2024

Silago, V., Oravcova, K. , Matthews, L. , Mshana, S. E., Claus, H. and Seni, J. (2024) Epidemiology and antimicrobial resistance trends of pathogens causing urinary tract infections in Mwanza, Tanzania: a comparative study during and after the implementation of the National Action Plan on Antimicrobial Resistance (2017-2022). International Journal of Infectious Diseases, 147, 107208. (doi: 10.1016/j.ijid.2024.107208) (PMID:39128601)

2023

Nthambi, M. , Lembo, T. , Davis, A. , Nasuwa, F., Mmbaga, B. T., Matthews, L. and Hanley, N. (2023) Quantifying farmers’ preferences for antimicrobial use for livestock diseases in northern Tanzania. Q Open, 3(1), qoac032. (doi: 10.1093/qopen/qoac032)

2022

Thorpe, H. A. et al. (2022) A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nature Microbiology, 7(12), pp. 2054-2067. (doi: 10.1038/s41564-022-01263-0) (PMID:36411354) (PMCID:PMC9712112)

Dykes, J. et al. (2022) Visualization for epidemiological modelling: challenges, solutions, reflections and recommendations. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380(2233), 20210299. (doi: 10.1098/rsta.2021.0299) (PMID:35965467) (PMCID:PMC9376715)

Mitchell, S. N. et al. (2022) FAIR Data Pipeline: provenance-driven data management for traceable scientific workflows. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380(2233), 20210300. (doi: 10.1098/rsta.2021.0300) (PMID:35965468) (PMCID:PMC9376726)

Chen, M. et al. (2022) RAMPVIS: Answering the challenges of building visualisation capabilities for large-scale emergency responses. Epidemics, 39, 100569. (doi: 10.1016/j.epidem.2022.100569) (PMID:35597098) (PMCID:PMC9045880)

Sondag, M., Turkay, C., Xu, K., Matthews, L. , Mohr, S. and Archambault, D. (2022) Visual analytics of contact tracing policy simulations during an emergency response. Computer Graphics Forum, 41(3), pp. 29-41. (doi: 10.1111/cgf.14520)

Kovacs, D., Silago, V., Msanga, D. R., Mshana, S. E., Seni, J., Oravcova, K. and Matthews, L. (2022) The hospital environment versus carriage: transmission pathways for third-generation cephalosporin-resistant bacteria in blood in neonates in a low-resource country healthcare setting. Scientific Reports, 12, 8347. (doi: 10.1038/s41598-022-11626-6) (PMID:35589773) (PMCID:PMC9120020)

Davis, A. et al. (2022) How public health crises expose systemic, day-to-day health inequalities in low- and-middle income countries: an example from East Africa. Antimicrobial Resistance and Infection Control, 11(1), 34. (doi: 10.1186/s13756-022-01071-5) (PMID:35164886) (PMCID:PMC8842514)

Hernandez-Castro, L. E. et al. (2022) Population genomics and geographic dispersal in Chagas disease vectors: landscape drivers and evidence of possible adaptation to the domestic setting. PLoS Genetics, 18(2), e1010019. (doi: 10.1371/journal.pgen.1010019) (PMID:35120121) (PMCID:PMC8849464)

2021

Sondag, M., Turkay, C., Mohr, S. , Matthews, L. , Xu, K. and Archambault, D. (2021) What is R? A graph drawer’s perspective? In: 29th International Symposium on Graph Drawing and Network Visualization, Tübingen, Germany, 14-17 Sep 2021, pp. 431-433. ISBN 9783030929305 (doi: 10.1007/978-3-030-92931-2_29)

Kovacs, D., Msanga, D. R., Mshana, S. E., Bilal, M., Oravcova, K. and Matthews, L. (2021) Developing practical clinical tools for predicting neonatal mortality at a neonatal intensive care unit in Tanzania. BMC Pediatrics, 21, 537. (doi: 10.1186/s12887-021-03012-4) (PMID:34852794) (PMCID:PMC8638252)

Silago, V., Kovacs, D., Samson, H., Seni, J., Matthews, L. , Oravcová, K. , Lupindu, A. M., Hoza, A. S. and Mshana, S. E. (2021) Existence of multiple ESBL genes among phenotypically confirmed ESBL producing Klebsiella pneumoniae and Escherichia coli concurrently isolated from clinical, colonization and contamination samples from neonatal units at Bugando Medical Center, Mwanza, Tanzania. Antibiotics, 10(5), 476. (doi: 10.3390/antibiotics10050476) (PMID:33919117) (PMCID:PMC8143173)

2020

Gilbert, M. et al. (2020) Distemper, extinction and vaccination of the Amur tiger. Proceedings of the National Academy of Sciences of the United States of America, 117(50), pp. 31954-31962. (doi: 10.1073/pnas.2000153117) (PMID:33229566) (PMCID:PMC7749280)

Rostal, M. K., Cleaveland, S. , Cordel, C., Staden, L. v., Matthews, L. , Anyamba, A., Karesh, W. B., Paweska, J. T., Haydon, D. T. and Ross, N. (2020) Farm-level risk factors of increased abortion and mortality in domestic ruminants during the 2010 Rift Valley fever outbreak in central South Africa. Pathogens, 9(11), 914. (doi: 10.3390/pathogens9110914) (PMID:33158214) (PMCID:PMC7694248)

Silago, V., Kovacs, D., Msanga, D. R., Seni, J., Matthews, L. , Oravcová, K. , Zadoks, R. N. , Lupindu, A. M., Hoza, A. S. and Mshana, S. E. (2020) Bacteremia in critical care units at Bugando Medical Centre, Mwanza, Tanzania: the role of colonization and contaminated cots and mothers’ hands in cross-transmission of multidrug resistant Gram-negative bacteria. Antimicrobial Resistance and Infection Control, 9, 58. (doi: 10.1186/s13756-020-00721-w) (PMID:32375857) (PMCID:PMC7201549)

Nickbakhsh, S. , Mair, C. , Matthews, L. , Reeve, R. , Johnson, P.C.D. , Thorburn, F., Von Wissmann, B., McMenamin, J., Gunson, R.N. and Murcia, P.R. (2020) Reply to Kloepfer and Gern: Independent studies suggest an arms race between influenza and rhinovirus: what next? Proceedings of the National Academy of Sciences of the United States of America, 117(13), pp. 6988-6989. (doi: 10.1073/pnas.2000903117) (PMID:32127475) (PMCID:PMC7132304)

Mohr, S. , Beard, R., Nisbet, A. J., Burgess, S. T.G., Reeve, R. , Denwood, M., Porphyre, T., Zadoks, R. N. and Matthews, L. (2020) Uptake of diagnostic tests by livestock farmers: a stochastic game theory approach. Frontiers in Veterinary Science, 7, 36. (doi: 10.3389/fvets.2020.00036) (PMID:32118060) (PMCID:PMC7012806)

Subbiah, M. et al. (2020) Antimicrobial resistant enteric bacteria are widely distributed amongst people, animals and the environment in Tanzania. Nature Communications, 11, 228. (doi: 10.1038/s41467-019-13995-5) (PMID:31932601) (PMCID:PMC6957491)

2019

Nickbakhsh, S. et al. (2019) Virus-virus interactions impact the population dynamics of influenza and the common cold. Proceedings of the National Academy of Sciences of the United States of America, 116(52), pp. 27142-27150. (doi: 10.1073/pnas.1911083116) (PMID:31843887) (PMCID:PMC6936719)

Mair, C. , Nickbakhsh, S. , Reeve, R. , McMenamin, J., Reynolds, A., Gunson, R. N., Murcia, P. R. and Matthews, L. (2019) Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models. PLoS Computational Biology, 15(12), e1007492. (doi: 10.1371/journal.pcbi.1007492) (PMID:31834896) (PMCID:PMC6934324)

Hodgkinson, J. E. et al. (2019) Refugia and anthelmintic resistance: concepts and challenges. International Journal for Parasitology, 10, pp. 51-57. (doi: 10.1016/j.ijpddr.2019.05.001) (PMID:31125837) (PMCID:PMC6531808)

Stefan, T., Matthews, L. , Prada, J. M., Mair, C. , Reeve, R. and Stear, M. J. (2019) Divergent Allele Advantage provides a quantitative model for maintaining alleles with a wide range of intrinsic merits. Genetics, 212(2), pp. 553-564. (doi: 10.1534/genetics.119.302022) (PMID:30952668) (PMCID:PMC6553829)

Chaters, G.L. et al. (2019) Analysing livestock network data for infectious disease control: an argument for routine data collection in emerging economies. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1776), 20180264. (doi: 10.1098/rstb.2018.0264) (PMID:31104601) (PMCID:PMC6558568)

2018

Caudell, M. A., Mair, C. , Subbiah, M., Matthews, L. , Quinlan, R. J., Zadoks, R. , Keyyu, J. and Call, D. R. (2018) Identification of risk factors associated with carriage of resistant Escherichia coli in three culturally diverse ethnic groups in Tanzania: a biological and socioeconomic analysis. Lancet Planetary Health, 2(11), e489-e497. (doi: 10.1016/S2542-5196(18)30225-0) (PMID:30396440) (PMCID:PMC6215761)

2017

Stewart, K., Matthews, L. , Scott, E. M. , Husmeier, D. and Mccowan, C. (2017) Preliminary Investigation of the Influences on Antimicrobial Resistance. RSS 2017 Annual Conference, Glasgow, Scotland, 04-07 Sep 2017.

Bush, A. et al. (2017) Connecting Earth observation to high-throughput biodiversity data. Nature Ecology and Evolution, 1, 0176. (doi: 10.1038/s41559-017-0176)

Caudell, M. A., Quinlan, M. B., Subbiah, M., Call, D. R., Roulette, C. J., Roulette, J. W., Roth, A., Matthews, L. and Quinlan, R. J. (2017) Antimicrobial use and veterinary care among agro-pastoralists in Northern Tanzania. PLoS ONE, 12(1), e0170328. (doi: 10.1371/journal.pone.0170328) (PMID:28125722) (PMCID:PMC5268417)

Prentice, J. C., Marion, G., Hutchings, M. R., MCneilly, T. N. and Matthews, L. (2017) Complex responses to movement-based disease control: when livestock trading helps. Journal of the Royal Society: Interface, 14(126), 20160531. (doi: 10.1098/rsif.2016.0531) (PMID:28077759) (PMCID:PMC5310727)

2016

Lupolova, N., Dallman, T. J., Matthews, L. , Bono, J. L. and Gally, D. L. (2016) Support vector machine applied to predict the zoonotic potential of E. coli O157 cattle isolates. Proceedings of the National Academy of Sciences of the United States of America, 113(40), pp. 11312-11317. (doi: 10.1073/pnas.1606567113) (PMID:27647883) (PMCID:PMC5056084)

Ahmad, A., Zachariasen, C., Christiansen, L. E., Græsbøll, K., Toft, N., Matthews, L. , Nielsen, S. S. and Olsen, J. E. (2016) Modeling the growth dynamics of multiple Escherichia coli strains in the pig intestine following intramuscular ampicillin treatment. BMC Microbiology, 16(1), 205. (doi: 10.1186/s12866-016-0823-3) (PMID:27599570) (PMCID:PMC5012095)

Ahmad, A., Zachariasen, C., Christiansen, L. E., Græsbøll, K., Toft, N., Matthews, L. , Olsen, J. E. and Nielsen, S. S. (2016) Multistrain models predict sequential multidrug treatment strategies to result in less antimicrobial resistance than combination treatment. BMC Microbiology, 16, 118. (doi: 10.1186/s12866-016-0724-5) (PMID:27338861) (PMCID:PMC4917987)

Mather, A. E., Reeve, R. , Mellor, D. J. , Matthews, L. , Reid-Smith, R. J., Dutil, L., Haydon, D. T. and Reid, S. W.J. (2016) Detection of rare antimicrobial resistance profiles by active and passive surveillance approaches. PLoS ONE, 11(7), e0158515. (doi: 10.1371/journal.pone.0158515) (PMID:27391966) (PMCID:PMC4938605)

Reeve, R. , Leinster, T., Cobbold, C. A. , Thompson, J., Brummitt, N., Mitchell, S. N. and Matthews, L. (2016) How to partition diversity. arXiv, (Unpublished)

2015

Ahmad, A., Zachariasen, C., Christiansen, L. E., Græsbøll, K., Toft, N., Matthews, L. , Damborg, P., Agersø, Y., Olsen, J. E. and Nielsen, S. S. (2015) Pharmacodynamic modelling of in vitro activity of tetracycline against a representative, naturally occurring population of porcine Escherichia coli. Acta Veterinaria Scandinavica, 57, 79. (doi: 10.1186/s13028-015-0169-0) (PMID:26603151) (PMCID:PMC4657295)

Gharbi, K., Matthews, L. , Bron, J., Roberts, R., Tinch, A. and Stear, M. (2015) The control of sea lice in Atlantic salmon by selective breeding. Journal of the Royal Society: Interface, 12(110), 20150574. (doi: 10.1098/rsif.2015.0574) (PMID:26289656) (PMCID:PMC4614468)

Toma, L., Low, J.C., Vosough Ahmadi, B., Matthews, L. and Stott, A.W. (2015) An analysis of cattle farmers' perceptions of drivers and barriers to on-farm control of Escherichia coli O157. Epidemiology and Infection, 143(11), pp. 2355-2366. (doi: 10.1017/S0950268814003045) (PMID:25427776)

Gilbert, M., Soutyrina, S. V., Seryodkin, I. V., Sulikhan, N., Uphyrkina, O. V., Goncharuk, M., Matthews, L. , Cleaveland, S. and Miquelle, D. G. (2015) Canine distemper virus as a threat to wild tigers in Russia and across their range. Integrative Zoology, 10(4), pp. 329-343. (doi: 10.1111/1749-4877.12137) (PMID:25939829)

Mair, C. , Matthews, L. , Prada J. de Cisneros, J., Stefan, T. and Stear, M. J. (2015) Multitrait indices to predict worm length and number in sheep with natural, mixed predominantly Teladorsagia circumcincta infection. Parasitology, 142(6), pp. 773-782. (doi: 10.1017/S0031182014001905) (PMID:25586410) (PMCID:PMC4413790)

Ahmad, A., Græsbøll, K., Christiansen, L. E., Toft, N., Matthews, L. and Nielsen, S. S. (2015) Pharmacokinetic-pharmacodynamic model to evaluate intramuscular tetracycline treatment protocols to prevent antimicrobial resistance in pigs. Antimicrobial Agents and Chemotherapy, 59(3), pp. 1634-1642. (doi: 10.1128/AAC.03919-14) (PMID:25547361)

Mair, C. , Stear, M., Johnson, P. , Denwood, M., Jimenez de Cisneros, J. P., Stefan, T. and Matthews, L. (2015) A Bayesian generalized random regression model for estimating heritability using overdispersed count data. Genetics Selection Evolution, 47, 51. (doi: 10.1186/s12711-015-0125-5) (PMID:26092676) (PMCID:PMC4473853)

2014

Ikeda, Y., Gilbert, M., Miquelle, D. G., Goodrich, J. M., Reeve, R. , Cleaveland, S. , Matthews, L. and Joly, D. O. (2014) Estimating the potential impact of canine distemper virus on the Amur tiger population (Panthera tigris altaica) in Russia. PLoS ONE, 9(10), e110811. (doi: 10.1371/journal.pone.0110811) (PMID:25354196) (PMCID:PMC4212977)

Prada Jimenez de Cisneros, J., Stear, M. J., Mair, C. , Singleton, D., Stefan, T., Stear, A., Marion, G. and Matthews, L. (2014) An explicit immunogenetic model of gastrointestinal nematode infection in sheep. Journal of the Royal Society: Interface, 11(99), p. 20140416. (doi: 10.1098/rsif.2014.0416) (PMID:25121649) (PMCID:PMC4233724)

Nickbakhsh, S. , Matthews, L. , Reid, S. and Kao, R.R. (2014) A metapopulation model for highly pathogenic avian influenza: implications for compartmentalization as a control measure. Epidemiology and Infection, 142(09), pp. 1813-1825. (doi: 10.1017/S0950268813002963)

Prada Jiménez de Cisneros, J., Matthews, L. , Mair, C. , Stefan, T. and Stear, M. J. (2014) The transfer of IgA from mucus to plasma and the implications for diagnosis and control of nematode infections. Parasitology, 141(7), pp. 875-879. (doi: 10.1017/S0031182013002321)

Herbert, L. J. et al. (2014) E. coli O157 on Scottish cattle farms: evidence of local spread and persistence using repeat cross-sectional data. BMC Veterinary Research, 10(1), p. 95. (doi: 10.1186/1746-6148-10-95)

2013

Matthews, L. et al. (2013) Predicting the public health benefit of vaccinating cattle against Escherichia coli O157. Proceedings of the National Academy of Sciences of the United States of America, 110(40), pp. 16265-16270. (doi: 10.1073/pnas.1304978110)

Call, D.R., Matthews, L. , Subbiah, M. and Liu, J. (2013) Do antibiotic residues in soils play a role in amplification and transmission of antibiotic resistant bacteria in cattle populations? Frontiers in Microbiology, 4(193), pp. 1-8. (doi: 10.3389/fmicb.2013.00193)

Nickbakhsh, S. , Matthews, L. , Dent, J.E., Innocent, G.T., Arnold, M.E., Reid, S.W.J. and Kao, R.R. (2013) Implications of within-farm transmission for network dynamics: consequences for the spread of avian influenza. Epidemics, 5(2), pp. 67-76. (doi: 10.1016/j.epidem.2013.03.001)

Strachan, N.J.C. et al. (2013) Identifying the seasonal origins of human campylobacteriosis. Epidemiology and Infection, 141(06), pp. 1267-1275. (doi: 10.1017/S0950268812002063)

2012

Denwood, M.J., Love, S., Innocent, G.T., Matthews, L. , McKendrick, I.J., Hillary, N., Smith, A. and Reid, S.W.J. (2012) Quantifying the sources of variability in equine faecal egg counts: Implications for improving the utility of the method. Veterinary Parasitology, 188(1-2), pp. 120-126. (doi: 10.1016/j.vetpar.2012.03.005) (PMID:22469484)

Mather, A.E. et al. (2012) The diversity of antimicrobial resistance is different in Salmonella Typhimurium DT104 from co-located animals and humans. Proceedings of the Royal Society of London Series B: Biological Sciences, 279(1740), pp. 2924-2925. (doi: 10.1098/rspb.2012.0614)

Codner, G.F., Stear, M.J., Reeve, R. , Matthews, L. and Ellis, S.A. (2012) Selective forces shaping diversity in the class I region of the major histocompatibility complex in dairy cattle. Animal Genetics, 43(3), pp. 239-249. (doi: 10.1111/j.1365-2052.2011.02239.x) (PMID:22486494)

Mather, A.E. et al. (2012) An ecological approach to assessing the epidemiology of antimicrobial resistance in animal and human populations. Proceedings of the Royal Society of London Series B: Biological Sciences, 279(1733), pp. 1630-1639. (doi: 10.1098/rspb.2011.1975)

Chase-Topping, M.E. et al. (2012) Pathogenic Potential to Humans of Bovine Escherichia coli O26, Scotland. Emerging Infectious Diseases, 18(3), pp. 439-448. (doi: 10.3201/eid1803.111236)

Stear, M.J., Nikbakht, G., Matthews, L. and Jonsson, N.N. (2012) Breeding for disease resistance in livestock and fish. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, 7(007), pp. 1-10. (doi: 10.1079/PAVSNNR20127007)

Bessell, P.R., Rotariu, O., Innocent, G.T., Smith-Palmer, A., Strachan, N.J.C., Forbes, K.J., Cowden, J.M., Reid, S.W.J. and Matthews, L. (2012) Using sequence data to identify alternative routes and risk of infection: a case-study of campylobacter in Scotland. BMC Infectious Diseases, 12(80), (doi: 10.1186/1471-2334-12-80)

2011

Denwood, M.J., Mather, A.E., Haydon, D.T. , Matthews, L. , Mellor, D.J. and Reid, S.W.J. (2011) From phenotype to genotype: a Bayesian solution. Proceedings of the Royal Society of London Series B: Biological Sciences, 278(1710), pp. 1434-1440. (doi: 10.1098/rspb.2010.1719)

Singleton, D.R., Stear, M.J. and Matthews, L. (2011) A mechanistic model of developing immunity to Teladorsagia circumcincta infection in lambs. Parasitology, 138(3), pp. 322-332. (doi: 10.1017/S0031182010001289) (PMID:20946694)

Mather, A.E., Denwood, M.J., Haydon, D.T. , Matthews, L. , Mellor, D.J. , Coia, J.E., Brown, D.J. and Reid, S.W.J. (2011) The prevalences of Salmonella Genomic Island 1 variants in human and animal Salmonella Typhimurium DT104 are distinguishable using a Bayesian approach. PLoS ONE, 6(11), e27220. (doi: 10.1371/journal.pone.0027220) (PMID:22125606) (PMCID:PMC3220677)

Nickbakhsh, S., Matthews, L. , Bessell, P.R., Reid, S.W.J. and Kao, R.R. (2011) Generating social network data using partially described networks: an example informing avian influenza control in the British poultry industry. BMC Veterinary Research, 7(66), (doi: 10.1186/1746-6148-7-66)

Stear, M.J., Singleton, D. and Matthews, L. (2011) An evolutionary perspective on gastrointestinal nematodes of sheep. Journal of Helminthology, 85(02), pp. 113-120. (doi: 10.1017/S0022149X11000058)

2010

O'Reilly, K.M., Low, J.C., Denwood, M.J., Gally, D.L., Evans, J., Gunn, G.J., Mellor, D.J. , Reid, S.W.J. and Matthews, L. (2010) Associations between the presence of virulence determinants and the epidemiology and ecology of zoonotic escherichia coli. Applied and Environmental Microbiology, 76(24), pp. 8110-8116. (doi: 10.1128/AEM.01343-10)

Bessell, P.R., Matthews, L. , Smith-Palmer, A., Rotariu, O., Strachan, N.J., Forbes, K.J., Cowden, J.M., Reid, S.W.J. and Innocent, G.T. (2010) Geographic determinants of reported human Campylobacter infections in Scotland. BMC Public Health, 10, p. 423. (doi: 10.1186/1471-2458-10-423)

Denwood, M.J., Reid, S.W.J., Love, S., Nielsen, M.K., Matthews, L. , McKendrick, I.J. and Innocent, G.T. (2010) Comparison of three alternative methods for analysis of equine Faecal Egg Count Reduction Test data. Preventive Veterinary Medicine, 93(4), pp. 316-323. (doi: 10.1016/j.prevetmed.2009.11.009)

Reeve, R. et al. (2010) Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus. PLoS Computational Biology, 6(12), e1001027. (doi: 10.1371/journal.pcbi.1001027) (PMID:21151576) (PMCID:PMC3000348)

Rotariu, O. et al. (2010) Putative household outbreaks of campylobacteriosis typically comprise single MLST genotypes. Epidemiology and Infection, 138(12), pp. 1744-1747. (doi: 10.1017/S0950268810001457)

Townsend, S.E., Haydon, D.T. and Matthews, L. (2010) On the generality of stability–complexity relationships in Lotka–Volterra ecosystems. Journal of Theoretical Biology, 267(2), pp. 243-251. (doi: 10.1016/j.jtbi.2010.08.018)

2009

Matthews, L. , Reeve, R. , Woolhouse, M.E.J., Mellor, D. , Pearce, M.C., Allison, L.J., Gunn, G.J., Low, J.C. and Reid, S.W.J. (2009) Exploiting strain diversity to expose transmission heterogeneities and predict the impact of targeting supershedding. Epidemics, 1(4), pp. 221-229. (doi: 10.1016/j.epidem.2009.10.002)

Gharbi, K., Glover, K.A., Stone, L.C., MacDonald, E.S., Matthews, L. , Grimholt, U. and Stear, M.J. (2009) Genetic dissection of MHC-associated susceptibility to Lepeophtheirus salmonis in Atlantic salmon. BMC Genetics, 10, p. 20. (doi: 10.1186/1471-2156-10-20)

Howey, R., Quan, M., Savill, N.J., Matthews, L. , Alexandersen, S. and Woolhouse, M. (2009) Effect of the initial dose of foot-and-mouth disease virus on the early viral dynamics within pigs. Journal of the Royal Society: Interface, 6(39), pp. 835-847. (doi: 10.1098/rsif.2008.0434)

Pearce, M.C. et al. (2009) Temporal and spatial patterns of bovine Escherichia coli O157 prevalence and comparison of temporal changes in the patterns of phage types associated with bovine shedding and human E. coli O157 cases in Scotland between 1998-2000 and 2002-2004. BMC Microbiology, 9, (doi: 10.1186/1471-2180-9-276)

Townsend, S.E., Newey, S., Thirgood, S.J., Matthews, L. and Haydon, D.T. (2009) Can parasites drive population cycles in mountain hares? Proceedings of the Royal Society of London Series B: Biological Sciences, 276(1662), pp. 1611-1617. (doi: 10.1098/rspb.2008.1669)

2008

Denwood, M.J., Stear, M.J., Matthews, L. , Reid, S.W.J., Toft, N. and Innocent, G.T. (2008) The distribution of the pathogenic nematode Nematodirus battus in lambs is zero-inflated. Parasitology, 135(10), pp. 1225-1235. (doi: 10.1017/S0031182008004708)

Chase-Topping, M., Gally, D., Low, C., Matthews, L. and Woolhouse, M. (2008) Super-shedding and the link between human infection and livestock carriage of Escherichia coli O157. Nature Reviews Microbiology, 6(12), pp. 904-912. (doi: 10.1126/science.1170587)

2007

Matthews, L. and Haydon, D. (2007) Introduction. Cross-scale influences on epidemiological dynamics: from genes to ecosystems. Journal of the Royal Society: Interface, 4(16), pp. 763-765. (doi: 10.1098/rsif.2007.1173) (PMCID:PMC2394559)

Stear, M., Innocent, G.T. and Matthews, L. (2007) Genetic disorders and the quest for candidate genes: Hypotheses worth testing. Veterinary Journal, 174(2), pp. 217-218. (doi: 10.1016/j.tvjl.2006.07.015)

Chase-Topping, M.E. et al. (2007) Risk factors for the presence of high-level shedders of Escherichia coli O157 on Scottish farms. Journal of Clinical Microbiology, 45, pp. 1594-1603. (doi: 10.1128/JCM.01690-06)

Jansen, P., Matthews, L. and Toft, N. (2007) Geographic risk factors for inter-river dispersal of Gyrodactylus salaris in fjord systems in Norway. Diseases of Aquatic Organisms, 74, pp. 139-149.

Liu, W.-C., Shaw, D.J., Matthews, L., Hoyle, D.V., Pearce, M.C., Yates, C.M., Low, J.C., Amyes, S.G.B., Gunn, G.J. and Woolhouse, M.E.J. (2007) Modelling the epidemiology and transmission of Verocytotoxin-producing Escherichia coli serogroups O26 and O103 in two different calf cohorts. Epidemiology and Infection, 135(8), pp. 1316-1323. (doi: 10.1017/S0950268806007722)

Liu, W., Matthews, L., Chase-Topping, M., Savill, N., Shaw, D. and Woolhouse, M. (2007) Metapopulation dynamics of Escherichia coli O157 in cattle: an exploratory model. Journal of the Royal Society: Interface, 4, pp. 917-924. (doi: 10.1098/rsif.2007.0219)

Stear, M., Fitton, L., Innocent, G., Murphy, L., Rennie, K. and Matthews, L. (2007) The dynamic influence of genetic variation on the susceptibility of sheep to gastrointestinal nematode infection. Journal of the Royal Society: Interface, 4(16), pp. 767-776. (doi: 10.1098/rsif.2007.1104)

2006

Haydon, D. et al. (2006) Low-coverage vaccination strategies for the conservation of endangered species. Nature, 443, pp. 692-695. (doi: 10.1038/nature05177)

Matthews, L. (2006) Super-shedding cattle and the transmission dynamics of Escherichia coli O157. Epidemiology and Infection, 134(1), pp. 131-142.

Matthews, L. et al. (2006) Heterogeneous shedding of Escherichia coli O157 in cattle and its implications for control. Proceedings of the National Academy of Sciences of the United States of America, 103(3), pp. 547-552. (doi: 10.1073/pnas.0503776103)

St Rose, S.G., Hunter, N., Matthews, L., Foster, J.D., Chase-Topping, M.E., Kruuk, L.E.B., Shaw, D.J., Rhind, S.M., Will, R.G. and Woolhouse, M.E.J. (2006) Comparative evidence for a link between Peyer's patch development and susceptibility to transmissible spongiform encephalopathies. BMC Infectious Diseases, 6, (doi: 10.1186/1471-2334-6-5)

Touzeau, S., Chase-Topping, M.E., Matthews, L., Lajous, D., Eychenne, F., Hunter, N., Foster, J.D., Simm, G., Elsen, J.-M. and Woolhouse, M.E.J. (2006) Modelling the spread of scrapie in a sheep flock: evidence for increased transmission during lambing seasons. Archives of Virology, 151(4), pp. 735-751. (doi: 10.1007/s00705-005-0666-y)

2005

Liu, W.C., Jenkins, C., Shaw, D.J., Matthews, L., Pearce, M.C., Low, J.C., Gunn, G.J., Smith, H.R., Frankel, G. and Woolhouse, M.E.J. (2005) Modelling the epidemiology of Verocytotoxin-producing Escherichia coli serogroups in young calves. Epidemiology and Infection, 133(3), pp. 449-458. (doi: 10.1017/S0950268804003644)

Matthews, L. (2005) Genotype-level variation in lifetime breeding success, litter size and survival of sheep in scrapie-affected flocks. Journal of General Virology, 86(Pt 4), pp. 1229-1238.

Matthews, L. and Woolhouse, M.E.J. (2005) New approaches to quantifying the spread of infection. Nature Reviews Microbiology, 3(7), pp. 529-536. (doi: 10.1038/nrmicro1178)

Taylor, L., Matthews, L., Shaw, D. and Haydon, D. (2005) Competitive suppression in rnixed-clone parasite cultures. Biology Letters, 1, pp. 108-111. (doi: 10.1098/rsbl.2004.0256)

Woolhouse, M., Shaw, D., Matthews, L., Liu, W., Mellor, D. and Thomas, M. (2005) Epidemiological implications of the contact network structure for cattle farms and the 20-80 rule. Biology Letters, 1, pp. 350-352. (doi: 10.1098/rsbl.2005.0331)

2003

Haydon, D. T. , Matthews, L. , Timms, R. and Colegrave, N. (2003) Top-down or bottom-up regulation of intra-host blood-stage malaria: do malaria parasites most resemble the dynamics of prey or predator? Proceedings of the Royal Society of London Series B: Biological Sciences, 270(1512), pp. 289-298. (doi: 10.1098/rspb.2002.2203)

Haydon, D.T., Chase-Topping, M., Shaw, D.J., Matthews, L. , Friar, J.K., Wilesmith, J. and Woolhouse, M.E.J. (2003) The construction and analysis of epidemic trees with reference to the 2001 UK foot-and-mouth outbreak. Proceedings of the Royal Society of London Series B: Biological Sciences, 270, pp. 121-127. (doi: 10.1098/rspb.2002.2191) (PMCID:PMC1691228)

Matthews, L., Haydon, D.T., Shaw, D., Chase-Topping, M.E., Keeling, M.J. and Woolhouse, M.E.J. (2003) Neighbourhood control policies and the spread of infectious diseases. Proceedings of the Royal Society of London Series B: Biological Sciences, 270(1525), pp. 1659-1666. (doi: 10.1098/rspb.2003.2429)

2002

Matthews, L. (2002) Comparative epidemiology of scrapie outbreaks in individual sheep flocks. Epidemiology and Infection, 128(3), pp. 513-521.

2001

Woolhouse, M.E.J., Coen, P., Matthews, L. , Foster, J.D., Elsen, J.-M., Lewis, R.M., Haydon, D.T. and Hunter, N. (2001) A centuries-long epidemic of scrapie in British sheep? Trends in Microbiology, 9(2), pp. 67-70. (doi: 10.1016/S0966-842X(00)01912-0)

Keeling, M.J., Woolhouse, M.E.J., Shaw, D.J., Matthews, L. , Chase-Topping, M., Haydon, D.T., Cornell, S.J., Kappey, J., Wilesmith, J. and Grenfell, B.T. (2001) Dynamics of the 2001 UK foot and mouth epidemic: stochastic dispersal in a heterogeneous landscape. Science, 294(5543), pp. 813-817. (doi: 10.1126/science.1065973) (PMID:11679661)

Matthews, L., Coen, P.G., Foster, J.D., Hunter, N. and Woolhouse, M.E.J. (2001) Population dynamics of a scrapie outbreak. Archives of Virology, 146(6), pp. 1173-1186. (doi: 10.1007/s007050170113)

Woolhouse, M. et al. (2001) Epidemiology - Foot-and-mouth disease under control in the UK. Nature, 411, pp. 258-259. (doi: 10.1038/35077149) (PMID:11357118)

2000

Matthews, L. , Woolhouse, M.E.J. and Hunter, N. (2000) The basic reproduction number for scrapie in a flock of Cheviot sheep. In: Thrusfield, M.V. and Goodall, E.A. (eds.) Proceedings of the Society for Veterinary Epidemiology and Preventive Medicine. Society for Veterinary Epidemiology and Preventive Medicine, pp. 183-197. ISBN 9780948073441

1999

Matthews, L. , Woolhouse, M. E. J. and Hunter, N. (1999) The basic reproduction number for scrapie. Proceedings of the Royal Society of London Series B: Biological Sciences, 266(1423), pp. 1085-1090. (doi: 10.1098/rspb.1999.0747) (PMCID:PMC1689932)

Woolhouse, M. E. J., Matthews, L. , Coen, P., Stringer, S. M., Foster, J. D. and Hunter, N. (1999) Population dynamics of scrapie in a sheep flock. Philosophical Transactions of the Royal Society B: Biological Sciences, 354(1384), pp. 751-756. (doi: 10.1098/rstb.1999.0427) (PMID:10365400) (PMCID:PMC1692552)

1998

Woolhouse, M.E.J., Stringer, S.M., Matthews, L. , Hunter, N. and Anderson, R.M. (1998) Epidemiology and control of scrapie within a sheep flock. Proceedings of the Royal Society of London Series B: Biological Sciences, 265(1402), pp. 1205-1210. (doi: 10.1098/rspb.1998.0421)

1997

Matthews, L. and Brindley, J. (1997) Patchiness in plankton populations. Dynamics and Stability of Systems, 12(1), pp. 39-59. (doi: 10.1080/02681119708806235)

Articles

Silago, V., Oravcova, K. , Matthews, L. , Mshana, S. E., Claus, H. and Seni, J. (2024) Epidemiology and antimicrobial resistance trends of pathogens causing urinary tract infections in Mwanza, Tanzania: a comparative study during and after the implementation of the National Action Plan on Antimicrobial Resistance (2017-2022). International Journal of Infectious Diseases, 147, 107208. (doi: 10.1016/j.ijid.2024.107208) (PMID:39128601)

Nthambi, M. , Lembo, T. , Davis, A. , Nasuwa, F., Mmbaga, B. T., Matthews, L. and Hanley, N. (2023) Quantifying farmers’ preferences for antimicrobial use for livestock diseases in northern Tanzania. Q Open, 3(1), qoac032. (doi: 10.1093/qopen/qoac032)

Thorpe, H. A. et al. (2022) A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nature Microbiology, 7(12), pp. 2054-2067. (doi: 10.1038/s41564-022-01263-0) (PMID:36411354) (PMCID:PMC9712112)

Dykes, J. et al. (2022) Visualization for epidemiological modelling: challenges, solutions, reflections and recommendations. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380(2233), 20210299. (doi: 10.1098/rsta.2021.0299) (PMID:35965467) (PMCID:PMC9376715)

Mitchell, S. N. et al. (2022) FAIR Data Pipeline: provenance-driven data management for traceable scientific workflows. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380(2233), 20210300. (doi: 10.1098/rsta.2021.0300) (PMID:35965468) (PMCID:PMC9376726)

Chen, M. et al. (2022) RAMPVIS: Answering the challenges of building visualisation capabilities for large-scale emergency responses. Epidemics, 39, 100569. (doi: 10.1016/j.epidem.2022.100569) (PMID:35597098) (PMCID:PMC9045880)

Sondag, M., Turkay, C., Xu, K., Matthews, L. , Mohr, S. and Archambault, D. (2022) Visual analytics of contact tracing policy simulations during an emergency response. Computer Graphics Forum, 41(3), pp. 29-41. (doi: 10.1111/cgf.14520)

Kovacs, D., Silago, V., Msanga, D. R., Mshana, S. E., Seni, J., Oravcova, K. and Matthews, L. (2022) The hospital environment versus carriage: transmission pathways for third-generation cephalosporin-resistant bacteria in blood in neonates in a low-resource country healthcare setting. Scientific Reports, 12, 8347. (doi: 10.1038/s41598-022-11626-6) (PMID:35589773) (PMCID:PMC9120020)

Davis, A. et al. (2022) How public health crises expose systemic, day-to-day health inequalities in low- and-middle income countries: an example from East Africa. Antimicrobial Resistance and Infection Control, 11(1), 34. (doi: 10.1186/s13756-022-01071-5) (PMID:35164886) (PMCID:PMC8842514)

Hernandez-Castro, L. E. et al. (2022) Population genomics and geographic dispersal in Chagas disease vectors: landscape drivers and evidence of possible adaptation to the domestic setting. PLoS Genetics, 18(2), e1010019. (doi: 10.1371/journal.pgen.1010019) (PMID:35120121) (PMCID:PMC8849464)

Kovacs, D., Msanga, D. R., Mshana, S. E., Bilal, M., Oravcova, K. and Matthews, L. (2021) Developing practical clinical tools for predicting neonatal mortality at a neonatal intensive care unit in Tanzania. BMC Pediatrics, 21, 537. (doi: 10.1186/s12887-021-03012-4) (PMID:34852794) (PMCID:PMC8638252)

Silago, V., Kovacs, D., Samson, H., Seni, J., Matthews, L. , Oravcová, K. , Lupindu, A. M., Hoza, A. S. and Mshana, S. E. (2021) Existence of multiple ESBL genes among phenotypically confirmed ESBL producing Klebsiella pneumoniae and Escherichia coli concurrently isolated from clinical, colonization and contamination samples from neonatal units at Bugando Medical Center, Mwanza, Tanzania. Antibiotics, 10(5), 476. (doi: 10.3390/antibiotics10050476) (PMID:33919117) (PMCID:PMC8143173)

Gilbert, M. et al. (2020) Distemper, extinction and vaccination of the Amur tiger. Proceedings of the National Academy of Sciences of the United States of America, 117(50), pp. 31954-31962. (doi: 10.1073/pnas.2000153117) (PMID:33229566) (PMCID:PMC7749280)

Rostal, M. K., Cleaveland, S. , Cordel, C., Staden, L. v., Matthews, L. , Anyamba, A., Karesh, W. B., Paweska, J. T., Haydon, D. T. and Ross, N. (2020) Farm-level risk factors of increased abortion and mortality in domestic ruminants during the 2010 Rift Valley fever outbreak in central South Africa. Pathogens, 9(11), 914. (doi: 10.3390/pathogens9110914) (PMID:33158214) (PMCID:PMC7694248)

Silago, V., Kovacs, D., Msanga, D. R., Seni, J., Matthews, L. , Oravcová, K. , Zadoks, R. N. , Lupindu, A. M., Hoza, A. S. and Mshana, S. E. (2020) Bacteremia in critical care units at Bugando Medical Centre, Mwanza, Tanzania: the role of colonization and contaminated cots and mothers’ hands in cross-transmission of multidrug resistant Gram-negative bacteria. Antimicrobial Resistance and Infection Control, 9, 58. (doi: 10.1186/s13756-020-00721-w) (PMID:32375857) (PMCID:PMC7201549)

Nickbakhsh, S. , Mair, C. , Matthews, L. , Reeve, R. , Johnson, P.C.D. , Thorburn, F., Von Wissmann, B., McMenamin, J., Gunson, R.N. and Murcia, P.R. (2020) Reply to Kloepfer and Gern: Independent studies suggest an arms race between influenza and rhinovirus: what next? Proceedings of the National Academy of Sciences of the United States of America, 117(13), pp. 6988-6989. (doi: 10.1073/pnas.2000903117) (PMID:32127475) (PMCID:PMC7132304)

Mohr, S. , Beard, R., Nisbet, A. J., Burgess, S. T.G., Reeve, R. , Denwood, M., Porphyre, T., Zadoks, R. N. and Matthews, L. (2020) Uptake of diagnostic tests by livestock farmers: a stochastic game theory approach. Frontiers in Veterinary Science, 7, 36. (doi: 10.3389/fvets.2020.00036) (PMID:32118060) (PMCID:PMC7012806)

Subbiah, M. et al. (2020) Antimicrobial resistant enteric bacteria are widely distributed amongst people, animals and the environment in Tanzania. Nature Communications, 11, 228. (doi: 10.1038/s41467-019-13995-5) (PMID:31932601) (PMCID:PMC6957491)

Nickbakhsh, S. et al. (2019) Virus-virus interactions impact the population dynamics of influenza and the common cold. Proceedings of the National Academy of Sciences of the United States of America, 116(52), pp. 27142-27150. (doi: 10.1073/pnas.1911083116) (PMID:31843887) (PMCID:PMC6936719)

Mair, C. , Nickbakhsh, S. , Reeve, R. , McMenamin, J., Reynolds, A., Gunson, R. N., Murcia, P. R. and Matthews, L. (2019) Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models. PLoS Computational Biology, 15(12), e1007492. (doi: 10.1371/journal.pcbi.1007492) (PMID:31834896) (PMCID:PMC6934324)

Hodgkinson, J. E. et al. (2019) Refugia and anthelmintic resistance: concepts and challenges. International Journal for Parasitology, 10, pp. 51-57. (doi: 10.1016/j.ijpddr.2019.05.001) (PMID:31125837) (PMCID:PMC6531808)

Stefan, T., Matthews, L. , Prada, J. M., Mair, C. , Reeve, R. and Stear, M. J. (2019) Divergent Allele Advantage provides a quantitative model for maintaining alleles with a wide range of intrinsic merits. Genetics, 212(2), pp. 553-564. (doi: 10.1534/genetics.119.302022) (PMID:30952668) (PMCID:PMC6553829)

Chaters, G.L. et al. (2019) Analysing livestock network data for infectious disease control: an argument for routine data collection in emerging economies. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1776), 20180264. (doi: 10.1098/rstb.2018.0264) (PMID:31104601) (PMCID:PMC6558568)

Caudell, M. A., Mair, C. , Subbiah, M., Matthews, L. , Quinlan, R. J., Zadoks, R. , Keyyu, J. and Call, D. R. (2018) Identification of risk factors associated with carriage of resistant Escherichia coli in three culturally diverse ethnic groups in Tanzania: a biological and socioeconomic analysis. Lancet Planetary Health, 2(11), e489-e497. (doi: 10.1016/S2542-5196(18)30225-0) (PMID:30396440) (PMCID:PMC6215761)

Bush, A. et al. (2017) Connecting Earth observation to high-throughput biodiversity data. Nature Ecology and Evolution, 1, 0176. (doi: 10.1038/s41559-017-0176)

Caudell, M. A., Quinlan, M. B., Subbiah, M., Call, D. R., Roulette, C. J., Roulette, J. W., Roth, A., Matthews, L. and Quinlan, R. J. (2017) Antimicrobial use and veterinary care among agro-pastoralists in Northern Tanzania. PLoS ONE, 12(1), e0170328. (doi: 10.1371/journal.pone.0170328) (PMID:28125722) (PMCID:PMC5268417)

Prentice, J. C., Marion, G., Hutchings, M. R., MCneilly, T. N. and Matthews, L. (2017) Complex responses to movement-based disease control: when livestock trading helps. Journal of the Royal Society: Interface, 14(126), 20160531. (doi: 10.1098/rsif.2016.0531) (PMID:28077759) (PMCID:PMC5310727)

Lupolova, N., Dallman, T. J., Matthews, L. , Bono, J. L. and Gally, D. L. (2016) Support vector machine applied to predict the zoonotic potential of E. coli O157 cattle isolates. Proceedings of the National Academy of Sciences of the United States of America, 113(40), pp. 11312-11317. (doi: 10.1073/pnas.1606567113) (PMID:27647883) (PMCID:PMC5056084)

Ahmad, A., Zachariasen, C., Christiansen, L. E., Græsbøll, K., Toft, N., Matthews, L. , Nielsen, S. S. and Olsen, J. E. (2016) Modeling the growth dynamics of multiple Escherichia coli strains in the pig intestine following intramuscular ampicillin treatment. BMC Microbiology, 16(1), 205. (doi: 10.1186/s12866-016-0823-3) (PMID:27599570) (PMCID:PMC5012095)

Ahmad, A., Zachariasen, C., Christiansen, L. E., Græsbøll, K., Toft, N., Matthews, L. , Olsen, J. E. and Nielsen, S. S. (2016) Multistrain models predict sequential multidrug treatment strategies to result in less antimicrobial resistance than combination treatment. BMC Microbiology, 16, 118. (doi: 10.1186/s12866-016-0724-5) (PMID:27338861) (PMCID:PMC4917987)

Mather, A. E., Reeve, R. , Mellor, D. J. , Matthews, L. , Reid-Smith, R. J., Dutil, L., Haydon, D. T. and Reid, S. W.J. (2016) Detection of rare antimicrobial resistance profiles by active and passive surveillance approaches. PLoS ONE, 11(7), e0158515. (doi: 10.1371/journal.pone.0158515) (PMID:27391966) (PMCID:PMC4938605)

Reeve, R. , Leinster, T., Cobbold, C. A. , Thompson, J., Brummitt, N., Mitchell, S. N. and Matthews, L. (2016) How to partition diversity. arXiv, (Unpublished)

Ahmad, A., Zachariasen, C., Christiansen, L. E., Græsbøll, K., Toft, N., Matthews, L. , Damborg, P., Agersø, Y., Olsen, J. E. and Nielsen, S. S. (2015) Pharmacodynamic modelling of in vitro activity of tetracycline against a representative, naturally occurring population of porcine Escherichia coli. Acta Veterinaria Scandinavica, 57, 79. (doi: 10.1186/s13028-015-0169-0) (PMID:26603151) (PMCID:PMC4657295)

Gharbi, K., Matthews, L. , Bron, J., Roberts, R., Tinch, A. and Stear, M. (2015) The control of sea lice in Atlantic salmon by selective breeding. Journal of the Royal Society: Interface, 12(110), 20150574. (doi: 10.1098/rsif.2015.0574) (PMID:26289656) (PMCID:PMC4614468)

Toma, L., Low, J.C., Vosough Ahmadi, B., Matthews, L. and Stott, A.W. (2015) An analysis of cattle farmers' perceptions of drivers and barriers to on-farm control of Escherichia coli O157. Epidemiology and Infection, 143(11), pp. 2355-2366. (doi: 10.1017/S0950268814003045) (PMID:25427776)

Gilbert, M., Soutyrina, S. V., Seryodkin, I. V., Sulikhan, N., Uphyrkina, O. V., Goncharuk, M., Matthews, L. , Cleaveland, S. and Miquelle, D. G. (2015) Canine distemper virus as a threat to wild tigers in Russia and across their range. Integrative Zoology, 10(4), pp. 329-343. (doi: 10.1111/1749-4877.12137) (PMID:25939829)

Mair, C. , Matthews, L. , Prada J. de Cisneros, J., Stefan, T. and Stear, M. J. (2015) Multitrait indices to predict worm length and number in sheep with natural, mixed predominantly Teladorsagia circumcincta infection. Parasitology, 142(6), pp. 773-782. (doi: 10.1017/S0031182014001905) (PMID:25586410) (PMCID:PMC4413790)

Ahmad, A., Græsbøll, K., Christiansen, L. E., Toft, N., Matthews, L. and Nielsen, S. S. (2015) Pharmacokinetic-pharmacodynamic model to evaluate intramuscular tetracycline treatment protocols to prevent antimicrobial resistance in pigs. Antimicrobial Agents and Chemotherapy, 59(3), pp. 1634-1642. (doi: 10.1128/AAC.03919-14) (PMID:25547361)

Mair, C. , Stear, M., Johnson, P. , Denwood, M., Jimenez de Cisneros, J. P., Stefan, T. and Matthews, L. (2015) A Bayesian generalized random regression model for estimating heritability using overdispersed count data. Genetics Selection Evolution, 47, 51. (doi: 10.1186/s12711-015-0125-5) (PMID:26092676) (PMCID:PMC4473853)

Ikeda, Y., Gilbert, M., Miquelle, D. G., Goodrich, J. M., Reeve, R. , Cleaveland, S. , Matthews, L. and Joly, D. O. (2014) Estimating the potential impact of canine distemper virus on the Amur tiger population (Panthera tigris altaica) in Russia. PLoS ONE, 9(10), e110811. (doi: 10.1371/journal.pone.0110811) (PMID:25354196) (PMCID:PMC4212977)

Prada Jimenez de Cisneros, J., Stear, M. J., Mair, C. , Singleton, D., Stefan, T., Stear, A., Marion, G. and Matthews, L. (2014) An explicit immunogenetic model of gastrointestinal nematode infection in sheep. Journal of the Royal Society: Interface, 11(99), p. 20140416. (doi: 10.1098/rsif.2014.0416) (PMID:25121649) (PMCID:PMC4233724)

Nickbakhsh, S. , Matthews, L. , Reid, S. and Kao, R.R. (2014) A metapopulation model for highly pathogenic avian influenza: implications for compartmentalization as a control measure. Epidemiology and Infection, 142(09), pp. 1813-1825. (doi: 10.1017/S0950268813002963)

Prada Jiménez de Cisneros, J., Matthews, L. , Mair, C. , Stefan, T. and Stear, M. J. (2014) The transfer of IgA from mucus to plasma and the implications for diagnosis and control of nematode infections. Parasitology, 141(7), pp. 875-879. (doi: 10.1017/S0031182013002321)

Herbert, L. J. et al. (2014) E. coli O157 on Scottish cattle farms: evidence of local spread and persistence using repeat cross-sectional data. BMC Veterinary Research, 10(1), p. 95. (doi: 10.1186/1746-6148-10-95)

Matthews, L. et al. (2013) Predicting the public health benefit of vaccinating cattle against Escherichia coli O157. Proceedings of the National Academy of Sciences of the United States of America, 110(40), pp. 16265-16270. (doi: 10.1073/pnas.1304978110)

Call, D.R., Matthews, L. , Subbiah, M. and Liu, J. (2013) Do antibiotic residues in soils play a role in amplification and transmission of antibiotic resistant bacteria in cattle populations? Frontiers in Microbiology, 4(193), pp. 1-8. (doi: 10.3389/fmicb.2013.00193)

Nickbakhsh, S. , Matthews, L. , Dent, J.E., Innocent, G.T., Arnold, M.E., Reid, S.W.J. and Kao, R.R. (2013) Implications of within-farm transmission for network dynamics: consequences for the spread of avian influenza. Epidemics, 5(2), pp. 67-76. (doi: 10.1016/j.epidem.2013.03.001)

Strachan, N.J.C. et al. (2013) Identifying the seasonal origins of human campylobacteriosis. Epidemiology and Infection, 141(06), pp. 1267-1275. (doi: 10.1017/S0950268812002063)

Denwood, M.J., Love, S., Innocent, G.T., Matthews, L. , McKendrick, I.J., Hillary, N., Smith, A. and Reid, S.W.J. (2012) Quantifying the sources of variability in equine faecal egg counts: Implications for improving the utility of the method. Veterinary Parasitology, 188(1-2), pp. 120-126. (doi: 10.1016/j.vetpar.2012.03.005) (PMID:22469484)

Mather, A.E. et al. (2012) The diversity of antimicrobial resistance is different in Salmonella Typhimurium DT104 from co-located animals and humans. Proceedings of the Royal Society of London Series B: Biological Sciences, 279(1740), pp. 2924-2925. (doi: 10.1098/rspb.2012.0614)

Codner, G.F., Stear, M.J., Reeve, R. , Matthews, L. and Ellis, S.A. (2012) Selective forces shaping diversity in the class I region of the major histocompatibility complex in dairy cattle. Animal Genetics, 43(3), pp. 239-249. (doi: 10.1111/j.1365-2052.2011.02239.x) (PMID:22486494)

Mather, A.E. et al. (2012) An ecological approach to assessing the epidemiology of antimicrobial resistance in animal and human populations. Proceedings of the Royal Society of London Series B: Biological Sciences, 279(1733), pp. 1630-1639. (doi: 10.1098/rspb.2011.1975)

Chase-Topping, M.E. et al. (2012) Pathogenic Potential to Humans of Bovine Escherichia coli O26, Scotland. Emerging Infectious Diseases, 18(3), pp. 439-448. (doi: 10.3201/eid1803.111236)

Stear, M.J., Nikbakht, G., Matthews, L. and Jonsson, N.N. (2012) Breeding for disease resistance in livestock and fish. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, 7(007), pp. 1-10. (doi: 10.1079/PAVSNNR20127007)

Bessell, P.R., Rotariu, O., Innocent, G.T., Smith-Palmer, A., Strachan, N.J.C., Forbes, K.J., Cowden, J.M., Reid, S.W.J. and Matthews, L. (2012) Using sequence data to identify alternative routes and risk of infection: a case-study of campylobacter in Scotland. BMC Infectious Diseases, 12(80), (doi: 10.1186/1471-2334-12-80)

Denwood, M.J., Mather, A.E., Haydon, D.T. , Matthews, L. , Mellor, D.J. and Reid, S.W.J. (2011) From phenotype to genotype: a Bayesian solution. Proceedings of the Royal Society of London Series B: Biological Sciences, 278(1710), pp. 1434-1440. (doi: 10.1098/rspb.2010.1719)

Singleton, D.R., Stear, M.J. and Matthews, L. (2011) A mechanistic model of developing immunity to Teladorsagia circumcincta infection in lambs. Parasitology, 138(3), pp. 322-332. (doi: 10.1017/S0031182010001289) (PMID:20946694)

Mather, A.E., Denwood, M.J., Haydon, D.T. , Matthews, L. , Mellor, D.J. , Coia, J.E., Brown, D.J. and Reid, S.W.J. (2011) The prevalences of Salmonella Genomic Island 1 variants in human and animal Salmonella Typhimurium DT104 are distinguishable using a Bayesian approach. PLoS ONE, 6(11), e27220. (doi: 10.1371/journal.pone.0027220) (PMID:22125606) (PMCID:PMC3220677)

Nickbakhsh, S., Matthews, L. , Bessell, P.R., Reid, S.W.J. and Kao, R.R. (2011) Generating social network data using partially described networks: an example informing avian influenza control in the British poultry industry. BMC Veterinary Research, 7(66), (doi: 10.1186/1746-6148-7-66)

Stear, M.J., Singleton, D. and Matthews, L. (2011) An evolutionary perspective on gastrointestinal nematodes of sheep. Journal of Helminthology, 85(02), pp. 113-120. (doi: 10.1017/S0022149X11000058)

O'Reilly, K.M., Low, J.C., Denwood, M.J., Gally, D.L., Evans, J., Gunn, G.J., Mellor, D.J. , Reid, S.W.J. and Matthews, L. (2010) Associations between the presence of virulence determinants and the epidemiology and ecology of zoonotic escherichia coli. Applied and Environmental Microbiology, 76(24), pp. 8110-8116. (doi: 10.1128/AEM.01343-10)

Bessell, P.R., Matthews, L. , Smith-Palmer, A., Rotariu, O., Strachan, N.J., Forbes, K.J., Cowden, J.M., Reid, S.W.J. and Innocent, G.T. (2010) Geographic determinants of reported human Campylobacter infections in Scotland. BMC Public Health, 10, p. 423. (doi: 10.1186/1471-2458-10-423)

Denwood, M.J., Reid, S.W.J., Love, S., Nielsen, M.K., Matthews, L. , McKendrick, I.J. and Innocent, G.T. (2010) Comparison of three alternative methods for analysis of equine Faecal Egg Count Reduction Test data. Preventive Veterinary Medicine, 93(4), pp. 316-323. (doi: 10.1016/j.prevetmed.2009.11.009)

Reeve, R. et al. (2010) Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus. PLoS Computational Biology, 6(12), e1001027. (doi: 10.1371/journal.pcbi.1001027) (PMID:21151576) (PMCID:PMC3000348)

Rotariu, O. et al. (2010) Putative household outbreaks of campylobacteriosis typically comprise single MLST genotypes. Epidemiology and Infection, 138(12), pp. 1744-1747. (doi: 10.1017/S0950268810001457)

Townsend, S.E., Haydon, D.T. and Matthews, L. (2010) On the generality of stability–complexity relationships in Lotka–Volterra ecosystems. Journal of Theoretical Biology, 267(2), pp. 243-251. (doi: 10.1016/j.jtbi.2010.08.018)

Matthews, L. , Reeve, R. , Woolhouse, M.E.J., Mellor, D. , Pearce, M.C., Allison, L.J., Gunn, G.J., Low, J.C. and Reid, S.W.J. (2009) Exploiting strain diversity to expose transmission heterogeneities and predict the impact of targeting supershedding. Epidemics, 1(4), pp. 221-229. (doi: 10.1016/j.epidem.2009.10.002)

Gharbi, K., Glover, K.A., Stone, L.C., MacDonald, E.S., Matthews, L. , Grimholt, U. and Stear, M.J. (2009) Genetic dissection of MHC-associated susceptibility to Lepeophtheirus salmonis in Atlantic salmon. BMC Genetics, 10, p. 20. (doi: 10.1186/1471-2156-10-20)

Howey, R., Quan, M., Savill, N.J., Matthews, L. , Alexandersen, S. and Woolhouse, M. (2009) Effect of the initial dose of foot-and-mouth disease virus on the early viral dynamics within pigs. Journal of the Royal Society: Interface, 6(39), pp. 835-847. (doi: 10.1098/rsif.2008.0434)

Pearce, M.C. et al. (2009) Temporal and spatial patterns of bovine Escherichia coli O157 prevalence and comparison of temporal changes in the patterns of phage types associated with bovine shedding and human E. coli O157 cases in Scotland between 1998-2000 and 2002-2004. BMC Microbiology, 9, (doi: 10.1186/1471-2180-9-276)

Townsend, S.E., Newey, S., Thirgood, S.J., Matthews, L. and Haydon, D.T. (2009) Can parasites drive population cycles in mountain hares? Proceedings of the Royal Society of London Series B: Biological Sciences, 276(1662), pp. 1611-1617. (doi: 10.1098/rspb.2008.1669)

Denwood, M.J., Stear, M.J., Matthews, L. , Reid, S.W.J., Toft, N. and Innocent, G.T. (2008) The distribution of the pathogenic nematode Nematodirus battus in lambs is zero-inflated. Parasitology, 135(10), pp. 1225-1235. (doi: 10.1017/S0031182008004708)

Chase-Topping, M., Gally, D., Low, C., Matthews, L. and Woolhouse, M. (2008) Super-shedding and the link between human infection and livestock carriage of Escherichia coli O157. Nature Reviews Microbiology, 6(12), pp. 904-912. (doi: 10.1126/science.1170587)

Matthews, L. and Haydon, D. (2007) Introduction. Cross-scale influences on epidemiological dynamics: from genes to ecosystems. Journal of the Royal Society: Interface, 4(16), pp. 763-765. (doi: 10.1098/rsif.2007.1173) (PMCID:PMC2394559)

Stear, M., Innocent, G.T. and Matthews, L. (2007) Genetic disorders and the quest for candidate genes: Hypotheses worth testing. Veterinary Journal, 174(2), pp. 217-218. (doi: 10.1016/j.tvjl.2006.07.015)

Chase-Topping, M.E. et al. (2007) Risk factors for the presence of high-level shedders of Escherichia coli O157 on Scottish farms. Journal of Clinical Microbiology, 45, pp. 1594-1603. (doi: 10.1128/JCM.01690-06)

Jansen, P., Matthews, L. and Toft, N. (2007) Geographic risk factors for inter-river dispersal of Gyrodactylus salaris in fjord systems in Norway. Diseases of Aquatic Organisms, 74, pp. 139-149.

Liu, W.-C., Shaw, D.J., Matthews, L., Hoyle, D.V., Pearce, M.C., Yates, C.M., Low, J.C., Amyes, S.G.B., Gunn, G.J. and Woolhouse, M.E.J. (2007) Modelling the epidemiology and transmission of Verocytotoxin-producing Escherichia coli serogroups O26 and O103 in two different calf cohorts. Epidemiology and Infection, 135(8), pp. 1316-1323. (doi: 10.1017/S0950268806007722)

Liu, W., Matthews, L., Chase-Topping, M., Savill, N., Shaw, D. and Woolhouse, M. (2007) Metapopulation dynamics of Escherichia coli O157 in cattle: an exploratory model. Journal of the Royal Society: Interface, 4, pp. 917-924. (doi: 10.1098/rsif.2007.0219)

Stear, M., Fitton, L., Innocent, G., Murphy, L., Rennie, K. and Matthews, L. (2007) The dynamic influence of genetic variation on the susceptibility of sheep to gastrointestinal nematode infection. Journal of the Royal Society: Interface, 4(16), pp. 767-776. (doi: 10.1098/rsif.2007.1104)

Haydon, D. et al. (2006) Low-coverage vaccination strategies for the conservation of endangered species. Nature, 443, pp. 692-695. (doi: 10.1038/nature05177)

Matthews, L. (2006) Super-shedding cattle and the transmission dynamics of Escherichia coli O157. Epidemiology and Infection, 134(1), pp. 131-142.

Matthews, L. et al. (2006) Heterogeneous shedding of Escherichia coli O157 in cattle and its implications for control. Proceedings of the National Academy of Sciences of the United States of America, 103(3), pp. 547-552. (doi: 10.1073/pnas.0503776103)

St Rose, S.G., Hunter, N., Matthews, L., Foster, J.D., Chase-Topping, M.E., Kruuk, L.E.B., Shaw, D.J., Rhind, S.M., Will, R.G. and Woolhouse, M.E.J. (2006) Comparative evidence for a link between Peyer's patch development and susceptibility to transmissible spongiform encephalopathies. BMC Infectious Diseases, 6, (doi: 10.1186/1471-2334-6-5)

Touzeau, S., Chase-Topping, M.E., Matthews, L., Lajous, D., Eychenne, F., Hunter, N., Foster, J.D., Simm, G., Elsen, J.-M. and Woolhouse, M.E.J. (2006) Modelling the spread of scrapie in a sheep flock: evidence for increased transmission during lambing seasons. Archives of Virology, 151(4), pp. 735-751. (doi: 10.1007/s00705-005-0666-y)

Liu, W.C., Jenkins, C., Shaw, D.J., Matthews, L., Pearce, M.C., Low, J.C., Gunn, G.J., Smith, H.R., Frankel, G. and Woolhouse, M.E.J. (2005) Modelling the epidemiology of Verocytotoxin-producing Escherichia coli serogroups in young calves. Epidemiology and Infection, 133(3), pp. 449-458. (doi: 10.1017/S0950268804003644)

Matthews, L. (2005) Genotype-level variation in lifetime breeding success, litter size and survival of sheep in scrapie-affected flocks. Journal of General Virology, 86(Pt 4), pp. 1229-1238.

Matthews, L. and Woolhouse, M.E.J. (2005) New approaches to quantifying the spread of infection. Nature Reviews Microbiology, 3(7), pp. 529-536. (doi: 10.1038/nrmicro1178)

Taylor, L., Matthews, L., Shaw, D. and Haydon, D. (2005) Competitive suppression in rnixed-clone parasite cultures. Biology Letters, 1, pp. 108-111. (doi: 10.1098/rsbl.2004.0256)

Woolhouse, M., Shaw, D., Matthews, L., Liu, W., Mellor, D. and Thomas, M. (2005) Epidemiological implications of the contact network structure for cattle farms and the 20-80 rule. Biology Letters, 1, pp. 350-352. (doi: 10.1098/rsbl.2005.0331)

Haydon, D. T. , Matthews, L. , Timms, R. and Colegrave, N. (2003) Top-down or bottom-up regulation of intra-host blood-stage malaria: do malaria parasites most resemble the dynamics of prey or predator? Proceedings of the Royal Society of London Series B: Biological Sciences, 270(1512), pp. 289-298. (doi: 10.1098/rspb.2002.2203)

Haydon, D.T., Chase-Topping, M., Shaw, D.J., Matthews, L. , Friar, J.K., Wilesmith, J. and Woolhouse, M.E.J. (2003) The construction and analysis of epidemic trees with reference to the 2001 UK foot-and-mouth outbreak. Proceedings of the Royal Society of London Series B: Biological Sciences, 270, pp. 121-127. (doi: 10.1098/rspb.2002.2191) (PMCID:PMC1691228)

Matthews, L., Haydon, D.T., Shaw, D., Chase-Topping, M.E., Keeling, M.J. and Woolhouse, M.E.J. (2003) Neighbourhood control policies and the spread of infectious diseases. Proceedings of the Royal Society of London Series B: Biological Sciences, 270(1525), pp. 1659-1666. (doi: 10.1098/rspb.2003.2429)

Matthews, L. (2002) Comparative epidemiology of scrapie outbreaks in individual sheep flocks. Epidemiology and Infection, 128(3), pp. 513-521.

Woolhouse, M.E.J., Coen, P., Matthews, L. , Foster, J.D., Elsen, J.-M., Lewis, R.M., Haydon, D.T. and Hunter, N. (2001) A centuries-long epidemic of scrapie in British sheep? Trends in Microbiology, 9(2), pp. 67-70. (doi: 10.1016/S0966-842X(00)01912-0)

Keeling, M.J., Woolhouse, M.E.J., Shaw, D.J., Matthews, L. , Chase-Topping, M., Haydon, D.T., Cornell, S.J., Kappey, J., Wilesmith, J. and Grenfell, B.T. (2001) Dynamics of the 2001 UK foot and mouth epidemic: stochastic dispersal in a heterogeneous landscape. Science, 294(5543), pp. 813-817. (doi: 10.1126/science.1065973) (PMID:11679661)

Matthews, L., Coen, P.G., Foster, J.D., Hunter, N. and Woolhouse, M.E.J. (2001) Population dynamics of a scrapie outbreak. Archives of Virology, 146(6), pp. 1173-1186. (doi: 10.1007/s007050170113)

Woolhouse, M. et al. (2001) Epidemiology - Foot-and-mouth disease under control in the UK. Nature, 411, pp. 258-259. (doi: 10.1038/35077149) (PMID:11357118)

Matthews, L. , Woolhouse, M. E. J. and Hunter, N. (1999) The basic reproduction number for scrapie. Proceedings of the Royal Society of London Series B: Biological Sciences, 266(1423), pp. 1085-1090. (doi: 10.1098/rspb.1999.0747) (PMCID:PMC1689932)

Woolhouse, M. E. J., Matthews, L. , Coen, P., Stringer, S. M., Foster, J. D. and Hunter, N. (1999) Population dynamics of scrapie in a sheep flock. Philosophical Transactions of the Royal Society B: Biological Sciences, 354(1384), pp. 751-756. (doi: 10.1098/rstb.1999.0427) (PMID:10365400) (PMCID:PMC1692552)

Woolhouse, M.E.J., Stringer, S.M., Matthews, L. , Hunter, N. and Anderson, R.M. (1998) Epidemiology and control of scrapie within a sheep flock. Proceedings of the Royal Society of London Series B: Biological Sciences, 265(1402), pp. 1205-1210. (doi: 10.1098/rspb.1998.0421)

Matthews, L. and Brindley, J. (1997) Patchiness in plankton populations. Dynamics and Stability of Systems, 12(1), pp. 39-59. (doi: 10.1080/02681119708806235)

Book Sections

Matthews, L. , Woolhouse, M.E.J. and Hunter, N. (2000) The basic reproduction number for scrapie in a flock of Cheviot sheep. In: Thrusfield, M.V. and Goodall, E.A. (eds.) Proceedings of the Society for Veterinary Epidemiology and Preventive Medicine. Society for Veterinary Epidemiology and Preventive Medicine, pp. 183-197. ISBN 9780948073441

Conference or Workshop Item

Stewart, K., Matthews, L. , Scott, E. M. , Husmeier, D. and Mccowan, C. (2017) Preliminary Investigation of the Influences on Antimicrobial Resistance. RSS 2017 Annual Conference, Glasgow, Scotland, 04-07 Sep 2017.

Conference Proceedings

Sondag, M., Turkay, C., Mohr, S. , Matthews, L. , Xu, K. and Archambault, D. (2021) What is R? A graph drawer’s perspective? In: 29th International Symposium on Graph Drawing and Network Visualization, Tübingen, Germany, 14-17 Sep 2021, pp. 431-433. ISBN 9783030929305 (doi: 10.1007/978-3-030-92931-2_29)