ArticleGenome biology2019
MPRAnalyze: statistical framework for massively parallel reporter assays.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
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Who cites it
83 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.Human mutation · 2019Pooled it
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- Massively parallel characterization of adolescent idiopathic scoliosis risk variants.Genome research · 2026Article
- The gene-regulatory evolution of the human skeleton.Nature · 2026Article
- Massively parallel assessment of gene regulatory activity at human cortical-structure-associated variants.Nature neuroscience · 2026Article
- Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.Genome research · 2026Article
- Dynamic neuro-immune regulation of psychiatric risk loci in human neurons.Nature communications · 2026Article
- Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions.HGG advances · 2026Article
- Influence ofGenome research · 2026Article
- Neural stem cell epigenomes and fate bias are temporally coordinated during mouse cortical development.Genes & development · 2026Article
- Combinatorial pioneer transcription factor binding reinforces bivalent epigenetic states to preserve lineage fidelity.bioRxiv : the preprint server for biology · 2026Article
- Massively parallel reporter assay-informed modeling improves prediction of context-specific enhancer-gene regulatory interactions.Nucleic acids research · 2026Article
- Single-nucleus epigenomic dysregulation unmasks genetic risk-associated neurodegenerative glia states.Nature communications · 2026Article
- Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.Nature communications · 2026Article
- Promoter mutagenesis and a massively parallel reporter screen of thebioRxiv : the preprint server for biology · 2026Article
- keju: powerful and accurate inference in Massively Parallel Reporter Assays.bioRxiv : the preprint server for biology · 2026Article
- Systematic functional dissection of germline noncoding risk variants impacting clonal hematopoiesis.bioRxiv : the preprint server for biology · 2026Article
- Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA.Nature communications · 2026Article
- Influence ofbioRxiv : the preprint server for biology · 2025Article
- Meta-analysis of genetic regulation of RNA editing in the human brain identifies new genes underlying neurological disease.medRxiv : the preprint server for health sciences · 2025Article
23 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Massively parallel reporter assays (MPRAs) can measure the regulatory function of thousands of DNA sequences in a single experiment. Despite growing popularity, MPRA studies are limited by a lack of a unified framework for analyzing the resulting data. Here we present MPRAnalyze: a statistical framework for analyzing MPRA count data. Our model leverages the unique structure of MPRA data to quantify the function of regulatory sequences, compare sequences' activity across different conditions, and provide necessary flexibility in an evolving field. We demonstrate the accuracy and applicability of MPRAnalyze on simulated and published data and compare it with existing methods.
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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.