ArticleGenome biology2020
tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing.
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, 70 citations in OpenAlex.
- Review
- EPBAM: annotation-robust detection of alternative splicing events and a systematic benchmarking of current tools.Briefings in bioinformatics · 2026Article
- IsoformSwitchAnalyzeR v2: analysis of functional isoform changes in long-read and single-cell sequencing data.NAR genomics and bioinformatics · 2026Article
- SpliceImpactR maps alternative RNA processing events driving protein functional diversity.Nucleic acids research · 2026Article
- Article
- A framework for identifying transcript orthologs: the evolution of sex bias in alternative transcript structure in Drosophila.bioRxiv : the preprint server for biology · 2026Article
- Improving gene isoform quantification with miniQuant.Nature biotechnology · 2026Article
- Hypatia: Comparative Isoform Profiling Across Cell Populations from Long-Read Single-Cell Transcriptomes.bioRxiv : the preprint server for biology · 2026Article
- Analyzing cell-type-specific isoform expression using IsoDiffR and long-read single-cell RNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- A cell type-specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage.Genes & development · 2025Article
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders.Nucleic acids research · 2025Article
- Quantification of single cell-type-specific alternative transcript initiation.bioRxiv : the preprint server for biology · 2025Article
- Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity.Genome research · 2025Article
- Unravelling genotype-phenotype correlations in Stargardt disease using patient-derived retinal organoids.Cell death & disease · 2025Article
- Steering research on mRNA splicing in cancer towards clinical translation.Nature reviews. Cancer · 2024Review
- Article
- Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation.Genome research · 2024Article
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Authors and funding
16 authors at 5 institutions in 4 countries.
Funding
Abstract
Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isoform-centered functional analysis. Here, we present tappAS, the first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, which is effective at revealing the functional impact of context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation of coding and non-coding functional domains, motifs, and sites, in combination with novel analysis methods to interrogate different aspects of the functional readout of transcript variants and isoform regulation. tappAS software and documentation are available at https://app.tappas.org.
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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.