ArticleGenes2012
Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays.
Article in Genes, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed, 44 citations in OpenAlex.
- Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data.bioRxiv : the preprint server for biology · 2025Article
- Methods for evaluating unsupervised vector representations of genomic regions.NAR genomics and bioinformatics · 2024Article
- Opportunities and challenges in sharing and reusing genomic interval data.Frontiers in genetics · 2023Article
- Characterization of chromatin accessibility patterns in different mouse cell types using machine learning methods at single-cell resolution.Frontiers in genetics · 2023Article
- Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs.Journal of animal science and biotechnology · 2022Article
- Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat.Genome biology · 2022Article
- PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments.NAR genomics and bioinformatics · 2021Article
- Rare Does Not Mean Worthless: How Rare Diseases Have Shaped Neurodevelopment Research in the NGS Era.Biomolecules · 2021Review
- Bedshift: perturbation of genomic interval sets.Genome biology · 2021Article
- Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine.Non-coding RNA · 2021Review
- Chromatin Accessibility of Human Mitral Valves and Functional Assessment of MVP Risk Loci.Circulation research · 2021Article
- Chromatin accessibility profiling methods.Nature reviews. Methods primers · 2021Article
- Article
- Frequency spectra characterization of noncoding human genomic sequences.Genes & genomics · 2020Article
- Enhancer prediction in the human genome by probabilistic modelling of the chromatin feature patterns.BMC bioinformatics · 2020Article
- Analytical Approaches for ATAC-seq Data Analysis.Current protocols in human genetics · 2020Article
- Regulatory variants: from detection to predicting impact.Briefings in bioinformatics · 2019Review
- LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.Nucleic acids research · 2018Article
- Computational Methods for Assessing Chromatin Hierarchy.Computational and structural biotechnology journal · 2018Review
- Novel method to ascertain chromatin accessibility at specific genomic loci from frozen brain homogenates and laser capture microdissected defined cells.Neuroepigenetics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
After finishing a human genome reference sequence in 2002, the genomics community has turned to the task of interpreting it. A primary focus is to identify and characterize not only protein-coding genes, but all functional elements in the genome. The effort includes both individual investigators and large-scale projects like the Encyclopedia of DNA Elements (ENCODE) project. As part of the ENCODE project, several groups have identified millions of regulatory elements in hundreds of human cell-types using DNase-seq and FAIRE-seq experiments that detect regions of nucleosome-free open chromatin. ChIP-seq experiments have also been used to discover transcription factor binding sites and map histone modifications. Nearly all identified elements are found in non-coding DNA, hypothesizing a function for previously unannotated sequence. In this review, we provide an overview of the ENCODE effort to define regulatory elements, summarize the main results, and discuss implications of the millions of regulatory elements distributed throughout the genome.
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.