ArticlePLoS computational biology2024
Cooltools: Enabling high-resolution Hi-C analysis in Python.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 221 papers.
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Who cites it
221 citing papers in PubMed.
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Comparative genomics reveals lineage-associated structural variation and diversification in a barley fungal pathogen.The New phytologist · 2026Article
- Chromosome-level phylogenomics and genome evolution of the grape family.Nature plants · 2026Article
- Article
- Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase.eLife · 2026Article
- Topoisomerase-mediated resolution of negative DNA supercoiling sustains human transcription and gene activation.bioRxiv : the preprint server for biology · 2026Article
- Spatial chromatin architecture and accessibility co-profiling of mammalian tissues.Nature methods · 2026Article
- Nested TAD hierarchy defines cohesion zones on replicated chromosomes.The EMBO journal · 2026Article
- Identification of differential topologically associating domains from low sequencing depth and pseudobulk chromatin contact maps.Genome research · 2026Article
- Influence of Histone Acetylation on Chromatin 3D Organization inInternational journal of molecular sciences · 2026Article
- Matrix Rigidity Mechanoprimes Microglia for Inflammation Through Cytoskeletal-to-Nuclear Signaling and 3D Spatio-Epigenomic Remodeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Single-cell mapping of chromosome breaks identifies multiple fragile site classes with distinct DNA replication timing landscapes.Nature communications · 2026Article
- Directionality of transcriptional regulatory elements.Nature communications · 2026Article
- Single-allele chromatin tracing reveals cytokine-dependent super-enhancer repositioning in CD4Immunity · 2026Article
- Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3.Nucleic acids research · 2026Article
- GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles.Nucleic acids research · 2026Article
- CTCF aligns single-cell TAD-like domain boundaries and stabilizes long-range active chromatin clusters.Science advances · 2026Article
- Cohesin promotes genomic stability by suppressing unequal sister chromatid exchange.bioRxiv : the preprint server for biology · 2026Article
- De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.Genome research · 2026Article
- dcHiChIP: a comprehensive Nextflow-based pipeline for multiscale analysis of chromatin architecture from HiChIP data.Bioinformatics (Oxford, England) · 2026Article
161 more citing papers are in PubMed but not listed here.
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11 authors.
Funding
Abstract
Chromosome conformation capture (3C) technologies reveal the incredible complexity of genome organization. Maps of increasing size, depth, and resolution are now used to probe genome architecture across cell states, types, and organisms. Larger datasets add challenges at each step of computational analysis, from storage and memory constraints to researchers' time; however, analysis tools that meet these increased resource demands have not kept pace. Furthermore, existing tools offer limited support for customizing analysis for specific use cases or new biology. Here we introduce cooltools (https://github.com/open2c/cooltools), a suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Cooltools leverages the widely-adopted cooler format which handles storage and access for high-resolution datasets. Cooltools provides a paired command line interface (CLI) and Python application programming interface (API), which respectively facilitate workflows on high-performance computing clusters and in interactive analysis environments. In short, cooltools enables the effective use of the latest and largest genome folding datasets.
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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.