Search Results - "Spouge, J L"

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements by Schäffer, A A, Aravind, L, Madden, T L, Shavirin, S, Spouge, J L, Wolf, Y I, Koonin, E V, Altschul, S F

“…PSI-BLAST is an iterative program to search a database for proteins with distant similarity to a query sequence. We investigated over a dozen modifications to…”
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Prediction of immunodominant helper T cell antigenic sites from the primary sequence by Margalit, H, Spouge, JL, Cornette, JL, Cease, KB, Delisi, C, Berzofsky, JA

“…We have used a data base of 23 known immunodominant helper T cell antigenic sites located on 12 proteins to systematically develop an optimized algorithm for…”
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Factors underlying spontaneous inactivation and susceptibility to neutralization of human immunodeficiency virus by Layne, S P, Merges, M J, Dembo, M, Spouge, J L, Conley, S R, Moore, J P, Raina, J L, Renz, H, Gelderblom, H R, Nara, P L

“…To determine the factors governing inactivation and neutralization, physical, chemical, and biological assays were performed on a molecular clone of human…”
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The efficient computation of position-specific match scores with the fast fourier transform by Rajasekaran, S, Jin, X, Spouge, J L

“…Historically, in computational biology the fast Fourier transform (FFT) has been used almost exclusively to count the number of exact letter matches between…”
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Statistical Analysis of Sparse Infection Data and its Implications for Retroviral Treatment Trials in Primates by Spoug, John L.

“…Reports on retroviral primate trials rarely publish any statistical analysis. Present statistical methodology lacks appropriate tests for these trials and…”
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AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes by Neuwald, A F, Aravind, L, Spouge, J L, Koonin, E V

“…Using a combination of computer methods for iterative database searches and multiple sequence alignment, we show that protein sequences related to the AAA…”
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Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins by Cornette, J L, Cease, K B, Margalit, H, Spouge, J L, Berzofsky, J A, DeLisi, C

“…Protein segments that form amphipathic alpha-helices in their native state have periodic variation in the hydrophobicity values of the residues along the…”
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Finding functional sequence elements by multiple local alignment by Frith, Martin C., Hansen, Ulla, Spouge, John L., Weng, Zhiping

“…Algorithms that detect and align locally similar regions of biological sequences have the potential to discover a wide variety of functional motifs. Two…”
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HIV requires multiple gp120 molecules for CD4-mediated infection by Layne, Scott P, Merges, Michael J, Dembo, Micah, Spouge, John L, Nara, Peter L

“…Binding of glycoprotein gp120 to the T cell-surface receptor CD4 is a crucial step in CD4-dependent infection of a target cell by the human immunodeficiency…”
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Strong conformational propensities enhance T cell antigenicity by Spouge, JL, Guy, HR, Cornette, JL, Margalit, H, Cease, K, Berzofsky, JA, DeLisi, C

“…The ability to predict T cell antigenic peptides would have important implications for the development of artificial vaccines. As a first step towards…”
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Quantifying the Infectivity of Human Immunodeficiency Virus by Layne, Scott P., Spouge, John L., Dembo, Micah

“…We have developed a mathematical model that quantifies lymphocyte infection by human immunodeficiency virus (HIV) and lymphocyte protection by blocking agents…”
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Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences by Frith, Martin C., Spouge, John L., Hansen, Ulla, Weng, Zhiping

“…The human genome encodes the transcriptional control of its genes in clusters of cis‐elements that constitute enhancers, silencers and promoter signals. The…”
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Blocking of human immunodeficiency virus infection depends on cell density and viral stock age by LAYNE, S. P, MERGES, M. J, SPOUGE, J. L, DEMBO, M, NARA, P. L

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Viral multiplicity of attachment and its implications for human immunodeficiency virus therapies by Spouge, J L

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HIV-1 infection kinetics in tissue cultures by Spouge, John L., Shrager, Richard I., Dimitrov, Dimiter S.

“…Despite intensive experimental work on HIV-1, very little theoretical work has focused on HIV-1 spread in tissue culture. This article uses two systems of…”
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Human plasma enhances the infectivity of primary human immunodeficiency virus type 1 isolates in peripheral blood mononuclear cells and monocyte-derived macrophages by Wu, S C, Spouge, J L, Conley, S R, Tsai, W P, Merges, M J, Nara, P L

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The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment by Sheetlin, Sergey, Park, Yonil, Spouge, John L.

“…The optimal gapped local alignment score of two random sequences follows a Gumbel distribution. The Gumbel distribution has two parameters, the scale parameter…”
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Alignments anchored on genomic landmarks can aid in the identification of regulatory elements by Tharakaraman, Kannan, Mariño-Ramírez, Leonardo, Sheetlin, Sergey, Landsman, David, Spouge, John L.

“…Motivation: The transcription start site (TSS) has been located for an increasing number of genes across several organisms. Statistical tests have shown that…”
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Tree models of aggregation: multiple particle and bond-types by Spouge, J. L.

“…This paper considers aggregation processes where particles bond pairwise to form tree-structures. The tree-structures may model chemical polymerization, the…”
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Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes by Silva, J C, Shabalina, S A, Harris, D G, Spouge, J L, Kondrashovi, A S

“…We analysed the distribution of transposable elements (TEs) in 100 aligned pairs of orthologous intergenic regions from the mouse and human genomes. Within…”
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