ArticlePloS one2009
Identifying cis-regulatory sequences by word profile similarity.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 27 citations in OpenAlex.
- The Resolved Mutual Information Function as a Structural Fingerprint of Biomolecular Sequences for Interpretable Machine Learning Classifiers.Entropy (Basel, Switzerland) · 2021Article
- Alignment-free method for DNA sequence clustering using Fuzzy integral similarity.Scientific reports · 2019Article
- CAFE: aCcelerated Alignment-FrEe sequence analysis.Nucleic acids research · 2017Article
- Fast and accurate phylogeny reconstruction using filtered spaced-word matches.Bioinformatics (Oxford, England) · 2017Article
- Progress and challenges in bioinformatics approaches for enhancer identification.Briefings in bioinformatics · 2016Review
- Estimating evolutionary distances between genomic sequences from spaced-word matches.Algorithms for molecular biology : AMB · 2015Article
- Evidence for deep regulatory similarities in early developmental programs across highly diverged insects.Genome biology and evolution · 2014Article
- Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation.Nucleic acids research · 2014Article
- Computational identification of active enhancers in model organisms.Genomics, proteomics & bioinformatics · 2013Review
- Alignment-free sequence comparison based on next-generation sequencing reads.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis.PLoS genetics · 2012Article
- Discriminative prediction of mammalian enhancers from DNA sequence.Genome research · 2011Article
- Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.Nucleic acids research · 2011Article
- Formation of regulatory modules by local sequence duplication.PLoS computational biology · 2011Article
- New powerful statistics for alignment-free sequence comparison under a pattern transfer model.Journal of theoretical biology · 2011Article
- An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.Bioinformatics (Oxford, England) · 2010Article
- Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundRecognizing regulatory sequences in genomes is a continuing challenge, despite a wealth of available genomic data and a growing number of experimentally validated examples. METHODOLOGY/PRINCIPAL
findingsWe discuss here a simple approach to search for regulatory sequences based on the compositional similarity of genomic regions and known cis-regulatory sequences. This method, which is not limited to searching for predefined motifs, recovers sequences known to be under similar regulatory control. The words shared by the recovered sequences often correspond to known binding sites. Furthermore, we show that although local word profile clustering is predictive for the regulatory sequences involved in blastoderm segmentation, local dissimilarity is a more universal feature of known regulatory sequences in Drosophila. CONCLUSIONS/SIGNIFICANCE: Our method leverages sequence motifs within a known regulatory sequence to identify co-regulated sequences without explicitly defining binding sites. We also show that regulatory sequences can be distinguished from surrounding sequences by local sequence dissimilarity, a novel feature in identifying regulatory sequences across a genome. Source code for WPH-finder is available for download at http://rana.lbl.gov/downloads/wph.tar.gz.
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