Publications

• 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 (abstract). 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 (pdf) J Immunol, 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. (pdf) In: Options for the control of influenza virus V, eds. , Excerpta Medica, International Congress Series 1263, Amsterdam, 145-148, 2004.

• D. J. Smith Applications of bioinformatics and computational biology to influenza surveillance and vaccine strain selection (pdf) 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 (pdf, postscript), and supplemental material (pdf, postscript), 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 (pdf, postscript), Bulletin of Mathematical Biology, Vol 60, 647-658, 1998.

• D. J. Smith, S. Forrest, and A. S. Perelson, Immunological memory is associative (pdf, postscript), 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 (Postscript single sided, double sided).

• D. J. Smith, S. Forrest, R. R. Hightower, and A. S. Perelson, Deriving Shape Space Parameters from Immunological Data (pdf, postscript), 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, May 1994.

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

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

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

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

• T. Shiple et al, Area Evaluation Metrics for Transistor Placement, in Proc. IEEE Intl. Conf. on Computer Design, New York NY, October 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, Nov. 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, June 1987.

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

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

Technical reports

• D. J. Smith, Towards a Model of Associative Recall in Immunological Memory, Masters thesis, Computer Science Department, University of New Mexico, Technical Report, 94-9, Albuquerque NM, May 1994.

• D. J. Smith, A Literature Review of Original Antigenic Sin, Computer Science Department, University of New Mexico, Technical Report, 94-10, Albuquerque NM, May 1994.

• S. S. Mahant-Shetti et al, Standard Pinout Smart Memory (SPISM) for Application Specific Massive Parallel Processing, Texas Instruments Technical Report #08-91-27, Dallas TX, August 1991.

• D. J. Smith, P. H. Stanford, and D. Hwang, Cache Coherency in One page of CSP, Texas Instruments Technical Report #08-91-26, Dallas TX, August 1991.

• S. S. Mahant-Shetti et al, Standard Pinout Smart Memory (SPISM) for Application Specific Massive Parallel Processing and Artificial Neural Networks, Texas Instruments Technical Report #08-90-42, Dallas TX, August 1990.

Patents

• S. S. Mahant-Stetti, D. J. Smith, et al., Distributed processing memory chip with embedded logic having both data memory and broadcast memory, US Patent Number 5,751,987, May 12, 1998.

• S. S. Mahant-Shetti et al, Apparatus, Systems and Methods for Implementing a Memory Embedded Search Arithmetic Logic Unit. US Patent Number 5,528,550, June 18, 1996.

• Doddington et al, Apparatus, System and Methods for Distributed Signal Processing, US Patent Number 5,500,828, May 19, 1996.

• B. I. Pawate et al, Apparatus, Systems and Methods for Distributed Signal Processing, US Patent Number 5,528,549, June 18, 1996.

• D. J. Smith et al, Devices, Systems and Methods for Implementing a Kanerva Memory, US Patent Number 5,390,139. February 14, 1995.

• D. J. Smith, Computation System and Method using Hamming Distance, June 1993, US Patent Number 5,216,750, June 1, 1993.