ReviewBriefings in functional genomics2018
Integrating ChIP-seq with other functional genomics data.
Review in Briefings in functional genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 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
39 citing papers in PubMed, 87 citations in OpenAlex.
- Motif-Cluster: Motif driven prioritization of transcription factor binding clusters.PLoS computational biology · 2026Article
- Dynamic Histone Modification Patterns in Key Transcription Factor Genes During Porcine Adipogenesis.Genes · 2026Article
- Article
- Advances in Artificial Intelligence (AI) Models and Generative Algorithms Represent a New Paradigm for Genomics Research.International journal of molecular sciences · 2025Review
- Neur-Ally: a deep learning model for regulatory variant prediction based on genomic and epigenomic features in brain and its validation in certain neurological disorders.NAR genomics and bioinformatics · 2025Article
- A transcription network underlies the dual genomic coordination of mitochondrial biogenesis.eLife · 2024Article
- Identifying hub genes and key functional modules in leaf tissue of Populus species based on WGCNA.Genetica · 2024Article
- Understanding relationships between epigenetic marks and their application to robust assignment of chromatin states.Briefings in bioinformatics · 2024Article
- A transcription network underlies the dual genomic coordination of mitochondrial biogenesis.bioRxiv : the preprint server for biology · 2024Article
- Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets.Briefings in bioinformatics · 2024Review
- Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.Epigenomes · 2024Review
- epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation.Briefings in bioinformatics · 2024Article
- Article
- Analyzing histone ChIP-seq data with a bin-based probability of being signal.PLoS computational biology · 2023Article
- Epstein-Barr virus evades restrictive host chromatin closure by subverting B cell activation and germinal center regulatory loci.Cell reports · 2023Article
- Bioinformatics for wet-lab scientists: practical application in sequencing analysis.BMC genomics · 2023Article
- Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines.iScience · 2023Article
- The GRN concept as a guide for evolutionary developmental biology.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2023Article
- DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma.Bioinformatics (Oxford, England) · 2022Article
- Article
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.
Funding
Abstract
Transcription is regulated by transcription factor (TF) binding at promoters and distal regulatory elements and histone modifications that control the accessibility of these elements. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard assay for identifying genome-wide protein-DNA interactions in vitro and in vivo. As large-scale ChIP-seq data sets have been collected for different TFs and histone modifications, their potential to predict gene expression can be used to test hypotheses about the mechanisms of gene regulation. In addition, complementary functional genomics assays provide a global view of chromatin accessibility and long-range cis-regulatory interactions that are being combined with TF binding and histone remodeling to study the regulation of gene expression. Thus, ChIP-seq analysis is now widely integrated with other functional genomics assays to better understand gene regulatory mechanisms. In this review, we discuss advances and challenges in integrating ChIP-seq data to identify context-specific chromatin states associated with gene activity. We describe the overall computational design of integrating ChIP-seq data with other functional genomics assays. We also discuss the challenges of extending these methods to low-input ChIP-seq assays and related single-cell assays.
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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.