ArticleNucleic acids research2016
Goldmine integrates information placing genomic ranges into meaningful biological contexts.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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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.
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Who cites it
27 citing papers in PubMed.
- scPASU: A computational protocol for quantifying polyadenylation site usage and alternative polyadenylation from 3' scRNA-seq data.STAR protocols · 2026Article
- A multi-modal diffusion model with dual-cross-attention for multi-omics data generation and translation.Nature communications · 2026Article
- PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing.Genome research · 2025Article
- HERV Dysregulation in a Case of Myalgic Encephalomyelitis and Multiple Sclerosis Responsive to Rituximab.International journal of molecular sciences · 2025Article
- HERV activation segregates ME/CFS from fibromyalgia while defining a novel nosologic entity.eLife · 2025Article
- GGNBP2 regulates MDA5 sensing triggered by self double-stranded RNA following loss of ADAR1 editing.Science immunology · 2024Article
- Injured inflammatory environment overrides the TET2 shaped epigenetic landscape of pluripotent stem cell derived human neural stem cells.Scientific reports · 2024Article
- Epigenetic regulation of asymmetric cell division by the LIBR-BRD4 axis.Nucleic acids research · 2024Article
- OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations.BMC bioinformatics · 2023Article
- Article
- The phenotype of the most common human ADAR1p150 Zα mutation P193A in mice is partially penetrant.EMBO reports · 2023Article
- Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells.PLoS genetics · 2023Article
- Altered hydroxymethylome in the substantia nigra of Parkinson's disease.Human molecular genetics · 2022Article
- Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential.NPJ Regenerative medicine · 2022Article
- MethReg: estimating the regulatory potential of DNA methylation in gene transcription.Nucleic acids research · 2022Article
- Dynamic transcriptional activity and chromatin remodeling of regulatory T cells after varied duration of interleukin-2 receptor signaling.Nature immunology · 2022Article
- GenomicDistributions: fast analysis of genomic intervals with Bioconductor.BMC genomics · 2022Article
- AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators.Scientific reports · 2021Article
- The majority of A-to-I RNA editing is not required for mammalian homeostasis.Genome biology · 2019Article
- Genome-wide brain DNA methylation analysis suggests epigenetic reprogramming in Parkinson disease.Neurology. Genetics · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Bioinformatic analysis often produces large sets of genomic ranges that can be difficult to interpret in the absence of genomic context. Goldmine annotates genomic ranges from any source with gene model and feature contexts to facilitate global descriptions and candidate loci discovery. We demonstrate the value of genomic context by using Goldmine to elucidate context dynamics in transcription factor binding and to reveal differentially methylated regions (DMRs) with context-specific functional correlations. The open source R package and documentation for Goldmine are available at http://jeffbhasin.github.io/goldmine.
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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.