ArticleNature communications2022
Stripenn detects architectural stripes from chromatin conformation data using computer vision.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Overcoming Artificial Structures in Resolution-Enhanced Hi-C Data by Signal Decomposition and Multi-Scale Attention.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Sequence design for three-dimensional genome folding using Akita Semifreddo.bioRxiv : the preprint server for biology · 2026Article
- De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion.Nature genetics · 2026Article
- 3D genetic architecture of schizophrenia risk across three neuronal subtypes.Molecular psychiatry · 2026Article
- DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID.Nature communications · 2026Article
- Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP.Nature communications · 2025Article
- Article
- MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets.bioRxiv : the preprint server for biology · 2025Article
- Architectural transcription factors collectively shape nuclear radial positioning of chromatin contacts.Science advances · 2025Article
- DeepNanoHi-C: deep learning enables accurate single-cell nanopore long-read data analysis and 3D genome interpretation.Nucleic acids research · 2025Article
- EBNA leader protein orchestrates chromatin architecture remodeling during Epstein-Barr virus-induced B cell transformation.Nucleic acids research · 2025Article
- StripePy: fast and robust characterization of architectural stripes.Bioinformatics (Oxford, England) · 2025Article
- Recipes and ingredients for deep learning models of 3D genome folding.Current opinion in genetics & development · 2025Review
- Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes.Communications biology · 2025Article
- Memory CD4+ T cells sequentially restructure their 3D genome during stepwise activation.Frontiers in cell and developmental biology · 2025Article
- Mapping the 3D genome architecture.Computational and structural biotechnology journal · 2025Review
- Perspective on recent developments and challenges in regulatory and systems genomics.Bioinformatics advances · 2025Review
- Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions.Nature communications · 2024Article
- Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
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Authors and funding
3 authors.
Funding
Abstract
Architectural stripes tend to form at genomic regions harboring genes with salient roles in cell identity and function. Therefore, the accurate identification and quantification of these features are essential for understanding lineage-specific gene regulation. Here, we present Stripenn, an algorithm rooted in computer vision to systematically detect and quantitate architectural stripes from chromatin conformation measurements using various technologies. We demonstrate that Stripenn outperforms existing methods and highlight its biological applications in the context of B and T lymphocytes. By comparing stripes across distinct cell types and different species, we find that these chromatin features are highly conserved and form at genes with prominent roles in cell-type-specific processes. In summary, Stripenn is a computational method that borrows concepts from widely used image processing techniques to demarcate and quantify architectural stripes.
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