ReviewComputational and structural biotechnology journal2018
Computational Methods for Assessing Chromatin Hierarchy.
Review in Computational and structural biotechnology journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 27 citations in OpenAlex.
- Establishing an optimized ATAC-seq protocol for the maize.Frontiers in plant science · 2024Article
- Chromatin accessibility profiling by ATAC-seq.Nature protocols · 2022Review
- Bibliometric review of ATAC-Seq and its application in gene expression.Briefings in bioinformatics · 2022Review
- Review
- Mouse genomic and cellular annotations.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Understanding the function of regulatory DNA interactions in the interpretation of non-coding GWAS variants.Frontiers in cell and developmental biology · 2022Review
- The 3D Genome: From Structure to Function.International journal of molecular sciences · 2021Review
- From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-seq Data.Genomics, proteomics & bioinformatics · 2021Article
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
- Chromatin accessibility profiling methods.Nature reviews. Methods primers · 2021Article
- A Comparative Overview of Epigenomic Profiling Methods.Frontiers in cell and developmental biology · 2021Review
- SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.Journal for immunotherapy of cancer · 2020Article
- Are We Meeting the Promise of Endotypes and Precision Medicine in Asthma?Physiological reviews · 2020Review
- Analytical Approaches for ATAC-seq Data Analysis.Current protocols in human genetics · 2020Article
- From reads to insight: a hitchhiker's guide to ATAC-seq data analysis.Genome biology · 2020Review
- Genetics and Genomics Approaches for Diagnosis and Research Into Hereditary Anemias.Frontiers in physiology · 2020Review
- The changing paradigm of intron retention: regulation, ramifications and recipes.Nucleic acids research · 2019Review
- Tales from topographic oceans: topologically associated domains and cancer.Endocrine-related cancer · 2019Review
- Gray-level co-occurrence matrix analysis of chromatin architecture in periportal and perivenous hepatocytes.Histochemistry and cell biology · 2019Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling "higher-order" and "primary-order" chromatin structures from both experimental and computational aspects. Experimental requirements and considerations specific for each method were highlighted. For computational analysis, we summarized a common analysis strategy for both levels of chromatin assessment, focusing on the characteristic computing steps and the tools. The recently developed single-cell level techniques based on Hi-C and ATAC-seq present great potential to reveal cell-to-cell variability in chromosome architecture. A brief discussion on these methods in terms of experimental and data analysis features is included. We also touch upon the biological relevance of chromatin organization and how the combination with other techniques uncovers the underlying mechanisms. We conclude with a summary and our prospects on necessary improvements of currently available methods in order to advance understanding of chromatin hierarchy. Our review brings together the analyses of both higher- and primary-order chromatin structures, and serves as a roadmap when choosing appropriate experimental and computational methods for assessing chromatin hierarchy.
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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.