ArticleGenome research2021
Correcting signal biases and detecting regulatory elements in STARR-seq data.
Article in Genome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 22 citations in OpenAlex.
- Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers.bioRxiv : the preprint server for biology · 2026Article
- SOSHI-seq: a high-throughput screening assay to test the functionality of putative response elements for nuclear hormone receptors.Scientific reports · 2025Article
- Comprehensive evaluation of diverse massively parallel reporter assays to functionally characterize human enhancers genome-wide.Genome biology · 2025Article
- Identification and application of bioparts for plant synthetic biology.Molecules and cells · 2025Review
- Applications of high-throughput reporter assays to gene regulation studies.Current opinion in structural biology · 2025Review
- Gene regulatory activity associated with polycystic ovary syndrome revealed DENND1A-dependent testosterone production.Nature communications · 2025Article
- Genome-Wide Silencer Screening Reveals Key Silencer Modulating Reprogramming Efficiency in Mouse Induced Pluripotent Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Uncovering the whole genome silencers of human cells via Ss-STARR-seq.Nature communications · 2025Article
- HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.BMC genomics · 2024Article
- MPRAbase: A Massively Parallel Reporter Assay Database.bioRxiv : the preprint server for biology · 2023Article
- From qualitative to quantitative: the state of the art and challenges for plant synthetic biology.Quantitative biology (Beijing, China) · 2023Review
- Challenges and considerations for reproducibility of STARR-seq assays.Genome research · 2023Article
- Leveraging massively parallel reporter assays for evolutionary questions.Genome biology · 2023Review
- AAV Deployment of Enhancer-Based Expression Constructs In Vivo in Mouse Brain.Journal of visualized experiments : JoVE · 2022Article
- Integration of Count Difference and Curve Similarity in Negative Regulatory Element Detection.Frontiers in genetics · 2022Article
- Annotating the Insect Regulatory Genome.Insects · 2021Review
Corrections and comments
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Authors and funding
9 authors at 1 institution in 2 countries.
Funding
Abstract
High-throughput reporter assays such as self-transcribing active regulatory region sequencing (STARR-seq) have made it possible to measure regulatory element activity across the entire human genome at once. The resulting data, however, present substantial analytical challenges. Here, we identify technical biases that explain most of the variance in STARR-seq data. We then develop a statistical model to correct those biases and to improve detection of regulatory elements. This approach substantially improves precision and recall over current methods, improves detection of both activating and repressive regulatory elements, and controls for false discoveries despite strong local correlations in signal.
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Registered trials
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