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In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection
BackgroundThe PmrAB (BasSR) two-component regulatory system is required for Salmonella typhimurium virulence. PmrAB-controlled modifications of the lipopolysaccharide (LPS) layer confer resistance toExpand
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Inferring transcriptional modules from ChIP-chip, motif and microarray data
Abstract'ReMoDiscovery' is an intuitive algorithm to correlate regulatory programs with regulators and corresponding motifs to a set of co-expressed genes. It exploits in a concurrent way threeExpand
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Inferring the transcriptional network of Bacillus subtilis.
The adaptation of bacteria to the vigorous environmental changes they undergo is crucial to their survival. They achieve this adaptation partly via intricate regulation of the transcription of theirExpand
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More robust detection of motifs in coexpressed genes by using phylogenetic information
BackgroundSeveral motif detection algorithms have been developed to discover overrepresented motifs in sets of coexpressed genes. However, in a noisy gene list, the number of genes containing theExpand
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A novel approach to identifying regulatory motifs in distantly related genomes
Although proven successful in the identification of regulatory motifs, phylogenetic footprinting methods still show some shortcomings. To assess these difficulties, most apparent when applyingExpand
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The Condition‐Dependent Transcriptional Network in Escherichia coli
Thanks to the availability of high‐throughput omics data, bioinformatics approaches are able to hypothesize thus‐far undocumented genetic interactions. However, due to the amount of noise in theseExpand
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IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data
BackgroundThe development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S rRNA gene ampliconExpand
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Genome-specific higher-order background models to improve motif detection.
Motif detection based on Gibbs sampling is a common procedure used to retrieve regulatory motifs in silico. Using a species-specific background model was previously shown to increase the robustnessExpand
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NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads
BackgroundThe popularity of new sequencing technologies has led to an explosion of possible applications, including new approaches in biodiversity studies. However each of these sequencingExpand
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