ArticleGenome biology2020
STARRPeaker: uniform processing and accurate identification of STARR-seq active regions.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Massively parallel functional profiling prioritizes breast cancer risk variants and implicates CCDC88C in ER-positive breast cancer.HGG advances · 2026Article
- A genome-wide survey reveals that a diverse array of enhancers coordinates theGenome research · 2026Article
- STARR-CRAAVT: A platform to identify cell type-specific regulatory elements for next-generation gene therapy.iScience · 2026Article
- Enhancer-based gene therapy: a new path for precision medicine.Hereditas · 2026Review
- Comprehensive Mapping of Functional Enhancers in Chinese Hamster Ovary Cells.Biotechnology and bioengineering · 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
- Quantifying the impact of genetic mutations on enhancer dynamics.bioRxiv : the preprint server for biology · 2025Article
- Applications of high-throughput reporter assays to gene regulation studies.Current opinion in structural biology · 2025Review
- A genome-wide survey reveals a diverse array of enhancers coordinate thebioRxiv : the preprint server for biology · 2025Article
- A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq.Genome research · 2025Article
- Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture.Bioinformatics (Oxford, England) · 2025Article
- ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types.Genome biology · 2025Article
- Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits.Nucleic acids research · 2025Article
- Abundant repressor binding sites in human enhancers are associated with the fine-tuning of gene regulation.iScience · 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
- Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators.Nature cell biology · 2024Article
- CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex.Cell reports · 2024Article
- Single-cell genomics and regulatory networks for 388 human brains.Science (New York, N.Y.) · 2024Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is non-uniform, overdispersed, and often confounded by sequencing biases, such as GC content. Furthermore, STARR-seq readout is confounded by RNA secondary structure and thermodynamic stability. To address these potential confounders, we developed a negative binomial regression framework for uniformly processing STARR-seq data, called STARRPeaker. Moreover, to aid our effort, we generated whole-genome STARR-seq data from the HepG2 and K562 human cell lines and applied STARRPeaker to comprehensively and unbiasedly call enhancers in them.
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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.