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» Genome-scale study of the importance of binding site context...
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BMCBI
2007
147views more  BMCBI 2007»
13 years 6 months ago
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining
Background: Cis-acting transcriptional regulatory elements in mammalian genomes typically contain specific combinations of binding sites for various transcription factors. Althoug...
Xochitl C. Morgan, Shulin Ni, Daniel P. Miranker, ...
BMCBI
2008
128views more  BMCBI 2008»
13 years 6 months ago
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor bindin
Background: Biologically active sequence motifs often have positional preferences with respect to a genomic landmark. For example, many known transcription factor binding sites (T...
Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mari...
BMCBI
2004
117views more  BMCBI 2004»
13 years 6 months ago
CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting
Background: All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome...
Henry R. Bigelow, Adam S. Wenick, Allan Wong, Oliv...
BMCBI
2010
167views more  BMCBI 2010»
13 years 6 months ago
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies
Background: Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription fa...
Denitsa Alamanova, Philip Stegmaier, Alexander E. ...
BMCBI
2007
149views more  BMCBI 2007»
13 years 6 months ago
Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
Background: Evolutionary conservation has been used successfully to help identify cis-acting DNA regions that are important in regulating tissue-specific gene expression. Motivate...
Xueping Yu, Jimmy J. Lin, Donald J. Zack, Jiang Qi...