SynthesisNature communications2022
ChIP-Hub provides an integrative platform for exploring plant regulome.
Synthesis in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 78 citations in OpenAlex.
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- Predicting transcriptional regulators in plants in the era of artificial intelligence.Current opinion in plant biology · 2026Review
- Integration of the D-Genome Reshapes Gene Transcription, Chromatin Architecture, and Metabolome of Allohexaploid Wheat, Leading to Enhanced Environmental Adaptability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.Plant communications · 2026Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- A cryptic START domain regulates deeply conserved transcription factors.The Plant cell · 2026Article
- BRANCHED1 acts as a rheostat of Nuclear Factor Y-dependent epigenetic regulation in axillary bud development.Nature communications · 2026Article
- SERRATE Regulates Floral Meristem Activity by Antagonizing SHOOT MERISTEMLESS and Repressing Cytokinin Signaling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Brassinosteroid signaling regulates shoot apical meristem homeostasis via orchestrating cytokinin and WUSCHEL activity.Science advances · 2026Article
- Article
- PCdb: A comprehensive plant genome-editing database integrating sgRNA efficiency, off-target predictions, and epigenomic landscapes.Plant communications · 2026Article
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Cross-species prediction of histone modifications in plants via deep learning.Genome biology · 2026Article
- PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms.bioRxiv : the preprint server for biology · 2025Article
- Evolutionary Diversification and Adaptive Evolution Analysis of the Plant HD-Zip IV Subfamily.Genes · 2025Article
- Rewiring of LEUNIG_HOMOLOG interaction networks marks regulatory shifts from meristem to organ growth in Arabidopsis flowers.The Plant journal : for cell and molecular biology · 2025Article
- Epigenetic crop improvement: Integrating ENCODE strategies into horticultural breeding.Horticulture research · 2025Article
- Review
- Cross-species modeling of plant genomes at single-nucleotide resolution using a pretrained DNA language model.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms the basis for most life on earth. A wealth of regulome and epigenome data have been generated in various plant species, but no common, standardized resource is available so far for biologists. Here, we present ChIP-Hub, an integrative web-based platform in the ENCODE standards that bundles >10,000 publicly available datasets reanalyzed from >40 plant species, allowing visualization and meta-analysis. We manually curate the datasets through assessing ~540 original publications and comprehensively evaluate their data quality. As a proof of concept, we extensively survey the co-association of different regulators and construct a hierarchical regulatory network under a broad developmental context. Furthermore, we show how our annotation allows to investigate the dynamic activity of tissue-specific regulatory elements (promoters and enhancers) and their underlying sequence grammar. Finally, we analyze the function and conservation of tissue-specific promoters, enhancers and chromatin states using comparative genomics approaches. Taken together, the ChIP-Hub platform and the analysis results provide rich resources for deep exploration of plant ENCODE. ChIP-Hub is available at https://biobigdata.nju.edu.cn/ChIPHub/ .
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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.