Personal Data

• Date of Birth: April 4, 1955
• Place of Birth: Sheffield, England
• Citizenship: American

• Work Address: 38A / 8S. 806, NLM, NIH, Bethesda MD 20894
• Work Phone: (301) 402-9310

• Home Address: 7208 Grinnell Drive, Rockville MD 20855-2725
• Home Phone: (301) 217-9527
• Marital Status: Married, Two Children

• Father: John Douglas Spouge
• Father's Home Address: 7820 Tweedsmuir Road, Richmond, BC, Canada
• Father's Home Phone: (604) 272-0972

Education

• 1971-1975
• University of British Columbia, Honors BSc Mathematics
• 1975-1979
• University of British Columbia, M.D.
• 1979-1983
• Oxford University, D. Phil., Mathematics

Thesis Title: A Probabilistic Approach to Coagulation
Supervisor: Dr. J. M. Hammersley

Selected Awards

• 1970
• lst Canadian Mathematical Olympiad
• 3rd in B.C. M.A.A. High School Math. Contest
• 2nd in Canada Waterloo Junior Math. Contest
• 1971
• 2nd Canadian Mathematical Olympiad
• 5th in North America; 2nd in Canada M.A.A. High School Math Contest
• 3rd in B. C. Canadian Association of Physicists Contest
• 1973
• 77th in North America William Lowell Putnam Math. Contest
• 1974
• 7th in North America William Lowell Putnam Math. Contest
• 1975
• 14th in North America William Lowell Putnam Math. Contest
• 1st on Dean's Honor Roll Faculty of Science, University of British Columbia
• 1979
• Rebecca and Samuel Nemetz Prize for student showing most promise in Medical research
• 98th percentile American Board exams for clinical medical subjects

Employment

• 1979-1983
• Postdoctoral Fellow of the Canadian Medical Research Council
• 1983-1985
• Postdoctoral Fellow

Theoretical Biology and Biophysics Group
Los Alamos National Laboratory, Los Alamos, NM
Sponsor: Dr. A.S. Perelson
• 1985-1988
• Visiting Associate

Laboratory of Mathematical Biology
National Institutes of Health
Sponsor: Dr. J.V. Maizel
• 1986 (on leave of absence from NIH, April 9 to July 31)
• Research Assistant

Institute of Science and Technology
University of Manchester
Sponsor: Prof. R.F. Stepto
• On Loan to:

Laboratory of Prof. W. Burchard
Institut fur Makromolekulare Chemie
Freiburg, West Germany
• 1989
• Visiting Scientist

National Center for Biotechnology Information
National Library of Medicine
Sponsor: Dr. D.A. Benson
• 1990-present
• Tenured Visiting Scientist

National Center for Biotechnology Information
National Library of Medicine
Sponsor: Dr. D.J. Lipman

Conference Speaker

• 1984
• Nice Conference on Kinetics of Gelation
• 1986
• UC Davis Conference on Statistical Mechanics
• 1987
• Santa Fe Conference on Theoretical Immunology
• 1988
• Santa Fe Conference on the Interaction of HIV with the Immune System
• 1991
• 4th Annual Island Meeting

National Cooperative Vaccine Development Groups for AIDS
• 1991
• NIH Conference on Models of Non-Classical Reaction Rates: Session Chairman
• 1991
• Annual Meeting of the Laboratory of Tumor Cell Biology on HIV
• 1992
• 5th Annual Meeting

National Cooperative Vaccine Development Groups for AIDS
• 1998
• Los Alamos National Laboratory

Frontiers of Combinatorics in Biology

Reviewer

• Bioinformatics
• Cell
• Circulation
• Computer Algorithms in the Biosciences
• Genome Research
• Israel Science Foundation
• Journal of AIDS
• Journal of Chemical Physics
• Journal of Computational Biology
• Journal of Molecular Biology
• Journal of Physical Chemistry
• Physical Review
• The Royal Society of Chemistry Journals

Publications

1. J. L. Spouge and P. A. Larkin
"A reason for pleomerism"
(1979) J. Fish. Res. Board Can. 36 : 255-269
2. J. L. Spouge and S. B. Easterbrook-Smith
"A reinterpretation of the evidence for an interaction between Clgand pairs of immunoglobulin molecules in an immune lattice"
(1982) Mol. Immunol. 19 : 253-256    
3. J. L. Spouge
"Equilibrium polymer size distributions"
(1983) Macromolecules 16 : 121-127
4. J. L. Spouge
"The size distribution for the A_gRB_f-g model of polymerization"
(1983) J. Stat. Phys. 31 : 363-378
5. J. L. Spouge
"Solutions and critical times for the monodisperse coagulation equationwhen a_ij = A + B(i + j) + Cij"
(1983) J. Phys. A: Math. Gen. 16 : 767-774
6. J. L. Spouge
"Asymmetric bonding of identical units: a general A[g]RB[f-g] polymermodel"
(1983) Macromolecules 16 : 831-835
7. J. L. Spouge
"Tree models of aggregation: multiple particle and bond-types"
(1983) Proc. Roy. Soc. Lond. 387 : 351-365
8. J. L. Spouge
"Solutions and critical times for the polydisperse coagulation equationwhen a(x,y) = A + B(x + y) + Cxy"
(1983) J. Phys. A: Math. Gen. 16 : 3127-3132
9. J. L. Spouge
"A branching process solution of the polydisperse coagulation equation"
(1983) Adv. Appl. Prob. 16 : 59-69
10. J. L. Spouge
"Improving sequence-matching algorithms by working from both ends"
(1984) J. Mol. Biol. 181 : 137-138    
11. J. L. Spouge
"Analytic results for finite systems of ringed Flory polymers"
(1984) Can. J. Chem. 62 : 1262-1264
12. J. L. Spouge
"Polymers and random graphs: Asymptotic equivalence to branching processes"
(1984) J. Stat. Phys. 38 : 573-587
13. J. L. Spouge
"Long range percolation in one dimension"
(1984) J. Phys. A: Math. Gen. 17 : 2349-2350
14. J. L. Spouge
"An existence theorem for the discrete coagulation fragmentation equations"
(1984) Proc. Camb. Phil. Soc. 96 : 351-357
15. J. L. Spouge
"An existence theorem for the discrete coagulation fragmentation equations. II. Inclusion of source and efflux terms"
(1985) Proc. Camb. Phil. Soc. 98 : 183-185
16. J. L. Spouge
"Cross-linking of identical particles by multiple ligand-types"
(1985) Proceedings of the conference on mathematical biology 1983,Bari, Italy V. Capasso, E. Grosso, and S. L. Paveri-Fontana, eds.,pp. 354-359
17. J. L. Spouge
"Random graph problems in polymer chemistry: Proceedings of the conference on random graphs 1983, Poznan, Poland"
(1985) Disc. Appl. Math. 28 : 251-262
18. J. L. Spouge
"Monte Carlo results for random coagulation"
(1985) J. Phys. A. Math. Gen. 107 : 38-43
19. J. L. Spouge
"Analytic solutions to Smoluchowski's equation: A combinatorial interpretation"
(1985) J. Phys. A. Math. Gen. 18 : 3063-3069
20. A. S. Perelson and L. A. Segel (appendix by J. L. Spouge)
"On a model for the structure of circular mitochondrial genomes inhigherplants"
(1985) IMAJ. Math. Appl. Med. Biol. 2 : 41-56    
21. E. M. Hendriks, J. L. Spouge, M. Eibl, and M. Schreckenberg
"Exact solutions for random coagulation processes"
(1985) Z. Phys. B 58 : 219-227
22. J. L. Spouge
"Increasing stability with complexity in a system composed of unstablesubsystems"
(1986) J. Math. Anal. Appl. 118 : 502-518
23. J. L. Spouge
"Equilibrium ring-formation in polymer solutions"
(1986) J. Stat. Phys. 43 : 143-196
24. J. L. Spouge and G. I. Bell
"Coagulation and total weight fractions over a threshold size"
(1986) J. Coll. Interface Sci. 110 : 446-452
25. J. L. Spouge
"Exact solutions for reaction-diffusion in one dimension"
(1987) Phys. Rev. Lett. 60 : 871-874
26. J. L. Spouge, H. R. Guy, J. L. Cornette, H. Margalit, K. B.Cease,J. A. Berzofsky, and C. DeLisi
"Strong conformational propensities enhance T-cell antigenicity"
(1987) J. Immunol. 138 : 204-212    
27. J. L. Spouge and J. A. Berzofsky
"Statistics in immunology and biochemistry: an application to T cellantigenic sites"
(1987) Proceedings of the Theoretical Immunology Workshop A.S. Perelson, ed., pp. 131-145
28. H. Margalit, J. L. Spouge, J. L. Cornette, K. B. Cease, J. A. Berzofsky,and C. DeLisi
"Prediction of T-cell antigenic sites from the primary sequence"
(1987) J. Immunol. 138 : 2213-2229    
29. J. L. Cornette, K. B. Cease, H. Margalit, J. L. Spouge, J. A. Berzofsky,and C. DeLisi
"Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins"
(1987) J. Mol. Biol. 195 : 659-685    
30. J. A. Berzofsky, K. B. Cease, J. L. Cornette, J. L. Spouge, H.Margalit, I. J. Berkower, M. F. Good, L. H. Miller, and C. DeLisi
"Protein antigenic structures recognized by T cells: potential application to vaccine design"
(1987) Immunol. Rev. 98 : 9-52    
31. C. DeLisi, J. L. Cornette, H. Margalit, K. B. Cease, J. L. Spouge , and J. A. Berzofsky
"The role of amphipathicity as an indicator of {T}-cell antigenic siteson proteins"
(1987) Immunogenicity of Protein Antigens: Repertoire and Regulation E. E. Secarz and J. A. Berzofsky, eds., pp. 35-42    
32. H. Margalit, J. L. Spouge, J. L. Cornette, K. B. Cease, J. A. Berzofsky, and C. DeLisi
"Prediction of T-cell antigenic sites from the protein sequence"
(1987) J. Cellular Biochem. 11C : 236
33. J. L. Spouge
"Exact solutions for reaction-diffusion in one dimension. II. Spatial Distributions"  
(1988) J. Phys. A: Math. Gen. 21 : 4183-4199
34. J. A. Berzofsky, I. J. Berkower. K. B. Cease, H. Margalit, J. L. Cornette, J.L. Spouge, C. Spencer, G. Buckenmeyer, H. Streicher, M. Kojima, andC. DeLisi
"The role of MHC and amphipathic structures in T cell recognition:Features determining immunodominance"
(1988) Processing and Presentation of Antigens H. Vogel, B.Pernis, and S. Silverstein, eds., pp. 125-131
35. J. L. Spouge
"Speeding up dynamic programming algorithms for finding optimal latticepaths"
(1989) SIAM J. Appl. Math. 49 : 1552-1566
36. J. L. Spouge, S. P. Layne, and M. Dembo
"Analytic results for quantifying HIV infectivity"
(1989) Bull. Math. Biol. 51 : 715-730
37. P. M. Hale, K. B. Cease, R. M. Houghten, C. Ouyang, S. Putney, K. Jahaverian, H. Margalit, J. L. Cornette, J. L. Spouge, C. DeLisi, and J. A.Berzofsky
"T cell multideterminant regiouns in the human immunodeficiency virusenvelope: towards overcoming the problem of major histocompatibility complexrestriction"
(1989) Int. Immunol. 1 : 409-415    
38. S. P. Layne, J. L. Spouge, and M. Dembo
"The kinetics of HIV infectivity"
(1989) Los Alamos Science 18 : 91-109
39. S. P. Layne, J. L. Spouge, and M. Dembo
"Quantifying the infectivity of human immunodeficiency virus"
(1989) Proc. Natl. Acad. Sci. USA 86 : 4644-4648    
40. S. P. Layne, M. J. Merges, M. Dembo, J. L. Spouge, and P. L. Nara
"HIV requires multiple gp120 molecules for CD4-mediated infection"
(1990) Nature 346 : 277-279    
41. J. L. Spouge
"Fast optimal alignment"
(1991) Comput. Appl. Biosci. 7 : 1-7
42. S. P. Layne, M. J. Merges, J. L. Spouge, M. Dembo, and P. L. Nara
"Blocking of human immunodeficiency virus infection depends on celldensity and viral stock age"
(1991) J. Virol. 65 : 3293-3300    
43. J. L. Spouge
"Statistical analysis of sparse infection data and its implicationsfor retroviral treatment trials in primates"
(1992) Proc. Natl. Acad. Sci. USA 89 : 7581-7585    
44. S. P. Layne, M. J. Merges, M. Dembo, J. L. Spouge, S. R. Conley, J. P. Moore, J. L. Raina, J. H. Renz, H. R. Gelderblom, and P. L. Nara
"Factors underlying spontaneous inactivation and susceptibility toneutralization of human immunodeficiency virus"
(1992) Virology 189 : 3293-3300    
45. J. L. Spouge
"Viral multiplicity of attachment and its implications for HIV therapies"
(1994) J.Virol. 68 : 1782-1789    
46. J. L. Spouge
"Computation of the gamma, digamma, and trigamma functions"
(1994) SIAM J. Numerical Anal. 31 : 931-944
47. S. C. Wu, J. L. Spouge, S. R. Conley, W. P. Tsai, and P. L.Nara
"Human plasma enhances the infectivity of primary human immunodeficiencyvirus type 1 isolates in peripheral blood mononuclear cells and monocyte-derived macrophages"
(1995) J.Virol. 69 : 6054-6062    
48. W. J. Wilbur, F. Major, S. Bryant, Appendix by J. L. Spouge
"The statistics of unique native states for random peptides"
(1995) Biopolymers 38 : 447-459
49. J. L. Spouge, R. I. Shrager, and D. S. Dimitrov
"HIV-1 infection kinetics in tissue cultures"
(1996) Math. Biosciences 138 : 1-22
50. P. L. Nara, S. C. Wu, M. J. Merges, and J. L. Spouge
"Plasma factors in human blood alter the entry properties of HIV-1:Implications for gp120-based vaccine approaches"
(1996) Vaccines 96 pp. 323-332
51. S. C. Wu, J. L. Spouge, M. J. Merges, S. R. Conley, and P. L. Nara
"A cytopathic infectivity assay of human immunodeficiency virus type1 for human primary macrophages"
(1996) J.Virol. Methods 59 : 45-55    
52. S. C. Wu, J. L. Spouge, and P. L. Nara
"Kinetics of human immunodeficiency virus entry affected by human plasmamicroenvironment"
(1996) 7th Asian-Pacific Congress on Chemical Engineering pp.532-536
53. J. L. Spouge, A. Szabo, G. H. Weiss
"Single particle survival in gated trapping"
(1996) Phys. Rev. E 54 : 2248-2255
54. J. L. Spouge
"Single particle survival in parallel gated trapping"
(1997) Phys. Rev. E 55 : 421-425
55. J. L. Spouge
"Stochastically Gated Chemical Reactions"
(1997) J. Phys. Chem. B 101 : 5026-5030
56. T. D. Schneider, Appendix by J. L. Spouge
"Information content of individual genetic sequences"
(1997) J.Theor. Biol. 189 : 427-441    
57. S. C. Wu, J. L. Spouge, and P. L. Nara
"Increase of primary HIV-1 production in human peripheral blood mononuclear cells by intermittent medium replenishment"
(1998) Biotechnol. Prog. 14 : 540-542    
58. A. F. Neuwald, L. Aravind, J. L. Spouge, and E. V. Koonin
"AAA+: A class of chaperone-like ATPases associated with the assembly,operation, and disassembly of protein complexes"
(1999) Genome Res. 9 : 27-43    
59. T. G. Wolfsberg, A. E. Gabrielian, M. J. Campbell, R. J. Cho, J. L.Spouge, D. Landsman
"Candidate regulatory sequence elements for cell cycle-dependent transcription in saccharomyces cerevisiae"
(1999) Genome Res. 9 : 775-792    
60. J. L. Spouge and S. P. Layne
"A practical method for simultaneously determining the effective burstsizes and cycle times of viruses"
(1999) Proc. Natl. Acad. Sci. USA 96 : 7017-7022

61. J. L. Spouge, A. Marchler-Bauer, and S. H. Bryant
"The combinatorics and extreme value statistics of protein threading"
(1999) Annals of Combinatorics 3 : 81-93
62. I. K. Jordan IK, K.S. Makarova, J.L. Spouge, Y.I.Wolf, E.V. Koonin "Lineage-specific gene expansions in bacterial and archaeal genomes"
    (2001) Genome Res. 11: 555-6
63. J. L. Spouge"Finite-size corrections to Poisson approximations of rare events in renewal processes"
    (2001) Journal of Applied Probability 38 : 1-16
64. A. A. Schaffer, L. Aravind, T. L. Madden, S. Shavarin, J. L. Spouge , Y. I. Wolf, E. V. Koonin, and S. F. Altschul
    "Improving the Accuracy of PSI-BLAST Protein Database Searches with Composition-Based Statistics and Other Refinements"
    (2001) Nucleic Acids Research to appear
65. S. Rajasekaran, X. Jin, and J. L. Spouge
    "The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform"
    (2001) Journal of Computational Biol. to appear

Invited Reviews

1. J. L. Spouge
"A model of HIV infection and its blockers: From complex to simple"
in Computer Modeling and Simulations of Complex Biological Systems
S.S. Iyengar, ed., Ch. 5, pp. 67-77
(1998) CRC Press, Boca Raton
2. J. L. Spouge
"Smoluchowski gating theory and its application to viral blocking"
(1999) Recent Research Developments in Physical Chemistry 3 : 291-322

Posters and Abstracts

1. S. P. Layne, M. J. Merges, M. Dembo, J. L. Spouge, and P. L. Nara
"HIV gp120 cooperativity: A new outlook on viral receptor / anti-receptor based interventive strategies"
(1990) Hopkins Conference on AIDS, Baltimore, Maryland, USAApr 1-4, Poster #2, p. 2
2. S. P. Layne, M. J. Merges, M. Dembo, J. L. Spouge, and P. L. Nara
"gp120 cooperativity: A new finding that pertains to vaccine developmentand receptor / anti-receptor therapies"
(1990) VI International Conference on AIDS, San Francisco, California, USA Jun 20-24, Poster F.A. 317, p. 155
3. S. P. Layne, M. J. Merges, M. Dembo, J. L. Spouge, and P. L. Nara
"Determining basic molecular requirements for blocking therapies andHIV vaccines in vitro"
(1990) Modern Approaches to New Vaccines, Cold Spring Harbor, NewYork Sep 12-16, Abstract, p. 32
4. S. P. Layne, M. J. Merges, M. Dembo, J. L. Spouge, and P. L. Nara
"Envelope shedding and high cell density: Barriers to vaccine and immunotherapy development"
(1991) International Conference on AIDS, Florence, Italy Jun16-21, Poster #M.A.1270, p. 159
5. S. P. Layne, M. J. Merges, M. Dembo, J. L. Spouge, H. Gelderblom, and P. L. Nara
"Relationships between envelope shedding, cell density, and humoralblocking activity"
(1991) Laboratory of Tumor Cell Biology Annual Meeting, Bethesda,Maryland, USA Sep 1-8, Abstract, p. 61
6. S. P. Layne, M. J. Merges, M. Dembo, J. L. Spouge, H. Gelderblom, and P. L. Nara
"Factors regulating the spontaneous inactivation of HIV and its susceptibility to neutralization"
(1992) Laboratory of Tumor Cell Biology Annual Meeting, Bethesda,Maryland, USA Aug 9-16, Abstract, p. 39
7. S. P. Layne, M. J. Merges, M. Dembo, J. L. Spouge, H. Gelderblom, and P. L. Nara
"HIV-1 gp120 cooperativity: New insights into HIV receptor/antireceptorbased interventive strategies"
(1992) NIH Research Festival, Bethesda, Maryland, USA Sep 21-22,Abstract
8. M. J. Merges, S. P. Layne, M. Dembo, J. L. Spouge, H. Gelderblom, and P. L. Nara
"Determining biologically relevant neutralization parameters of humanimmunodeficiency virus type-1 through physicochemical analysis"
(1992) Laboratory of Tumor Cell Biology Annual Meeting, Bethesda,Maryland, USA Aug 9-16, Poster #B1
9. P. L. Nara, M. J. Merges, J. L. Spouge, S. R. Conley, and S. P.Layne
"Determinants of both viral and cellular origin in addition to thebiophysical properties of immunoglobulin influence the neutralization ofHIV-1"
(1992) Modern Approaches to New Vaccines Including Prevention ofAIDS,Cold Spring Harbor, New York Sep 16-20, p. 102
10. J. L. Spouge, P. L. Nara, M. J. Merges, and S. P. Layne
"Viral multiplicity of adsorption: A quantitative analogue of target-cell multiplicity of infection"
(1993) Laboratory of Tumor Cell Biology Annual Meeting, Bethesda,Maryland, USA Abstract
11. S. P. Layne, M. J. Merges, J. L. Spouge, H. Gelderblom, andP. L.Nara
"Extensive and fundamental investigations of how humoral immunity blocksHIV infection"
(1993) IX International Conference on AIDS, Berlin, GermanyJun 7-11, Abstract
12. M. J. Merges, S. P. Layne, J. L. Spouge, and P. L. Nara
"V3-specific neutralization: Valency, reversibility, and the stateof thevirion determine in vitro efficacy"
(1993) Laboratory of Tumor Cell Biology Annual Meeting, Bethesda,Maryland, USA Aug 22-28, Abstract
13. M. J. Merges, S. P. Layne, J. L. Spouge, and P. L. Nara
"Valency, reversibility, and the state of the virion determine in vitroHIV-1 V3-specific neutralization efficacy"
(1993) The 1st Annual National Conference on Human Retrovirusesand Related Infections, Washington, D.C., USA Dec 12-16, Poster #71
14. M. J. Merges, S. P. Layne, J. L. Spouge, and P. L. Nara
"Viral multiplicity of attachment and its implications for HIV therapies"
(1993) The 1st Annual National Conference on Human Retrovirusesand Related Infections, Washington, D.C., USA Dec 12-16, Poster #604
15. M. J. Merges, S. P. Layne, J. L. Spouge, and P. L. Nara
"Valency, reversibility, and the state of the virion determine in vitroHIV-1 V3-specific neutralization efficacy"
(1994) AIDS Weekly, Research Report Feb 14, p. 19
16. J. L. Spouge, G. P. Englund, R. I. Shrager, and D. S. Dimitrov
"Mathematical modeling of HIV-1 infection in tissue cultures: predictionand observation of oscillations in viral load"
(1995) AIDS Res. and Human Retr. 11 Laboratory ofTumor Cell Biology Annual Meeting, Bethesda, Maryland, USA Abstract#210 : p. s117
17. J. L. Spouge, G. P. Englund, R. I. Shrager, and D. S. Dimitrov
"Mathematical modeling of HIV-1 infection in tissue cultures: predictionand observation of oscillations in viral load"
(1995) NIH Research Festival, Bethesda, Maryland, USA Sep 18-19,p. 36, Poster #E-02
18. P. L. Nara, S. C. Wu, M. J. Merges, and J. L. Spouge
"Plasma factors in human blood alter the entry properties of HIV-1:Implications for gp120-based vaccine approaches"
(1996) Vaccines 96 pp. 323-332
19. J. F. Gibrat, T. Madej, J. L. Spouge, and S. H. Bryant
"The vast protein structure comparison method"
(1997) Biophysical J. 72 : MP298-MP298, Part 2

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