coli strains harbouring Shiga toxin-producing E. coli (STEC)-associated virulence factors (stx1, stx2, eae, ehxA) from very young calves in the North Island of New Zealand. Epidemiology and Infection. doi: http://dx.doi.org/10.1017/S0950268814000089

Jancloes, M.F., Bertherat, E., Scheider, C., Belmain, S., Munoz-Zanzi, C., Hartskeerl, R., Costa, F., Denis, J., & Benschop, J. 2014. Towards a “One Health” Strategy Against Leptospirosis. Planet@Risk, 2(3), 204-206. http://planet-risk.org/index.php/pr/article/view/94

Jaros, P., Cookson, A., Campbell, D., Duncan, G., Prattley, D., Carter, P., Besser, T., Shiringi, S., Hathaway, S., Marshall, J., & French, N. 2014. Geographic divergence of bovine and human Shiga toxin-producing Escherichia coli O157:H7 genotypes in New Zealand. Emerging Infectious Diseases, 20(12). http://dx.doi.org/10.3201/eid2012.140281

Kalaris, T., Fieselmann, D., Magarey, R., Colunga-Garcia, M., Roda, A., Hardie, D., Cogger, N., Hammond, N., Martin, P. T. & Whittle, P. 2014. The Role of Surveillance Methods and Technologies in Plant Biosecurity. The Handbook of Plant Biosecurity. Springer Netherlands.

Kim, H., Yoon, H., Moon, O-K., Han, J-H., Lee, K., Jeong, W., Choi, J., Cho, Y-M., Kang, Y-M., Ahn, H-Y., Kim, D-S., Carpenter, T.E. 2014. Economic impacts of foot-and-mouth disease, experienced in five epidemics in the Republic of Korea from 2000 to 2011, Journal of Preventive Veterinary Medicine,

Kvalsvig, A., Baker, M.G., Sears, A. & French, N. 2014 Bacteria: Campylobacter. In: Encyclopedia of Food Safety, Elsevier, Academic Press, 369-380.

Lal, A., Lill, A., Mcintyre, M., Baker, M., Hales, S., & French, N. 2014. Environmental change and enteric zoonoses in New Zealand: A systematic review of the evidence. Australian and New Zealand Journal of Public Health, doi: 10.1111/1753-6405.12274

Lam, J., Chan, G., Morgan, W. H., Hazelton, M., Betz-Stablein, B., & Yu, D. Y. 2014. Analysis of venous pulsations in the human retina using ocular coherence tomography. Clinical and experimental ophthalmology Vol. 42, pp. 45-45.

Liu, Y., Rainey, P. B., Zhang, X., 2014. Mini-Tn7 vectors for studying post-transcriptional gene expression in Pseudomonas. Journal of Microbiological Methods, Vol 107,pp 182-185, ISSN 0167-7012, http://dx.doi.org/10.1016/j.mimet.2014.10.015

Loerbroks A, Bosch J.A., Douwes J., Angerer P., & Li J. 2014. Job insecurity is associated with adult asthma in Germany during Europe’s recent economic crisis: a prospective cohort study. Journal of Epidemiology & Community Health. doi:10.1136/jech-2014-204274

Lindgreen S, Umu, S U, Lai A S-W, Eldai H, Liu W, McGimpsey S, Wheeler N, Biggs, P.J., Thomson N, Barquist L, Poole A M, Gardner P P. 2014. Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling” PLoS Comp Biol, DOI: 10.1371/journal.pcbi.1003907

Mansell, C., & Benschop, J. 2014. Leptospirosis is an important multi-species zoonotic disease in New Zealand. Invited editorial. New Zealand Medical Journal, 127 (1388). http://journal.nzma.org.nz/journal/127-1388/5980/

Mardones F.O., Martínez-López B., Valdés-Donoso P., Carpenter T.E., & Perez A.M., 2014. The role of fish movements in the spread of infectious salmon anemia in Chile, 2007-2009, Preventive Veterinary Medicine. 114(7), 37-46. http://dx.doi.org/10.1016/j.prevetmed.2014.01.012

McDougall S, Heuer C, Morton J, Brownlie T. 2014. Use of herd management programmes to improve the reproductive performance of dairy cattle. Animal, 8(1), 199-210.  doi: 10.1017/S1751731114000457

McLean, D., Biggs, P., Leblanc-Maridor, M., Hall, R., French, N., Pearce, N., & Douwes, J. 2014. 0164 Metagenomic detection of bacteria in aerosol samples in animal slaughterhouses to develop exposure profiles for an epidemiological analysis.. Occup Environ Med. , A21. doi: 10.1136/oemed-2014-102362.65

Morgan, W., Abdul-Rahman, A., Yu, D. Y., Hazelton, M., Betz-Stablein, B., & Lind, C. 2014. New photo-plethysmographic technique accurately detects retinal vessel pulsation. Cinical and experimental ophthalmology Vol. 42, pp. 19-19.

Morgan W. H., Hazelton M. L., Betz-Stablein B. D., Yu D. Y., Lind C. R.,Ravichandran V., House P. H. 2014. Photoplethysmographic measurement of various retinal vascular pulsation parameters and measurement of the venous phase delay. Invest Ophthalmol Vis Sci 55: 5998–6006. doi: 10.1167/iovs.14-15104. pmid:25183767

Mughini-Gras, L., Smid, J. H., Wagenaar, J., De Boer, A., Havelaar, A. H., Friesema, I.H.M.,. French, N.P., Graziani, C., Busani, L., & van Pelt, W. 2014. Campylobacteriosis in travellers returning to The Netherlands: multilocus sequence types, risk factors, and evidence for person-to-person transmission of exotic strains in domestically acquired infections. Epidemiology and Infection. 142(6), 1277-1288. doi:  http://dx.doi.org/10.1017/S0950268813002069

O'Brien, J. M., O'Brien, C. S., MCcarthy, C. and Carpenter, T. E. 2014. Incorporating foray behavior into models estimating contact risk between bighorn sheep and areas occupied by domestic sheep. Wildlife Society Bulletin, 38: 321–331. doi: 10.1002/wsb.387

Olival, K.J., & Hayman, D.T.S. 2014. Filoviruses in Bats: Current Knowledge and Future Directions. Viruses. 6(4), 1759-1788. doi:10.3390/v6041759

O’Shea, T.J., Cryan, P,M., Cunningham, A.A., Fooks, A.R., Hayman, D.T.S., Luis, A.D., Peel, A.J., Plowright, R.K., & Wood, J.L.N. 2014. Bat flight and zoonotic viruses. Emerging infectious diseases. 20(5), 741-745. doi:10.3201/eid2005.130539

Peel, A.J., Pulliam, J. R. C., Luis, A. D., Plowright, R. K., O'Shea, T. J., Hayman, D. T. S., Wood, J. L. N., Webb, C. T., & Restif, O. 2014. The effect of seasonal birth pulses on pathogen persistence in wild mammal populations. Proceedings of the Royal Society B: Biological Sciences. 281(1786). doi:10.1098/rspb.2013.2962 1471-2954

Prangle, D., Fearnhead, P., Cox, M., Biggs, P., & French, N. 2014. Semi-automatic selection of summary statistics for ABC model choice. Statistical Applications in Genetics and Molecular Biology. 13(1), 67-82. doi: 10.1515/sagmb-2013-0012

Preziuso, S., Pinho, M.D., Attili, A.R., Melo-Cristino, J., Acke, E., Midwinter, A.C., Cuteri, V., Ramirez, M. 2014. PCR based differentiation between Streptococcus dysgalactiae subsp. equisimilis strains isolated from humans and horses. Comparative Immunology, Microbiology and Infectious Diseases. doi: http://dx.doi.org/10.1016/j.cimid.2014.04.001

Ranta, A., Yang, C. F., Funnell, M., Cariga, P., Murphy-Rahal, C., Cogger, N. 2014. Utility of a primary care based transient ischaemic attack electronic decision support tool: a prospective sequential comparison. BMC family practice, 15(1), 86.

Rainey, P.B., & De Monte, S. 2014. Resolving Social Conflicts and the Evolution of Multicellularity. Annual Review of Ecology, Evolution, and Systematics. 45(1)

Rainey, P.B., Desprat, N., Driscoll, W.W., & Zhang, X.-X. 2014. Microbes are not bound by sociobiology: Response to Kummerli and Ross-Gillespie (2013) Evolution, doi: 10.1111/evo.12508 

Richards, K., Hazelton, M., Stevenson, M., Lockhart, C., Pinto, J., & Nguyen, L. 2014. Using exceedance probabilities to detect anomalies in routinely recorded animal health data, with particular reference to foot-and-mouth disease in Viet Nam. Spatial and Spatio-temporal Epidemiology. 11, 125-133 doi: 10.1016/j.sste.2014.08.002

Ritchie, S.R., Thomas, M.G., & Rainey, P.B. 2014. The Genetic Structure of Staphylococcus aureus Populations from the Southwest Pacific. PLoS ONE, 9(7), e100300 

Roberts, M.G., & Heesterbeek, J.A.P. 2014. Mathematical models in epidemiology. In J.A. Filar (Ed.) Mathematical Models. Oxford: EOLSS Publishers Ltd 

Roche, S.E., Cogger, N., Garner, M.G., Putra, A.A.G., & Toribio, J.A.L.M.L. 2014. Assessing the risk of highly pathogenic avian influenza H5N1 transmission through poultry movements in Bali, Indonesia. Preventive Veterinary Medicine. 113(4), 599-607. doi:tp://dx.doi.org/10.1016/j.prevetmed.2013.11.017

Roe, W. D., Mayhew, I. G., Jolly, R. D., Marshall, J., & Chilvers, B. L. 2014. Traumatic brain injury, axonal injury and shaking in New Zealand sea lion pups. The Veterinary Journal, 200(1), 96-102. doi: http://www.sciencedirect.com/science/article/pii/S1090023314000501  

Rosanowski, S.M.,Cogger,N., Rogers,C.W., Bolwell, C.F. 2014.Prevalence and risk factors for respiratory disease on Thorougbred and Standardbred stud farms in New Zealand. Proceedings of the New Zealand Society of Animal Production, Volume 74, Napier, p.5-10. 

Salgado, M., Verdugo, C., Heuer, C., Castillo, P., & Zamorano, P. 2014. A novel low-cost method for Mycobacterium avium subsp paratubercuiosis DNA extraction from an automated broth culture system for real-time PCR analysis. Journal of Veterinary Science. 15(2), 233-239. doi:10.4142/jvs.2014.15.2.233

Sanhueza, J., Heuer, C., Jackson, R., Hughes, P., Anderson, P., Kelly, K., & Walker, G. 2014. Pregnancy rates of beef cattle are not affected by Campylobacter fetus subsp. venerealis real-time PCR-positive breeding sires in New Zealand. New Zealand Veterinary Journal. 62(5), 237-243  http://www.sciquest.org.nz/node/93632

Shao, H., Lam, W. H. K., Sumalee, A., Chen, A., Hazelton, M. L., 2014.Estimation of mean and covariance of peak hour origin–destination demands
from day-to-day traffic counts. Transportation Research Part B: Methodological 68, 52–75.

Shrestha, R.D., Grinberg, A., Dukkipati, V.S.R., Pleydell, E.J., Prattley, D.J., & French, N.P. 2014. Infections with multiple Cryptosporidium species and new genetic variants in young dairy calves on a farm located within a drinking water catchment area in New Zealand. Veterinary Parasitology. 202, 287-291 http://dx.doi.org/10.1016/j.vetpar.2014.03.034/j.vetpar.2014.03.034

Smith, M., Hazelton, M.L., Lo, H.K., Cantarella, G.E., & Watling, D.P. (2014). The long term behaviour of day-to-day traffic assignment models. Transportmetrica A:Transport Science. 10(7), 647-660 doi:10.1080/18128602.2012.751683

Smith S.L., Wilson P.R., Collett M.G., Heuer C, West D.M, Stevenson M, Chambers J.P. 2014. Liver Biopsy Histopathology for Diagnosis of Johne's Disease in Sheep. Veterinary Pathology. 51(5), 915-918. doi: 10.1177/0300985813516644

Souther, S., Tingley, M.W., Popescu, V. D., Hayman, D.T.S., Ryan, M.E., Graves, T.A., Hartl, B., & Terrell, K. 2014. Biotic impacts of energy development from shale: research priorities and knowledge gaps. Frontiers in Ecology and the Environment, 12(6), 330-338. doi: 10.1890/130324 

’t Mannetje A., Coakley J., Bridgen P., Smith A.H., Read D., Pearce N., & Douwes J. 2014. Estimated infant intake of persistent organic pollutants through breast milk in New Zealand. New Zealand Medical Journal. 127 (1401): 56-68. http://europepmc.org/abstract/med/25225757

VanWormer, E., Miller, M.A., Conrad, P.A., Grigg, M.E., Rejmanek, D., Carpenter, T.E., & Mazet, J.A.K. 2014. Using Molecular Epidemiology to Track Toxoplasma gondii from Terrestrial Carnivores to Marine Hosts: Implications for Public Health and Conservation. PLoS Neglected Tropical Diseases. 8(5) doi: 10.1371/journal.pntd.0002852

Verhaar, N. , Rogers, C. W., Gee, E. K., Bolwell, C. F., Rosanowski, S. M. 2014. The Feeding Practices and Estimated Workload in a Cohort of New Zealand Competition Horses. Journal of Equine Veterinary Science 34 (2014) 1257-1262. doi:10.1016/j.jevs.2014.08.008 

Whiteson, K.L., Bailey, B., Bergkessel, M., Conrad, D., Delhaes, L., Felts, B., Harris, J.K., Hunter, R., Lim, Y.W., Maughan, H., Quinn, R., Salamon, P., Sullivan, J., Wagner, B.D., & Rainey, P.B. 2014. The Upper Respiratory Tract as a Microbial Source for Pulmonary Infections in Cystic Fibrosis. Parallels from Island Biogeography. American journal of respiratory and critical care medicine, 189(11), 1309-1315. doi: 10.1164/rccm.201312-2129PP 

Yıldırım, Y., Patel, S., Millar, C.D., Rainey, P. B. 2014. Microsatellite development for a tetrodotoxin-containing sea slug (Pleurobranchaea maculata). Biochemical Systematics and Ecology, Vol 55, pp 342-345, ISSN 0305-1978. http://dx.doi.org/10.1016/j.bse.2014.04.001

Zhang, X.X, Ritchie, S.R., & Rainey, P.B. 2014. Urocanate as a potential signaling molecule for bacterial recognition of eukaryotic hosts. 71(4) 541-547. http://link.springer.com/article/10.1007%2Fs00018-013-1527-6

2013

Ahmed, I., Matthews, P.J., Biggs, P.J., Naeem, M., McLenachan, P.A., & Lockhart, P.J. 2013. Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa. Molecular Ecology Resources. 13(5), 929-937. doi: 10.1111/1755-0998.12128

Akhtar, S., & Carpenter, T.E. 2013. Stochastic modelling of intra-household transmission of hepatitis C virus: Evidence for substantial non-sexual infection. Journal of Infection. 66(2), 179-183 http://www.sciencedirect.com/science/article/pii/S0163445312003064

Almawly, J., Prattley, D., French, N.P., Lopez-Villalobos, N., Hedgespeth, B., & Grinberg, A. 2013. Utility of halofuginone lactate for the prevention of natural cryptosporidiosis of calves, in the presence of co-infection with rotavirus and Salmonella Typhimurium. Veterinary Parasitology  197(1-2), 59-67. http://www.sciencedirect.com/science/article/pii/S0304401713002410

Bailey, S., Dettman, J. R., Rainey, P. B., & Kassen, R.  2013.  Competition both drives and impedes diversification in a model adaptive radiation. Proceedings of the Royal Society (London) B.  280. doi: 10.1098/rspb.2013.1253 

Baker, K.S., Marsh G.A., Todd S., Crameri G., Barr .J, Kamins A.O., Peel A.C., Yu M, Hayman D.T.S., Nagjm B., Mtove G., Amos B., Reyburn H., Nyarko E.O., Suu-Ire R., Murcia P.R., Cunningham A.A., Wood J.L.N., Wang L.F. 2013. Novel potentially-zoonotic paramyxoviruses from the African straw-coloured fruit bat, Eidolon helvum. Journal of Virology, 87:1348-1358. doi: 10.1128/JVI.01202-12.

Banda, M.E., Howe, L.J., & French, N. 2013. A cluster of avian malaria cases in a kiwi management program. New Zealand Veterinary Journal 61(3), 121-126. doi/abs/10.1080/00480169.2012.736130

Betz-Stablein, B.D., Morgan, W.H., House, P.H., &  Hazelton, M.L. 2013. Spatial Modeling of Visual Field Data for Assessing Glaucoma Progression. Investigative Ophthalmology & Visual Science 54(2), 1544-1553.

Brooks, C., Pearce, N., & Douwes, J. 2013. The hygiene hypothesis in allergy and asthma: An update. Current Opinion in Allergy and Clinical Immunology. 13(1), 70-77. doi 10.1097/ACI.0b013e32835ad0d2  

Brooks, C.R., Gibson, P.G., Douwes, J., Van Dalen, C.J., & Simpson, J.L. 2013.  Relationship between airway neutrophilia and ageing in asthmatics and non-asthmatics. Respirology 18(5), 857-865   doi: 10.1111/resp.12079  

Carpenter T, Kim, H., Yoon, H., Moon, O-K., Han, J-H., Lee, K., Jeong, W., Choi, J., Cho, Y-M., Kang, Y-M., Ahn, H-Y., Kim, D-S. [2013] Direct costs of five foot-and-mouth disease epidemics in the Republic of Korea, from 2000 to 2011. Journal of Preventive Veterinary Medicine. 37. 163-168. doi: 10.13041/jpvm.2013.37.4.163 

Coakley, J.D., Harrad, J., Goosey, E., Ali, N., Dirtu, A., Van den Eede, N., Covaci, A., Douwes, J., & Mannetje, A. 2013. Concentrations of polybrominated diphenyl ethers in matched samples of indoor dust and breast milk in New Zealand. Environment International, 59, 255-61 10.1016/j.envint.2013.06.020   

Conrad, D., Haynes, M., Salamon, P., Rainey, P.B., Youle, M., & Rohwer, F. 2013. Cystic fibrosis therapy: a community ecology perspective. American Journal of Respiratory and Critical Care Medicine 48(2), 150-156. doi: 10.1165/rcmb.2012-0059PS

Davies, T.M., & Hazelton, M.L. 2013. Assessing minimum contrast parameter estimation for spatial and spatiotemporal log-Gaussian Cox processes. Statistica Neerlandica, 67(4), 355-389. doi: 10.1111/stan.12011 

Davis, M.A., Moore, D.l., Baker,K.N.K., French,N.P., Patnode.M., Hensley,J., MacDonald,K., & Besser, T.E. 2013. Risk factors for campylobacteriosis in two Washington State counties with high numbers of dairy farms. Journal of Clinical Microbiology. 51(2): 3921 doi: 10.1128/JCM.01433-13   

Durr, S., zu Dohna, H., Di Labio, E., Carpenter, T.E., & Doherr, M.G. 2013. Evaluation of control and surveillance strategies for classical swine fever using a simulation model. Preventive Veterinary Medicine. 108(1), 73-84 http://www.sciencedirect.com/science/article/pii/S0167587712002310  

Frean, M. Rainey, P. B. & Traulsen, A. 2013. The effect of population structure on the rate of evolution.  Proceedings of the Royal Society (London) B. 280. doi: 10.1098/rspb.2013.0211 

Ferguson, G.C., Bertels, F., & Rainey, P.B. 2013.  Adaptive divergence in experimental populations of Pseudomonas fluorescens. V. Genetic and phenotypic bases of Fuzzy Spreader fitness and revision of niche specialisation during the Pseudomonas radiation.  Genetics, 195(4): 1319-35. doi: 10.1534/genetics.113.154948

Gartrell, B., French, N., Howe, L.J., Nelson, N., Houston, M., Burrows, L., Russel, J., Anderson, S.H. 2013. First detection of Chlamydia psittaci from a wild native passerine bird in New Zealand. New Zealand Veterinary Journal 61(3), 174-176. doi/0.1080/00480169.2012.740656

Gilbert A., Fooks A.R., Hayman D.T.S., Horton D.L., Müller T., Plowright R.K., Peel A., Bowen R., Wood J.L.N., Mills J.N., Cunningham A.A., & Rupprecht C.E. 2013. The utility and limitations of serologic testing: implications for the study of wildlife diseases. EcoHealth.

Gilpin, B., Walsh, G., On, S.L., Smith, D., Marshall, J., French, N.P. 2013. Application of molecular epidemiology to understanding campylobacteriosis in the Canterbury region of New Zealand. Epidemiology and Infection 141(6), 1253-1266.  doi:10.1017/S0950268812001719

Grinberg, A., Biggs, P.J., Dukkipati, V.S.R., & George, T.T. 2013. Extensive intra-host genetic diversity uncovered in Cryptosporidium parvum using Next Generation Sequencing. Infection, Genetics and Evolution. 15, 18-24. http://www.sciencedirect.com/science/article/pii/S1567134812002869

Harland, A.L., Cave, N.J., Jones,  B.R., Benschop, J., Donald, J.J., Midwinter, A.C., Squires, R.A. & Collins-Emerson, J.M. 2013. A serological survey of leptospiral antibodies in dogs in New Zealand. New Zealand Veterinary Journal 61(2), 98-106 doi:10.1080/00480169.2012.719212  

Hayman, D.T.S., Bowen, R.A., Cryan, P.M., McCracken, G.F., O’Shea, T.J., Peel, A.J., Gilbert, A., Webb, C.T. & Wood, J.L.N. 2013. Ecology of Zoonotic Infectious Diseases in Bats: Current Knowledge and Future Directions. Zoonoses and Public Health. 60, 2–21. doi: 10.1111/zph.12000

Hayman, D.T.S., McDonald, K.D., & Kosoy, K.Y. 2013. Evolutionary history of rat-borne Bartonella: the importance of commensal rats in the dissemination of bacterial infections globally, Ecology and Evolution. 3(10), 3195–3203. doi: 10.1002/ece3.702 

Hall R. J., Leblanc-Maridor, M., Wang, J., Ren, X., Moore, N.E., Brooks, C.R., Peacey, M., Douwes, J., & McLean, D.J. 2013. Metagenomic Detection of Viruses in Aerosol Samples from Workers in Animal Slaughterhouses  PLOS ONE 8(8), e72226. doi:10.1371/journal.pone.0072226

Han, J., Collins, L.J., Biggs, P.J., White, W.T. & Penny, D. 2013. Are Signature Proteins the Key to Evaluating Eukaryotic Phylogeny? Rev Bioinform Biometr 2(2), 37-44.

Hennebelle, J., Sykes, J.E., Carpenter, T.E., & Foley, J. 2013. Spatial and temporal patterns of Leptospira infection in dogs from northern California: 67 cases (2001-2010). Journal of the American Veterinary Medical Association. 242(7), 941-947 http://avmajournals.avma.org/doi/abs/10.2460/javma.242.7.941

Jaros, P., Cookson, A., Campbell, D., Besser,T., Shiringi, S., Mackereth, G. F., Lim.E., Lopez.L., Dufour,M., Marshall, J.,Baker,M., Hathaway,S.,  French, N.P. 2013. A prospective case-control and molecular epidemiological study of human cases of Shiga toxin-producing Escherichia coli in New Zealand. BMC Infectious Diseases 13, 450. doi:10.1186/1471-2334-13-450 

Lal, A., Baker, M.G., Hales, S., French, N.P. 2013. Potential effects of global environmental changes on cryptosporidiosis and giardiasis transmission. Trends in Parasitology 29, 83-90. doi/10.1016/j.pt.2012.10.005

Lal, A, Ikeda, T, French, N, Baker, MG, & Hales, S. 2013. Climate Variability, Weather and Enteric Disease Incidence in New Zealand: Time Series Analysis. PlosOne, 8(12):e83484. doi: 10.1371/journal.pone.0083484

Libby, E., Rainey, P.B. 2013. A conceptual framework for the evolutionary origins of multicellularity. Physical Biology 10(3) 035001 

Luis A.D., Hayman D.T.S., O’Shea T.J., Cryan P.M., Gilbert A.T., Pulliam J.R.C., Mills J.N., Willis C.K.R., Timonin M.E., Cunningham A.A., Fooks A.R., Rupprecht C.E., Wood J.L.N., & Webb C.T. 2013. A comparison of bats and rodents as reservoirs of zoonotic viruses: Are bats special? Proceedings of the Royal Society B: Biological Sciences, 280(1756): doi: 10.1098/rspb.2012.2753 

Mannetje, A., Coakley, J., Bridgen, P., Brooks, C., Harrad, S., Smith, A.H., Pearce, N., & Douwes, J. 2013 Current concentrations, temporal trends and determinants of persistent organic pollutants in breast milk of New Zealand women. The Science of the Total Environment.  458-460, 399-407. doi: 10.1016/j.scitotenv.2013.04.055    

Mardones, F.O., Jansen, P.A., Valdes-Donoso, P., Jarpa, M., Lyngstad, T.M., Jimenez, D., Carpenter, T.E., & Perez, A.M. 2013. Within-farm spread of infectious salmon anemia virus (ISAV) in Atlantic salmon Salmo salar farms in Chile. Disease of Aquatic Organisims. 106(1), 7-16. doi:10.3354/dao02639

Mardones, F.O., zu Donha, H., Thunes, C., Velez, V., & Carpenter, T.E. 2013. The value of animal movement tracing: A case study simulating the spread and control of foot-and-mouth disease in California. Preventive Veterinary Medicine. 110(2), 133-138 http://www.sciencedirect.com/science/article/pii/S0167587712004011

McCann, H., Rikkerink, E.H., Bertels, F., Fiers, M., Lu, A., Rees-George, J., Andersen, M.T., Gleave, A.P., Haubold, B., Wohlers, Guttman, D. S., Wang, P., Vanneste, J., Rainey, P.B., & Templeton, M.D.  2013. Genomic analysis of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insights into the origins of an emergent plant disease.  PLoS Pathogens 9(7), e1003503. doi:10.1371/journal.ppat.100350 

Mohan, V., Stevenson, M., Marshall, J., Fearnhead, P., Holland, B., Hotter, G., & French, N.P. 2013. Campylobacter jejuni colonisation and population structure in urban populations of ducks and starlings in New Zealand. MicrobiologyOpen 2(4) 659-673. doi: 10.1002/mbo3.102

Muellner, P., Pleydell, E., Pirie, R., Baker, M., Campbell, D., Carter, P., French, N., 2013. Molecular-based surveillance of campylobacteriosis in New Zealand - from source attribution to genomic epidemiology. Eurosurveillance 18(3), pii=20365 http://www.eurosurveillance.org/images/dynamic/EE/V18N03/art20365.pdf

Mughini-Gras, L., Smid, J., Wagenaar, J., de Boer, A., Havelaar, A., Friesema, I., French, N., Graziani, C., Busani, L., van Pelt, W. 2013. Increased risk for Campylobacter jejuni and C. coli infection of pet origin in dog owners and evidence for genetic association between strains causing infection in humans and their pets. Epidemiology and Infection, 141 (12), 2526-2535. doi:10.1017/S0950268813000356

On, S.L.W., Brandt, S.M., Cornelius, A.J., Fusco, V., Quero, G.M., Maćkiw, E., Houf, K., Bilbao, A., Díaz, A.I., Benejat, L., Megraud, F., Collins-Emerson, J., French, N.P., Gotcheva, V., Angelov, A., Alakomi, H.L., Saarela, M., & Paulin, S.M. 2013. PCR revisited: a case for revalidation of PCR assays for microorganisms using identification of Campylobacter species as an exemplar. Quality Assurance and Safety of Crops & Foods 5, 49-62. 

Parry, K., & Hazelton, M.L. 2013. Bayesian inference for day-to-day dynamic traffic models. Transportation Research Part B-methodological, 104-115. http://www.sciencedirect.com/science/article/pii/S0191261513000143 

Pearce, N., Douwes, J. 2013. Research at the interface between human and veterinary health. Preventive Veterinary Medicine.111(3-4), 187-193. http://www.sciencedirect.com/science/article/pii/S0167587713001736

Pearce, N., & Douwes, J. 2013 Lifestyle changes and childhood asthma. Indian journal of pediatrics  80(1),   S95-9. doi: 10.1007/s12098-012-0764-2 

Peel, A.J., McKinley, T.J., Baker, K.S., Barr, J.A., Crameri, G., Hayman, D.T.S., Feng, Y-R., Broder, C.C., Wang, L-F., Cunningham, A.A., & Wood, J.L.N. 2013. Use of cross-reactive serological assays for detecting novel pathogens in wildlife: Assessing an appropriate cutoff for henipavirus assays in African bats. Journal of Virological Methods. 193, 295-303. http://dx.doi.org/10.1016/j.jviromet.2013.06.030

Roberts, M.G. 2013. Epidemic models with uncertainty in the reproduction number. Journal of Mathematical Biology 66, 1463-1474. doi/10.1007%2Fs00285-012-0540-y

Roberts, M.G. Heesterbeek, J.A.P., 2013, Characterizing the next-generation matrix and basic reproduction number in ecological epidemiology. Journal of Mathematical Biology 66(4-5), 1045-1064. doi/10.1007%2Fs00285-012-0602-1

Roberts, M.G. 2013. A two-strain epidemic model with uncertainty in the interaction. ANZIAM Journal 54(1-2), 108-115. http://dx.doi.org/10.1017/S1446181112000326

Roe, W.D., Howe, L., Baker, E.J., Burrows, L., & Hunter, S.A. 2013. An atypical genotype of Toxoplasma gondii as a cause of mortality in Hector's dolphins (Cephalorhynchus hectori). Veterinary Parasitology. 192(1-3), 67-74. doi:10.1016/j.vetpar.2012.11.00

Sheppard, S.K., Didelot, X., Jolley, K.A., Darling, A.E., Pascoe, B., Meric, G., Kelly, D.J., Cody, A., Colles, F.M., Strachan, N.J., Ogden, I.D., Forbes, K., French, N.P., Carter, P., Miller, W.G., McCarthy, N.D., Owen, R., Litrup, E., Egholm, M., Affourtit, J.P., Bentley, S.D., Parkhill, J., Maiden, M.C., Falush, D., 2013. Progressive genome-wide introgression in agricultural Campylobacter coli. Molecular Ecology 22, 1051-1064. doi/10.1111/mec.12162

Simpson, J.L., Roberts, M.G. 2013. Modelling the effect of vaccination on the Meningococcal B epidemic in New Zealand. ANZIAM Journal 54(1-2), 74-88 http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8912415

Smid, J.H., Mughini Gras, L., de Boer, A.G., French, N.P., Havelaar, A.H., Wagenaar, J.A., van Pelt, W., 2013. Practicalities of using non-local or non-recent multilocus sequence typing data for source attribution in space and time of human campylobacteriosis. PLoS One 8(2), e55029. doi: 10.1371/journal.pone.0055029

Thornley, C.N., Hewitt, J., Perumal, L., Van Gessel, S.M., Wong, J., David, S.A., Rapana, J.P., Li, S., Marshall, J.C., & Greening, GE. 2013. Multiple outbreaks of a novel norovirus GII.4 linked to an infected post-symptomatic food handler. Epimiology and Infection. 141(8), 1585-1597 doi: http://dx.doi.org/10.1017/S0950268813000095

Valdes-Donoso, P., Mardones, F.O., Jarpa, M., Ulloa, M., Carpenter, T.E., & Perez, A.M. 2013. Co-infection patterns of infectious salmon anaemia and sea lice in farmed Atlantic salmon, Salmo salar L., in southern Chile (2007-2009). Journal of Fish Diseases. 36(3), 353-360. doi: 10.1111/jfd.12070 

VanWormer, E., Conrad, P.A., Miller, M.A., Melli, A.C., Carpenter, T.E., & Mazet, J.A.K. 2013. Toxoplasma gondii, Source to Sea: Higher Contribution of Domestic Felids to Terrestrial Parasite Loading Despite Lower Infection Prevalence. EcoHealth. , 1-13. http://link.springer.com/article/10.1007%2Fs10393-013-0859-x#

Vaughan, T.G., & Alexei J.D. 2013. A Stochastic Simulator of Birth-death Master Equations with Application to Phylodynamics. Molecular Biology and Evolution 30 (6) (June): 1480–1493. doi:10.1093/molbev/mst057

Wagenaar, J., French, N.P., & Havelaar, A.H. 2013. Preventing Campylobacter at the source - why is it so difficult? Clinical Infectious Diseases, 57(11), 1600-1606. doi: 10.1093/cid/cit555

Wang, J., McLenachan, P.A., Biggs, P.J., Winder, L.H., Schoenfeld, B.I., Narayan, V.V., Phiri, B.J., & Lockhart, P.J. 2013. Environmental bio-monitoring with high-throughput sequencing.. Brief Bioinform. 14(5), 575-588. doi:10.1093/bib/bbt032

Zhang, X-X., Rainey, P.B. 2013. Exploring the social biology of pyoverdin producing Pseudomonas. Evolution, 67(11): 3161-3174. DOI: 10.1111/evo.12183

2012

Choi, Y-K, Johnson W.O., Jones, G., Perez, A. and Thurmond, M.C. 2012. Modeling and predicting temporal frequency of foot-and-mouth disease (FMD) cases in countries with endemic FMD. Journal of the Royal Statistical Society: Series A (Statistics in Society) 175(2):619-636.

Collins-Emerson, J. and Abdul-Careem, M.F. 2012. Chapter 4. Microbiology. Section 4.8. "Molecular microbiology as a diagnostic tool." pp290-305. In "The Veterinary Laboratory and Field Manual." 2nd Edition.Editors: S.C. Cork and R.W. Halliwell. Nottingham University Press, 2012. ISBN 978-1-908062-09-3

Fernando, W.T.P.S, Ganesalingam, S. and Hazelton, M.L. 2012. A comparison of estimators of the geographical relative risk function. Journal of Statistical Computation and Simulation, online 14 Dec 2012. doi/abs/10.1080/00949655.2012.748055

Gerth, M.L., Ferla, M.P., Rainey, P.B. 2012. The origin and ecological significance of multiple branches for histidine utilisation in Pseudomonas aeruginosa PAO1. Environmental Microbiology. 14(8), 1929-1940  doi/10.1111/j.1462-2920.2011.02691 

Irshad, H., Cookson, A., Hotter, G., Besser, T., On, S. and French, N. Epidemiology of Shiga toxin producing Escherichia coli O157 in very young calves in the North Island of New Zealand. New Zealand Veterinary Journal 60, 21-26. doi: 10.1080/00480169.2011.627063

Jones, G., Johnson, W. O., Vink, W. D. and French, N. 2012. A Framework for the Joint Modeling of Longitudinal Diagnostic Outcome Data and Latent Infection Status: Application to Investigating the Temporal Relationship between Infection and Disease. Biometrics 68, 371-379. doi: 10.1111/j.1541-0420.2011.01687

Kidd, T.J., Ritchie, S.R., Ramsay, K.A., Grimwood, K., Bell, S.C., Rainey, P.B. 2012. Pseudomonas aeruginosa exhibits frequent recombination, but only a limited association between genotype and ecological setting. PLoS One, 7(9): e44199.

Lal, A., Baker, M.G., French, N., Dufour, M., Hales, S. 2012. The Epidemiology of Human Salmonellosis in New Zealand, 1997-2008. Epidemiology and Infection 140(9):1685-94. doi/10.1017/S0950268811002470

Lal, A., Hales, S., French, N. and Baker, M. 2012. Seasonality in Human Enteric Diseases: A Systematic Review. PLoS ONE 7(4): e31883. doi:10.1371/journal.pone.0031883

Lee, K., French, N. P., Jones, G., Hara-Kudo, Y., Iyoda, S., Kobayashi, H., Sugita-Konishi, Y., Tsubone, H. and Kumagai, S. 2012. Variation in stress-resistance patterns among stx genotypes and genetic lineages in Shiga toxin-producing Escherichia coli O157. Applied and Environmental Microbiology 78(9), 3361-8. doi: 10.1128/​AEM.06646-11

Mughini Gras, L., Smid, J.H., Wagenaar, J.A., de Boer, A.G., Havelaar, A.H., Friesema, I.H.M., French, N.P., Busani, L., van Pelt, W., 2012. Risk Factors for Campylobacteriosis of Chicken, Ruminant, and Environmental Origin: A Combined Case-Control and Source Attribution Analysis. PLoS One7(8), e42599. 

Phiri, B. J., Benschop, J., Stevenson, M., Swai, E. S., Karimuribo, E. D. and French, N. P. 2012. Spatiosurvival analysis of mortality on smallholder dairy farms in Tanga and Iringa regions of Tanzania. Tropical Animal Health Production 44(4), 827-834.

Pleydell, E.J., Souphavanh, K., Hill, K.E., French, N.P., Prattley, D. 2012. Descriptive epidemiological study of the use of antimicrobial drugs by companion animal veterinarians in New Zealand. New Zealand Veterinary Journal 60(2), 115-122. eprint/3RNVw8H2Br4w7v3KhDmN/full

Rapp, D., Ross, C.M., Pleydell, E.J., Muirhead, R.W. 2012. Differences in the fecal concentrations and genetic diversities of Campylobacter jejuni populations among individual cows in two dairy herds. Applied and Environmental Microbiology 78, 7564-71. doi: 10.1128/​AEM.01783-12

Redondo-Niece, M., Barret, M., Morrisey, J., Germaine, K., Martinez-Garner, F., Brahman, E., Navazo, A., Sanchez-Contraries, M., Moynihan, J. A., Giddens, S. R., Coppoolse, E. R., Muriel, C., Stiekema, W. J., Rainey, P.B., Dowling, D., O'Hare, F., Martin, M., Rival, R. 2012. Genome sequence of the biocontrol strain Pseudomonas fluorescens F113. Journal of Bacteriology. 194(5), 1273-1274. doi: 10.1128/ JB.06601-11 

Rodgers, J.D., Lawes, J.R., Vidal, A.B., Ellis-Iversen, J., Ridley, A., Pleydell, E., Powell, L.F., Toszeghy, M., Stapleton, K. and Clifton-Hadley, F.A. 2012. Characteristics and comparative performance of direct culture, direct PCR and enumeration methods for detection and quantification of Campylobacter spp. in broiler caeca. 2012. Veterinary Microbiology 159(3-4):390-6. doi: 10.1016/j.vetmic.2012.04.011

Simpson, J.L., Roberts, M.G. 2012. Modelling heterogeneous host immune response in a multi-strain system. Journal of Theoretical Biology 304, 60-65. http://dx.doi.org/10.1016/j.jtbi.2012.03.006

Souther, S., Tingley, M. W., Popescu, V. D., Hayman, D. T. S., Ryan, M. E., Graves, T. A., Hartl, B., & Terrell, K. 2014. Biotic impacts of energy development from shale: research priorities and knowledge gaps. Frontiers in Ecology and the Environment, 12(6), 330-338. doi: 10.1890/130324

Spencer, S., Marshall, J., Pirie, R., Campbell, D., Baker, M.G., French, N. 2012. The spatial and temporal determinants of campylobacteriosis notifications in New Zealand, 2001-2007. Epidemiology and Infection 140(9), 1663-1677 http://dx.doi.org/10.1017/S0950268811002159

Subharat, S., Wilson, P. R., Heuer, C., & Collins-Emerson, J. M. 2012. Growth response and shedding of Leptospira spp. in urine following vaccination for leptospirosis in young farmed deer. New Zealand Veterinary Journal, 60(1), 14-20. doi:10.1080/00480169.2011.624985 

Subharat, S., Wilson, P.R., Heuer, C. & Collins-Emerson, J.M. 2012. Longitudinal serological survey and herd-level risk factors for Leptospira spp. serovars Hardjo-bovis and Pomona on deer farms with sheep and/or beef cattle. New Zealand Veterinary Journal 60(4), 215-22 http://dx.doi.org/10.1080/00480169.2012.663323 

Willner, D., Haynes, M. R., Furlan, M., Hanson, N., Kirby, B., Lim, Y.W., Rainey, P.B., Schmieder, R., Yule, M., Conrad, D., Rohwer, F. 2012. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. American Journal of Respiratory Cell and Molecular Biology. 46(2), 127-131. doi:10.1165/2011-0253OC 

Yu, S., Fearnhead, P., Holland, B., Biggs, P., Maiden, M. and French, N. 2012. Estimating the relative roles of recombination and point mutation to the generation of single locus variants in Campylobacter jejuni and Campylobacter coli. Journal of Molecular Evolution 74(5-6), 273-280. doi/10.1007%2Fs00239-012-9505-4

Zhang, X-X., Chang, H., Tran, S.L., Gauntlett, J.C., Cook, G.M., Rainey, P.B. 2012. Variation in transporter genes explains polymorphism of histidine and urocanate utilisation in natural populations of Pseudomonas. Environmental Microbiology 14(8):1941-5. doi/10.1111/j.1462-2920.2011.02692 

2011

Bertels, F., Rainey, P.B., 2011. Within-genome evolution of REPINs: a new family of miniature mobile DNA in bacteria. PLoS Genet 7, e1002132.

Best, N., Fraser, J.D., Rainey, P.B., Roberts, S.A., Thomas, M.G., Ritchie, S.R., 2011. Nasal carriage of Staphylococcus aureus in healthy Aucklanders. N Z Med J 124, 31-39.

Biggs, P., Fearnhead, P., Hotter, G.S., Mohan, V., Collins-Emerson, J., Kwan, E., Besser, T., Cookson, A., Carter, P., French, N., 2011. Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage. PLoS One.

Carpenter, T.E., O'Brien, J.M., Hagerman, A.D., McCarl, B.A., 2011. Epidemic and economic impacts of delayed detection of foot-and-mouth disease: a case study of a simulated outbreak in California. J Vet Diagn Invest 23, 26-33.

Davies, T.M., Hazelton, M.L. and Marshall, J.C., 2011. sparr: Analyzing spatial relative risk using fixed and adaptive kernel density estimation in R. Journal of Statistical Software, 39, 1-14.

Douwes, J., Brooks, C., Pearce, N., 2011. Asthma nervosa: old concept, new insight. Eur Respir 37:986-990

Douwes, J., Brooks, C., van Dalen, C., Pearce, N., 2011. Importance of allergy in asthma: an epidemiologic perspective. Curr Allergy Asthma Rep 11, 434-444.

Ekong, P.S., Ducheyne, E., Carpenter, T.E., Owolodun, O.A., Oladokun, A.T., Lombin, L.H., Berkvens, D., 2011. Spatio-temporal epidemiology of highly pathogenic avian influenza (H5N1) outbreaks in Nigeria, 2006-2008. Prev Vet Med.

Eng, A., 't Mannetje, A., Pearce, N., Douwes, J., 2011. Work-related Stress and Asthma: Results from a Workforce Survey in New Zealand. J Asthma 48:783-9. 

Grove-White, D.H., Leatherbarrow, A.J., Cripps, P.J., Diggle, P.J., French, N.P., 2011. Molecular epidemiology and genetic diversity of Campylobacter jejuni in ruminants. Epidemiol Infect, 1-11.

Hepworth, P.J., Ashelford, K.E., Hinds, J., Gould, K.A., Witney, A.A., Williams, N.J., Leatherbarrow, H., French, N.P., Birtles, R.J., Mendonca, C., Dorrell, N., Wren, B.W., Wigley, P., Hall, N., Winstanley, C., 2011. Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes. Environ Microbiol 13, 1549-1560.

James, A., Brown, R., Basse, B., Bourdot, G., Lamoureaux, S., Roberts, M.G., and Saville, D.J., 2011. Application of a spatial meta-population model with stochastic parameters to the management of the invasive grass Nassella trichotoma in North Canterbury, New Zealand. Ecological Modelling 222, 1030-1037.

Jimenez, D.F., Perez, A.M., Carpenter, T.E., Martinez, A., 2011. Factors associated with infection by Campylobacter fetus in beef herds in the Province of Buenos Aires, Argentina. Prev Vet Med 101, 157-162.

Jones, G., Johnson, W.O., Vink, W.D., French, N.P., 2011. A framework for the joint modeling of longitudinal diagnostic outcome data and latent infection status: application to investigating the temporal relationship between infection and disease. Biometrics.

Kidd, T.J., Grimwood, K., Ramsay, K.A., Rainey, P.B., Bell, S.C., 2011. Comparison of three molecular techniques for typing Pseudomonas aeruginosa isolates in sputum samples from patients with cystic fibrosis. J Clin Microbiol 49, 263-268.

Lee, K., French, N.P., Hara-Kudo, Y., Iyoda, S., Kobayashi, H., Sugita-Konishi, Y., Tsubone, H., Kumagai, S., 2011. Multivariate analyses revealed distinctive features differentiating human and cattle isolates of Shiga toxin-producing Escherichia coli O157 in Japan. J Clin Microbiol 49, 1495-1500.

Leon, M.E., Beane Freeman, L.E., Douwes, J., Hoppin, J.A., Kromhout, H., Lebailly, P., Nordby, K.C., Schenker, M., Schuz, J., Waring, S.C., Alavanja, M.C., Annesi-Maesano, I., Baldi, I., Dalvie, M.A., Ferro, G., Fervers, B., Langseth, H., London, L., Lynch, C.F., McLaughlin, J., Merchant, J.A., Pahwa, P., Sigsgaard, T., Stayner, L., Wesseling, C., Yoo, K.Y., Zahm, S.H., Straif, K., Blair, A., 2011. AGRICOH: a consortium of agricultural cohorts. Int J Environ Res Public Health 8, 1341-1357.

Li, J., Zu Dohna, H., Cardona, C.J., Miller, J., Carpenter, T.E., 2011. Emergence and genetic variation of neuraminidase stalk deletions in avian influenza viruses. PLoS One 6, e14722.

Libby, E., Rainey, P.B., 2011. Exclusion rules, bottlenecks and the evolution of stochastic phenotype switching. Proc Biol Sci 278, 3574-3583.

Mann, J., Roberts, M., 2011. Modelling the epidemiology of hepatitis B in New Zealand. J Theor Biol 269, 266-272.

't Mannetje, A., Eng, A., Douwes, J., Ellison-Loschmann, L., McLean, D., Pearce, N., 2011. Determinants of nonresponse in an occupational exposure and health survey in New Zealand. The Australian & New Zealand Journal of Public Health 35:256-63. 

Mardones, F.O., Perez, A.M., Valdes-Donoso, P., Carpenter, T.E., 2011. Farm-level reproduction number during an epidemic of infectious salmon anemia virus in southern Chile in 2007-2009. Prev Vet Med 102, 175-184.

McDonald, M.J., Cooper, T.F., Beaumont, H.J., Rainey, P.B., 2011. The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens. Biol Lett 7, 98-100.

Mendell, M.J., Mirer, A.G., Cheung, K., Tong, M., Douwes, J., 2011. Respiratory and allergic health effects of dampness, mold, and dampness-related agents: a review of the epidemiologic evidence. Environ Health Perspect 119, 748-756.

Minh, P., Stevenson, M., Jewell, C., French, N., Schauer, B., 2011. Spatio-temporal analyses of highly pathogenic avian influenza H5N1 outbreaks in the Mekong River Delta, Vietnam, 2009. Spatial and Spatio-temporal Epidemiology  2, 49-57.

Muellner, P., Marshall, J., Spencer, S., Noble, A.D., Shadbolt, T., Collins-Emerson, J., Midwinter, A.C., Carter, P., Pirie, R., Wilson, D.J., Campbell, D., Stevenson, M.A., French, N., 2011a. Utilising a combination of molecular and spatial tools to assess the effect of a public health intervention. Preventive Veterinary Medicine.

Muellner, P., Zadoks, R., Perez, A., Spencer, S., Schukken, Y., French, N., 2011b. The integration of molecular tools into veterinary and spatial epidemiology.   . Spatial and Spatio-temporal Epidemiology.

Rainey, P.B., Beaumont, H.J., Ferguson, G.C., Gallie, J., Kost, C., Libby, E., Zhang, X.X., 2011. The evolutionary emergence of stochastic phenotype switching in bacteria. Microb Cell Fact 10 Suppl 1, S14.

Ritchie, S.R., Fraser, J.D., Libby, E., Morris, A.J., Rainey, P.B., Thomas, M.G., 2011. Demographic variation in community-based MRSA skin and soft tissue infection in Auckland, New Zealand. N Z Med J 124, 21-30.

Roberts, M.G., Nishiura, H., 2011. Early estimation of the reproduction number in the presence of imported cases: pandemic influenza H1N1-2009 in New Zealand. PLoS One 6, e17835.

Sanson, R.L., Harvey, N., Garner, M.G., Stevenson, M.A., Davies, T.M., Hazelton, M.L., O'Connor, J., Dube, C., Forde-Folle, K.N., Owen, K., 2011. Foot and mouth disease model verification and 'relative validation' through a formal model comparison. Rev Sci Tech 30, 527-540.

Sears, A., Baker, M.G., Wilson, N., Marshall, J., Muellner, P., Campbell, D.M., Lake, R.J., French, N.P., 2011. Marked campylobacteriosis decline after interventions aimed at poultry, new zealand. Emerg Infect Dis 17, 1007-1015.

Spencer, S., Marshall, J., Pirie, R., Campbell, D., French, N., 2011. The detection of spatially localised outbreaks in campylobacteriosis notification data. Spatial and Spatio-temporal Epidemiology.

Williams, N.J., Sherlock, C., Jones, T.R., Clough, H.E., Telfer, S.E., Begon, M., French, N., Hart, C.A., Bennett, M., 2011. The prevalence of antimicrobial-resistant Escherichia coli in sympatric wild rodents varies by season and host. J Appl Microbiol.

Willner, D., Haynes, M.R., Furlan, M., Hanson, N., Kirby, B., Lim, Y.W., Rainey, P.B., Schmieder, R., Youle, M., Conrad, D., Rohwer, F., 2011a. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. Am J Respir Cell Mol Biol.

Willner, D., Haynes, M.R., Furlan, M., Schmieder, R., Lim, Y.W., Rainey, P.B., Rohwer, F., Conrad, D., 2011b. Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J.

Yee, K.S., Novick, C.A., Halvorson, D.A., Dao, N., Carpenter, T.E., Cardona, C.J., 2011. Prevalence of low pathogenicity avian influenza virus during 2005 in two U.S. live bird market systems. Avian Dis 55, 236-242.

2010

Benschop, J., Spencer, S., Alban, L., Stevenson, M., French, N., 2010. Bayesian zero-inflated predictive modelling of herd-level Salmonella prevalence for risk-based surveillance. Zoonoses Public Health 57 Suppl 1, 60-70.

Brooks, C.R., Weinkove, R., Hermans, I.F., van Dalen, C.J., Douwes, J., 2010. Invariant natural killer T cells and asthma: immunologic reality or methodologic artifact? J Allergy Clin Immunol 126, 882-885.

Davies, T.M., Hazelton, M.L., 2010. Adaptive kernel estimation of spatial relative risk. Stat Med 29, 2423-2437.

Diekmann, O., Heesterbeek, J.A., Roberts, M.G., 2010. The construction of next-generation matrices for compartmental epidemic models. J R Soc Interface 7, 873-885.

Douwes, J., Brooks, C., Pearce, N., 2010. Stress and asthma: Hippocrates revisited. J Epidemiol Community Health 64, 561-562.

Elvin, A.J., Laing, C.R., McLachlan, R.I., and Roberts, M.G., 2010. Exploiting the Hamiltonian structure of a neural field model. Physica D 239, 537-546

Eng, A., A, T.M., Cheng, S., Douwes, J., Ellison-Loschmann, L., McLean, D., Gander, P., Laird, I., Legg, S., Pearce, N., 2010a. The New Zealand workforce survey I: self-reported occupational exposures. Ann Occup Hyg 54, 144-153.

Eng, A., A, T.M., Douwes, J., Cheng, S., McLean, D., Ellison-Loschmann, L., Pearce, N., 2010b. The New Zealand workforce survey II: occupational risk factors for asthma. Ann Occup Hyg 54, 154-164.

Fryer, H.R., Frater, J., Duda, A., Roberts, M.G., Phillips, R.E., McLean, A.R., 2010. Modelling the evolution and spread of HIV immune escape mutants. PLoS Pathog 6, e1001196.

Grove-White, D.H., Leatherbarrow, A.J., Cripps, P.J., Diggle, P.J., French, N.P., 2010. Temporal and farm-management-associated variation in the faecal-pat prevalence of Campylobacter jejuni in ruminants. Epidemiol Infect 138, 549-558.

Hotter, G.S., Li, I.H., French, N.P., 2010. Binary genomotyping using lipooligosaccharide biosynthesis genes distinguishes between Campylobacter jejuni isolates within poultry-associated multilocus sequence types. Epidemiol Infect 138, 992-1003.

John, K., Fitzpatrick, J., French, N., Kazwala, R., Kambarage, D., Mfinanga, G.S., MacMillan, A., Cleaveland, S., 2010. Quantifying risk factors for human brucellosis in rural northern Tanzania. PLoS One 5, e9968.

Li, J., zu Dohna, H., Miller, J., Cardona, C.J., Carpenter, T.E., 2010. Identifying errors in avian influenza virus gene sequences and implications for data usage of public databases. Genomics 95, 29-36.

Lockhart, C.Y., Stevenson, M.A., Rawdon, T.G., Gerber, N., French, N.P., 2010. Patterns of contact within the New Zealand poultry industry. Prev Vet Med 95, 258-266.

Mullner, P., Collins-Emerson, J.M., Midwinter, A.C., Carter, P., Spencer, S.E., van der Logt, P., Hathaway, S., French, N.P., 2010a. Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry. Appl Environ Microbiol 76, 2145-2154.

Mullner, P., Shadbolt, T., Collins-Emerson, J.M., Midwinter, A.C., Spencer, S.E., Marshall, J., Carter, P.E., Campbell, D.M., Wilson, D.J., Hathaway, S., Pirie, R., French, N.P., 2010b. Molecular and spatial epidemiology of human campylobacteriosis: source association and genotype-related risk factors. Epidemiol Infect 138, 1372-1383.

Nishiura, H., Roberts, M.G., 2010. Estimation of the reproduction number for 2009 pandemic influenza A(H1N1) in the presence of imported cases. Euro Surveill 15.

Phiri, B.J., Benschop, J., French, N.P., 2010. Systematic review of causes and factors associated with morbidity and mortality on smallholder dairy farms in eastern and southern Africa. Prev Vet Med 94, 1-8.

Pineda-Krch, M., O'Brien, J.M., Thunes, C., Carpenter, T.E., 2010. Potential impact of introduction of foot-and-mouth disease from wild pigs into commercial livestock premises in California. Am J Vet Res 71, 82-88.

Pleydell, E., Rogers, L., Kwan, E., French, N., 2010a. Evidence for the clustering of antibacterial resistance phenotypes of enterococci within integrated poultry companies. Microb Ecol 59, 678-688.

Pleydell, E.J., Rogers, L., Kwan, E., French, N.P., 2010b. Low levels of antibacterial drug resistance expressed by Gram-negative bacteria isolated from poultry carcasses in New Zealand. N Z Vet J 58, 229-236.

Rainey, P.B., Kerr, B., 2010. Cheats as first propagules: a new hypothesis for the evolution of individuality during the transition from single cells to multicellularity. Bioessays 32, 872-880.

Refardt, D., Rainey, P.B., 2010. Tuning a genetic switch: experimental evolution and natural variation of prophage induction. Evolution 64, 1086-1097.

Teh, K.H., Flint, S., French, N., 2010. Biofilm formation by Campylobacter jejuni in controlled mixed-microbial populations. Int J Food Microbiol 143, 118-124.

Whitworth, J., Zhang, Y., Bono, J., Pleydell, E., French, N., Besser, T., 2010. Diverse genetic markers concordantly identify bovine origin Escherichia coli O157 genotypes underrepresented in human disease. Appl Environ Microbiol 76, 361-365.

Yoon, H., Moon, O.K., Her, M., Carpenter, T.E., Kim, Y.J., Jung, S., Lee, S.J., 2010. Impact of bovine brucellosis eradication programs in the Republic of Korea. Prev Vet Med 95, 288-291.

Zhang, X.X., Liu, Y.H., Rainey, P.B., 2010. CbrAB-dependent regulation of pcnB, a poly(A) polymerase gene involved in polyadenylation of RNA in Pseudomonas fluorescens. Environ Microbiol 12, 1674-1683.

Zhang, X.X., Rainey, P.B., 2010. Bet hedging in the underworld. Genome Biol 11, 137.