ReviewBriefings in bioinformatics2022
Bibliometric review of ATAC-Seq and its application in gene expression.
Review in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
30 citing papers in PubMed, 56 citations in OpenAlex.
- Profiling chromatin accessibility responses to seasonal heat stress in Angora rabbit testes.BMC genomics · 2026Article
- Single-Cell CRISPR: An Efficient Strategy for Decoding Plant Cis-Regulatory Complexity.Plant biotechnology journal · 2026Review
- An Integrative ATAC-Seq and RNA-Seq Analysis of Spleen Tissues from Largemouth Bass (International journal of molecular sciences · 2026Article
- ATAC-seq and RNA-seq reveal key genes and pathways regulating lactation in the mammary gland of Yili horses.BMC genomics · 2026Article
- Multi-omics analysis of somatic mutants reveals TCP7 allelically regulates multiple carotenogenic genes in citrus.Molecular horticulture · 2026Article
- ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species.BMC bioinformatics · 2026Article
- Cancer Reversion Therapy: Prospects, Progress and Future Directions.Current issues in molecular biology · 2025Review
- Probiotics derived sodium benzoate improves social behavior of offspring exposed in the maternal immune activation through regulation of histone lysine benzoylation in astrocytes.Molecular psychiatry · 2025Article
- The integration of genome-wide and transcriptome-wide association studies in neurodegenerative diseases: opportunities, challenges, and current methodological innovations.Briefings in bioinformatics · 2025Review
- Integration ATAC-Seq and RNA-Seq Analysis of Mammary Placodes in Erhualian and Bamaxiang Pigs Identified Candidate Genes Influencing Pig Teat Number Variation.Evolutionary applications · 2025Article
- Epigenetics factors in schizophrenia: future directions for etiologic and therapeutic study approaches.Annals of general psychiatry · 2025Review
- An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the α-globin regulatory elements and α-thalassemia--SEA deletion.Annals of hematology · 2025Article
- Advances on the Role of Lung Macrophages in the Pathogenesis of Chronic Obstructive Pulmonary Disease in the Era of Single-Cell Genomics.International journal of medical sciences · 2025Review
- A review of Ribosome profiling and tools used in Ribo-seq data analysis.Computational and structural biotechnology journal · 2024Review
- Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.eLife · 2024Article
- Article
- Androgen signaling inhibitsZoological research · 2024Article
- Dynamics of Chromatin Opening across Larval Development in the Urochordate AscidianInternational journal of molecular sciences · 2024Article
- 3D genome structural variations play important roles in regulating seed oil content of Brassica napus.Plant communications · 2024Article
- Dissecting the Immune System through Gene Regulation.Advances in experimental medicine and biology · 2024Article
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 at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With recent advances in high-throughput next-generation sequencing, it is possible to describe the regulation and expression of genes at multiple levels. An assay for transposase-accessible chromatin using sequencing (ATAC-seq), which uses Tn5 transposase to sequence protein-free binding regions of the genome, can be combined with chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) and ribonucleic acid sequencing (RNA-seq) to provide a detailed description of gene expression. Here, we reviewed the literature on ATAC-seq and described the characteristics of ATAC-seq publications. We then briefly introduced the principles of RNA-seq, ChIP-seq and ATAC-seq, focusing on the main features of the techniques. We built a phylogenetic tree from species that had been previously studied by using ATAC-seq. Studies of Mus musculus and Homo sapiens account for approximately 90% of the total ATAC-seq data, while other species are still in the process of accumulating data. We summarized the findings from human diseases and other species, illustrating the cutting-edge discoveries and the role of multi-omics data analysis in current research. Moreover, we collected and compared ATAC-seq analysis pipelines, which allowed biological researchers who lack programming skills to better analyze and explore ATAC-seq data. Through this review, it is clear that multi-omics analysis and single-cell sequencing technology will become the mainstream approach in future research.
Indexed as
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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.