ArticleGenome biology2022
Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed, 10 citations in OpenAlex.
- CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.Genome biology · 2026Article
- A 3D Genome Atlas of Genetic Variants and Their Pathological Effects in Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles.Briefings in bioinformatics · 2024Review
- MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.Nucleic acids research · 2024Article
- 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages.Nature structural & molecular biology · 2024Article
- Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression.bioRxiv : the preprint server for biology · 2023Article
- EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions.Nucleic acids research · 2022Article
- Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies.Genome biology · 2022Article
- Understanding the function of regulatory DNA interactions in the interpretation of non-coding GWAS variants.Frontiers in cell and developmental biology · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. To analyze these large and complex datasets, computational methods are undergoing rapid and expansive evolution. Thus, a thorough evaluation of these analytical pipelines is necessary to identify which commonly used algorithms and processing pipelines need to be improved. Here we present a comprehensive benchmark framework, Bacon, to evaluate the performance of several computational methods. Finally, we provide practical recommendations for users working with HiChIP and/or ChIA-PET analyses.
Indexed as
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.