List of Publications 2011

Allebrandt KV, Amin N, Müller-Myhsok B, Esko T, Teder-Laving M, Azevedo RV, Hayward C, van Mill J, Vogelzangs N, Green EW, Melville SA, Lichtner P, Wichmann HE, Oostra BA, Janssens AC, Campbell H, Wilson JF, Hicks AA, Pramstaller PP, Dogas Z, Rudan I, Merrow M, Penninx B, Kyriacou CP, Metspalu A, van Duijn CM, Meitinger T, Roenneberg T. - A K(ATP) channel gene effect on sleep duration: from genome-wide association studies to function in Drosophila, Mol Psychiatry. doi: 10.1038/mp.2011.142. file
Allen, J.E. and Maizels, R.M. - Diversity and Dialogue in Immunity to Helminths. Nature Reviews Immunology. 11:375-88. file
Allen J.E. and Wynn T.A. - Evolution of Th2 Immunity: A Rapid Repair Response to Tissue Destructive Pathogens. PLoS Pathog 7(5): e1002003. file
Anderson, N.E., Mubanga, J., Fèvre, E.M., Picozzi, K., Eisler, M.C., Thomas, R., & Welburn, S.C. - Characterisation of the wildlife reservoir community for human and animal trypanosomiasis in the Luangwa Valley, Zambia. Public Library of Science Neglected Tropical Diseases, 5(6):e1211 file
Archer J., Rambaut A., Taillon BE, Harrigan PR, Lewis M & Robertson DL - The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time - An Ultra-Deep Approach. PLoS Comput Biol 6, e1001022. file
Aricò E, Monque DM, D'Agostino G, Moschella F, Venditti M, Kalinke U, Allen DJ, Nash AA, Belardelli F and Ferrantini M. - MHV-68 producing mIFNα1 is severely attenuated in vivo and effectively protects mice against challenge with wt MHV-68., Vaccine. 2011 May 23;29(23):3935-44. Epub 2011 Apr 8. file
Atkins KE, Read AF, Savill NJ, Renz KG, Walkden-Brown SW, Woolhouse ME. - Modelling Marek’s Disease Virus (MDV) infection: parameter estimates for mortality rate and infectiousness, BMC Vet Res. 11;7:70. file
Ayres D, Darling A, Zwickl D, Beerli P, Holder M, Lewis P, Huelsenbeck JP, Ronquist F, Swofford D, Cummings MP, Rambaut A and Suchard MA  - BEAGLE: a common application programming inferface and high-performance computing library for statistical phylogenetics. Syst Biol. 2012 Jan 1;61(1):170-3. file
Babayan, S.A., Allen, J.E., Bradley, J.E., Geuking, M., Graham, A.L., Grencis, R.K., Kaufman, J., McCoy, K.D., Paterson, S., Smith, K.G.C., Turnbaugh, P.J., Viney, M.E., Maizels, R.M. and Pedersen, A.B. - Wild Immunology: converging on the ‘real world’. Annals of the New York Academy of Sciences. 1236(1):17-29. file
Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, Halpin RA, Stockwell TB, Lin X, Wentworth DE, Ghedin E, Guan Y, Peiris JS, Riley S, Rambaut A, Holmes EC, Smith GJ. - Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans., Proc Natl Acad Sci U S A. 2011 Nov 29;108(48):19359-64. file
Bai, J., McAteer, S. P., Paxton, E. Mahajan, A., Gally, D. L. and Tree, J. J. - Screening of an E. coli O157:H7 bacterial artificial chromosome library by comparative genomic hybridization to identify genomic regions contributing to growth in bovine gastrointestinal mucus and epithelial cell colonization. Frontiers in Cellular and Infection Microbiology, 2:168. file
Baker RH, Buschbaum S, Matthews JB, McKendrick IJ, Schnieder T, Strube C, Nisbet AJ. - GTP-cyclohydrolase and development in Teladorsagia circumcincta and Dictyocaulus viviparus (Nematoda: Strongylida).  Exp. Parasitol. 128(4):309-17. file
Baxter, S. W., Davey JW, Johnston JS, Shelton AM, Heckel DG, Jiggins CD and Blaxter ML. - Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism. PLoS One 6 (4) file
Benjamin, L., Lewthwaite, P., Vasanthapuram, R., Zhao, G., Sharp, C. P., Simmonds, P., Wang, D. and Solomon, T. - Human parvovirus 4 (PARV4) causes encephalitis in children in Southern India. Emerg. Infect Dis. Vol. 17, No 8 1484-1487 file
Bennett S, Harvala H, Witteveldt J, McWilliam Leitch EC, McLeish N, Templeton K, Gunson R, Carman WF and Simmonds P, - Rapid Simultaneous Detection of Enterovirus and Parechovirus RNAs in Clinical Samples by One-Step Real-Time Reverse Transcription-PCR Assay. Journal of Clincal Microbiology ;49(7):2620-4. file
Bielejec F, Rambaut A, Suchard MA and Lemey P - SPREAD: Spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics 27, 2910-2912. file
Blaxter, M. - Nematodes: the worm and its relatives. PLoS Biol 9 (4) file
Blaxter, M. and Sunnucks, P. - Velvet worms. Curr Biol 21, R238-240 file
Borger JG, Cardenas-Maestre JM, Zamoyska R, Sanchez-Martin RM. - Novel Strategy for Microsphere-Mediated DNA Transfection, Bioconjug Chem. 19;22(10):1904-8. file
Boros A, Pankovics P, Simmonds P, Reuter G. -  Novel Positive-Sense, Single-Stranded RNA (+ssRNA) Virus with Di-Cistronic Genome from Intestinal Content of Freshwater Carp (Cyprinus carpio) PLoS One. 2011;6(12). file
Bourke, C.D., Maizels, R.M. and Mutapi, F. - Acquired immune heterogeneity and its sources in human helminth infection. Parasitology. 2011 Feb;138(2):139-59. file
Brockhurst, M.A. Colegrave, N and Rosen DE. - Next-generation sequencing as a tool to study microbial evolution. Molecular Ecology, 20(5):972-80 file
Brown SP and Levin D. - Social dilemmas among supergenes: intragenomic sexual conflict and a selfing solution in Oenothera. Evolution. 65(12):3360-7.  file
Brown, R.J.P., Peters, P.J., Caron, C., Gonzalez-Perez, M.P., Stones, L., Ankghuambom, C., Pondei, K., McClure, C.P., Alemnji, G., Taylor, S., Sharp, P.M., Clapham, P.R., Ball, J.K. 2011. Intercompartmental Recombination of HIV-1 Contributes to env Intrahost Diversity and Modulates Viral Tropism and Sensitivity to Entry Inhibitors. Journal of Parasitology 85(12) pp6024-6037 file

Buchrieser C, Rusniok C, Garrido P, Hain T, Scortti M, Lampidis R, Kärst U, Chakraborty T, Cossart P, Kreft J, Vazquez-Boland JA, Goebel W, Glaser P. - Complete Genome Sequence of the Animal Pathogen Listeria ivanovii,
Which Provides Insights into Host Specificities and Evolution of the Genus Listeria
, J Bacteriol. 2011 Dec;193(23):6787-8. file
Calderón-Gómez E, Lampropoulou V, Shen P, Neves P, Roch T, Stervbo U, Rutz S, Kühl AA, Heppner FL, Loddenkemper C, Anderton SM, Kanellopoulos JM, Charneau P and Fillatreau S. - Reprogrammed quiescent B cells provide an effective cellular therapy against chronic experimental autoimmune encephalomyelitis, Eur J Immunol. 2011 Jun;41(6):1696-708. Epub 2011 May 25. file
Charleston B, Bankowski BM, Gubbins S, Chase-Topping ME, Schley D, Howey R, Barnett PV, Gibson D, Juleff ND and Woolhouse ME. - Relationship between clinical signs and transmission of an infectious disease and the implications for control. Science  6;332(6030):726-9. file
Childs DZ, Coulson TN, Pemberton JM, Clutton-Brock TH, Rees M. - Predicting trait values and measuring selection in complex life histories: reproductive allocation decisions in Soay sheep, Ecol Lett. 2011 Oct;14(10):985-92 file
Claessens A, Ghumra A, Gupta AP, Mok S, Bozdech Z, Rowe JA. - Design of a variant surface antigen-supplemented microarray chip for whole transcriptome analysis of multiple Plasmodium falciparum cytoadherent strains, and identification of strain-transcendent rif and stevor genes, Malar J. 10:180.file
Colgan TJ, Carolan JC, Bridgett SJ, Sumner S, Blaxter ML, Brown MJ.- Polyphenism in social insects: Insights from a transcriptome-wide analysis of gene expression in the life stages of the key pollinator, Bombus terrestris. BMC Genomics. 2011 Dec 20;12(1):623. file
Coltherd, J.C., Babayan, S.A., Bünger, L., Kyriazakis, I., Allen, J.E. and Houdijk, J.G.M. - Interactive effects of protein nutrition, genetic growth potential and Heligmosomoides bakeri infection pressure on resilience and resistance in mice. Parasitology. 138: 1305-15. file
Cowan GJ, Creasey AM, Dhanasarnsombut K, Thomas AW, Remarque EJ and Cavanagh DR. - A malaria vaccine based on the polymorphic block 2 region of MSP-1 that elicits a broad serotype-spanning immune response. PLoS One. 2011;6(10):e26616. file
Culleton R, Coban C, Zeyrek FY, Cravo P, Kaneko A, Randrianarivelojosia M, Andrianaranjaka V, Kano S, Farnert A, Paula Arez A,  Sharp PM, Carter R and Tanabe K - The Origins of African Plasmodium vivax; Insights from Mitochondrial Genome Sequencing. PLoS ONE 6(12) file
Culleton R.L., Inoue M., Reece S.E., Cheeseman S. & Carter R. - Strain-specific immunity to the pre-erythrocytic stages of Plasmodium chabaudi. Parasite Immunology, 33(1): 73-8 file
Davey, JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM and Blaxter ML. - Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12 (7), 499-510 file
de las Heras A, Cain RJ, Bielecka MK, Vázquez-Boland JA.- Regulation of Listeria virulence: PrfA master and commander, Curr Opin Microbiol. 201 Regulation of Listeria virulence 14(2):118-27 Review file

Decaestecker, E., Labbé, P., Ellegaard, K., Allen, J.E. and Little T. - Candidate innate immune system gene expression in the ecological model Daphnia. Developmental and Comparative Immunology. 35, 10, 1068-1077. file

Díaz, A., Casaravilla, C., Allen, J.E., Sim, R.B. and Ferreira, A.M. - Understanding the laminated layer of larval Echinococcus. II: Immunology. Trends in Parasitology. 27:264-73. file

Donegan KL, Walker AS, Dunn D, Judd A, Pillay D, Menson E, Lyall H, Tudor-Williams G, Gibb DM; Collaborative HIV Paediatric Study; UK HIV Drug Resistance Database. - The prevalence of darunavir-associated mutations in HIV-1-infected children in the UK. Antivir Ther. 2012;17(4):599-603. file

Douradinha B, Augustijn KD, Moore SG, Ramesar J, Mota MM, Waters AP, Janse CJ and Thompson J - Plasmodium berghei Cysteine Repeat Modular Proteins 3 and 4 are essential for parasite transmission from the mosquito to the host. Malaria J. 10:71 file
Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O'Connell TC, Coxon P, Monaghan N, Valdiosera CE, Lorenzen ED, WIllerslev E, Baryshnikov GF, Rambaut A, Thomas MG, Bradley DG & Shapiro B - Multiple hybridizations between ancient brown and polar bears and an Irish origin for the modern polar bear matriline. Current Biology 15, 1251-1258. file
Elsworth, B., Wasmuth, J. and Blaxter, M. - NEMBASE4: The nematode transcriptome resource. Int J Parasitol, 41(8):881-94 file
Gaunt, E. R., Jansen, R. R., Poovorawan, Y., Templeton, K. E., Toms, G. L. and Simmonds,  P. - Molecular epidemiology and evolution of human respiratory syncytial virus and human metapneumovirus. PLoS. ONE. 6:e17427  file
Ghumra A,  Khunrae P,  Ataide R,  Raza A,  Rogerson SJ,  Higgins MK and Rowe JA. - Immunisation with Recombinant PfEMP1 Domains Elicits Functional Rosette-Inhibiting and Phagocytosis-Inducing Antibodies to Plasmodium falciparum. PLoS ONE 6(1): e16414. file
Griffiths E.C., Pedersen A.B., Fenton A. and Petchey O.L. - The nature and consequences of coinfection in humans. Journal of Infection 2011 Sep;63(3):200-6. Epub 2011 Jun 6 file
Handel I.G., Bronsvoort C., Forbes J.F., Woolhouse M.E.J. - Risk-Targeted Selection of Agricultural Holdings for Post-Epidemic Surveillance:
Estimation of Efficiency Gains.
PLoS ONE 6(5): e20064. file
Harrison A, Lemey P, Hurles M, Moyes C, Horn S, Pryor J, Malani J, Sapuri M, Masta A, Teriboriki B, Toatu T, Penny D, Rambaut A and Shapiro B - Genomic analysis of Hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Viruses 3, 83-101. file
Harvala, H., Sharp, C. P., Ngole, E. M., Delaporte, E., Peeters, M. and Simmonds,  P.Detection and genetic characterisation of enteroviruses circulating among wild populations of chimpanzees in Cameroon; relationship with human and simian enteroviruses. J Virol. ePub, 6th February, 2011  file
Hewitson JP, Harcus Y, Murray J, van Agtmaal M, Filbey KJ, Grainger JR, Bridgett S, Blaxter ML, Ashton PD, Ashford DA, Curwen RS, Wilson RA, Dowle AA, Maizels RM. - Proteomic analysis of secretory products from the model gastrointestinal nematode Heligmosomoides polygyrus reveals dominance of venom allergen-like (VAL) proteins. J Proteomics. 2011 Aug 24;74(9):1573-94. file
Hewitson JP, Filbey KJ, Grainger JR, Dowle AA, Pearson M, Murray J, Harcus Y, Maizels RM. - Heligmosomoides polygyrus elicits a dominant nonprotective antibody response directed against restricted glycan and peptide epitopes. J Immunol. 2011 Nov 1;187(9):4764-77. file
Higon, M., Cowan, G., Nausch, N., Cavanagh, D., Oleaga, A., Toledo, R., Stothard, J.R., Antúnez, O., Marcilla, A., Bruchmore, R. and Mutapi, F. - Screening trematodes for novel intervention targets: a proteomic and immunological comparison of Schistosoma haematobium, Schistosoma bovis and Echinostoma caproni. Parasitology 2011 Jun 10:1-13 [E-pub ahead of print] file
Huffman JE, Knezevic A, Vitart V, Kattla J, Adamczyk B, Novokmet M, Igl W, Pucic M, Zgaga L, Johannson Å, Redzic I, Gornik O, Zemunik T, Polasek O, Kolcic I, Pehlic M, Koeleman CA, Campbell S, Wild SH, Hastie ND, Campbell H, Gyllensten U, Wuhrer M, Wilson JF, Hayward C, Rudan I, Rudd PM, Wright AF, Lauc G. - Polymorphisms in B3GAT1, SLC9A9 and MGAT5 are associated with variation within the human plasma N-glycome of 3533 European adults, Hum Mol Genet. 15;20(24):5000-11. file
Imai, N., Rujeni, N., Nausch, N., Bourke, C.D., Appleby, L.J., Cowan, G., Gwisai, R., Midzi, N., Cavanagh, D., Mduluza, T., Taylor, D., Mutapi, F. - Exposure, infection, systemic cytokine levels and antibody responses in young children concurrently exposed to schistosomiasis and malaria. Parasitology 2011 Aug 4:1-15. [Epub ahead of print] file
Imhof I., and Simmonds P. - Genotype differences in susceptibility and resistance development of hepatitis C virus to protease inhibitors telaprevir (VX-950) and danoprevir (ITMN-191). Hepatology. 53(4):1090-9. file
Jenkins, S.J., Ruckerl, D., Cook, P.C., Jones, L.H., Finkelman, F.D., van Rooijen, N., MacDonald, A.S., and Allen, J. E. - Local Macrophage Proliferation, Rather than Recruitment from the Blood, Is a Signature of TH2 Inflammation. Science 332: 1284-1288 file
Jones, M., Ghoorah, A. and Blaxter, M. - jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units. PLoS One 6, e19259 file
Jones, M. O., Koutsovoulos, G. D. and Blaxter, M. L. - iPhy: an integrated phylogenetic workbench for supermatrix analyses. BMC Bioinformatics 12, 30 file
Kaczanowski S., Sajid M. and Reece S.E. - Evolution of apotosis like programmed cell death in unicellular protozoan parasites. Parasites & Vectors, 25;4:44 file
Kapoor A, Simmonds P, Dubovi EJ, Qaisar N, Henriquez JA, Medina J, Shields S, Lipkin WI. -  Characterization of a canine homolog of human Aichivirus. J Virol. 85(21):11520-5. file
Kapoor A, Simmonds P, Gerold G, Qaisar N, Jain K, Henriquez JA, Firth C, Hirschberg DL, Rice CM, Shields S, Lipkin WI. - Characterization of a canine homolog of hepatitis C virus. Proceedings of the National Academy of Sciences of the United States of America 108(28):11608-13. file
Kumar S, Schiffer PH, Blaxter M.- 959 Nematode Genomes: a semantic wiki for coordinating sequencing projects. Nucleic Acids Res. 2012 Jan;40(Database issue):D1295-300. file
Lahtinen, A., Kivela, P., Hedman, L., Kumar, A., Kantele, A., Lappalainen, M., Liitsola, K., Ristola, M., Delwart, E., Sharp, C., Simmonds, P., Soderlund-Venermo, M. and Hedman, K. - Serodiagnosis of primary infections with human parvovirus 4, Finland. Emerg. Infect Dis. 17:79-82  file
Leigh Brown AJ, Lycett SJ, Weinert L, Hughes GJ, Fearnhill E, Dunn DT; UK HIV Drug Resistance Collaboration. - Transmission network parameters estimated from HIV sequences for a nationwide epidemic. J Infect Dis. 2011 Nov;204(9):1463-9. file

Lohse, K., Sharanowski, B., Blaxter, M., Nicholls, J. A. and Stone, G. N. - Developing EPIC markers for chalcidoid Hymenoptera from EST and genomic data. Mol Ecol Resour 11, 521-529 file

Longdon B, Hadfield JD, Webster CL, Obbard DJ, Jiggins FM - Host phylogeny determines viral persistence and replication in novel hosts PLoS Pathogens 7(9) file
Longdon B, Wilfert L, Osei-Poku J, Cagney H, Obbard DJ and Jiggins FM - Host-switching by a vertically transmitted rhabdovirus in Drosophila, Biology Letters (Advance Online Pub From 30th March 2011) file

Longdon B, Wilfert L, Obbard DJ and Jiggins FM - Vertically transmitted insect viruses: the recent sweep of a rhabdovirus through populations of Drosophila obscura, Genetics (Advance Online Pub) file

Lu JP, Kneževic A, Wang YX, Rudan I, Campbell H, Zou ZK, Lan J, Lai QX, Wu JJ, He Y, Song MS, Zhang L, Lauc G, Wang W. - Screening novel biomarkers for metabolic syndrome by profiling human plasma N-glycans in Chinese Han and Croatian populations, J Proteome Res.10(11):4959-69. file


MacGregor, P.,  Savill, N.J.,  Hall, D. and  Matthews, K.R.  - Transmission stages dominate trypanosome 1 within-­host dynamics during chronic infections, Cell, Host and Microbe, 9(4): 310-318 file
Maizels, R.M. and Allen, J.E. - Forestalling obesity by eosinophils and helminths. Science 332 : 186-187 file
Maizels, R.M., Hewitson, J.P. and Gause, W.C. (2011). Heligmosomoides polygyrus: one species still. Trends in Parasitology 27: 100-101 file
Mahajan A and Gally D. - Escherichia coli and the mucosal immune system Expert Rev Clin Immunol. 2011 Nov;7(6):743-5. file

Makita, K., Fèvre, E.M., Waiswa, C., Kaboyo, W., Eisler, M.C., and Welburn, S.C. - Spatial epidemiology of hospital-diagnosed brucellosis in Kampala, Uganda. International Journal of Health Geographics, 10: 52. file
Makita, K., Fèvre, E.M., Waiswa, C., Kaboyo, W., Eisler, M.C., and Welburn, S.C. - Evidence-based identification of the most important livestock-related zoonotic diseases in Kampala, Uganda. Journal of Veterinary Medical Science, 73, pp. 991-1000. file
Martin, J. G. A., Nussey, D. H., Wilson, A. J. & Réale, D. - Measuring individual differences in reaction norms in field and experimental studies: a power analysis of random regression models. Methods in Ecology and Evolution (2011), on-line early. file
Matthews JB. - Facing the threat of equine parasitic disease. Equine Vet. J. 43: 126-32. file
Matthews JB, McArthur C, Robinson A, Jackson F. - The in vitro diagnosis of anthelmintic resistance in cyathostomins, Vet Parasitol. 185(1):25-31 file
Matthews, K.R. - Controlling and co-ordinating development in vector-transmitted parasites, Science. Vol. 331 no. 6021 pp. 1149-1153 file
McArthur CL, Bartley DJ, Shaw DJ, Matthews JB.- Assessment of ivermectin efficacy against gastrointestinal nematodes in cattle on four Scottish farms,
Vet Rec.169(25):658 file
McFadden N, Bailey D, Carrara G, Benson A, Chaudhry Y, Shortland A, Heeney J, Yarovinsky F, Simmonds P, Macdonald A, Goodfellow I. -  Norovirus regulation of the innate immune response and apoptosis occurs via the product of the alternative open reading frame 4. PLoS Pathog. 7(12). file
McLeish NJ, Simmonds P, Robertson C, Handel I, McGilchrist M, Singh BK, Kerr S, Chase-Topping ME, Sinka K, Bronsvoort M, Porteous DJ, Carman W, McMenamin J, Leigh-Brown A and Woolhouse ME. - Sero-prevalence and incidence of A/H1N1 2009 influenza infection in Scotland in winter 2009-2010, PLoS One. 2011;6(6):e20358. Epub 2011 Jun 8. file
McWilliam Leitch EC, Cabrerizo M, Cardosa J, Harvala H, Ivanova OE, Koike S, Kroes AC, Lukashev A, Perera D, Roivainen M, Susi P, Trallero G, Evans DJ, Simmonds P. -  The association of recombination events in the founding and emergence of subgenogroup evolutionary lineages of human enterovirus J Virol. 2012 Mar, 86(5):2676-85 file
Mideo N., Nelson W.A., Reece S.E., Bell A.S, Read A.F. and Day T. - Bridging Scales in the Evolution of Infectious Disease Life Histories: Application. Evolution, 65(11): 3298-3310 file
Mideo N, Savill NJ, Chadwick W, Schneider P, Read AF, Day T, Reece SE. - Causes of variation in malaria infection dynamics: insights from theory and data. Am Nat. 178(6):E174-88. file
Midzi, N., Mtapuri-Zinyowera, S., Mapingure, M.P., Paul, N.H., Sangweme, D., Hlerema, G., Mutsaka, M.J., Tongogara, F., Makware, G., Chadukura, V., Brouwer, K.C., Mutapi, F., Kumar, N. and Mduluza, T. - Knowledge Attitudes and Practices of grade three primary schoolchildren in relation to schistosomiasis, soil transmitted helminthiasis and malaria in Zimbabwe. BMC Infect Dis 11(1): 169. file
Midzi, N., Mtapuri-Zinyowera, S., Sangweme, D., Paul, N.H., Makware, G., Mapingure, M.P., Brouwer, K.C., Mudzori, J., Hlerema, G., Chadukura, V., Mutapi, F., Kumar, N. and Mduluza, T. - Efficacy of integrated school based de-worming and prompt malaria treatment on helminths-Plasmodium falciparum co-infections: A 33 months follow up study. BMC Int Health Hum Rights 11(1): 9. file
Miranda-Casoluengo R, Miranda-Casoluengo AA, O'Connell EP, Fahey RJ, Boland CA, Vázquez-Boland JA, Meijer WG. - The vapA co-expressed virulence plasmid gene vcgB (orf10) of the intracellular actinomycete Rhodococcus equi, Microbiology. 157(Pt 8):2357-68. file
Mitchell KM, Mutapi F, Savill NJ, Woolhouse ME. - Explaining observed infection and antibody age-profiles in populations with urogenital schistosomiasis. PLoS Comput Biol. 7(10):e1002237. file
Mott GA, Wilson R, Fernando A, Robinson A, MacGregor P, Kennedy D, Schaap D, Matthews JB, Matthews KR. - Targeting cattle-borne zoonoses and cattle pathogens using a novel trypanosomatid-based delivery system, PLoS Pathog. 7(10) file

Moyes, K., Nussey, D. H., Clements, M. N., Guinness, F. E., Morris, A., Morris, S., Pemberton, J. M., Kruuk, L. E. B. & Clutton-Brock, T. H. - Advancing breeding phenology in response to environmental change in a wild red deer population. Global Change Biology (2011), on-line early. file

Mutapi, F. - Improving diagnosis of urogenital schistosome infection. Expert Rev Anti Infect Ther 9(10): 863-865. file
Mutapi, F., Bourke, C., Harcus, Y., Midzi, N., Mduluza, T., Turner, C.M., Burchmore, R. and Maizels, R.M. - Differential recognition patterns of Schistosoma haematobium adult worm antigens by the human antibodies IgA, IgE, IgG1 and IgG4.  Parasite Immunology  33: 181-192 file
Mutapi, F., Imai, N., Nausch, N., Bourke, C.D., Rujeni, N., Mitchell, K., Midzi, N., Woolhouse, M., Maizels, R. and Mduluza, T. - Schistosome infection intensity is inversely related to auto-reactive antibody levels. PLoS one. 6(5): e19149. file
Mutapi, F., Rujeni, N., Nausch, N., Bourke, C., Mitchell, K., Appleby, L.J., Midzi, N. and Mduluza, T. - Schistosoma haematobium treatment in 1-5 year old children: safety and effiecency of the antihelminthic drug praziquantel. PLoS NTD 5(5): e1143. file
Nair H, Brooks WA, Katz M, Roca A, Berkley JA, Madhi SA, Simmerman JM, Gordon A, Sato M, Howie S, Krishnan A, Ope M, Lindblade KA, Carosone-Link P, Lucero M, Ochieng W, Kamimoto L, Dueger E, Bhat N, Vong S, Theodoratou E, Chittaganpitch M, Chimah O, Balmaseda A, Buchy P, Harris E, Evans V, Katayose M, Gaur B, O'Callaghan-Gordo C, Goswami D, Arvelo W, Venter M, Briese T, Tokarz R, Widdowson MA, Mounts AW, Breiman RF, Feikin DR, Klugman KP, Olsen SJ, Gessner BD, Wright PF, Rudan I, Broor S, Simões EA, Campbell H. - Global burden of respiratory infections due to seasonal influenza in young children: a systematic review and meta-analysis, Lancet 378(9807):1917-30. file
Nadeau NJ, Whibley A, Jones RT, Davey JW, Dasmahapatra KK, Baxter SW, Quail MA, Joron M, Ffrench-Constant RH, Blaxter ML, Mallet J, Jiggins CD. - Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing. Philos Trans R Soc Lond B Biol Sci. 2012 Feb 5;367(1587):343-53. file
Nausch, N., Midzi, N., Mduluza, T., Maizels, R.M. and Mutapi, F. - Regulatory and activated T cells in human Schistosoma haematobium infections. PLOS One 6: e16860 file
Nelson MI, Lemey P, Yi Tan, Vincent A, Tsan-Yuk Lam, Detmer S, Viboud C, Suchard MA, Rambaut A, Holmes EC and Gramer M - Spatial Dynamics of Human-origin H1 Influenza A Virus in North American Swine.PLoS Pathog 7 (6) file
Nisbet AJ, Zarlenga DS, Knox DP, Meikle LA. Wildblood LA, Matthews JB. - A calcium-activated apyrase from Teladorsagia circumcincta: an excretory/secretory antigen capable of modulating host immune responses? Parasite Immunol. 33: 236-43. file
Nussey DH, Coulson T, Delorme D, Clutton-Brock TH, Pemberton JM, Festa-Bianchet M, Gaillard JM. - Patterns of body mass senescence and selective disappearance differ among three species of free-living ungulates, Ecology. 2011 Oct;92(10):1936-47 file
O’Donnell, A., Schneider, P., McWatters, H. and Reece, S. - Fitness costs of disrupting circadian rhythms in malaria parasites. Proceedings of the Royal Society London B (2011), published on-line January 5th file
Palin K, Campbell H, Wright AF, Wilson JF, Durbin R. - Identity-by-descent-based phasing and imputation in founder populations using graphical models. Genet Epidemiol 35(8):853-60. file
Pedersen A. B. and Babayan, S. A. - Wild Immunology. Molecular Ecology 20, 872–880 file
Pollitt, L.C., MacGregor, P., Matthews,K., Reece, S.E. - Malaria and trypanosome transmission: different parasites, same rules? Trends in Parasitology 2011 Feb 21. [Epub ahead of print] file
Pollitt L.C., Mideo N., Drew D.R., Schneider P., Colegrave N., and Reece S.E. - Competition and the evolution of reproductive restraint in malaria parasites. Am Nat 177:358-367 file
Pucic M, Knezevic A, Vidic J, Adamczyk B, Novokmet M, Polasek O, Gornik O, Supraha-Goreta S, Wormald MR, Redzic I, Campbell H, Wright A, Hastie ND, Wilson JF, Rudan I, Wuhrer M, Rudd PM, Josic D, Lauc G. - High throughput isolation and glycosylation analysis of IgG-variability and heritability of the IgG glycome in three isolated human populations. Mol Cell Proteomics. 10(10) file
Raghwani J, Rambaut A, Holmes EC, Vu Ty Hang, Tran Tinh Hien, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR & Simmons CP - Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission. PLoS Pathogenes 7(6) file
Rankin DJ, McGinty SE, Nogueira T, Touchon M, Taddei F, Rocha EPC and Brown SP - Bacterial cooperation controlled by mobile elements: kin selection and infectivity are part of the same process. Heredity 107, 279-281. file
Ramiro R.S., Alpedrinha J., Carter L., Gardner A. and Reece S.E. - Sex and Death: The Effects of Innate Immune Factors on the Sexual Reproduction of Malaria Parasites. PLoS Pathogens, 7:3, e1001309 file
Rayner, J., Liu, W., Peeters, M., Sharp, P.M., and Hahn, B.H.  - A plethora of Plasmodium species in wild apes: a source of human infection? Trends in Parasitology 27(5) pp222-229 file
Reece SE, Pollitt LC, Colegrave N and Gardner A. - The meaning of death: evolution and ecology of apoptosis in protozoan parasites. PLoS Pathog. 2011 Dec; 7(12) file

Reed DL, Currier RW, Walton SF, Conrad M, Sullivan SA, Carlton JM, Read TD, Severini A, Tyler S, Eberle R, Johnson WE, Silvestri G, Clarke IN, Lagergård T, Lukehart SA, Unemo M, Shafer WM, Beasley RP, Bergström T, Norberg P, Davison AJ, Sharp PM, Hahn BH and Blomberg J. - The evolution of infectious agents in relation to sex in animals and humans: brief discussions of some individual organisms Ann. N.Y. Acad. Sci. 1230 (2011) 74–107 file

Relf VE, Morgan ER, Hodgkinson JE, Matthews JB - A questionnaire study on parasite control practices on UK breeding Thoroughbred studs, Equine Vet J. 2011 Nov 2 file
Ricci V, Loman N, Pallen M, Ivens A, Fookes M, Langridge GC, Wain J, Piddock LJ. - The TCA cycle is not required for selection or survival of multidrug-resistant Salmonella.  Antimicrob Chemother 67(3):589-99 file
Rudicell RS, Piel AK, Stewart F, Moore DL, Learn GH, Li Y, Takehisa J, Pintea L, Shaw GM, Moore J, Sharp PM and Hahn BH. - High prevalence of simian immunodeficiency virus infection in a community of savanna chimpanzees. J Virol. 2011 Oct;85(19):9918-28. file
Salmond RJ, Zamoyska R. - The influence of mTOR on T helper cell differentiation and dendritic cell function, Eur J Immunol.41(8):2137-41. file
Saunders NJ, Trivedi UH, Thomson ML, Doig C, Laurenson IF and Blaxter ML. -  Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background. J Infect 62, 212-217 file
Shan T, Li L, Simmonds P, Wang C, Moeser A, Delwart E. -  The fecal virome of pigs on a high-density farm. J Virol. 85(22):11697-708. file
Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG & Rambaut A - A Bayesian phylogenetic method to estimate unknown sequence ages. Mol Biol Evol 28, 879-887. file
Sharp CP, Lail A, Donfield S, Gomperts ED, Simmonds P. - Virologic and clinical features of primary infection with human parvovirus 4 in subjects with hemophilia: frequent transmission by virally inactivated clotting factor concentrates. Transfusion. 2011 Nov 2.doi: 10.1111/j.1537-2995.2011.03420.x. file
Sharp PM and Hahn BH. - Origins of HIV and the AIDS Pandemic. Cold Spring Harb Perspect Med. 2011 Sep;1(1) file
Sharp PM, Liu W, Learn GH, Rayner JC, Peeters M and Hahn BH. - Source of the human malaria parasite Plasmodium falciparum. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):E744-5. file
Sharp, P.M. and Simmonds, P. - Evaluating the evidence for virus/host co-evolution  Current Opinion in Virology 2011, 1(5) 436–441 file
Simmonds P, Domingo E. - Virus evolution. Curr Opin Virol. 2011 Nov;1(5):410-2. Epub 2011 Nov 9. file
Sivakumaran S, Agakov F, Theodoratou E, Prendergast JG, Zgaga L, Manolio T, Rudan I, McKeigue P, Wilson JF, Campbell H. - Abundant pleiotropy in human complex diseases and traits. Am J Hum Genet. 89(5):607-18. file
Siu, R. W., Fragkoudis, R., Simmonds, P., Donald, C. L., Chase-Topping, M. E., Barry, G., Attarzadeh-Yazdi, G., Rodriguez-Andres, J., Nash, A. A., Merits, A., Fazakerley, J. K. and Kohl,  A.  - Antiviral RNA Interference Responses Induced by Semliki Forest Virus Infection of Mosquito Cells: Characterization, Origin, and Frequency-Dependent Functions of Virus-Derived Small Interfering RNAs. J Virol. 85:2907-2917 file
Smith, K.A. and Maizels, R.M. - Defeating sepsis by misleading MyD88.  Nature Immunology  12: 284-286 file
Smith PH, Mwangi JM, Afrane YA, Yan G, Obbard DJ, Ranford-Cartwright LC and Little TJ - Alternative splicing of the Anopheles gambiae Dscam gene in diverse Plasmodium falciparum infections Malaria Journal 2011, 10:156 file
Spence PJ, Cunningham D, Jarra W, Lawton J, Langhorne JL and Thompson J. - Transformation of the rodent malaria parasite, Plasmodium chabaudi. Nature Protocols. 6: 553-561 file
Stapleton, J. T., Foung, S., Muerhoff, A. S., Bukh, J. and Simmonds, P.  - The GB viruses: a review and proposed classification of GBV-A, GBV-C (HGV), and GBV-D in genus Pegivirus within the family Flaviviridae. J Gen. Virol. 92:233-246  file
Stjernman, M and T.J Little. - Genetic variation for Maternal effects on parasite resistance. J Evol Biol. 2011 Nov;24(11):2357-63. file
Stopher, K.V., Nussey, D.H., Clutton-Brock, T.H., Guinness, F., Morris, A. and  Pemberton, J.M. - The red deer rut revisited: female excursions but no evidence females move to mate with preferred males. Behavioural Ecology, 22: 808-818. file
Stothard, J.R., Sousa-Figueiredo, J.C., Betson, M., Green, H.K., Seto, E.Y., Garba, A., Sacko, M., Mutapi, F., Vaz Nery, S., Amin, M.A., Mutumba-Nakalembe, M., Navaratnam, A., Fenwick, A., Kabatereine, N.B., Gabrielli, A.F., Montresor A. - Closing the praziquantel treatment gap: new steps in epidemiological monitoring and control of schistosomiasis in African infants and preschool-aged children. Parasitology 138(12): 1593-1606.  file
Stratford CA, McGorum BC, Pickles KJ, Matthews JB. - An update on cyathostomins: anthelmintic resistance and diagnostic tools. Equine Vet. J. 43:133-9. file
Surakka I, Isaacs A, Karssen LC, Laurila P-PP, Middelberg RPS, et al. - A Genome-Wide Screen for Interactions Reveals a New Locus on 4p15 Modifying the Effect of Waist-to-Hip Ratio on Total Cholesterol. PLoS Genet 7(10) file
Sutherland, T.E., Andersen, O.A., Betou, M., Eggleston, I.M., Maizels, R.M., van Aalten D. and Allen, J.E. - Analyzing airway inflammation with chemical biology: dissection of acidic mammalian chitinase function with a selective drug-like inhibitor. Chem Biol. 2011 May 27;18(5):569-79. file
Tildesley MJ, Volkova VV, Woolhouse ME. - Potential for epidemic take-off from the primary outbreak farm via livestock movements, BMC Vet Res. 7:76. file
Tree, J.J., Roe, A.J., Flockhart, A., McAteer, S. P., Xu, X., Shaw, D., Mahajan, A., Beatson, S.A., Best, A., Lotz, S., Woodward, M.j., LaRagione, R., Murphy, K.C., Leong, J.M., and Gally, D.L. - Transcriptional regulators of the GAD acid stress island are carried by effector protein-encoding prophages and indirectly control type III secretion in enterohemorrhagic Escherichia coli O157:H7 Molecular Microbiology 80(5): 1349-1365 file
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van der Werf, N., Redpath, S. A., Phythian-Adams, A. T., Azuma, M., Allen, J. E., Maizels, R. M., MacDonald, A. S. and Taylor, M. - Th2 Responses to Helminth Parasites Can Be Therapeutically Enhanced by, but Are Not Dependent upon, GITR-GITR Ligand Costimulation In Vivo The Journal of Immunology. doi:10.4049/jimmunol.1100834 file
Volkova VV, Bessell PR, Woolhouse ME, Savill NJ. - Evaluation of risks of foot-and-mouth disease in Scotland to assist with decision making during the 2007 outbreak in the UK. Vet Rec. 169(5):124. file
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Walrad PB, Capewell P, Fenn K, Matthews KR. - The post-transcriptional trans-acting regulator, TbZFP3, co-ordinates transmission-stage enriched mRNAs in Trypanosoma brucei, Nucleic Acids Res. 2011 Dec 2. file
Wang D, Zetterström C. E., Gabrielsen M., Beckham K. S., Tree J. J., Macdonald S. E., Byron O, Mitchell T. J., Gally D. L., Herzyk P., Mahajan A., Uvell H., Burchmore R., Smith B. O., Elofsson M. and Roe, A. J. - Identification of Bacterial Target Proteins for the Salicylidene Acylhydrazide Class of Virulence-blocking Compounds. Journal of Biological Chemistry 286:29922-31. file
Whyte, C.S., Bishop, E.T., Rückerl, D., Gaspar-Pereira, S., Barker, R.N., Allen, J.E., Rees, A.J. and Wilson, H.M. - Suppressor of Cytokine Signaling (SOCS)1 is a key determinant of differential macrophage activation and function. Journal of Leukocyte Biology. May 31. 90(5):845-54. file
Woolhouse M. - Promoting good practice in epidemiology. Veterinary Record  168:156-157 file

Woolhouse M. - How to make predictions about future infectious disease risks. Philosophical Transactions of the Royal Society B Biological Sciences 12;366(1573):2045-54. file

Zhang XS and Woolhouse ME. - Escherichia coli O157 infection on Scottish cattle farms: dynamics and control. Journal of the Royal Society Interface 6;8(60):1051-8. file

Zonneveld-Huijssoon, E., Roord, S.T., de Jager, W., Klein, M., Albani, S., Anderton, S.M., Kuis, W., van Wijk, F. and Prakken, B.J. - Bystander suppression of experimental arthritis by nasal administration of a heat shock protein peptide. Ann Rheum Dis. 2011 Dec;70(12):2199-206. file


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