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John Spouge

Research Profile

Procedures

Occupations

Activities & Behaviors

Software

Chemicals & Drugs

Living Beings

HIV-1

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Genes & Molecular Sequences

Regulatory Elements, Transcriptional

Co-author Network

Publications

TOP 3
Conrad L Schoch; Keith A Seifert; John L Spouge; Wen Chen; Sabine M Huhndorf; C André Levesque; Vincent Robert
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.
Susanta Tewari; John L Spouge
Coalescent: an open-source and scalable framework for exact calculations in coalescent theory.
Yonil Park; Sergey L Sheetlin; Ning Ma; Thomas L Madden; John L Spouge
New finite-size correction for local alignment score distributions.

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All Publications

2012: Conrad L Schoch; Keith A Seifert; John L Spouge; Wen Chen; Sabine M Huhndorf; C André Levesque; Vincent Robert
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(16):6241-6.
2012: Susanta Tewari; John L Spouge
Coalescent: an open-source and scalable framework for exact calculations in coalescent theory.
BMC bioinformatics 2012;13():257.
2012: Yonil Park; Sergey L Sheetlin; Ning Ma; Thomas L Madden; John L Spouge
New finite-size correction for local alignment score distributions.
BMC research notes 2012;5():286.
2012: John L Spouge; Leonardo Mariño-Ramírez
The practical evaluation of DNA barcode efficacy.
Methods in molecular biology (Clifton, N.J.) 2012;858():365-77.
2011: Sergey L Sheetlin; Yonil Park; John L Spouge
Objective method for estimating asymptotic parameters, with an application to sequence alignment.
Physical review. E, Statistical, nonlinear, and soft matter physics 2011;84(3 Pt 1):031914.
2010: Hyrum D Carroll; Maricel G Kann; Sergey L Sheetlin; John L Spouge
Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics.
Bioinformatics (Oxford, England) 2010;26(14):1708-13.
2009: Leonardo Mariño-Ramírez; Kannan Tharakaraman; Olivier Bodenreider; John L Spouge; David Landsman
Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.
Methods in molecular biology (Clifton, N.J.) 2009;541():1-22.
2009: Leonardo Mariño-Ramírez; Kannan Tharakaraman; John L Spouge; David Landsman
Promoter analysis: gene regulatory motif identification with A-GLAM.
Methods in molecular biology (Clifton, N.J.) 2009;537():263-76.
2008: Martin C Frith; Yonil Park; Sergey L Sheetlin; John L Spouge
The whole alignment and nothing but the alignment: the problem of spurious alignment flanks.
Nucleic acids research 2008;36(18):5863-71.
2008: Kannan Tharakaraman; Olivier Bodenreider; David Landsman; John L Spouge; Leonardo Mariño-Ramírez
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.
Nucleic acids research 2008;36(8):2777-86.
2008: Nak-Kyeong Kim; Kannan Tharakaraman; Leonardo Mariño-Ramírez; John L Spouge
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites.
BMC bioinformatics 2008;9():262.
2007: Maricel G Kann; Sergey L Sheetlin; Yonil Park; Stephen H Bryant; John L Spouge
The identification of complete domains within protein sequences using accurate E-values for semi-global alignment.
Nucleic acids research 2007;35(14):4678-85.
2006: Nak-Kyeong Kim; Kannan Tharakaraman; John L Spouge
Adding sequence context to a Markov background model improves the identification of regulatory elements.
Bioinformatics (Oxford, England) 2006;22(23):2870-5.
2006: Kannan Tharakaraman; Leonardo Mariño-Ramírez; Sergey L Sheetlin; David Landsman; John L Spouge
Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements.
BMC bioinformatics 2006;7():408.
2005: Kannan Tharakaraman; Leonardo Mariño-Ramírez; Sergey L Sheetlin; David Landsman; John L Spouge
Alignments anchored on genomic landmarks can aid in the identification of regulatory elements.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i440-8.
2005: Sergey L Sheetlin; Yonil Park; John L Spouge
The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment.
Nucleic acids research 2005;33(15):4987-94.
2004: Leonardo Mariño-Ramírez; John L Spouge; Gavin C Kanga; David Landsman
Statistical analysis of over-represented words in human promoter sequences.
Nucleic acids research 2004;32(3):949-58.
2003: Joana Carneiro Da Silva; Svetlana A Shabalina; D G Harris; John L Spouge; A S Kondrashovi
Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes.
Genetical research 2003;82(1):1-18.
2002: Yonil Park; John L Spouge
The correlation error and finite-size correction in an ungapped sequence alignment.
Bioinformatics (Oxford, England) 2002;18(9):1236-42.
2001: Alejandro A Schäffer; L Aravind; Thomas L Madden; S Shavirin; John L Spouge; Yuri I Wolf; Eugene V Koonin; Stephen F Altschul
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.
Nucleic acids research 2001;29(14):2994-3005.
2001: I King Jordan; Kira S Makarova; John L Spouge; Yuri I Wolf; Eugene V Koonin
Lineage-specific gene expansions in bacterial and archaeal genomes.
Genome research 2001;11(4):555-65.
1999: Tyra G Wolfsberg; AE Gabrielian; M J Campbell; R J Cho; John L Spouge; David Landsman
Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae.
Genome research 1999;9(8):775-92.
1999: John L Spouge; S P Layne
A practical method for simultaneously determining the effective burst sizes and cycle times of viruses.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(12):7017-22.
1998: S C Wu; John L Spouge; P L Nara
Increase of primary HIV-1 production in human peripheral blood mononuclear cells by intermittent medium replenishment.
Biotechnology progress 1998;14(3):540-2.
1996: S C Wu; John L Spouge; M J Merges; S R Conley; PL Nara
A cytopathic infectivity assay of human immunodeficiency virus type 1 in human primary macrophages.
Journal of virological methods 1996;59(1-2):45-55.
1996: W John Wilbur; François Major; John L Spouge; S Bryant
The statistics of unique native states for random peptides.
Biopolymers 1996;38(4):447-59.
1995: S C Wu; John L Spouge; S R Conley; W P Tsai; M J Merges; PL Nara
Human plasma enhances the infectivity of primary human immunodeficiency virus type 1 isolates in peripheral blood mononuclear cells and monocyte-derived macrophages.
Journal of virology 1995;69(10):6054-62.
1994: John L Spouge
Viral multiplicity of attachment and its implications for human immunodeficiency virus therapies.
Journal of virology 1994;68(3):1782-9.
1992: John L Spouge
Statistical analysis of sparse infection data and its implications for retroviral treatment trials in primates.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(16):7581-5.
1992: S P Layne; M J Merges; micah dembo; John L Spouge; S R Conley; J P Moore; J L Raina; H Renz; H R Gelderblom; PL Nara
Factors underlying spontaneous inactivation and susceptibility to neutralization of human immunodeficiency virus.
Virology 1992;189(2):695-714.
1991: S P Layne; M J Merges; John L Spouge; micah dembo; PL Nara
Blocking of human immunodeficiency virus infection depends on cell density and viral stock age.
Journal of virology 1991;65(6):3293-300.
1991: John L Spouge
Fast optimal alignment.
Computer applications in the biosciences : CABIOS 1991;7(1):1-7.
1990: S P Layne; M J Merges; micah dembo; John L Spouge; PL Nara
HIV requires multiple gp120 molecules for CD4-mediated infection.
Nature 1990;346(6281):277-9.
1989: S P Layne; John L Spouge; micah dembo
Quantifying the infectivity of human immunodeficiency virus.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(12):4644-8.
1989: John L Spouge; S P Layne; micah dembo
Analytic results for quantifying HIV infectivity.
Bulletin of mathematical biology 1989;51(6):715-30.
1985: A S Perelson; L A Segel; John L Spouge
On a model for the structure of circular mitochondrial genomes in higher plants.
IMA journal of mathematics applied in medicine and biology 1985;2(1):41-56.