The Center for Pathogen Evolution

Publications by Group Members

For queries relating to publications, please contact:


Watanabe, T; Zhong, G; Hanson, T; Neumann, G; Hatta, M; Imai, M; Watanabe, S; Maher, S; Nakajima, N; Paulson, J; McBride, R; Russell, C; Smith, D; Burke, D; Satoshi, F; Tomita, Y; Kawaoka, Y. Circulating avian influenza viruses closely related to the 1918 virus have pandemic potential. Cell-Host-Microbe -D-14-00061R; in press due June 2014.

Smith, DJ; van Boheemen, S; de Rijck, JCWM; van Nieuwkoop, S: Excessive production and extreme editing of Human Metapneumovirus Defective Interfering RNA is Associated with Type I Interferon Induction. Journal of General Virology: 2014 Apr 23. doi: 10.1099/vir.0.066100-0. [Epub ahead of print]

Koopmans, M; Zhang, Y;  Lu,J; Guan, D; Zeng, X; Wu, J; Yi, L; Zou, L; Liang, L; Ni, H; Zhang, X; Song, T; Kang, M; Zhong, H;  He, J; Lin, J; Smith, DJ; Burke, D; Fouchier, R; Ke, C. Influenza A/H7N9 virus emergence in poultry and humans in Guangdong China. The Lancet, Infectious Diseases; In press March 2014.

Philippe Lemey, Andrew Rambaut; Trevor Bedford; Nuno Faria; Filip Bielejec; Guy Baele; Colin Russell; Derek Smith; Oliver Pybus; Dirk Brockmann; Marc Suchard: Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2. PLOS Pathogens: February 20, 2014; DOI: 10.1371/journal.ppat.1003932

Barr, I; Russell, C; Besselaar, TG; Zhiping Ye; McCauley, J; Daniels, R; Cox, N; Kelso, A; Takato Odagiri; Grohmann, G; Othmar, E; Webby, R; Jones, T; Smith, DJ, et al: WHO recommendations for the viruses used in the 2013-14 Northern Hemisphere Influenza Vaccine: Epidemiology, antigenic and genetic characteristics of influenza A(H1N1)pdm09, A(H3N2) and B influenza viruses collected from October 2012 to January 2013. Vaccine. In press


Westgeest, K; Russell, C; Lin, X; Spronken, M; Bestebroer, T; Bahl, J; van Beek, R; Skepner, E; Halpin, R; de Jong, J; Rimmelzwaan, G; Osterhaus, A; Smith, D; Wentworth, D; Fouchier, R; De Graaf, M. Genome-wide Analysis of Reassortment and Evolution of Human Influenza A(H3N2) Viruses Circulating between 1968 and 2011. ASM Journals.J Virol. 2014 Mar; 88(5):2844-57. doi: 10.1128/JVI.02163-13. Epub 2013 Dec 26..

Bedford, T; Suchard, MA; Lemey, P; Dudas, G; Gregory, V; Hay, AJ; McCauley, JW; Russell, CA; Smith, DJ; Rambaut, A. Integrating influenza antigenic dynamics with molecular evolution. Elife. 20 Feb 2014;3:e01914. doi: 10.7554/eLife.01914. Epub 2014 Feb 4.

Beyer WEP, McElhaney J, Smith DJ, Monto AS, Nguyen-Van-Tam JS, Osterhaus ADME. Cochrane re-arranged: Support for policies to vaccinate elderly people against influenza. Vaccine 2013 Oct 3. pii: S0264-410X(13)01339-X. doi: 10.1016/j.vaccine.2013.09.063 [epub ahead of print]

Richard M, Schrauwen EJ, de Graaf M, Bestebroer TM, Spronken MI, van Boheemen S, de Meulder D, Lexmond P, Linster M, Herfst S, Smith DJ, van den Brand JM, Burke DF, Kuiken T, Rimmelzwaan GF, Osterhaus AD, Fouchier RA. Limited airborne transmission of H7N9 influenza A virus between ferrets. Nature. 2013 Sep 26; 501(7468):560-3. doi: 10.1038/nature12476. Epub 2013 Aug 7.

Ludi, A; Horton, D; Li, Y; Mahapatra, M; King, D; Knowles, N; Russell, C; Paton, D; Wood, J; Smith, D; Hammond, J. Antigenic Variation of Foot-and-Mouth Disease Virus Serotype A. Journal of General Virology 2014 Feb; 95(Pt 2):384-92. doi: 10.1099/vir.0.057521-0. Epub 2013 Nov 1.

Koel, BF; Burke, DF; Bestebroer, TM; van der Vliet, S; Zondag, GCM; Vervaet, G; Skepner, E; Lewis, NS; Spronken, MIJ; Russell, CA; Eropkin, MY; Hurt, AC; Barr, IG; de Jong, JC; Rimmelzwaan, GF; Osterhaus, ADME; Fouchier, RAM; Smith, DJ. Substitutions near the receptor binding site determine major antigenic change during influenza virus evolution. Science. 2013 Nov 22; 342, 976 (2013); DOI: 10.1126/science.1244730

Fouchier, RAM; Kawaoka, Y; Cardona C; Compans, RW; García-Sastre, A; Govorkova, EA; Y Guan; Herfst, S; Orenstein, WA; Peiris, MJS; Perez, DR; Richt, JA; Russell, C; Schultz-Cherry, SL; Smith, DJ; Steel, J; Tompkins, SM; Topham, DJ; Treanor, JJ; Tripp, RA; Webby, RJ; Webster, RG. Gain-of-Function Experiments on H7N9. Science. 2013 August 9; Vol 341: 612-3.

Fouchier, RAM; Kawaoka, Y; Cardona C; Compans, RW; García-Sastre, A; Govorkova, EA; Y Guan; Herfst, S; Orenstein, WA; Peiris, MJS; Perez, DR; Richt, JA; Russell, C; Schultz-Cherry, SL; Smith, DJ; Steel, J; Tompkins, SM; Topham, DJ; Treanor, JJ; Tripp, RA; Webby, RJ; Webster, RG. Gain-of-function experiments on H7N9 Nature 2013 August 8; Vol 500: 150-1.

Al Busaidy, S; Al-Gohary, A; Ampofo, WK; Bekshin, Z; Cerkaoui, I; Claes, F; Cox, NJ; Cracknell, W; Cui, L; Paiva, TM; de Wit, M; Diep, LDT; Donabedian, A; Donis, R; Dormitzer, PR; Eichelberger, M; El Kholy, N; Engelhardt, O; Engelmann, HB; Eropkin, MY; Fasce, R; Fontaine, L; Ghadakchi, HF; Ghedin, E; Giovanni, MY; Golding, H; da Silva, HC; Gysin, R; Hamilton, K; Hauge, SH; Hay, A; Huang, S; Hungnes, O; Ibrahim, SSS; Immamura, T; Inglis, SC; Kadjo, H; Katz, J; Kawaoka, Y; Kelso, A; Khan, MI; Kilander, A; Klimov, A; Kreij, K; Kusmiaty, D; Linde, A; Liu, MT; Lupulescu, E; Mai, LQ; Martinez, VR; McCauley, J; Meyer, Q; Modi, R; Mohammadi, AA; Mokhtari-Azad, T; Mol, E; Music, T; Nelson, K; Neuhaus, E; Neumeier, ER; Niang, MN; Odagiri, T; Peiris, M; Pohlmann, A; Popow-Kraupp, T; Trilar, KP; Rabadan, R; Rambaut, A; Robertson, JS; Rolls, C; Sampurno, OD; Savy, V; Sawanpanyaltert, P; Schmid, G; Schweiger, B; Shapira, S; Shinde, V; Shu, Y; Siqueira, M; Smith, D; Spiro, D; Stevens, J; Takizawa, K; Tashiro, M; Taylor, B; Thomas, Y; Tsai, T; Van der Werf, S; Venter, M; Waddell, AL; Wan, XF; Wang, D; Webby, R; Weir, JP; Wentworth, D; Wickramasinghe, G; Ye, ZP; Zambon, M; Ziegler, T. Strengthening the influenza vaccine virus selection and development process Outcome of the 2nd WHO Informal Consultation for Improving Influenza Vaccine Virus Selection held at the Centre International de Conferences (CICG) Geneva, Switzerland, 7 to 9 December 2011. Vaccine. 2013 June 11; 31 (32):3209-3221; 10.1016/ j.vaccine.2013.05.049 JUL 11 2013

Lewis N.S, Javakhishvili Z, Russell C.A, Machablishvili A, Lexmond P, et al. (2013) Avian Influenza Virus Surveillance in Wild Birds in Georgia: 2009–2011. PLoS ONE 8(3): e58534. doi:10.1371/journal.pone.0058534.


Westgeest KB, de Graaf M, Fourment M, Bestebroer TM, van Beek R, Spronken MI, de Jong JC, Rimmelzwaan GF, Russell CA, Osterhaus AD, Smith GJ, Smith DJ, Fouchier RA. Genetic evolution of the neuraminidase of influenza A (H3N2) viruses from 1968 to 2009 and its correspondence to hemagglutinin evolution. J Gen Virol. 2012 Sep;93(Pt 9):1996-2007. doi: 10.1099/vir.0.043059-0. Epub 2012 Jun 20.

Russell CA, Fonville JM, Brown AE, Burke DF, Smith DL, James SL, Herfst S, van Boheemen S, Linster M, Schrauwen EJ, Katzelnick L, Mosterín A, Kuiken T, Maher E, Neumann G, Osterhaus AD, Kawaoka Y, Fouchier RA, Smith DJ. The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host. Science. 2012 Jun 22; 336(6088): 1541-7.

Herfst S, Schrauwen EJ, Linster M, Chutinimitkul S, de Wit E, Munster VJ, Sorrell EM, Bestebroer TM, Burke DF, Smith DJ, Rimmelzwaan GF, Osterhaus AD, Fouchier RA. Airborne transmission of influenza A/H5N1 virus between ferrets. Science. 2012 Jun 22;336(6088):1534-41.

Wilks S, de Graaf M, Smith DJ, Burke DF, A review of influenza haemagglutinin receptor binding as it relates to pandemic properties. Vaccine 30(29):4369-4376 19 Jun 2012.


Sandbulte MR, Westgeest KB, Gao J, Xu XY, Klimov AI, Russell CA, Burke DF, Smith DJ, Fouchier RAM, Eichelberger MC, Discordant antigenic drift of neuraminidase and hemagglutinin in H1N1 and H3N2 influenza viruses, P NATL ACAD SCI USA 108(51):20748-20753 20 Dec 2011.

A. Vincent, L. Awada, I. Brown, H. Chen, F. Claes, G. Dauphin, R. Donis, M. Culhane, K. Hamilton, N. Lewis, E. Mumford, T. Nguyen, S. Parchariyanon, J. Pasick, G. Pavade, A. Pereda, M. Peiris, T. Saito, S. Swenson, K. Van Reeth, R.Webby, F. Wong and J. Ciacci-Zanella Review of Influenza A Virus in Swine Worldwide: A Call for Increased Surveillance and Research. Zoonoses and Public Health DOI: 10.11.11/zph.12049.

Lewis NS, Daly JM, Russell CA, Horton DL, Skepner E, Bryant NA, Burke DF, Rash AS, Wood JL, Chambers TM, Fouchier RA, Mumford JA, Elton DM, Smith DJ. The antigenic and genetic evolution of equine influenza A(H3N8) virus from 1968-2007  J Virol 2011 Sep 21. [Epub ahead of print].

Nfon, C. K., Y. Berhane, T. Hisanaga, S. Zhang, K. Handel, H. Kehler, O. Labrecque, N. S. Lewis, A. L. Vincent, J. Copps, S. Alexandersen, and J. Pasick. (2011) Characterization of H1N1 swine influenza viruses circulating in Canadian pigs in 2009. Journal of Virology 85:8667-8679.

Abbas MA, Spackman E, Fouchier R, Smith D, Ahmed Z, Siddique N, Sarmento L, Naeem K, McKinley ET, Hameed A, Rehmani S, Swayne DE. H7 avian influenza virus vaccines protect chickens against challenge with antigenically diverse isolates. Vaccine 2011 Jul 29. [Epub ahead of print].

Bodewes R, de Mutsert G, van der Klis FR, Ventresca M, Wilks S, Smith DJ, Koopmans M, Fouchier RA, Osterhaus AD, Rimmelzwaan GF. Prevalence of antibodies against seasonal influenza A and B viruses in children in Netherlands. Clin Vaccine Immunol 2011 Mar;18(3):469-76. Epub 2011 Jan 5.

Lorusso A, Vincent AL, Harland ML, Alt D, Bayles DO, Swenson SL, Gramer MR, Russell CA, Smith DJ, Lager KM, Lewis NS. Genetic and antigenic characterization of H1 influenza viruses from United States swine from 2008.
J Gen Virol. 2011 Apr;92(Pt 4):919-30. Epub 2010 Dec 22.

WHO/OIE/FAO H5N1 Evolution Working Group. Continuing progress towards a unified nomenclature for the highly pathogenic H5N1 avian influenza viruses: divergence of clade 2.2 viruses. Influenza Other Respi Viruses. 2009 Mar;3(2):59-62.

Huang SWKiang D, Smith DJWang JR. Evolution of re-emergent virus and its impact on enterovirus 71 epidemics. Exp Biol Med 2011 Aug 1;236(8):899-908.

Lorusso A, Vincent AL, Harland ML, Alt D, Bayles DO, Swenson SL, Gramer MR, Russell CA, Smith DJ,  Lager KM, Lewis NS. Genetic and antigenic characterization of H1 influenza viruses from United States swine from 2008 J Gen Virol. 2011 April; 92(Pt 4): 919–930. doi: 10.1099/vir.0.027557-0.


Chutinimitkul S, Herfst S, Steel J, Lowen AC, Ye J, van Riel D, Schrauwen EJA, Bestebroer TM,  Koel B, Burke DF, Sutherland-Cash KH, Whittleston CS, Russell CA, Wales DJ, Smith DJ, Jonges M, Meijer A, Koopmans M, Rimmelzwaan GF, Kuiken T, Osterhaus ADME, García-Sastre A, Perez DR, Fouchier RAM
Virulence-Associated Substitution D222G in the Hemagglutinin of 2009 Pandemic Influenza A(H1N1) Virus Affects Receptor Binding J Virol. 2010 November; 84(22): 11802–11813. 

Van Kerkhove MD, Asikainen T, Becker NG, Bjorge S, Desenclos JC, dos Santos T, Fraser C, Leung GM, Lipsitch M, Longini IM Jr, McBryde ES, Roth CE, Shay DK, Smith DJ, Wallinga J, White PJ, Ferguson NM, Riley S. Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling.
PLoS Medicine, 2010, Jun 1;7(6):e1000275.

Bryant, N. A., R. Paillot, A. S. Rash, E. Medcalf, F. Montesso, J. Ross, J. Watson, M. Jeggo, N. S. Lewis, J. R. Newton, and D. M. Elton. (2010) Comparison of two modern vaccines and previous influenza infection against challenge with an equine influenza virus from the Australian 2007 outbreak. Veterinary Research 41:19.

Fouchier RAM and DJ Smith. Use of antigenic cartography in vaccine seed strain selection. Avian diseases, 2010 Mar; 54(1 supp): 222-3.


Barr IG, J McCauley, N Cox, R Daniels, OG Engelhardt, K Fukuda, G Grohmann, A Hay, A Kelso, A Klimov, T Odagiri, D Smith, C Russell, M Tashiro, R Webby, J Wood, Z Ye, W Zhang. 2010 Epidemiological, antigenic and genetic characteristics of seasonal influenza A(H1N1), A(H3N2) and B influenza viruses: basis for the WHO recommendation on the composition of influenza vaccines for use in the 2009-2010 Northern Hemisphere season.  Vaccine, 2010 Feb 3;28(5):1156-67. Epub 2009 Dec 9.

Park AW, Daly JM, Lewis NS, Smith DJ, Wood DLN, Grenfell BT, Quantifying the impact of immune escape on transmission dynamics of influenza, Science, 2009; 326: 726-728.

Voordouw  ACG , WEP Beyer, DJ Smith, MCJM Sturkenboom , BHCh Stricker, Evaluation of serological trials submitted for annual relicensure of influenza vaccines to regulatory authorities between 1992-2002, Vaccine, in press.

Huang, S-W, Y-W Hsu, D Kiang, H-P Tsai, P-H Kuo, K-H Lin, S-M Wang, C-C Liu, DJ Smith, I-J Su, J-R Wang, Reemerging of Enterovirus 71 in 2008 in Taiwan: Dynamics of Genetic and Antigenic Evolution from 1998 to 2008, American Society for Microbiology, in press.

Fouchier, RAM and DJ Smith. 2009. Use of Antigenic Cartography in Vaccine Seed Strain Selection. Avian Diseases
(in press).

Murilo Novaes Gomes, Antonio Miguel Vieira Monteiro, Nicola Lewis, Celso Alberto Goncalves, Vladimir de Souza Nogueira Filho Gomes, M.N., et al.,Landscape risk factors for attacks of vampire bats on cattle in Sao Paulo, Brazil. Prev. Vet. Med. (2009), doi:10.1016/j.prevetmed.2009.10.06

Bryant, N. A., A. S. Rash, C. A. Russell, J. Ross, A. Cooke, S. Bowman, S. MacRae, N. S. Lewis, R. Paillot, R. Zanoni, H. Meier, L. A. Griffiths, J. M. Daly, A. Tiwari, T. M. Chambers, J. R. Newton, and D. M. Elton. (2009) Antigenic and genetic variations in European and North American equine influenza virus strains (H3N8) isolated from 2006 to 2007. Veterinary Microbiology 138:41-52.

Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RA, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD Jr, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI, Cox NJ (2009). Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans, Science, doi 10.1126/science.1176225.

Donis RO, GJD Smith, ML Perdue, IH Brown, H Chen, RAM Fouchier, Y Kawaoka, J Mackenzie, Y Shu, I Capua, NJ Cox, T Davis, R Garten, Y Guan, E Mumford, CA Russell, C Smith, D Smith, D Vijaykrishna. 2008.Continuing progress towards a unified nomenclature for the highly pathogenic H5N1 avian influenza viruses: divergence of clade 2.2 viruses.WHO/OIE/FAO H5N1 Evolution Working Group. Influenza Other Respi Viruses. 2009 Mar;3(2):59-62.


Russell CA, TC Jones, IG Barr, NJ Cox, R Garten, V Gregory, I Gust, AW Hampson, AJ Hay, AC Hurt, JC de Jong, AI Klimov, T Kageyama, N Komadina, AS Lapedes, YP Lin, A Mosterin, M Obuchi, T Odagiri, ADME Osterhaus, GF Rimmelzwaan, MW Shaw, E Skepner, K Stohr, M Tashiro, RAM Fouchier, DJ Smith. 2008. The global circulation of seasonal influenza A(H3N2) viruses. Science, Vol. 320, No. 5874. (18 April 2008), pp. 340-346.

Bryant NA, AS Rash, CA Russell, J Ross, A Cooke, S Bowman, L Griffiths, S MacRae, R Zanoni, H Meier, R Paillot, JM Daly, TM Chambers, JR Newton, DM Elton. 2009. Equine influenza virus surveillance in North America and Europe from 2006 to 2007. Veterinary Microbiology 2009 Jul 2;138(1-2):41-52.

Bryant, N., A. Rash, N. Lewis, D. Elton, F. Montesso, J. Ross, R. Newton, R. Paillot, J. Watson, and M. Jeggo. (2008) Australian equine influenza: vaccine protection in the UK. Vet Rec 162:491-492.

Russell CA, TC Jones, IG Barr, NJ Cox, R Garten, V Gregory, I Gust, AW Hampson, AJ Hay, AC Hurt, JC de Jong, AI Klimov, T Kageyama, N Komadina, AS Lapedes, YP Lin, A Mosterin, M Obuchi, T Odagiri, ADME Osterhaus, GF Rimmelzwaan, MW Shaw, E Skepner, K Stohr, M Tashiro, RAM Fouchier, DJ Smith. 2008. Influenza vaccine strain selection and recent studies on the global migration of seasonal influenza viruses. Vaccine, 26:D31-34.

Donis RO, GJD Smith, ML Perdue, IH Brown, H Chen, RAM Fouchier, Y Kawaoka, J Mackenzie, Y Shu, I Capua, NJ Cox, T Davis, R Garten, Y Guan, E Mumford, CA Russell, C Smith, D Smith, D Vijaykrishna. 2008. Towards a unified nomenclature for highly pathogenic avian influenza H5N1 viruses. Emerging Infectious Diseases, Jul 2008.

Furnham N, de Bakker PIW, Gore S, Burke DF and Blundell TL 2008 Comparative modelling by restraint-based conformational sampling BMC Structural Biology 8:7. doi:10.1186/1472-6807-8-7.

Hayman DTS, Fooks AR, Horton D, Suu-Ire R, Breed AC, Cunningham AA, et al. Antibodies against Lagos bat virus in megachiroptera from West Africa. Emerging Infectious Diseases 2008 Jun.

Fitzmaurice TJ., Burke DF, Hopkins L, Yang S, Yu S, Sy M-S , Thackray AM. and Bujdoso R 2008 *The stability and aggregation of ovine prion protein associated with classical and atypical scrapie correlates with the ease of unwinding of helix-2 Biochem J 409(2):367-75 doi:10.1042/BJ20071122.

Jones NG, Nietlispach D, Sharma R, Burke DF, Eyres I, Mues M, Mott HR and Carrington M 2008 Structure of a GPI-anchored VSG C-terminal domain J.Biol.Chem. 283(6):3584-93. doi:10.1074/jbc.M706207200.

Smith DJ, JC de Jong, AS Lapedes, TC Jones, CA Russell, TM Bestebroer, GF Rimmelzwaan, ADME Osterhaus, RAM Fouchier. 2008. Antigenic relationships among influenza A(H3N2) viruses. Novartis Foundation Symposium Proceedings.


J.C. de Jong, D.J. Smith, A.S. Lapedes, I. Donatelli, L. Campitelli, G. Barigazzi, K. Van Reeth, T.C. Jones, G.F. Rimmelzwaan, A.D.M.E. Osterhaus, and R.A.M. Fouchier, Antigenic and genetic evolution of swine influenza A H3N2 viruses in Europe, Journal of. Virology. 81(8): 4315-22

J. Philippa, C. Baas, W. Beyer, T. Bestebroer, R.A.M. Fouchier,  D.J. Smith, W. Schaftenaar, A.D.M.E. Osterhaus, Vaccination against highly pathogenic avian influenza h5n1 virus in zoos using an adjuvanted inactivated H5n2 vaccine, Vaccine, forthcoming

Worth CL, Bickerton R, Cheng T, Lee S, Gong SS, Schreyer A, Burke DF and Blundell TL 2007 Predicting the functional effects of mutations using structural bioinformatics J.Bioinf.Comp.Biol 5(6),1297-1318 DOI:10.1142/S0219720007003120

Burke DF, Worth C, Prego EM, Cheng T, Smink L, Todd J and Blundell TL (2007) Large scale bioinformatic analysis of non-synonymous SNPs BMC Bioinformatics 8:301 doi:10.1186/1471-2105-8-301


D. J. Smith.  Predictability and preparedness in influenza control.  Science, 312, 392-394

Deans, A., Lyke, K. E., Mahamadou, T. E., Plowe, C. V., Kone, A., Ogobara, D. K., Kai, O., Marsh, K., Mackinnon, M. J., Raza, A., Rowe, J.A.(in press). Plasmodium falciparum multiplication rate and red cell selectivity are not associated with malaria virulence in African children.  2006.  Am. J. Trop. Med. Hyg.

Ali,E.,  Mackinnon,M.J., Abdel-Muhsin,A.M., Ahmed,S., Walliker,D. and Babiker,H.A.  Increased gametocytaemia following drug treatment of Plasmodium falciparum in Sudan (2006)  Trans. R. Soc. Trop. Med. Hyg. 100(2):176-183

Ferguson,H.F., Gandon,S., Mackinnon, M.J. and Read, A.F. 2006 Malaria parasite virulence in mosquitoes and its implications for the introduction and efficacy of GMM malaria control programmes. In ‘Genetically modified mosquitoes for malaria control’ Ed. Boete, C.  Landes Bioscience

Worth CL, Burke DF and Blundell TL (2006) Estimating the effects of single nucleotide polymorphisms on protein structure: how good are we at identifying likely disease associated mutations? Proceedings of Molecular Interactions - Bringing Chemistry to Life

Smith RE, Burke DF, Lovell SC, Montalvao RW, Blundell TL. 2007 ANDANTE: Reducing rotamer search space during comparative modelling using environmental-specific substitution probabilities. Bioinformatics

Blundell TL, Sibanda BL, Montalvao RW, Brewerton S, Chelliah V, Worth C, Harmer N, Davies O and Burke DF (2006) Structural Biology and Bioinformatics in Drug Design: Opportunities and Challenges for Target identification and Lead Discovery Philosophical Transactions of the Royal Society B: Biological Sciences 361(1467):413-23

Russell CA, LA Real, DL Smith. 2006. Utilizing natural barriers to optimize containment strategies for infectious diseases. Public Library of Science: Biology


R.A.M. Fouchier, V. Munster, A. Wallensten, T.M. Bestebroer, S. Herfst, D.J. Smith, G.F. Rimmelzwwaan, B.Olsen, A.D.M.E. Osterhaus. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. Journal of Virology, 79, 2814-2822

G.F. Rimmelzwaan, E.G.M. Berkhoff, N. Nieuwkoop, D.J. Smith, R.A.M. Fouchier and A.D.M.E. Osterhaus. Multiple clustered comutations are required for full functional compensation of a detrimental mutation in an influenza virus CTL epitope. Journal of General Virology, 86, 1801-5

D. J. Smith, A. S. Lapedes, J. C. de Jong, T. M. Bestebroer, T. C. Jones, G. F. Rimmelzwaan, A. D. M. E. Osterhaus, and R. A. M. Fouchier. Influenza virus surveillance: antigenic cartography and the influenza archipelago. Infectieziekten Bulletin, 9, 330-335

Mackinnon, M.J., Mwangi, T., Snow, R., Marsh,K. & Williams, T.N. (2005) Heritability of malaria in Africa. PloS Medicine 2 (12) e340

Babiker, H.A. and Mackinnon, M.J. (2005) Editors of ‘Drug resistance in malaria: population biology and implications for control’.  Special Edition of Acta Tropica 94: 161-280

Mackinnon, M.J. (2005) Drug resistance models in malaria.  Acta Trop. 94: 207-217

Mackinnon, M.J., Bell, A. and Read, A.F.  (2005) The effects of mosquito transmission and population bottlenecking on virulence, multiplication rate and rosetting in rodent malaria.  Int. J. Parasitol. 35: 145-153

Martinelli, A., Cheesman, S.J., Hunt, P., Culleton, R., Raza, A., Mackinnon, M.J. and Carter, R. (2005).  A genetic approach to the de novo identification of targets of strain-specific immunity in malaria parasites. Proc. Natl. Acad. Sci. USA  102: 814-819

Bujdoso R, Burke DF and Thackray A (2005) Structural differences between allelic variants of the ovine prion protein revealed by molecular dynamics simulations Proteins: Structure, Function and Bioinformatics61(4)

Gore S, Burke DFand Blundell TL (2005) PROVAT: A tool for Voronoi Tesellation Analysis of Macromolecular structures Bioinformatics  21(15):3316-7

Russell CA, DL Smith, JE Childs, LA Real. 2005. Predictive spatial dynamics and strategic planning for raccoon rabies emergence in Ohio. Public Library of Science: Biology, 3, e88.

Real LA, C Russell, L Waller, D Smith, J Childs. 2005. Spatial dynamics and molecular ecology of North American rabies. Journal of Heredity, 96:1-8.

Smith DL, LA Waller, CA Russell, JE Childs, LA Real. 2005. Assessing the role of long distance translocation and spatial heterogeneity in the raccoon rabies epidemic in Connecticut. Preventive Veterinary Medicine, 71:225-240.


D. J. Smith, A. S. Lapedes, J. C. de Jong, T. M. Bestebroer, G. F. Rimmelzwaan, A. D. M. E. Osterhaus, and R. A. M. Fouchier. Mapping the Antigenic and Genetic Evolution of Influenza Virus. Science, 305, 371-376

A.C.M.Boon, G. de Mutsert, D. van Baarle, D.J. Smith, A.S. Lapedes, R.A.M. Fouchier, K. Sintnicolaas, A.D.M.E. Osterhaus, and G.F. Rimmelzwaan. Recognition of homo- and heterosubtypic variants of influenza A viruses by human CD8+ T lymphocytes, Journal of Immunology, 172, 2453-2460

A.C.G. Voordouw, M.C.J.M. Sturkenboom, J.P. Dieleman, T. Stijnen, D.J. Smith, J. van der Lei, B.H.C. Stricker. Annual revaccination against influenza effectively reduces mortality risk in community dwelling elderly. Journal of the American Medical Association, 292, 2089-2095

D. J. Smith, A. S. Lapedes, J. C. de Jong, T. M. Bestebroer, T. C. Jones, G. F. Rimmelzwaan, A. D. M. E. Osterhaus, and R. A. M. Fouchier. Mutations, drift, and the influenza archipelago. Discovery Medicine, 4, 371-377

Mackinnon, M.J. and Read, A.F. (2004) Immunity promotes virulence evolution in a malaria model.  PloS  Biology. 2 (9) e230, pp1286-1292

Mackinnon, M. J. and Read, A. F. (2004) Virulence evolution in malaria: an evolutionary perspective.  Phil. Trans. R. Soc. Lond. B. 359: 965-986

Read, A. F., Gandon, S., Nee, S. and Mackinnon, M. J.  (2004) The evolution of pathogen virulence in response to animal and public health interventions. In: Dronamraj, K. (ed.) Evolutionary Aspects of Infectious Diseases. Cambridge University Press, Cambridge. pp. 265-292

Cockburn, I.A., Mackinnon, M.J., O'Donnell, A., Allen, S.J., Moulds, J.M., Baisor, M., Bockarie, M., Reeder, J.C. and Rowe, J.A. (2004) A human complement receptor one polymorphism that reduces Plasmodium falciparum rosetting confers protection against severe malaria.  Proc. Natl. Acad. Sci. USA 101:272-277

Abdel-Muhsin, A. A., Mackinnon, M.J., Ali, E., Nassir, E.A., Suleiman, S., Ahmed, S., Walliker, D. and Babiker, H.A.  (2004) Evolution of drug-resistance genes in Plasmodium falciparum in an area of seasonal malaria transmission in eastern Sudan. J. Infect. Dis. 189: 1239-1244

Paganotti, G.M., Babiker, H.A., Modiano, D., Sirima, B.S., Verra, F., Konate, A., Ouedraogo, A..L.., Diarra, A., Mackinnon, M.J., Coluzzi, M. and Walliker, D. (2004)  Genetic complexity of Plasmodium falciparum in two ethnic groups of Burkina Faso with marked differences in susceptibility to malaria.  Am. J. Trop. Med. Hyg. 71:173-178

Russell CA, DL Smith, LA Waller, JE Childs, LA Real. 2004. A priori prediction of disease invasion dynamics in a novel environment. Proceedings of the Royal Society, London, Series B, 271:21-24.


D.J.Smith.  Applications of bioinformatics and computational biology to influenza surveillance and vaccine strain selection. Invited manuscript. Vaccine 21:1758-1761

Ferguson, H. M., Mackinnon, M. J., Chan, B. H. K. & Read A. F. (2003) Mosquito mortality and the evolution of malaria virulence.  Evolution  57:2792-2804

De Roode J. C., Mackinnon, M.J. and Read, A. F.  (2003) Rodent malaria parasites suffer from the presence of conspecific clones in three-clone Plasmodium chabaudi infections  Parasitology 127:411-418

Gandon, S., Mackinnon, M.J., Nee, S. and Read, A. F.  (2003)  Imperfect vaccination: some epidemiological and evolutionary consequences.  Proc. Roy. Soc. Lond. Ser. B. 270:1129-1136

Abdel-Muhsin, A., Mackinnon, M.J., Awadalla, P., Ali, E., Suleiman, S., Ahmed, S., Walliker, D. and Babiker, H.A. (2003) Local differentiation in Plasmodium falciparum drug resistance genes in Sudan. Parasitology 126:391-400

Mackinnon, M.J. and Read, A.F. (2003) The effects of host immunity on virulence-transmissibility relationships in the rodent malaria parasite Plasmodium chabaudi. Parasitology. 126:103-112

Evans PC, Smith TS, Lai MJ, Williams MG, Burke DF, Heyninck K, Kreike M, Beyaert R, Blundell TL and Killshaw PJ (2003) Cezanne: A novel deubiquitinating enzyme J.Biol.Chem 278(25) 23180-6

Bakker de P, De Pristo MA, Burke DF, Blundell TL (2003) Ab initio construction of polypeptide fragments:II Accuracy of loop decoy descrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model Proteins Structure, Function and Genetics  51(1):21-40


Mackinnon, M.J., Walker, P.R., and Rowe, J.A. (2002) Plasmodium chabaudi: Rosetting in a rodent malaria model. Experimental Parasitology 101:121-128

Mackinnon, M.J., Gaffney, D.J., & Read, A.F.  (2002).  Virulence in rodent malaria: host genotype by parasite genotype interactions.  Infection, Genetics and Evolution 1:287-296

Gandon, S., Mackinnon, M.J., Nee, S. and Read, A. F.  (2002) Reply to Antitoxin vaccines and pathogen virulence.  Nature 417:610

Read, A.F., Mackinnon, M.J., Anwar, M.A. and Taylor, L.H. (2002) Kin selection models as evolutionary explanations of malaria.  In: Dieckmann, U., Metz, J.A.J., Sabelis, M.W. and Sigmund, K. (eds).  Pp 165-178 Virulence Management: The Adaptive Dynamics of Pathogen-Host Interactions. Cambridge: Cambridge University Press


D.J.Smith, S.Forrest, D.H.Ackley, A.S.Perelson, Modeling the effect of prior infection on vaccine efficacy, in Proc.  IEEE Intl. Conf. on Systems, Man, and Cybernetics, Orlando, Florida,  363-368 (1997).  Also, in Artificial Immune Systems and their Applications (Dasgupta, Editor), Springer, Berlin 144-153

*Gandon, S., *Mackinnon, M.J., Nee, S. and Read, A. F. (2001) Imperfect vaccines and the evolution of pathogen virulence.  Nature 414:751-756.  *  denotes joint first authorship

Cravo, P., Culleton, R., Hunt, P., Walliker, D. and Mackinnon, M.J.  Anti-malarial drugs clear resistant parasites from partially immune hosts (2001). Antimicrobial Agents and Chemotherapy 45:2897-2901

Ofosu-Okyere, A., Mackinnon, M.J., Sowa, M.P.K., Koram, K.A., Nkrumah,F., Osei, Y.D., Hill, W.G., Wilson, M.D. and Arnot, D.E.  Novel Plasmodium falciparum clones and rising clone multiplicities are associated with the increase in malaria morbidity in Ghanaian children during the transition into the high transmission season (2001). Parasitology 123:113-123

Awadalla, P., Mackinnon, M.J., Babiker, H.A. and Walliker, D.  (2001) The question of Plasmodium falciparum population structure  Trends in Parasitology 17:351-353

Babiker, H.A., Pringle, S.J., Abdel-Muhsin, A., Mackinnon, M.J., Hunt, P. and Walliker, D.  (2001) High-level chloroquine resistance in Sudanese isolates of Plasmodium falciparum is associated with mutations in the chloroquine resistance transporter gene Pfcrt and the multi-drug resistance gene Pfmdr1.  J. Infect. Dis. 183:1535-1538

Burke DF and Deane CM (2001) Improved Loop prediction from sequence alone Protein Engineering – Vol 14(7) 473-478

Williams MG, Shirai H, Shi J, Nagendra HG, Mueller J, Mizuguchi K, Miguel RN, Lovell SC, Innis cA, Deane CM, Chen L, Campillo N, Burke DF, de Bakker PIW and Blundell TL(2001) Homologue Recognition by Iterative Alignment Refinement and Comparative Modelling Proteins:Structure, Function and Genetics 45 Suppl 5:92-7

Bakker de PIW, Bateman A, Burke DF, Mizuguchi K, Miguel RN, Shirai H, Shi J and Blundell TL (2001) HOMSTRAD: Adding sequence information to structure-based alignments of homologous protein families Bioinfomatics 17: 748-749

Pellegrini L, Burke DF and Blundell TL(2001) Activation mechanism of fibroblast growth factor receptor tyrosine kinase revealed by crystal structure of fibroblast growth factor receptor ectodomain bound to fibroblast growth factor and heparin Insulin and Related Proteins pp189-200 Kluwer Academic Publishers Federwisch M, Leyck Dieken M and  De Meyts P (eds)

Nagendra HG, Harrington AE, Harmer NJ, Blundell TL, Pelligrini L and Burke DF (2001) Analysis of sequences and structures of Fly and Worm fibroblast growth factor receptors indicate that the determinants of FGF and heparin binding are retained in evolution Febs Letters 501(1), 51-58


Mackinnon, M.J., Gunawardena, D. M., Rajakaruna, J., Weerasingha, S. W., Mendis, K. N., and Carter, R.  (2000)  Quantifying genetic and non-genetic contributions to malarial infection in a Sri Lankan population. Proc. Natl. Acad. Sci. USA 97:12661-12666

Babiker, H. A., Abdel-Muhsin, A. A., Hamad, A., Mackinnon, M.J., Hill, W. G. and Walliker, D.  (2000)  Population dynamics of Plasmodium falciparum in an unstable area of eastern Sudan.  Parasitology 120: 105-111

Burke DF, Deane CM and Blundell TL( 2000) A browsable and searchable web interface to the SLoop database of structurally-classified loops connecting elements of protein secondary structure Bioinformatics 16(6), 513-519

Blundell TL, Burke DF, Chirgadze D, Dhanaraj V, Hyvonen M, Innis CA, Parisini E, Pellegrini L, Sayed M, Sibanda BL (2000) Protein-protein interactions in receptor activation and intracellular signalling Biological Chemistry 381, 955-959

PelligriniL, Burke DF, Mulloy B and Blundell TL (2000) The structure of the Fibroblast growth factor receptor, FGF and heparin complex Nature 407, 1029-1034


D.J.Smith, S.Forrest, D.H.Ackley, A.S.Perelson, Variable efficacy of repeated influenza vaccination, Proceeding of the National Academy of Sciences (USA) 96:14001-14006

D.J.Smith, S.Forrest, D.H.Ackley, A.S.Perelson, Modeling the effect of prior infection on vaccine efficacy. In: Artificial Immune Systems and their Applications (Dasgupta, Editor), Springer, Berlin 144-153

Mackinnon, M.J. and Read, A.F. (1999).  Genetic relationships between parasite virulence and transmission in the rodent malaria Plasmodium chabaudi.  Evolution 53: 689-703

Mackinnon, M.J. and Read, A.F. (1999).  Selection for high and low virulence in the malaria parasite Plasmodium chabaudi. Proc. Roy. Soc. Lond. B.  266: 741-748

Burke DF, Deane CM, Nagarajaram HA, Campillo N, Martin-Martinez M, Mendes J, Molina F, Perry J, Reddy BVB, Soares CM, Steward RE, Williams MG, Carrondo M-A, Blundell TL and Mizuguchi K (1999) An Improved Structure Assisted Approach to Sequence Alignment and Comparative Modelling Proteins Structure,Functions and Genetics suppl 3:1-6 


D.J.Smith, S.Forrest, A.S.Perleson. Using lazy evaluation to simulate realistic-size repertoires in models of the immune system. Bulletin of Mathematical Biology 60:647-658

Mackinnon, M.J. and Hastings, I.M. (1998)  The evolution of multiple drug resistance in malaria parasites.  Trans. Roy.  Soc. Trop. Med. Hyg. 92: 188-195

Hastings, I.M. and Mackinnon, M.J. (1998)  The emergence of drug resistant malaria.  Parasitology  117:411-417

Taylor, L.H., Mackinnon, M.J. and Read, AF (1998)  Virulence of mixed-clone and single-clone infections of the rodent malaria Plasmodium chabaudiEvolution 52:583-591

Carlton, J. M-R., M. J. Mackinnon and D. Walliker.  (1998) A chloroquine resistance locus in the rodent malaria parasite Plasmodium chabaudi.   Mol. Biochem. Parasitol.  93:57-72

Mackinnon, M.J. and Georges, M.A.J. (1998)  Marker-assisted pre-selection of young dairy sires prior to progeny testing.  Livest. Prod. Sci.  54: 229-250

Coppieters, W, Mackinnon, M.J. and Georges, M.  (1998) The effect of mixed selected and unselected samples on the power of QTL mapping.  J. Heredity 89:193-195

Coppieters, W, Kvasz, A, Farnir, F, Arranz, J. J., Grisart, B, Mackinnon, M.J. and Georges, M. (1998).  A rank-based nonparametric method for mapping quantitative trait loci in outbred half-sib pedigrees: Application to milk production in a granddaughter design.  Genetics 149:1547-1555

Burke DF, Wilkes D, Blundell TL and Malcolm S (1998) Fibroblast growth factor receptor- lessons from the genes TIBS 23  59-62

Sowdhamini R, Burke DF, Huang JF, Mizuguchi K, Nagarajaram HA, Srinivasan N, Steward RE and Blundell TL (1998) CAMPASS A database of structurally aligned protein superfamilies Structure 6(9):1087-94

Sowdhamini R, Burke DF, Deane CM, Huang JF, Mizuguchi K, Nagarajaram HA,, Overington JP, Srinivasan N, Steward RE and Blundell TL (1998) Protein 3D structural databases: domains,structurally aligned homologues and superfamilies Acta Crystallophica D D54, 1168 – 1177

Pellegrini L, Commander P, Mulloy B, Martin-Martinez M, Blundell TL, Burke DF (1998) The role of heparin in the complex formation between fibroblast growth factor 2 and its high affinity receptor: comparative modelling and biochemical studies Biochemical Society Transactions, 26(3), pp545- 549


D.J.Smith, S.Forrest, R.R.Hightower, A.S.Perelson. Deriving Shape Space Parameters from Immunological Data. Journal of Theoretical Biology 189:141-150

Mackinnon, M.J. (1997)  Survival probability of drug resistant mutants in malaria parasites.  Proc. Roy. Soc. Lond. B.  264: 53-59

Visscher, P. M., Mackinnon, M.J. and Haley, C. S.  (1997) Efficiency of marker assisted selection.  Animal Biotechnology 8: 99-106

Burke DF, Laughton CA, Neidle S (1997) Homology modelling of the enzyme P450 17a-hydroxylase/17,20-lyase A target for prostate cancer chemotherapy--from the crystal structure of P450BM-3 Anticancer Drug Des 12 (2) 113-123

Sowdhamini R, Srinivasan N, Burke DF, Mizuguchi K,Nagarajaram HA, Steward R, Rodionov Mand Blundell TL (1997) Protein Superfamilies, fold recognition and the identification of functions from genome sequences" WATOC conference of MGMS

© 2007, The Antigenic Cartography Group, Last modified 7 August, 2014