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» DNA binding sites: representation and discovery
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BMCBI
2010
95views more  BMCBI 2010»
13 years 6 months ago
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
Background: ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of prot...
Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A. Wilson...
TCBB
2008
103views more  TCBB 2008»
13 years 6 months ago
DNA Motif Representation with Nucleotide Dependency
The problem of discovering novel motifs of binding sites is important to the understanding of gene regulatory networks. Motifs are generally represented by matrices (PWM or PSSM) o...
Francis Y. L. Chin, Henry C. M. Leung
BMCBI
2006
110views more  BMCBI 2006»
13 years 6 months ago
Design of a combinatorial DNA microarray for protein-DNA interaction studies
Background: Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Rec...
Julian Mintseris, Michael B. Eisen
BIB
2004
48views more  BIB 2004»
13 years 6 months ago
In silico representation and discovery of transcription factor binding sites
Giulio Pavesi, Giancarlo Mauri, Graziano Pesole
BMCBI
2010
121views more  BMCBI 2010»
13 years 3 months ago
Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites
Background: DNA instability profiles have been used recently for predicting the transcriptional start site and the location of core promoters, and to gain insight into promoter ac...
Miriam R. Kantorovitz, Zoi Rapti, Vladimir Gelev, ...