ArticleBioinformatics (Oxford, England)2012
CLARE: Cracking the LAnguage of Regulatory Elements.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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.
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Who cites it
12 citing papers in PubMed.
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Article
- Computational methods for identifying enhancer-promoter interactions.Quantitative biology (Beijing, China) · 2023Review
- A comprehensive review of computational prediction of genome-wide features.Briefings in bioinformatics · 2020Article
- Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties.PLoS computational biology · 2018Article
- A new method for enhancer prediction based on deep belief network.BMC bioinformatics · 2017Article
- Article
- Perspectives on Gene Regulatory Network Evolution.Trends in genetics : TIG · 2017Review
- Mechanisms of Evolutionary Innovation Point to Genetic Control Logic as the Key Difference Between Prokaryotes and Eukaryotes.Journal of molecular evolution · 2015Article
- Identification and computational analysis of gene regulatory elements.Cold Spring Harbor protocols · 2015Review
- Integrating diverse datasets improves developmental enhancer prediction.PLoS computational biology · 2014Article
- Identifying transcriptional cis-regulatory modules in animal genomes.Wiley interdisciplinary reviews. Developmental biologyReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
unlabelledCLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it learns the sequence code of the input set and builds a predictive model from features specific to those elements. The resulting model can then be applied to user-supplied genomic regions to identify novel candidate regulatory elements. CLARE's model also provides a detailed analysis of transcription factors that most likely bind to the elements, making it an invaluable tool for understanding mechanisms of tissue-specific gene regulation. AVAILABILITY: CLARE is freely accessible at http://clare.dcode.org/.
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Identifiers
What OpenQuestion holds
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.