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Publications

2016 Publications

For queries relating to publications, please contact: group@antigenic-cartography.org

James SL, Blacksell SD, Nawtaisong P, Tanganuchitcharnchai A, Smith DJ, Day NP, Paris DH:.Antigenic relationships among human pathogenic Orientia tsutsugamushi isolates from Thailand. PLOS Neglected Tropical Diseases, 2016 Jun 1;10(6):e0004723. doi: 10.1371/journal.pntd.0004723.

Mosterín Höpping A, Fonville JM, Russell CA, James S, Smith DJ. Influenza B vaccine lineage selection—An optimized trivalent vaccine. Vaccine. 2016 Mar 18;34(13):1617-22. doi: 10.1016/j.vaccine.2016.01.042. Epub 2016 Feb 16.

2015 Publications

  • Mosterín Höpping A, McElhaney J, Fonville JM, Powers DC, Beyer WE, Smith DJ. The confounded effects of age and exposure history in response to influenza vaccination. Vaccine. 2015 Dec 5. pii: S0264-410X(15)01724-7. doi: 10.1016/j.vaccine.2015.11.058. [Epub ahead of print]
  • Huang SW, Tai CH, Fonville JM, Lin CH, Wang SM, Liu CC, Su IJ, Smith DJ, Wang JR. Mapping Enterovirus A71 Antigenic Determinants from Viral Evolution. J Virol. 2015 Nov 15;89(22):11500-6. doi: 10.1128/JVI.02035-15. Epub 2015 Sep 2.
  • Althouse M Benjamin, Scarpino V Samuel, Meyers Lauren, Ayers W John, Bargsten Marisa, Baumbach Joan, Brownstein S John, Castro Lauren, Clapham Hannah, Cummings Derek, Del Valle Sara, Eubank Stephen, Fairchild Geoffrey, Finelli Lyn, Generous Nicholas, George Dylan, Harper R David, Hébert-Dufresne Laurent, Johansson A Michael, Konty Kevin, Lipsitch Marc, Milinovich Gabriel, Miller D Joseph, Nsoesie O Elaine, Olson R Donald, Paul Michael, Polgreen M Philip, Priedhorsky Reid, Read M Jonathan, Rodríguez-Barraquer Isabel, Smith J Derek, Stefansen Christian, Swerdlow L David, Thompson Deborah, Vespignani Alessandro, Wesolowski Amy: Enhancing disease surveillance with novel data streams: challenges and opportunities. EPJ Data Science. In press, October 2015.
  • Katzelnick LC, Fonville JM, Gromowski GD, Arriaga JB, Green A, James SL, Lau L, Montoya M, Wang C, VanBlargan LA, Russell CA, Thu HM, Pierson TC, Buchy P, Aaskov JG, Muñoz-Jordán JL, Vasilakis N, Gibbons RV, Tesh RB, Osterhaus AD, Fouchier RA, Durbin A, Simmons CP, Holmes EC, Harris E, Whitehead SS, Smith DJ. Dengue viruses cluster antigenically but not as discrete serotypes. Science. 2015 Sep 18;349(6254):1338-43. doi: 10.1126/science.aac5017
  • Bedford T, Riley S, Barr IG, Broor S, Chadha M, Cox NJ, Daniels RS, Gunasekaran C, Hurt AC, Kelso A, Klimov A, Lewis NS, Li X, McCauley JW, Odagiri T, Potdar V, Rambaut A, Shu Y, Skepner E, Smith DJ, Suchard MA, Tashiro M, Wang D, Xu X, Lemey P, Russell CA. Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature. 2015 Jul 9;523(7559):217-20. doi: 10.1038/nature14460. Epub 2015 Jun 8.

 

  • Ruben O. Donis, Gavin J.D. Smith, World Health Organization/World Organisation for Animal Health/Food and Agriculture Organization (WHO/OIE/FAO) H5 Evolution Working Group incl. DJ Smith. Nomenclature updates resulting from the evolution of avian influenza A(H5) virus clades 2.1.3.2a, 2.2.1, and 2.3.4 during 2013-2014. Influenza and Other Respiratory Viruses. DOI: 10.1111/irv.12324.
  • Koel, B; Mögling, R; Chutinimitkul, S; Fraaij, P; Burke, D; Van der Vliet, S; de Wit, E; Bestebroer, T; Rimmelz- waan, G; Osterhaus, A; Smith, D; Fouchier, R; De Graaf, M. Identification of amino acid substitutions supporting antigenic change of A(H1N1)pdm09 viruses. ASM Journal of Virology. 2015 Apr;89(7):3763-75. doi: 10.1128/JVI.02962-14. Epub 2015 Jan 21.
  • Swayne, D; Suarez, D; Spackman, E; Jadhao, S; Dauphin, G; Kim-Torchetti, M; McGrane, J; Weaver, J; Daniels, P; Wong, F; Selleck, P; Wiyono, A; Indriani, R; Yupiana, Y; Siregar, ES; Prajitno, T; Smith, D; Fouchier, R. Antibody Titer Has Positive Predictive Value for Vaccine Protection against Challenge with Natural Antigenic Drift Variants of H5N1 High Pathogenicity Avian Influenza Viruses from Indonesia. ASM Journal of Virology. 2015 Apr;89(7):3746-62. doi: 10.1128/JVI.00025-15. Epub 2015 Jan 21.

 

2014 Publications

  • Gilbert et al. Serological evidence for non-lethal exposures of Mongolian wild birds to highly pathogenic avian influenza H5N1 virus. PLOS ONE. 15 December 15, 2014; 10.1371/journal.pone.0113569

  • Schultz-Cherry et al. Influenza Gain of Function (GOF) experiments: their role in vaccine virus recommendation and pandemic preparedness. mBio.12 December 2014; vol. 5 no. 6 e02430-14.

  • Burke, DF; Smith, DJ. A Recommended Numbering Scheme for Influenza A HA Subtypes. PLOS ONE November 12, 2014, DOI: 10.1371/journal. pone. 0112302.

  • Fonville, JM; Wilks, SH; James, SL; Fox, A; Ventresca, M; Aban, M; Xue, L; Jones, TC; Le, NMH; Pham, QT; Tran, ND; Wong, Y; Mosterin, A; Katzelnick, LC; Labonte, D; Le, TT; van der Net, G; Skepner, E; Russell, CA; Kaplan, TD; Rimmelzwaan, GF; Masurel, N; de Jong, JC; Palache, A; Beyer, WEP; Le, QM; Nguyen, TH; Wertheim, HFL; Hurt, AC; Osterhaus, ADME; Barr, IG; Fouchier, RAM; Horby, PW; Smith, DJ. Antibody landscapes after influenza virus infection or vaccination. Science: 21 November 2014: Vol. 346 no. 6212 pp. 996-1000; DOI: 10.1126/science.1256427.

  • Watanabe, T; Zhong, G; Hanson, T; Neumann, G; Hatta, M; Imai, M; Watanabe, S; Maher, S; Nakajima, N; Paulson, J; McBride, R; Russell, C;; Burke, D; Satoshi, F; Tomita, Y; Smith, D; Kawaoka, Y. Circulating avian influenza viruses closely related to the 1918 virus have pandemic potential. Cell-Host-Microbe -D-14-00061R; Volume 15, Issue 6, p692–705, 11 June 2014.

  • Koel BF, van der Vliet S, Burke DF, Bestebroer TM, Bharoto EE, Yasa IW, Herliana I, Laksono BM, Xu K, Skepner E, Russell CA, Rimmelzwaan GF, Perez DR, Osterhaus AD, Smith DJ, Prajitno TY, Fouchier RA. Antigenic variation of clade 2.1 H5N1 virus is determined by a few amino acid substitutions immediately adjacent to the receptor binding site. MBio. 2014 Jun 10;5(3):e01070-14. doi: 10.1128/mBio.01070-14. Erratum in: MBio. 2014;5(4):e01645-14.

  • van den Hoogen, GB; van Boheemen, S; de Rijck, J; van Nieuwkoop, S; Smith, DJ; Lasono, B; Gultayev, A; Osterhaus, ADME; Fouchier, RAM 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].

  • Changwen Ke, Jing Lu, Jie Wu, Dawei Guan, Lirong Zou, Tie Song, Lina Yi, Xianqiao Zeng, Lijun Liang, Hanzhong Ni, Min Kang, Xin Zhang, Haojie Zhong, Jianfeng He, Jinyan Lin, Derek Smith, David Burke, Ron A.M. Fouchier, Marion Koopmans, and Yonghui Zhang. Circulation of Reassortant Influenza A(H7N9) Viruses in Poultry and Humans, Guangdong Province, China, 2013; Emerging Infectious Diseases; doi -10.3201/eid2012.140765.

  • Lemey, P; Rambaut, A; Bedford, T; Faria, N; Bielejec, F; Baele, G; Russell, CA; Smith, DJ; Pybus, OG; Brockmann, D; Suchard, MA.   Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2. Plos Pathogens, Feb 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. 2014 Aug 20;32(37):4713-25. doi: 10.1016/j.vaccine.2014.02.014. Epub 2014 Feb 28.

  • 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. 2014;3:e01914. doi: 10.7554/eLife.01914. Epub 2014 Feb 4.

2013 Publications

  • 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.

  • 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(6161):976-9. doi: 10.1126/science.1244730.

  • 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 paper. 2014 Feb; 95(Pt 2):384-92. doi: 10.1099/vir.0.057521-0. Epub 2013 Nov 1.

  • Fonville JM, Burke DF, Lewis NS, Katzelnick LC, Russell CA. Quantifying the fitness advantage of polymerase substitutions in influenza A/H7N9 viruses during adaptation to humans. PLoS ONE 2013 (8): e76047.

  • Fonville JM, Carter CL, Pizarro L, Steven RT, Palmer AD, Griffiths RL, Lalor PF, Lindon JC, Nicholson JK, Holmes E, Bunch J. Hyperspectral visualization of mass spectrometry imaging data. Analytical Chemistry 2013 (85): 1415–1423.

  • 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.

  • 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 NS, Javakhishvili Z, Russell CA, Machablishvili A, Lexmond P, Verhagen JH, Vuong O, Onashvili T, Donduashvili M, Smith DJ, Fouchier RA. Avian influenza virus surveillance in wild birds in Georgia: 2009-2011. PLoS One. 2013;8(3):e58534. doi: 10.1371/journal.pone.0058534. Epub 2013 Mar 13.

2012 Publications

  • 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.
  • Fonville JM, Carter CL, Cloarec O, Nicholson JK, Lindon JC, Bunch J, Holmes, E. Robust data processing and normalization strategy for MALDI mass spectrometric imaging. Analytical Chemistry 2012 (84): 1310–1319.

  • Fonville JM, Swart M, Vokáčová Z, Sychrovský V, Šponer JE, Šponer J, Hilbers CW, Bickelhaupt FM, Wijmenga SS. Chemical shifts in nucleic acids studied with density functional theory calculations and comparison with experimentChemistry – a European Journal 2012 (18): 12372–12387.

  • Maher AD, Fonville JM, Coen M, Lindon JC, Rae CD, Nicholson JK. Statistical total correlation spectroscopy scaling for enhancement of metabolic information recovery in biological NMR spectra. Analytical Chemistry 2012 (84): 1083–1091.

  • Ferguson LS, Wulfert F, Wolstenholme R, Fonville JM, Clench MR, Carolan VA, Francese S. Direct detection of peptides and small proteins in fingermarks and determination of sex by MALDI  mass spectrometry profiling. Analyst 2012 (137): 4686–4692.

 

2011 and Earlier Publications

  • 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
  • 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.
  • Mansfield KL, Horton DL, Johnson N, Li L, Barrett ADT, Smith DJ, Galbraith SE, Solomon T, Fooks AR; Flavivirus-induced antibody cross-reactivity, J Gen Virol. 2011 Dec; 92:2821-2829.
  • 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.
  • 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. Clinical Vaccine Immunology. 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, SW; Kiang, D; Smith DJ; Wang, 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 Medecine, 2010, Jun 1; 7(6):e1000275.

  • 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, JM Daly, NS Lewis, DJ Smith, DLN Wood, BT Grenfell. Quantifying the impact of immune escape on transmission dynamics of influenza, Science.2009; 326(5953):726-8.

  • 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. 28(2):392-7. Epub 2009 Oct 28.

  • 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, J Clin Microbiol. 47(11):3653-62. Epub 2009 Sep 23.

  • 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, 2009 Jul 10; 325(5937):197-201. Epub 2009 May 22doi 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, Jones TC, Barrd IG, Cox NJ, Gartene RJ, Gregoryf V, Gust ID, Hampsond AW, Hay AJ, Hurtd AC, de Jong JC Kelso A , Klimove AI, Kageyama T, Komadinad T, Lapedes AS,. Lin YP, Mosterin A,  Obuchig M, Odagirig T, Osterhaus A. D.M.E., Rimmelzwaan GF,  Shawe MW, Skepner E, Stohr K, Tashiro M,. Fouchier RAM, Smith DJ, Influenza vaccine strain selection and recent studies on the global migration of seasonal influenza viruses Vaccine vol. 26, no 4 (75 p.) 8375, 2008.

  • 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. 5874pp. 340–346, 2008.

  • 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 system for highly pathogenic avian influenza H5N1 viruses.  Emerging Infectious Diseases, Volume 14, 2008.

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

  • Berkhoff EG, Geelhoed–Mieras MM, Jonges M, Smith DJ, Fouchier RA, Osterhaus AD, Rimmelzwaan GF. An amino acid substitution in the influenza A virus hemagglutinin associated with escape from recognition by human virus–specific CD4(+) T–cells. Virus Res, 126(1–2):282–7, 2007.

  • 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, Vol. 81, p. 4315–4322, 2007.

  • 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, 25(19):3800–8, 2007.

  • D. J. Smith. Predictability and preparedness in influenza control. Science Vol 312, 392–394, 2006.

  • 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, Vol 9, 330–335, 2005.

  • G.F. Rimmelzwaan, E.G.M. Berkhoff, N. Nieuwkoop, D.J. Smith, R.A.M. Fouchier and A.D.M.E. Osterhaus. Full restoration of viral fitness by multiple compensatory co–mutations in the nucleoprotein of influenza A virus cytotoxic T–lymphocyte escape mutants. Journal of General Virology, Vol 86, 1801–1805, 2005.

  • 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, Vol 79, 2814–2822, 2005.

  • 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, Vol 4, 371–377, 2004.

  • 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. (pdf at JAMA). Journal of the American Medical Association, Vol 292, 2089–2095, 2004.

  • 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 Vol 305, 371–376, 2004.

  • 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, Vol 172, 2453–2460, 2004.

  • G.F. Rimmelzwaan, A.C.M.Boon, G. de Mutsert, R.A.M. Fouchier, D. van Baarle, D.J. Smith, A.S. Lapedes, K. Sintnicolaas, A.D.M.E. Osterhaus. Recognition of influenza virus epitope variants by human CTL. In: Options for the control of influenza virus V, eds., Excerpta Medica, International Congress Series 1263, Amsterdam, 145, 2004.

  • D. J. Smith Applications of bioinformatics and computational biology to influenza surveillance and vaccine strain selection  Vaccine, Vol 21, 1758–1761, 2003.

  • D. J. Smith, A. S. Lapedes, S. Forrest, J. C. deJong, A. D. M. E. Osterhaus, R. A. M. Fouchier, N. J. Cox, and A. S. Perelson, Modeling the effects of updating the influenza vaccine on the efficacy of repeated vaccination (pdf, postscript), In: Options for the control of influenza virus IV, eds. A.D.M.E. Osterhaus, N. Cox, and A. Hampson, Excerpta Medica, International Congress Series 1219, Amsterdam, 655–660, 2001.

  • D. J. Smith, S. Forrest, D. H. Ackley, and A. S. Perelson, Variable Efficacy of Repeated Annual Influenza Vaccination, Proceedings of the National Academy of Sciences, Vol 96, 14001–14006, 1999.

  • D. J. Smith, S. Forrest, and A. S. Perelson, Using lazy evaluation to simulate realistic–size repertoires in models of the immune system, Bulletin of Mathematical Biology, Vol 60, 647–658, 1998.

  • D. J. Smith, S. Forrest, and A. S. Perelson, Immunological memory is associative, in Artificial Immune Systems and their Applications (Dasgupta, Editor), Springer, Berlin, 105–112, 1998 (and Intnl. Conf. on Multiagent Systems, Workshop notes, 62–70, Kyoto, Japan, 1996).

  • D. J. Smith, The Cross–Reactive Immune Response: Analysis, Modeling, and Application to Vaccine Design, PhD Thesis, University of New Mexico, NM, 1997

  • D. J. Smith, S. Forrest, R. R. Hightower, and A. S. Perelson, Deriving Shape Space Parameters from Immunological Data, Journal of Theoretical Biology, Vol. 189, No. 2, 141–150, Nov. 1997.

  • D. J. Smith, S. Forrest, D. H. Ackley, and A. S. Perelson, Modeling the effects of prior infection on vaccine efficacy, in Artificial Immune Systems and their Applications (Dasgupta, Editor), Springer, Berlin, 144–152, 1998 (and Proc. IEEE Intnl. Conf. on Systems, Man, and Cybernetics, Orlando, Florida, 1997).

  • P. H. Stanford and D. J. Smith, The Multidimensional Scatter Code: A Data Fusion Technique with Exponential Capacity, in Proc. Intl. Conf. on Artificial Neural Networks, Vol. II, pp. 1432–1435, Sorrento Italy, 1994.

  • D. J. Smith et al, A VLSI Implementation of the Nestor RCE Neural Network, Texas Instruments Technical Journal, Vol. 7, No. 6, 1990.

  • D. J. Smith and P. H. Stanford, A Random Walk in Hamming Space, in Proc. IEEE Intl. Conf. on Neural Networks, Vol. II, pp. 465–470, San Diego CA, 1990.

  • B. I. Pawate et al, Memory Based Digital Signal Processing, in Proc. IEEE Intl. Conf. on Application Specific Signal Processing, Albuquerque NM, 1990.

  • S. Lusky et al, A Unified Design Representation Can Work, in Proc. ACM/IEEE Design Automation Conf., Las Vegas Nevada, 1989.

  • B. Kapoor et al, Logic Optimization Using Pattern Matching, in Proc. IEEE Intl. Workshop on Logic Synthesis, North Carolina, 1989.

  • T. Shiple et al, Area Evaluation Metrics for Transistor Placement, in Proc. IEEE Intl. Conf. on Computer Design, New York NY, 1988.

  • T. Yoshino and D. J. Smith and D. J. Matzke, An RTL Simulator Based on Functional Programming, Texas Instruments Technical Journal, Vol. 4, No. 3, 139–145, 1987.

  • I. Oliver, D. J. Smith, and J. R. H. Holland, A Study of Permutation Crossover Operators on the Traveling Salesman Problem, in Proc. Intl. Conf. on Genetic Algorithms, Boston MA, 1987.

  • D. J. Smith, Bin Packing with Adaptive Search, in Proc. Intl. Conf. on Genetic Algorithms, Pittsburgh PA, 1985.

  • D. J. Smith and L. Davis, Adaptive Search for Layout Synthesis, in Proc. Texas Instruments Semiconductor Group Technical Meeting, Dallas TX, 1985.

Public and Animal Health Documents

  • CA Russell, E Skepner, Smith DJ. 2014. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2015. World Health Organization, Geneva, Switzerland.

  • Lewis NS, DJ Smith. 2014. “Report for the 2014 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. OIE headquarters, Paris, France.

  • CA Russell, E Skepner, Smith DJ. 2014. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2014-2015. World Health Organization, Geneva, Switzerland.

  • CA Russell, E Skepner, Smith DJ. 2013. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2014. World Health Organization, Geneva, Switzerland.

  • Lewis NS, DJ Smith. 2013. “Report for the 2013 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. OIE headquarters, Paris, France.

  • CA Russell, E Skepner, Smith DJ. 2013. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2013-2014. World Health Organization, Geneva, Switzerland.

  • CA Russell, E Skepner, Smith DJ. 2012. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2013. World Health Organization, Geneva, Switzerland.

  • Lewis NS, DJ Smith. 2012. “Report for the 2012 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. OIE headquarters, Paris, France.

  • CA Russell, E Skepner, Smith DJ. 2012. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2012-2013. World Health Organization, Geneva, Switzerland.

  • CA Russell, E Skepner, Smith DJ. 2011. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2012. Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia.

  • Lewis NS, DJ Smith. 2011. “Report for the 2011 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. OIE headquarters, Paris, France.

  • CA Russell, E Skepner, Smith DJ. 2011. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2011-2012. World Health Organization, Geneva, Switzerland.

  • Lewis NS, DJ Smith, CA Russell. 2010. “Report for the 2010 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. National Institute for Medical Research, Mill Hill, UK.

  • Smith DJ, E Skepner, CA Russell. 2010. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2011. Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza vaccines for use in the 2010 influenza season (southern hemisphere winter). Weekly Epidemiological Record vol. 84, 41 (pp 421–436), 2009.

  • Smith DJ, E Skepner, CA Russell. 2009. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2009-2010. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza vaccines for use in the 2009-2010 influenza season (northern hemisphere winter). Weekly Epidemiological Record vol. 84, 9 (pp 65–76), 2009.

  • Lewis NS, CA Russell, DJ Smith. 2009. “Report for the 2008 International Meeting of OIE Experts on Control of Equine Influenza”. OIE Equine Influenza Vaccine Strain Selection Meeting. National Institute for Medical Research, Mill Hill, UK.

  • Smith DJ, E Skepner, CA Russell. 2008. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2009. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2009 southern hemisphere influenza season. Weekly Epidemiological Record vol. 83, 41 (pp 365–372), 2008.

  • Smith DJ, E Skepner, CA Russell. 2008. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2008-2009. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2008–2009 influenza season. Weekly Epidemiological Record vol. 83, 9 (pp 77–88). 2008.

  • Smith DJ, E Skepner, CA Russell. 2007. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2008. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2009 southern hemisphere influenza season. Weekly Epidemiological Record vol. 82, 40 (pp 345–356) 2009.

  • Smith DJ, E Skepner, CA Russell. 2007. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2007-2008. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2007–2008 influenza season. Weekly Epidemiological Record vol. 82, 9 (pp 69–76) 2009.

  • Smith DJ, E Skepner, CA Russell. 2006. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2007. World Health Organization, Geneva, Switzerland.

  • Smith DJ, E Skepner, CA Russell. 2007. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2008. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2009 southern hemisphere influenza season. Weekly Epidemiological Record vol. 82, 40 (pp 345–356) 2009.

  • Smith DJ, E Skepner, CA Russell. 2007. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2007-2008. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2007–2008 influenza season. Weekly Epidemiological Record vol. 82, 9 (pp 69–76) 2009.

  • Smith DJ, E Skepner, CA Russell. 2006. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2007. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2007 influenza season. Weekly Epidemiological Record vol. 81, 41 (pp 385–396), 2006.

  • Smith DJ, E Skepner, CA Russell. 2006. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2006-2007. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2006-2007 influenza season. Weekly Epidemiological Record vol. 81, 41 (pp 82–86). 2006.

  • Smith DJ, TC Jones. 2005, “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2006. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2006 influenza season. Weekly Epidemiological Record vol. 80, 40 (pp 341-352), 2005.

  • Smith DJ, TC Jones. 2005. “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Northern Hemisphere 2005-2006. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2006 influenza season. Weekly Epidemiological Record vol. 80, 40 (pp 341-352), 2005.

  • Smith DJ, TC Jones. 2004, “Information for the World Health Organization Consultation on the Composition of Influenza Vaccines”. World Health Organization Consultation on the Composition of Influenza Vaccine for the Southern Hemisphere 2005. World Health Organization, Geneva, Switzerland.

  • WHO Vaccine Consultation Meeting report. Recommended composition of influenza virus vaccines for use in the 2005 influenza season. Weekly Epidemiological Record vol. 79, 41 (pp 369–376), 2004.


Other Scientific Writing

  • ESWI’s General strategy towards young scientists, European Scientific Working Group on Influenza, Bulletin #24, 2008.

  • Access Science Q&A by Science Online, 2006.

  • Mapping the flu virus, Science and Public Affairs, a publication of the British Association for the Advancement of Science, 2006.

  • Mapping the antigenic and genetic evolution of influenza virus, European Scientific Working Group on Influenza, Influenza bulletin #19, 2004.

  • Influenza database tutorials, European Scientific Working Group on Influenza, Bulletin #17, 2002