ArticleBioinformatics (Oxford, England)2020
Cooler: scalable storage for Hi-C data and other genomically labeled arrays.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,177 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
1,177 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cross-platform Hi-C meta-analysis identifies functional insulators that actively block enhancer-promoter interactions.Nature communications · 2026Pooled it
- Article
- Translocation-induced enhancer rewiring reveals cryptic oncogenic circuits in multiple myeloma.Science advances · 2026Article
- 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
- Nested TAD hierarchy defines cohesion zones on replicated chromosomes.The EMBO journal · 2026Article
- Matrix Rigidity Mechanoprimes Microglia for Inflammation Through Cytoskeletal-to-Nuclear Signaling and 3D Spatio-Epigenomic Remodeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Influence of Histone Acetylation on Chromatin 3D Organization inInternational journal of molecular sciences · 2026Article
- A scaffolding element rewires local 3D chromatin architecture during differentiation.Nature communications · 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
- cPRC1.2 and CTCF-mediated transition from poised to active chromatin loops at bivalent genes.EMBO reports · 2026Article
- De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.Genome research · 2026Article
- hnRNPK condensates facilitate enhancer-promoter looping and RNA polymerase II recruitment.Nature genetics · 2026Article
- Cohesin promotes genomic stability by suppressing unequal sister chromatid exchange.bioRxiv : the preprint server for biology · 2026Article
- dcHiChIP: a comprehensive Nextflow-based pipeline for multiscale analysis of chromatin architecture from HiChIP data.Bioinformatics (Oxford, England) · 2026Article
- Bacteriophage PAK_P3 genome structuration and dynamics during infection ofScience advances · 2026Article
- Enhanced chromatin compaction is associated with de novo expression of a nuclear microprotein, global loss of H3 acetylation and local transcriptional changes in retinal rod photoreceptors.Research square · 2026Article
- Article
- Topological mixing and irreversibility in animal chromosome evolution.Science advances · 2026Article
1,117 more citing papers are in PubMed but not listed here.
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
motivationMost existing coverage-based (epi)genomic datasets are one-dimensional, but newer technologies probing interactions (physical, genetic, etc.) produce quantitative maps with two-dimensional genomic coordinate systems. Storage and computational costs mount sharply with data resolution when such maps are stored in dense form. Hence, there is a pressing need to develop data storage strategies that handle the full range of useful resolutions in multidimensional genomic datasets by taking advantage of their sparse nature, while supporting efficient compression and providing fast random access to facilitate development of scalable algorithms for data analysis.
resultsWe developed a file format called cooler, based on a sparse data model, that can support genomically labeled matrices at any resolution. It has the flexibility to accommodate various descriptions of the data axes (genomic coordinates, tracks and bin annotations), resolutions, data density patterns and metadata. Cooler is based on HDF5 and is supported by a Python library and command line suite to create, read, inspect and manipulate cooler data collections. The format has been adopted as a standard by the NIH 4D Nucleome Consortium. AVAILABILITY AND IMPLEMENTATION: Cooler is cross-platform, BSD-licensed and can be installed from the Python package index or the bioconda repository. The source code is maintained on Github at https://github.com/mirnylab/cooler. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
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.