Bibliography of John L. Spouge
Titles link to *.pdf
files.
Citations link to Medline abstracts.
Publications
85. N. Kim, K.
Tharakaraman, L. Mariño-Ramírez, J.L. Spouge
"Finding sequence
motifs with Bayesian models incorporating positional information: an
application to transcription factor binding sites."
(2008) BMC Bioinformatics 9:262.
84. Tharakaraman, O.
Bodenreider, D. Landsman, J.L.
Spouge, L. Mariño-Ramírez
"The
biological function of some human transcription factor binding motifs varies
with position relative to the transcription start site."
(2008) Nucleic Acids Res. 36:2777-2786.
83. J.L. Spouge
"Markov additive processes and repeats in sequences”
(2007) Journal of Applied Probability 44: 514-527
82. J.L. Spouge
"Inequalities
on the overshoot beyond a boundary for independent summands with differing
distributions”
(2007) Statistics and Probability Letters 77:
1486-1489
81. M.G. Kann, S.L. Sheetlin, Y. Park, S.H.
Bryant, J.L. Spouge
"The
identification of complete domains within protein sequences using accurate
E-values for semi-global alignment”
(2007) Nucleic Acids Res 35: 4678-4685
80. N.K. Kim, K. Tharakaraman, J.L. Spouge
"Adding
sequence context to a Markov background model improves the identification of
regulatory elements”
(2006) Bioinformatics 22: 2870-2875
Supporting materials: AGLAM
1.6 : 2006-07-19
79. K. Tharakaraman,
L. Marino-Ramirez, S. Sheetlin, D. Landsman, J.L. Spouge
“Scanning sequences
after Gibbs sampling to find multiple occurrences of functional elements”
(2006) BMC Bioinformatics 8;408
Supporting materials: AGLAM
1.1 : 2006-06-11
78. S. Sheetlin, Y. Park, J.L. Spouge
"The
Gumbel pre-factor k for gapped local alignment can be estimated from
simulations of global alignment"
(2005) Nucleic Acids Research 33: 4987-4994
Supporting materials: Code
for Computing the BLAST Gumbel Parameters : 2008-02-14
Supporting materials: Code
for Computing the BLAST Gumbel Parameters : 2007-10-17
77.
Y. Park, S. Sheetlin, J.L.
Spouge
"Accelerated convergence and robust asymptotic regression of the Gumbel
scale parameter for gapped sequence alignment".
(2005) Journal of Physics A – Mathematics
and General 38: 97-108
76.
K.
Tharakaraman, L.
Marino-Ramirez, S. Sheetlin, D.
Landsman, J.L. Spouge
"Alignments anchored on genomic landmarks can aid in the identification of
regulatory elements"
(2005) Bioinformatics 21 Suppl 1: i440-i448
AWARD FOR BEST PAPER AT ISMB 2005 CONFERENCE
Supporting materials: AGLAM 1.0 : 2005-02-08
75.
Y. Park and J.L. Spouge
"Searching for multiple words in a Markov sequence"
(2004) INFORMS Journal on
Computing 16: 341-347
74.
J.L. Spouge
"Path reversal, islands, and the gapped alignment of random
sequences"
(2004) Journal of Applied Probability 41: 975-983
73.
J.L. Spouge
"Finite-size corrections to Poisson approximations in general
renewal-success processes"
(2004) Journal of Mathematical Analysis and Applications 301: 401-418
72. L. Marino-Ramirez, J.L. Spouge, G. C. Kanga, D.
Landsman
"Statistical analysis of over-represented words in human promoter
sequences"
(2004) Nucleic Acid
Research 32: 949-958
Supporting materials: 2004-08-22
71. M. C. Frith, U. Hansen, J.L. Spouge, Z. Weng
"Finding functional sequence elements by multiple local alignment"
(2004) Nucleic Acid
Research 32: 189-200
70. J. C. Silva, S. A. Shabalina,
D. G. Harris, J.L. Spouge, A. S. Kondrashov
"Conserved Fragments Of Transposable Elements In Intergenic Regions:
Evidence For Widespread Recruitment Of Mir- And L2-Derived Sequences Within The
Mouse And Human Genomes"
(2003) Genetical
Research 82: 1-18
69.
J.L. Spouge, H. Wan, and W.J. Wilbur
"Least squares isotonic regression in two dimensions"
(2003) Journal of Optimization Theory and Applications 117: 585-605
68.
Y. Park and J.L. Spouge
"The correlation error and finite-size correction in an
ungapped sequence alignment"
(2002) Bioinformatics 18: 1236-1242
67.
M. C. Frith, J.L. Spouge, U. Hansen, and Z. Weng
"Statistical Significance of Clusters of Motifs Represented by Position
Specific Scoring Matrices in Nucleotide Sequences"
(2002) Nucleic Acids Research 30: 3214-3224
66.
S. Rajasekaran,
X. Jin, and J.L. Spouge
"The Efficient Computation of Position-Specific Match Scores
with the Fast Fourier Transform"
(2002) Journal of Computational Biol. 9: 23-33
65.
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 29: 2994-3005
64.
J.L. Spouge
"Finite-size corrections to Poisson approximations of rare events in
renewal processes"
(2001) Journal of Applied Probability 38: 554-569
63. 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
62.
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
61.
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
60.
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
59.
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
58.
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
57. T. D. Schneider,
Appendix by J.L. Spouge
"Information content of individual genetic sequences"
(1997) J.Theor. Biol. 189 : 427-441
56.
J.L. Spouge
"Stochastically Gated Chemical Reactions"
(1997) J. Phys. Chem. B101 : 5026-5030
55.
J.L. Spouge
"Single particle survival in parallel gated trapping"
(1997) Phys. Rev. E55 : 421-425
54.
J.L. Spouge, A. Szabo, G. H. Weiss
"Single particle survival in gated trapping"
(1996) Phys. Rev. E 54 : 2248-2255
53.
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
52.
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
51.
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
50. J.L. Spouge,
R. I. Shrager, and D. S. Dimitrov
"HIV-1 infection kinetics in tissue cultures"
(1996) Math.
Biosciences 138 : 1-22
49.
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
48.
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
47.
J.L. Spouge
"Computation of the gamma, digamma, and trigamma
functions"
(1994) SIAM J. Numerical Anal. 31 : 931-944
46. J.L. Spouge
"Viral multiplicity of attachment and its implications for HIV
therapies"
(1994) J.Virol. 68 : 1782-1789
45.
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
44.
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
43.
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
42. J.L. Spouge
"Fast optimal alignment"
(1991) Comput. Appl. Biosci.7 : 1-7
41.
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
40.
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
39.
S. P. Layne, J.L. Spouge, and M. Dembo
"The kinetics of HIV infectivity"
(1989) Los Alamos Science 18 : 91-109
38.
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
37. J.L. Spouge,
S. P. Layne, and M. Dembo
"Analytic results for quantifying HIV infectivity"
(1989) Bull. Math. Biol. 51 : 715-730
36. J.L. Spouge
"Speeding up dynamic programming algorithms for finding optimal latticepaths"
(1989) SIAM J. Appl. Math. 49 : 1552-1566
35.
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, and C. 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
34. J.L. Spouge
"Exact solutions for reaction-diffusion in one dimension. II. Spatial
Distributions"
(1988) J. Phys. A: Math. Gen. 21 : 4183-4199
33.
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
32.
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
31.
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
30.
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
29.
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
28.
J.L. Spouge and J. A. Berzofsky
"Statistics in immunology and biochemistry: an application to T cell
antigenic sites"
(1987) Proceedings of the Theoretical Immunology Workshop A.S. Perelson, ed., pp. 131-145
27.
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
26.
J.L. Spouge
"Exact solutions for reaction-diffusion in one dimension"
(1987) Phys. Rev. Lett 60 : 871-874
25.
J.L. Spouge and G. I. Bell
"Coagulation and total weight fractions over a threshold size"
(1986) J. Coll. Interface Sci. 110 : 446-452
24.
J.L. Spouge
"Equilibrium ring-formation in polymer solutions"
(1986) J. Stat. Phys. 43 : 143-196
23. J.L. Spouge
"Increasing stability with complexity in a system composed of unstable
subsystems"
(1986) J. Math.
Anal. Appl. 118 : 502-518
22.
E. M. Hendriks,
J.L. Spouge, M. Eibl, and M. Schreckenberg
"Exact solutions for random coagulation processes"
(1985) Z. Phys. B58 : 219-227
21. A. S. Perelson and L. A. Segel
(appendix by J.L. Spouge)
"On a model for the structure of circular mitochondrial genomes in higher
plants"
(1985) IMAJ. Math. Appl. Med. Biol. 2 : 41-56
20.
J.L. Spouge
"Improving sequence-matching algorithms by working from both ends"
(1985) J. Mol. Biol. 181 : 137-138
19.
J.L. Spouge
"Analytic solutions to Smoluchowski's equation:
A combinatorial interpretation"
(1985) J. Phys. A. Math. Gen. 18 : 3063-3069
18. J.L. Spouge
"Monte Carlo results for random coagulation"
(1985) J. Phys. A. Math. Gen. 107
: 38-43
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
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
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
14. J.L. Spouge
"An existence theorem for the discrete coagulation fragmentation
equations"
(1984) Proc. Camb. Phil. Soc. 96 : 351-357
13. J.L. Spouge
"Long range percolation in one dimension"
(1984) J. Phys.
A: Math. Gen. 17 : 2349-2350
12.
J.L. Spouge
"Polymers and random graphs: Asymptotic equivalence to branching
processes"
(1984) J. Stat. Phys. 38 : 573-587
11.
J.L. Spouge
"Analytic results for finite systems of ringed Flory polymers"
(1984) Can. J. Chem. 62 : 1262-1264
10.
J.L. Spouge
"Improving sequence-matching algorithms by working from both ends"
(1984) J. Mol. Biol. 181 : 137-138
9.
J.L. Spouge
"A branching process solution of the polydisperse
coagulation equation"
(1983) Adv. Appl. Prob. 16 : 59-69
8.
J.L. Spouge
"Solutions and critical times for the polydisperse
coagulation equation when a(x,y) = A + B(x + y)+
Cxy"
(1983) J. Phys. A: Math. Gen. 16 : 3127-3132
7.
J.L. Spouge
"Tree models of aggregation: multiple particle and bond-types"
(1983) Proc. Roy . Soc. Lond.
387 : 351-365
6.
J.L. Spouge
"Asymmetric bonding of identical units: a general A[g]RB[f-g]
polymer model"
(1983) Macromolecules 16 : 831-835
5.
J.L. Spouge
"Solutions and critical times for the monodisperse
coagulation equation when aij =
A + B(i + j) + Cij"
(1983) J. Phys. A: Math. Gen. 16 : 767-774
4.
J.L. Spouge
"The size distribution for the AgRBf-g
model of polymerization"
(1983) J. Stat. Phys. 31 : 363-378
3.
J.L. Spouge
"Equilibrium polymer size distributions"
(1983) Macromolecules 16 : 121-127
2. J.L. Spouge and
S. B. Easterbrook-Smith
"A reinterpretation of the evidence for an interaction between Clg and pairs of immunoglobulin molecules in an immune
lattice"
(1982) Mol. Immunol. 19 : 253-256
1.
J.L. Spouge and P. A. Larkin
"A reason for pleomerism"
(1979) J. Fish. Res. Board Can. 36 : 255-269
Invited
Reviews
2.
J.L. Spouge
"Smoluchowski gating theory and its application to viral
blocking"
(1999) Recent Research Developments in Physical Chemistry 3: 291-322
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
Posters
and Abstracts
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
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
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
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.11Laboratory ofTumor
Cell Biology Annual Meeting, Bethesda, Maryland, USA Abstract #210 : p. s117
15.
M. J. Merges, S. P. Layne, J.L.
Spouge, and P. L. Nara
"Valency, reversibility, and the state of the virion determine in vitro HIV-1 V3-specific neutralization
efficacy"
(1994) AIDS Weekly, Research Report Feb 14, p. 19
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
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
12.
M. J. Merges, S. P. Layne, J.L.
Spouge, and P. L. Nara
"V3-specific neutralization: Valency,
reversibility, and the stateof the virion determine in vitro efficacy"
(1993) Laboratory of Tumor Cell Biology Annual Meeting, Bethesda,Maryland,
USA Aug 22-28, Abstract
11.
S. P. Layne, M. J. Merges, J.L.
Spouge, H. Gelderblom, andP. L.Nara
"Extensive and fundamental investigations of how humoral
immunity blocks HIV infection"
(1993) IX International Conference on AIDS, Berlin ,
GermanyJun
7-11, Abstract
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
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
8.
M. J. Merges, S. P. Layne, M. Dembo, J.L.
Spouge, H. Gelderblom,
and P. L. Nara
"Determining biologically relevant neutralization parameters of