ArticleQuantitative biology (Beijing, China)2013
Computational methodology for ChIP-seq analysis.
Article in Quantitative biology (Beijing, China), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions.Hepatology communications · 2021Pooled it
- Characterization of Protein Co-Localization and Histone Modifications at Enhancers Anchored in Chromatin Loops.Biology · 2026Article
- BayesPI-FLY: a Bayesian neural network approach for inferring feature weighted TF-DNA interaction.Briefings in bioinformatics · 2026Article
- Article
- 2,3,7,8-Tetrachlorodibenzo-p-dioxin induces multigenerational alterations in the expression of microRNA in the thymus through epigenetic modifications.PNAS nexus · 2023Article
- Statistical Analysis in ChIP-seq-Related Applications.Methods in molecular biology (Clifton, N.J.) · 2023Article
- CpG content-dependent associations between transcription factors and histone modifications.PloS one · 2021Article
- RECOGNICER: A coarse-graining approach for identifying broad domains from ChIP-seq data.Quantitative biology (Beijing, China) · 2020Article
- FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues.Nature protocols · 2020Article
- Article
- HMMRATAC: a Hidden Markov ModeleR for ATAC-seq.Nucleic acids research · 2019Article
- Facilitating Analysis of Publicly Available ChIP-Seq Data for Integrative Studies.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2019Article
- Distinct DNA Sequence Preference for Histone Occupancy in Primary and Transformed Cells.Cancer informatics · 2019Article
- Epigenetic control of gene regulation during development and disease: A view from the retina.Progress in retinal and eye research · 2018Review
- Loss of the Hematopoietic Stem Cell Factor GATA2 in the Osteogenic Lineage Impairs Trabecularization and Mechanical Strength of Bone.Molecular and cellular biology · 2018Article
- MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps.BMC bioinformatics · 2016Article
- Genome-wide analysis of HIF-2α chromatin binding sites under normoxia in human bronchial epithelial cells (BEAS-2B) suggests its diverse functions.Scientific reports · 2016Article
- Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles.Nature medicine · 2016Article
- Single molecule and single cell epigenomics.Methods (San Diego, Calif.) · 2015Review
- Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.Cell cycle (Georgetown, Tex.) · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of DNA binding proteins such as transcription factors or modified histones. As more and more experimental laboratories are adopting ChIP-seq to unravel the transcriptional and epigenetic regulatory mechanisms, computational analyses of ChIP-seq also become increasingly comprehensive and sophisticated. In this article, we review current computational methodology for ChIP-seq analysis, recommend useful algorithms and workflows, and introduce quality control measures at different analytical steps. We also discuss how ChIP-seq could be integrated with other types of genomic assays, such as gene expression profiling and genome-wide association studies, to provide a more comprehensive view of gene regulatory mechanisms in important physiological and pathological processes.
Identifiers
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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.