Discovering regulatory elements in non-coding sequences by analysis of spaced dyads.

By Jacques van Helden, Alma. F. Rios, Julio Collado-Vides. Nucleic Acids Research, 2000

355 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b7e21654d680ba67a9bf98614936ff95122cf698

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In Molecular Biology

Citations in the corpus

DWE: Discriminating Word Enumerator (2005, methodology): “Other motif discovery algorithms that use word-counting methods are reported previously (Van Helden et al., 1998, 2000; Sinha and Tompa, 2002).”
Regulatory Sequence Analysis Tools (2003, background): “A second program, dyadanalysis (8), specifically detects such spaced motifs, which are typical of many bacterial transcription factors, and of the fungal binuclear zinc cluster proteins.”
Finding composite regulatory patterns in DNA sequences (2002, methodology): “The forth related work is the RSA-dyad algorithm by van Helden et al. (2000), which compares observed frequencies of pairs of spaced trinucleotides to the expected frequencies of the pairs.”
An improved map of conserved regulatory sites for Saccharomyces cerevisiae (2006, background): “The factor Dal82 is now predicted to have a specificity of AAaNwT-Selected (GATAAG) is likely to represent the binding specificities of Gln3, Gat1, and Dal80, which are known to co-regulate allophanate/oxalurate-dependent genes along with Dal82 [19].”
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling (2001, methodology): “These methods can be divided in two major classes: methods based on word counting (Jensen and Knudsen, 2000; Vanet et al., 2000; van Helden et al., 1998, 2000 ) and methods based on probabilistic sequence models (Bailey and Elkan, 1995; Hughes et al., 2000; Lawrence et al., 1993; Liu et al., 1995; ”
A survey of DNA motif finding algorithms (2007, neutral): “[24] extended their method to find”
LOGOS: a modular Bayesian model for de novo motif detection (2003, background): “, 2001; Bailey and Elkan, 1995], or imposing explicit “shape” [Helden et al., 2000] or entropy constraints [Kechris et al.”
A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes (2001, neutral): “In these tests, we used the higher-order background models compiled from the upstream regions of all the annotated genes in the yeast genome (van Helden et al. , 2000b).”