ArticleNature communications2020
ASCOT identifies key regulators of neuronal subtype-specific splicing.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
69 citing papers in PubMed, 148 citations in OpenAlex.
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- scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution.Nature methods · 2025Article
- Distinct and convergent effects ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Ptbp1 is not required for retinal neurogenesis and cell fate specification.bioRxiv : the preprint server for biology · 2025Article
- Large-scale RNA-Seq mining reveals ciclopirox olamine induces TDP-43 cryptic exons.Nature communications · 2025Article
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.bioRxiv : the preprint server for biology · 2025Article
- TDP-43 pathology induces CD8bioRxiv : the preprint server for biology · 2025Article
- Evaluating the representational power of pre-trained DNA language models for regulatory genomics.Genome biology · 2025Article
- Inhibition of nonsense-mediated decay in TDP-43 deficient neurons reveals novel cryptic exons.bioRxiv : the preprint server for biology · 2025Article
- Reactivating the phototransduction cascade with a mutation agnostic gene therapy preserves vision in rod-cone dystrophies.iScience · 2025Article
- Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina.Genome research · 2025Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 2 institutions in 1 country.
Funding
Abstract
Public archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by scientists. Here, we present ASCOT, a resource that uses annotation-free methods to rapidly analyze and visualize splice variants across tens of thousands of bulk and single-cell data sets in the public archive. To demonstrate the utility of ASCOT, we identify novel cell type-specific alternative exons across the nervous system and leverage ENCODE and GTEx data sets to study the unique splicing of photoreceptors. We find that PTBP1 knockdown and MSI1 and PCBP2 overexpression are sufficient to activate many photoreceptor-specific exons in HepG2 liver cancer cells. This work demonstrates how large-scale analysis of public RNA-Seq data sets can yield key insights into cell type-specific control of RNA splicing and underscores the importance of considering both annotated and unannotated splicing events.
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What OpenQuestion holds
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.