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    BMCBI
    2007
    233views more  BMCBI 2007»
    160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
    13 years 5 months ago
    160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
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    Background: To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching s...
    Isaac T. S. Li, Warren Shum, Kevin Truong
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    BMCBI
    2005
    169views more  BMCBI 2005»
    MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
    13 years 5 months ago
    MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
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    Background: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. Th...
    Voichita D. Marinescu, Isaac S. Kohane, Alberto Ri...
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    BMCBI
    2005
    113views more  BMCBI 2005»
    Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks
    13 years 5 months ago
    Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks
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    Background: Biological processes are carried out by coordinated modules of interacting molecules. As clustering methods demonstrate that genes with similar expression display incr...
    Cecily J. Wolfe, Isaac S. Kohane, Atul J. Butte
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    BMCBI
    2004
    115views more  BMCBI 2004»
    Quantifying the relationship between co-expression, co-regulation and gene function
    13 years 5 months ago
    Quantifying the relationship between co-expression, co-regulation and gene function
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    Background: It is thought that genes with similar patterns of mRNA expression and genes with similar functions are likely to be regulated via the same mechanisms. It has been diff...
    Dominic J. Allocco, Isaac S. Kohane, Atul J. Butte
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    BMCBI
    2005
    144views more  BMCBI 2005»
    Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in
    13 years 5 months ago
    Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in
    Download  www.biomedcentral.com
    Background: Comparison of data produced on different microarray platforms often shows surprising discordance. It is not clear whether this discrepancy is caused by noisy data or b...
    Scott L. Carter, Aron C. Eklund, Brigham H. Mecham...
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