ArticleNature methods2018
GIGGLE: a search engine for large-scale integrated genome analysis.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
What it found
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Who cites it
135 citing papers in PubMed.
- Epigenetic profiling identifies markers of endocrine resistance and therapeutic options for metastatic castration-resistant prostate cancer.Cell reports. Medicine · 2025Trial
- Androgen receptor drives divergent chromatin accessibility programs in benign and malignant prostate epithelial cells.Nucleic acids research · 2026Article
- Analysis of isoform complexity in pan-transcriptome graphs with atroplex.bioRxiv : the preprint server for biology · 2026Article
- Nuclear-specific reductive carboxylation of alpha-ketoglutarate fuels histone acetylation to induce chromatin accessibility and gene activation.Nature communications · 2026Article
- Genomic sequence evolution underlying human neocortical interareal diversification.Genome biology · 2026Article
- A TAD-informed aging-brain xQTL atlas of multi-modal and cell-type-resolved regulatory variation.medRxiv : the preprint server for health sciences · 2026Article
- T-ChroNet: Time-aware chromatin network reconstruction to detect dynamic regulatory programs in longitudinal epigenetic dataset.NAR genomics and bioinformatics · 2026Article
- Transposable elements shape stemness in normal and leukemic hematopoiesis.Nature genetics · 2026Article
- RPS19 and RPL5 haploinsufficient models reveal divergent ribosomal subunit controls of fetal hematopoiesis.Nature communications · 2026Article
- A Double-Negative Prostate Cancer Subtype Is Vulnerable to SWI/SNF-Targeting Degrader Molecules.Cancer research · 2026Article
- Functional genomic analysis of non-canonical DNA regulatory elements of the aryl hydrocarbon receptor.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- Distal enhancers regulate mammalian early embryonic lineage differentiation through long-range interactions.Nucleic acids research · 2026Article
- ViMIC 2.0: an updated database of human disease-related viral mutations, integration sites, and multi-omics data.Nucleic acids research · 2026Article
- Article
- Investigating the Physiological Regulation of Transposable Elements In Vivo: Nuclei Preparation from Primary Mouse Tissues for Epigenomic Analyses and Computational Approaches to Interrogate the Repeat Genome.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Computational Analyses and Challenges of Single-cell ATAC-seq.Genomics, proteomics & bioinformatics · 2025Review
- Distinct transcription factor interactions drive HOXB13 activity in different stages of prostate cancer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genomic Crosstalk Between Nuclear Receptors in Hormone-dependent Cancers.Endocrinology · 2025Review
- A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice.Nature immunology · 2025Article
- Remodelling bivalent chromatin is essential for mouse peri-implantation embryogenesis.Nature cell biology · 2025Article
75 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation.
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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.