ReviewNucleic acids research2006
Computational identification of transcriptional regulatory elements in DNA sequence.
Review in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
60 citing papers in PubMed, 130 citations in OpenAlex.
- Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer.bioRxiv : the preprint server for biology · 2026Article
- An explainable AI framework integrating machine and deep learning models for multi-species DNA functional group classification.Scientific reports · 2026Article
- DNA-Protein Binding is Dominated by Short Anchoring Elements.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Screening and Validation of p38 MAPK Involved in Ovarian Development ofFrontiers in veterinary science · 2022Article
- Quantifying the tissue-specific regulatory information within enhancer DNA sequences.NAR genomics and bioinformatics · 2021Article
- SCOUR: a stepwise machine learning framework for predicting metabolite-dependent regulatory interactions.BMC bioinformatics · 2021Article
- Article
- Anchor: trans-cell type prediction of transcription factor binding sites.Genome research · 2019Article
- Leveraging human genetic and adverse outcome pathway (AOP) data to inform susceptibility in human health risk assessment.Mammalian genome : official journal of the International Mammalian Genome Society · 2018Article
- Deciphering transcriptional regulations coordinating the response to environmental changes.BMC bioinformatics · 2016Article
- PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets.BioMed research international · 2016Article
- Article
- Sequence information gain based motif analysis.BMC bioinformatics · 2015Article
- Genome-wide analysis of transcription factor binding sites and their characteristic DNA structures.BMC genomics · 2015Article
- Improving MEME via a two-tiered significance analysis.Bioinformatics (Oxford, England) · 2014Article
- Article
- Bayesian centroid estimation for motif discovery.PloS one · 2013Article
- SPIC: a novel similarity metric for comparing transcription factor binding site motifs based on information contents.BMC systems biology · 2013Article
- Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters.PloS one · 2013Article
- Evidence classification of high-throughput protocols and confidence integration in RegulonDB.Database : the journal of biological databases and curation · 2013Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification and annotation of all the functional elements in the genome, including genes and the regulatory sequences, is a fundamental challenge in genomics and computational biology. Since regulatory elements are frequently short and variable, their identification and discovery using computational algorithms is difficult. However, significant advances have been made in the computational methods for modeling and detection of DNA regulatory elements. The availability of complete genome sequence from multiple organisms, as well as mRNA profiling and high-throughput experimental methods for mapping protein-binding sites in DNA, have contributed to the development of methods that utilize these auxiliary data to inform the detection of transcriptional regulatory elements. Progress is also being made in the identification of cis-regulatory modules and higher order structures of the regulatory sequences, which is essential to the understanding of transcription regulation in the metazoan genomes. This article reviews the computational approaches for modeling and identification of genomic regulatory elements, with an emphasis on the recent developments, and current challenges.
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Registered trials
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.