ArticleNucleic acids research2011
A new framework for identifying cis-regulatory motifs in prokaryotes.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.Patterns (New York, N.Y.) · 2024Article
- CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq.Briefings in bioinformatics · 2023Article
- Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites.Nucleic acids research · 2020Article
- Exacerbated obesogenic response in female mice exposed to early life stress is linked to fat depot-specific upregulation of leptin protein expression.American journal of physiology. Endocrinology and metabolism · 2020Article
- Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1.Scientific reports · 2020Article
- Identifying Plant Pentatricopeptide Repeat Coding Gene/Protein Using Mixed Feature Extraction Methods.Frontiers in plant science · 2018Article
- An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.BMC genomics · 2016Article
- Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses.Scientific reports · 2016Article
- cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.Nucleic acids research · 2015Article
- Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum.Nucleic acids research · 2015Article
- DMINDA: an integrated web server for DNA motif identification and analyses.Nucleic acids research · 2014Article
- Global O-GlcNAc Levels Modulate Transcription of the Adipocyte Secretome during Chronic Insulin Resistance.Frontiers in endocrinology · 2014Article
- Article
- DOOR 2.0: presenting operons and their functions through dynamic and integrated views.Nucleic acids research · 2014Article
- Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress.Biotechnology for biofuels · 2013Article
- A fast weak motif-finding algorithm based on community detection in graphs.BMC bioinformatics · 2013Article
- Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions.Nucleic acids research · 2013Article
- Phylogenetic footprinting: a boost for microbial regulatory genomics.Protoplasma · 2012Review
- Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis.BMC plant biology · 2012Article
- QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.PloS one · 2012Article
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4 authors.
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Abstract
We present a new algorithm, BOBRO, for prediction of cis-regulatory motifs in a given set of promoter sequences. The algorithm substantially improves the prediction accuracy and extends the scope of applicability of the existing programs based on two key new ideas: (i) we developed a highly effective method for reliably assessing the possibility for each position in a given promoter to be the (approximate) start of a conserved sequence motif; and (ii) we developed a highly reliable way for recognition of actual motifs from the accidental ones based on the concept of 'motif closure'. These two key ideas are embedded in a classical framework for motif finding through finding cliques in a graph but have made this framework substantially more sensitive as well as more selective in motif finding in a very noisy background. A comparative analysis shows that the performance coefficient was improved from 29% to 41% by our program compared to the best among other six state-of-the-art prediction tools on a large-scale data sets of promoters from one genome, and also consistently improved by substantial margins on another kind of large-scale data sets of orthologous promoters across multiple genomes. The power of BOBRO in dealing with noisy data was further demonstrated through identification of the motifs of the global transcriptional regulators by running it over 2390 promoter sequences of Escherichia coli K12.
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