Bibliography

Articles

A 114. J.L. Spouge "A comprehensive estimation of country-level basic reproduction numbers R0 for COVID-19: Regime regression can automatically estimate the end of the exponential phase in epidemic data" (2021) PLoS One

A 113. J.L. Spouge, J.M. Ziegelbauer, and M.W. Gonzalez "A linear-time algorithm that avoids inverses and computes jackknife (leave-one-out) products like convolutions or other operators in commutative semigroups" (2020) Algorithms for Molecular Biology

A 112. M.P. Martin, P.P. Daniels, D. Erickson, and J.L. Spouge "Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera" (2020) PLoS ONE 15(1):e0227127

A 111. K.A. Melzak, J.L. Spouge, C. Boecker, F. Kirschhöfer, G. Brenner-Weiss, and K. Bieback "Hemolysis Pathways during Storage of Erythrocytes and Inter-Donor Variability in Erythrocyte Morphology" (2020) Transfusion Medicine and Hemotherapy

A 110. V. Patel and J.L. Spouge "Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects" (2020) PLoS ONE 15(1):e0227127

A 109. M.T.V. Hoang, L. Irinyi, S.C.A. Chen, T. Sorrell, ISHAM Barcoding of Medical Fungi Working Group incl. J.L. Spouge, and W. Meyer "Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections" (2019) Frontiers in Microbiology 10: 1647

A 108. A. Manzourolajdad and J.L. Spouge "Structural Prediction of RNA Switches using Conditional Base-Pair Probabilities" (2019) PLoS ONE 14(6):e0217625

A 107. J.L. Spouge "An accurate approximation for the expected site frequency spectrum in a Galton-Watson process under an infinite sites mutation model" (2019) Theoretical Population Biology 127 : 7-15

A 106. H.D. Carroll, M.W. Gonzalez, and J.L. Spouge "MultiDomainBenchmark: a multi-domain query and subject database suite" (2019) BMC Bioinformatics 20 : 77

A 105. K. Tang, J. Ren, R. Cronn, D.L. Erickson, B.G. Milligan, M. Parker-Forney, J.L. Spouge, and F. Sun "Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA" (2018) BMC Genomics

A 104. T. Tagawa, S. Gao, V.N. Koparde, M. Gonzalez, J.L. Spouge, A.P. Serquiña, K. Lurain, R. Ramaswami, T.S. Uldrick, R. Yarchoan, and J.M. Ziegelbauer "Discovery of Kaposi's sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA" (2018) PNAS

A 103. I. Gauran, J. Park, J. Lim, D. Park, J. Zylstra, T. Peterson, M. Kann, and J.L. Spouge "Empirical Null Estimation using Zero-inflated Discrete Mixture Distributions and its Application to Protein Domain Data" (2018) Biometrics PMC5862774

A 102. M. Mengistu, A.H. Tang, J.S. Foulkes, T.A. Blanpied, M.W. Gonzalez, J.L. Spouge, R.C. Gallo, G.K. Lewis, and A.L. DeVico "Patterns of conserved gp120 epitope presentation on attached HIV-1 virions" (2017) PNAS

A 101. M.W. Gonzalez, A.L. DeVico, and J.L. Spouge "Conserved signatures indicate HIV-1 transmission is under strong selection and thus is not a "stochastic" process" (2017) Retrovirology 24:13

A 100. N. Acevedo-Luna, L. Mariño-Ramírez, A. Halbert, U. Hansen, D. Landsman, and J.L. Spouge "Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules" (2016) BMC Bioinformatics 17:479

A 99. S.L. Sheetlin, Y. Park, M.C. Frith, and J.L. Spouge "ALP & FALP: C++ Libraries for pairwise local alignment E-values" (2016) Bioinformatics

A 98. A. Manzourolajdad, M.W. Gonzalez, and J.L. Spouge "Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic" (2016) PLoS One

A 97. H.D. Carroll, A.C. Williams, A.G. Davis, and J.L. Spouge "Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate" (2015) IEEE/ACM Trans Comput Biol Bioinform 8213 : 194-201 PMC4568567

A 96. J.C. Silva, A. Egan, C. Arze, J.L. Spouge, and D.G. Harris "A new method for estimating species age supports the co-existence of malaria parasites and their mammalian hosts" (2015) Molecular Biology and Evolution PMC4408405

A 95. S. Tewari and J.L. Spouge "Coalescent: an Open-Science framework for Importance Sampling in Coalescent Theory" (2015) PeerJ PMC4548476

A 94. M.W. Gonzalez, A.L. DeVico, G.K. Lewis, and J.L. Spouge "Conserved molecular signatures in HIV gp120 are associated with the preferential transmission of HIV-1, SHIV, and SIV transmitted/founder viruses" (2015) J Virology 89 : 3619-3629 PMC4403421

A 93. S.L. Sheetlin, Y. Park, M.C. Frith, and J.L. Spouge "Frameshift alignment: statistics and post-genomic applications" (2014) Bioinformatics PMC4253828

A 92. S.L. Sheetlin, L. Mariño-Ramírez, and J.L. Spouge "Searching for Repeats, as an Example of Using the Generalized Ruzzo-Tompa Algorithm to Find Optimal Subsequences with Gaps" (2014) International Journal of Bioinformatics Research and Applications 10 : 384-408 PMC4135518

A 91. J.L. Spouge "Within a Sample from a Population, the Distribution of the Number of Descendants of a Subsample's Most Recent Common Ancestor" (2014) Theoretical Population Biology 92 : 51-54 PMC3944932

A 90. N.-K. Kim, R.V. Jayatillake, and J.L. Spouge "NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data" (2013) BMC Genomics 14 : 349 PMC3672025

A 89. N. Suwannasai, M.P. Martín, C. Phosri, P. Sihanonth, A.J.S. Whalley and J.L. Spouge "Fungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera" (2013) PLoS One 8 : e54529 PMC3563529

A 88. M.W. Gonzalez and J.L. Spouge "Domain Analysis of Symbionts and Hosts (DASH) in a genome-wide survey of pathogenic human viruses" (2013) BMC Research Notes 6 : 209 PMC3672079

A 87. CBOL Protist Working Group [Member : J.L. Spouge] "Barcoding eukaryotic richness beyond the animal, plant and fungal kingdoms" (2012) PLoS Biol 10 :e1001419 PMC3491025

A 86. Y. Park, S.L. Sheetlin, N. Ma, T.L. Madden, and J.L. Spouge "New Finite-Size Correction for Local Alignment Score Distributions" (2012) BMC Research Notes 5 : 286 PMC3483159

A 85. CBOL Fungal Working Group [Member : J.L. Spouge] "The nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi" (2012) PNAS 109 : 6241-6246 PMC3341068

A 84. S. Tewari and J.L. Spouge "An Open-Source and Scalable Framework for Exact Calculations in Coalescent Theory" (2012) BMC Bioinformatics 13: 257 PMC3575375

A 83. J.L. Spouge and L. Mariño-Ramírez "The practical evaluation of DNA barcode efficacy" (2012) Methods Mol Biol 858 : 365-377 PMC3410705

A 82. S.L. Sheetlin, Y. Park, and J.L. Spouge "An objective method for estimating asymptotic parameters, with application to biological sequence alignment" (2011) Physics Review E 84 : 031914 PMC3233989

A 81. H.D. Carroll, M.G. Kann, S.L. Sheetlin, and J.L. Spouge "Threshold Average Precision (TAP-k): a Measure of Retrieval Efficacy Designed for Bioinformatics" (2010) Bioinformatics 26 : 1708-1713 PMC2894514

A 80. CBOL Plant Working Group [Member : J.L. Spouge] "A DNA barcode for land plants" (2009) Proc Natl Acad Sci USA 106 : 12794-12797 PMC2722355

A 79. L. Mariño-Ramírez, K. Tharakaraman, J.L. Spouge, and D. Landsman "Promoter analysis: gene regulatory motif identification with A-GLAM" (2009) Methods Mol Biol 537 : 263-276 PMC2702474

A 78. Y. Park, S. Sheetlin, and J.L. Spouge "Estimating the Gumbel scale parameter for local alignment of random sequences by importance sampling with stopping times" (2009) Ann Stat 37 : 3697-3714 PMC2818155

A 77. D.L. Erickson, J.L. Spouge, A. Resch, L.A. Weight, and J.W. Kress "DNA barcoding in land plants: developing standards to quantify and maximize success" (2008) Taxon 54 : 1304-1316

A 76. M.C. Frith, Y. Park, S.L. Sheetlin, and J.L. Spouge "The whole alignment and nothing but the alignment: the problem of spurious alignment flanks" (2008) Nucl Acids Res 36 : 5863-5871 PMC2566872

A 75. N. Kim, K. Tharakaraman, L. Mariño-Ramírez, and J.L. Spouge "Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites" (2008) BMC Bioinformatics 9 : 262 PMC2432075

A 74. Tharakaraman, O. Bodenreider, D. Landsman, J.L. Spouge, and L. Mariño-Ramírez "The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site" (2008) Nucl Acids Res 36 : 2777-2786 PMC2377430

A 73. J.L. Spouge "Correction to Markov additive processes and repeats in sequences" (2007) J Appl Prob 44 : 1122

A 72. J.L. Spouge "Markov additive processes and repeats in sequences" (2007) J Appl Prob 44 : 514-527

A 71. J.L. Spouge "Inequalities on the overshoot beyond a boundary for independent summands with differing distributions" (2007) Stat and Prob Letters 77 : 1486-1489 PMC2683021

A 70. M.G. Kann, S.L. Sheetlin, Y. Park, S.H. Bryant, and J.L. Spouge "The identification of complete domains within protein sequences using accurate E-values for semi- global alignment" (2007) Nucl Acids Res 35 : 4678-4685 PMC1950549

A 69. N.K. Kim, K. Tharakaraman, and J.L. Spouge "Adding sequence context to a Markov background model improves the identification of regulatory elements" (2006) Bioinformatics 22 : 2870-2875

A 68. K. Tharakaraman, L. Mariño-Ramírez, S. Sheetlin, D. Landsman, and J.L. Spouge "Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements" (2006) BMC Bioinformatics 8 : 408 PMC1599759

A 67. S. Sheetlin, Y. Park, and J.L. Spouge "The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment" (2005) Nucl Acids Res 33 : 4987-4994 PMC1199557

A 66. J.L. Spouge "Finite-size corrections to Poisson approximations" (2005) J Math Anal Appl 301 : 401-418

A 65. Y. Park, S. Sheetlin, and J.L. Spouge "Accelerated convergence and robust asymptotic regression of the Gumbel scale parameter for gapped sequence alignment" (2005) J Phys A : Math Gen 38 : 97-108

A 64. Y. Park and J.L. Spouge "Searching for multiple words in a Markov sequence" (2004) INFORMS J on Computing 16 : 341-347

A 63. J.L. Spouge "Path reversal, islands, and the gapped alignment of random sequences" (2004) J Appl Prob 41 : 975-983

A 62. L. Mariño-Ramírez, J.L. Spouge, G.C. Kanga, and D. Landsman "Statistical analysis of over-represented words in human promoter sequences" (2004) Nucl Acid Res 32 : 949-958 PMC373387

A 61. M.C. Frith, U. Hansen, J.L. Spouge, and Z. Weng "Finding functional sequence elements by multiple local alignment" (2004) Nucl Acid Res 32 : 189-200

A 60. J.C. Silva, S. A. Shabalina, D.G. Harris, J.L. Spouge, and 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 Res 82 : 1-18

A 59. J.L. Spouge, H. Wan, and W.J Wilbur "Least squares isotonic regression in two dimensions" (2003) J Optimization Theory Appl 117 : 585-605 Free Full Text in PubMed Central

A 58. Y. Park and J.L. Spouge "The correlation error and finite-size correction in an ungapped sequence alignment" (2002) Bioinformatics 18 : 1236-1242

A 57. M.C. Frith, J.L. Spouge, U. Hansen, and and Z. Weng "Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences" (2002) Nucl Acids Res 30 : 3214-3224 PMC135758

A 56. S. Rajasekaran, X. Jin, and J.L. Spouge "The efficient computation of position-specific match scores with the Fast Fourier Transform" (2002) J Computational Biol 9 : 23-33

A 55. 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) Nucl Acids Res 29 : 2994-3005 PMC55814

A 54. J.L. Spouge "Finite-size corrections to Poisson approximations of rare events in renewal processes" (2001) J Appl Prob 38 : 554-569

A 53. I.K. Jordan, K.S. Makarova, J.L. Spouge, Y.I.Wolf, and E.V. Koonin "Lineage-specific gene expansions in bacterial and archaeal genomes" (2001) Genome Res 11 : 555-565 PMC311027

A 52. J.L. Spouge, A. Marchler-Bauer, and S.H. Bryant "The combinatorics and extreme value statistics of protein threading" (1999) Ann Combinatorics 3 : 81-93

A 51. J.L. Spouge and S.P. Layne "A practical method for simultaneously determining the effective burst sizes and cycle times of viruses" (1999) Proc Natl Acad Sci USA 96 : 7017-7022 PMC22041

A 50. T.G. Wolfsberg, A.E. Gabrielian, M.J. Campbell, R.J. Cho, J.L. Spouge, and D. Landsman "Candidate regulatory sequence elements for cell cycle-dependent transcription in saccharomyces cerevisiae" (1999) Genome Res 9 : 775-792 PMC310804

A 49. A.F. Neuwald, L. Aravind, J.L. Spouge, and 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

A 48. 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

A 47. T.D. Schneider and Appendix by J.L. Spouge "Information content of individual genetic sequences" (1997) J Theor Biol 189 : 427-441

A 46. J.L. Spouge "Stochastically gated chemical reactions" (1997) J Phys Chem b 101 : 5026-5030

A 45. J.L. Spouge "Single particle survival in parallel gated trapping" (1997) Phys Rev E 55 : 421-425

A 44. J.L. Spouge, A. Szabo, and G.H. Weiss "Single particle survival in gated trapping" (1996) Phys Rev E 54 : 2248-2255

A 43. S.C. Wu, J.L. Spouge, M.J. Merges, S.R. Conley, and P.L. Nara "A cytopathic infectivity assay of human immunodeficiency virus type 1 for human primary macrophages" (1996) J Virol Methods 59 : 45-55

A 42. J.L. Spouge, R.I. Shrager, and D.S. Dimitrov "HIV-1 infection kinetics in tissue cultures" (1996) Math Biosciences 138 : 1-22

A 41. W. J Wilbur, F. Major, S.H. Bryant, and Appendix by J.L. Spouge "The statistics of unique native states for random peptides" (1995) Biopolymers 38 : 447-459

A 40. 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 189502

A 39. J.L. Spouge "Computation of the gamma, digamma, and trigamma functions" (1994) SIAM J Num Anal 31 : 931-944

A 38. J.L. Spouge "Viral multiplicity of attachment and its implications for HIV therapies" (1994) J Virol 68 : 1782-1789 PMC236639

A 37. 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 to neutralization of human immunodeficiency virus" (1992) Virology 189 : 3293-3300

A 36. J.L. Spouge "Statistical analysis of sparse infection data and its implications for retroviral treatment trials in primates" (1992) Proc Natl Acad Sci USA 89 : 7581-7585 PMC49754

A 35. S.P. Layne, M.J. Merges, J.L. Spouge, M. Dembo, and P.L. Nara "Blocking of human immunodeficiency virus infection depends on cell density and viral stock age" (1991) J Virol 65 : 3293-3300 PMC240987

A 34. J.L. Spouge "Fast optimal alignment" (1991) Comput Appl Biosci 7 : 1-7

A 33. 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

A 32. 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 PMC287327

A 31. S.P. Layne, J.L. Spouge, and M. Dembo "The kinetics of HIV infectivity" (1989) Los Alamos Science 18 : 91-109

A 30. S.P. Layne, J.L. Spouge, and M. Dembo "Measuring HIV infectivity. Mathematical and statistical approaches to AIDS epidemiology" (1989) Lecture Notes in Biomath 83: 90-110, Springer, Berlin

A 29. J.L. Spouge, S.P. Layne, and M. Dembo "Analytic results for quantifying HIV infectivity" (1989) Bull Math Biol 51 : 715-730

A 28. J.L. Spouge "Speeding up dynamic programming algorithms for finding optimal lattice paths" (1989) SIAM J Appl Math 49 : 1552-1566

A 27. J.L. Spouge "Exact solutions for reaction-diffusion in one dimension. II. Spatial distributions" (1988) J Phys A : Math Gen 21 : 4183-4199

A 26. 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

A 25. 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

A 24. 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

A 23. J.L. Spouge "Exact solutions for reaction-diffusion in one dimension" (1987) Phys Rev Lett 60 : 871-874

A 22. J.L. Spouge and G.I. Bell "Coagulation and total weight fractions over a threshold size" (1986) J Coll Interface Sci 110 : 446-452

A 21. J.L. Spouge "Equilibrium ring-formation in polymer solutions" (1986) J Stat Phys 43 : 143-196

A 20. J.L. Spouge "Increasing stability with complexity in a system composed of unstable subsystems" (1986) J Math Anal Appl 118 : 502-518

A 19. E.M. Hendriks, J.L. Spouge, M. Eibl, and M. Schreckenberg "Exact solutions for random coagulation processes" (1985) Z Phys b 58 : 219-227

A 18. A.S. Perelson, L.A. Segel, and 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

A 17. J.L. Spouge "Improving sequence-matching algorithms by working from both ends" (1985) J Mol Biol 181 : 137-138

A 16. J.L. Spouge "Analytic solutions to Smoluchowski's equation : a combinatorial interpretation" (1985) J Phys A : Math Gen 18 : 3063-3069

A 15. J.L. Spouge "Monte Carlo results for random coagulation" (1985) J Phys A : Math Gen 107 : 38-43

A 14. 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

A 13. J.L. Spouge "An existence theorem for the discrete coagulation fragmentation equations" (1984) Proc Camb Phil Soc 96 : 351-357

A 12. J.L. Spouge "Long range percolation in one dimension" (1984) J Phys A : Math Gen 17 : 2349-2350

A 11. J.L. Spouge "Polymers and random graphs : Asymptotic equivalence to branching processes" (1985) J Stat Phys 38 : 573-587

A 10. J.L. Spouge "Analytic results for finite systems of ringed Flory polymers" (1984) Can J Chem 62 : 1262-1264

A 9. J.L. Spouge "A branching process solution of the polydisperse coagulation equation" (1983) Adv Appl Prob 16 : 59-69

A 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

A 7. J.L. Spouge "Tree models of aggregation : multiple particle and bond-types" (1983) Proc Roy Soc Lond 387 : 351-365

A 6. J.L. Spouge "Asymmetric bonding of identical units : a general AgRBf-g polymer model" (1983) Macromolecules 16 : 831-835

A 5. J.L. Spouge "Solutions and critical times for the monodisperse coagulation equation when ai,j = A + B(i + j) + Cij" (1983) J Phys A : Math Gen 16 : 767-774

A 4. J.L. Spouge "The size distribution for the AgRBf-g model of polymerization" (1983) J Stat Phys 31 : 363-378

A 3. J.L. Spouge "Equilibrium polymer size distributions" (1983) Macromolecules 16 : 121-127

A 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

A 1. J.L. Spouge and P.A. Larkin "A reason for pleomerism" (1979) J Fish Res Board Can 36 : 255-269

Reviews

R 8. J.L. Spouge "Measurement of a Barcode's Accuracy in Identifying Species" (2016) DNA Barcoding in Marine Perspectives Ch. 2, pp. 29-43 S. Trivedi, A.A. Ansari, S.K. Ghosh & H. Rehman, eds., Springer Nature

R 7. J.L. Spouge "Smoluchowski gating theory and its application to viral blocking" (1999) Recent Research Developments in Physical Chemistry 3 : 291-322

R 6. J.L. Spouge "A model of HIV infection and its blockers : From complex to simple" (1998) Computer Modeling and Simulations of Complex Biological Systems Ch. 5, pp. 67-77 S.S. Iyengar, ed., CRC Press, Boca Raton

R 5. 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

R 4. 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 regions in the human immunodeficiency virus envelope: towards overcoming the problem of major histocompatibility complex restriction" (1989) Int Immunol 1 : 409-415

R 3. 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, pp. 125-131 H. Vogel, b. Pernis, and S. Silverstein, eds.

R 2. 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 sites on proteins" (1987) Immunogenicity of Protein Antigens: Repertoire and Regulation, pp. 35-42 E.E. Secarz and J.A. Berzofsky, eds. Abstract in PubMed Central

R 1. 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

Proceedings

CP 8. H.D. Carroll, A.C. Williams, A.G. Davis, and J.L. Spouge "False Discovery Rate for Homology Searches" (2014) Advances In Bioinformatics And Computational Biology, J. C. Setubal, and N. F. Almeida (Eds.) 8213 : 194-201

CP 7. S.L. Sheetlin, L. Mariño-Ramírez, and J.L. Spouge "The Ruzzo-Tompa Algorithm Can Find The Maximal Paths In Weighted, Directed Graphs On A One-Dimensional Lattice" (2012) IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences ICCABS

CP 6. J.C. Zamora, F. de Diego Calonge, J.L. Spouge, and M.P. Martin "Exploring DNA Barcoding Regions in Geastrum (Agaricomycetes)" (2011) Fourth International Barcode of Life Conference

CP 5. K. Tharakaraman, L. Mariño-Ramírez, S. Sheetlin, D. Landsman, and J.L. Spouge "Alignments anchored on genomic landmarks can aid in the identification of regulatory elements" (2005) Bioinformatics 21 Suppl 1 : i440-i448 PMC1317086 Award for Best Paper at ISMB 2005 Conference

CP 4. S. C. Wu, J.L. Spouge, and 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

CP 3. 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, pp. 131-145 A.S. Perelson, ed.

CP 2. J.L. Spouge "Cross-linking of identical particles by multiple ligand-types" (1985) Proceedings of the Conference on Mathematical Biology 1983, Bari, Italy, pp. 354-359 V. Capasso, E. Grosso, and S.L. Paveri-Fontana, eds.

CP 1. J.L. Spouge "Random graph problems in polymer chemistry" (1985) Proceedings of the Conference on Random Graphs 1983, Poznan, Poland Disc Appl Math 28 : 251-262

Abstracts and Posters

AP 18. 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

AP 17. J.L. Spouge, G.P. Englund, R.I. Shrager, and D.S. Dimitrov "Mathematical modeling of HIV-1 infection in tissue cultures: prediction and observation of oscillations in viral load" (1995) NIH Research Festival, Bethesda, Maryland, USA Sep 18-19, p. 36, Poster #E-02

AP 16. 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

AP 15. M.J. Merges, S.P. Layne, J.L. Spouge, and P.L. Nara "Viral multiplicity of attachment and its implications for HIV therapies" (1993) 1st Annual National Conference on Human Retroviruses and Related Infections, Washington, D.C., USA, Dec 12-16, Poster #604

AP 14. 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" (1993) 1st Annual National Conference on Human Retroviruses and Related Infections, Washington, D.C., USA, Dec 12-16, Poster #71

AP 13. 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

AP 12. S.P. Layne, M.J. Merges, J.L. Spouge, H. Gelderblom, and P.L. Nara "Extensive and fundamental investigations of how humoral immunity blocks HIV infection" (1993) IX International Conference on AIDS, Berlin , Germany, Jun 7-11, Abstract

AP 11. 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

AP 10. P.L. Nara, M.J. Merges, J.L. Spouge, S.R. Conley, and and S.P. Layne "Determinants of both viral and cellular origin in addition to the biophysical properties of immunoglobulin influence the neutralization of HIV-1" (1992) Modern Approaches to New Vaccines Including Prevention of AIDS, Cold Spring Harbor, New York Sep 16-20, p. 102

AP 9. M.J. Merges, S.P. Layne, M. Dembo, J.L. Spouge, H. Gelderblom, and 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

AP 8. S.P. Layne, M.J. Merges, M. Dembo, J.L. Spouge, H. Gelderblom, and and P.L. Nara "HIV-1 gp120 cooperativity : New insights into HIV receptor/antireceptor-based interventive strategies" (1992) NIH Research Festival, Bethesda, Maryland, USA, Sep 21-22, Abstract

AP 7. S.P. Layne, M.J. Merges, M. Dembo, J.L. Spouge, H. Gelderblom, and 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

AP 6. S.P. Layne, M.J. Merges, M. Dembo, J.L. Spouge, H. Gelderblom, and 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

AP 5. S.P. Layne, M.J. Merges, M. Dembo, J.L. Spouge, and and P.L. Nara "Envelope shedding and high cell density : Barriers to vaccine and immunotherapy development" (1991) International Conference on AIDS, Florence, Italy, Jun 16-21, Poster #M.A.1270, p. 159

AP 4. S.P. Layne, M.J. Merges, M. Dembo, J.L. Spouge, and and P.L. Nara "Determining basic molecular requirements for blocking therapies and HIV vaccines in vitro" (1990) Modern Approaches to New Vaccines, Cold Spring Harbor, New York, Sep 12-16, Abstract, p. 32

AP 3. S.P. Layne, M.J. Merges, M. Dembo, J.L. Spouge, and 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

AP 2. S.P. Layne, M.J. Merges, M. Dembo, J.L. Spouge, and 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, USA, Apr 1-4, Poster #2, p. 2

AP 1. 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