ArticleNucleic acids research2007
The Gibbs Centroid Sampler.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2.Nucleic acids research · 2023Article
- Prediction of Structure and Molecular Interaction with DNA of BvrR, a Virulence-Associated Regulatory Protein ofMolecules (Basel, Switzerland) · 2019Article
- Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome.Nucleic acids research · 2019Article
- Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.Nature microbiology · 2018Article
- NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.Nucleic acids research · 2017Article
- Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis.PloS one · 2017Article
- On the comparison of regulatory sequences with multiple resolution Entropic Profiles.BMC bioinformatics · 2016Article
- DynaMIT: the dynamic motif integration toolkit.Nucleic acids research · 2016Article
- The MEME Suite.Nucleic acids research · 2015Article
- Multiple novel promoter-architectures revealed by decoding the hidden heterogeneity within the genome.Nucleic acids research · 2014Article
- Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity.Nucleic acids research · 2014Article
- DMINDA: an integrated web server for DNA motif identification and analyses.Nucleic acids research · 2014Article
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- Article
- Comprehensive experimental fitness landscape and evolutionary network for small RNA.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Bayesian centroid estimation for motif discovery.PloS one · 2013Article
- The zinc-responsive regulon of Neisseria meningitidis comprises 17 genes under control of a Zur element.Journal of bacteriology · 2012Article
- Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks.Proteome science · 2011Article
- coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq data.Bioinformatics (Oxford, England) · 2011Article
- Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.Nucleic acids research · 2011Article
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Authors and funding
5 authors.
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Abstract
The Gibbs Centroid Sampler is a software package designed for locating conserved elements in biopolymer sequences. The Gibbs Centroid Sampler reports a centroid alignment, i.e. an alignment that has the minimum total distance to the set of samples chosen from the a posteriori probability distribution of transcription factor binding-site alignments. In so doing, it garners information from the full ensemble of solutions, rather than only the single most probable point that is the target of many motif-finding algorithms, including its predecessor, the Gibbs Recursive Sampler. Centroid estimators have been shown to yield substantial improvements, in both sensitivity and positive predictive values, to the prediction of RNA secondary structure and motif finding. The Gibbs Centroid Sampler, along with interactive tutorials, an online user manual, and information on downloading the software, is available at: http://bayesweb.wadsworth.org/gibbs/gibbs.html.
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