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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.