ArticleGenome research2002
Discovery of regulatory elements by a computational method for phylogenetic footprinting.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers.
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Who cites it
131 citing papers in PubMed, 328 citations in OpenAlex.
- Genome-wide discovery ofeLife · 2026Article
- Computational inference of Rhizobium phaseoli transcriptional regulatory network predicts Transcription Factors involved in nodulation.Briefings in functional genomics · 2025Article
- Deep learning the cis-regulatory code for gene expression in selected model plants.Nature communications · 2024Article
- Graphylo: A deep learning approach for predicting regulatory DNA and RNA sites from whole-genome multiple alignments.iScience · 2024Article
- A multi-million-year natural experiment: Comparative genomics on a massive scale and its implications for human health.Evolution, medicine, and public health · 2024Article
- A survey on algorithms to characterize transcription factor binding sites.Briefings in bioinformatics · 2023Review
- BLSSpeller to discover novel regulatory motifs in maize.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Classification of Long Noncoding RNAs by k-mer Content.Methods in molecular biology (Clifton, N.J.) · 2021Article
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- Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1.Scientific reports · 2020Article
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- Transcriptional Regulation of Carotenoid Biosynthesis in Plants: So Many Regulators, So Little Consensus.Frontiers in plant science · 2019Review
- BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization.BMC bioinformatics · 2018Article
- Unsupervised statistical discovery of spaced motifs in prokaryotic genomes.BMC genomics · 2017Article
- An Intronic Enhancer Element Regulates Angiotensin II Type 2 Receptor Expression during Satellite Cell Differentiation, and Its Activity Is Suppressed in Congestive Heart Failure.The Journal of biological chemistry · 2016Article
- An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.BMC genomics · 2016Article
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- Article
- BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.Bioinformatics (Oxford, England) · 2015Article
- Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis.The Plant cell · 2014Article
71 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.