A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
By Gert Thijs, Magali Lescot, Kathleen Marchal, Stephane Rombauts, B. De Moor, Pierre Rouzé, Yves Moreau. Bioinform., 2001
437 citations recorded by the source corpus.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/8ff9c70376444bd0e5c861606d461b087d5f2d32
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Genetics
In Molecular Biology
- Joanne Chory
- Todd C. Mockler
- S. Harmer
- B. De Moor
- Jacques van Helden
- Todd P. Michael
- Kathleen Marchal
- Yves Moreau
Citations in the corpus
- The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. (2007, methodology): “A third use for HAYSTACK is to seed promoter analysis using ELEMENT or other promoter element discovery programs such as Promomer (Toufighi et al. 2005), SIFT (Hudson and Quail 2003), or MotifSampler (Thijs et al. 2001, 2002).”
- RSAT: regulatory sequence analysis tools (2008, methodology): “Reciprocally, the demo workflows on the RSAT web server include some example of multi-program pattern discovery combining oligoanalysis (RSAT), dyad-analysis (RSAT) andMotifSampler (TOUCAN).”
- A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes (2001, positive): “Currently, we have constructed an independent background model for Arabidopsis thaliana (based on the sequences in Araset [Pavy et al. , 1999] and PlantGene [Thijs et al. , 2001]) and also for Saccharomyces cerevisiae ( www.ucmb.ulb.ac.be/bioinformatics/rsa-tools/ ).”
- STAMP: a web tool for exploring DNA-binding motif similarities (2007, methodology): “Currently supported STAMP input formats include the output files from motif-finder programs like SOMBRERO (19), BioProspector (18), MDScan (20), AlignACE (21), MEME (22), Weeder (23), MotifSampler ( 24 ), YMF (25), ANN-Spec (26), Consensus (27), Improbizer and Co-Bind (28).”
- Interdependency of Brassinosteroid and Auxin Signaling in Arabidopsis (2004, methodology): “Improvements on these methods use so-called higher-order models based on Markov chain statistics (Thijs et al. 2001, 2002; Marchal et al. 2003), building the background model by estimating the probability at each nucleotide position based on the previous bases in the sequence.”
- Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development (2008, background): “2 [92,93]) and an exhaustive in silico testing of 6-mer and 8-mer nucleotide sequences.”