FAIR Genomics: Standards, Repositories, and Reproducibility in Chromatin and Genome Research

This Research Topic is part of our FAIR series. For other Research Topics in the series, please see below:FAIR Metabolomics: Open Datasets, Shared Standards, and the Road to AI-Ready DataFAIR RNA Data: Open Resources for Transcriptomics, Structure, and Regulatory Network ResearchFAIR Cell Biology Data: From Image Archives to Interoperable Signalling DatasetsFAIR Mitochondrial Data: Open Resources for Integrative Research in Bioenergetics and DiseaseFAIR Structural Data in the Age of AI: From Deposition to DiscoveryMaking Glycan Data FAIR: Addressing the Interoperability Gap in GlycoscienceGenome organisation research, spanning chromatin architecture, epigenomics, transcription factor binding, and 3D genome structure, routinely produces large, multi-modal datasets deposited in repositories such as GEO, SRA, ENCODE, and the 4D Nucleome. Yet FAIR compliance across these resources varies considerably, and integration between datasets generated by different platforms or research groups remains technically challenging.This Research Topic invites contributions addressing the practical implementation of FAIR principles in genome organisation research, including metadata harmonisation across sequencing technologies, ontologies for chromatin state annotation, and interoperability between 3D genome data formats such as .hic and .cool. Contributions addressing pipeline standardisation and parameter reporting — ensuring that published analyses can be reproduced from raw reads — are of particular importance. Contributions addressing the deposition of intermediate processed files alongside raw reads, to maximise the range of researchers who can engage with shared data, are of particular importance.We also welcome submissions on FAIR-compliant sharing of single-cell epigenomics data, TAD and enhancer-promoter interaction datasets, and regulatory element catalogues. Studies demonstrating novel insights enabled by cross-study data integration, and FAIR² Data Articles presenting curated, analysis-ready genomics datasets, are especially encouraged. Reproducible bioinformatics workflows built entirely on open data, and designed so that others can rerun analyses from raw reads to biological interpretation, are of high interest. KEY THEMESMetadata harmonisation across Hi-C, ATAC-seq, ChIP-seq, and CUT&RUN datasetsInteroperability between 3D genome data formats (.hic, .cool, .pairs)Ontologies and controlled vocabularies for chromatin state and regulatory element annotationFAIR-compliant deposition of TAD, enhancer-promoter, and insulator interaction dataReproducible bioinformatics workflows built on openly deposited raw dataFAIR practices for single-cell epigenomics and multi-modal genome dataCross-tissue and cross-condition integration of genome organisation datasetsLinking genome organisation data to gene expression and disease-relevant phenotypes Topic editors: Audesh Bhat, Jack DiGiovanna Source: https://www.frontiersin.org/research-topics/82999/fair-genomics-standards-repositories-and-reproducibility-in-chromatin-and-genome-research