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Improved benchmarks for computational motif discovery
(Journal article; Peer reviewed, 2007-06-08)
Background An important step in annotation of sequenced genomes is the identification of transcription factor binding sites. More than a hundred different computational methods have been proposed, and it is difficult ...
Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication
(Journal article; Peer reviewed, 2013)
A ChIP-Seq Benchmark Shows That Sequence Conservation Mainly Improves Detection of Strong Transcription Factor Binding Sites
(Journal article; Peer reviewed, 2011)
Background: Transcription factors are important controllers of gene expression and mapping transcription factor binding sites (TFBS) is key to inferring transcription factor regulatory networks. Several methods for ...
Assessment of composite motif discovery methods
(Journal article; Peer reviewed, 2008)
Background: Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have ...
The eGenVar data management system-cataloguing and sharing sensitive data and metadata for the life sciences
(Journal article; Peer reviewed, 2014)
Systematic data management and controlled data sharing aim at increasing reproducibility, reducing redundancy in work, and providing a way to efficiently locate complementing or contradicting information. One method of ...
Cell-type specificity of ChIP-predicted transcription factor binding sites
(Journal article; Peer reviewed, 2012)
Background Context-dependent transcription factor (TF) binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing ...