ArticleProceedings of the National Academy of Sciences of the United States of America2018
JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Sam68 stimulates polymerase theta-mediated end-joining by suppressing poison exon inclusion in Polq mRNA.Nucleic acids research · 2026Article
- Integrative multiomic analysis reveals co-ordinated alternative splicing in human bone marrow stromal stem cells.Scientific reports · 2026Article
- Pervasive non-triplet alternative splicing drives functional isoform diversity.Nature communications · 2026Article
- Alternative pre-mRNA Splicing and Gene Expression Patterns in Midbrain Lineage Cells Carrying Familial Parkinson's Disease Mutations.bioRxiv : the preprint server for biology · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Regulated microexon alternative splicing in single neurons tunes synaptic function.EMBO reports · 2025Article
- Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.Nature communications · 2025Article
- Structural insights into spliceosome fidelity: DHX35-GPATCH1- mediated rejection of aberrant splicing substrates.Cell research · 2025Article
- Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms.Nucleic acids research · 2025Article
- Shiba: A versatile computational method for systematic identification of differential RNA splicing across platforms.bioRxiv : the preprint server for biology · 2025Article
- Conserved role for spliceosomal component PRPF40A in microexon splicing.RNA (New York, N.Y.) · 2024Article
- Spliceosomal vulnerability of MYCN-amplified neuroblastoma is contingent on PRMT5-mediated regulation of epitranscriptomic and metabolomic pathways.Cancer letters · 2024Article
- Conserved role for spliceosomal component PRPF40A in microexon splicing.bioRxiv : the preprint server for biology · 2024Article
- Detecting haplotype-specific transcript variation in long reads with FLAIR2.Genome biology · 2024Article
- Co-transcriptional splicing facilitates transcription of gigantic genes.PLoS genetics · 2024Article
- rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data.Nature protocols · 2024Review
- Two distinct waves of transcriptome and translatome changes drive Drosophila germline stem cell differentiation.The EMBO journal · 2024Article
- A mutation in the low-complexity domain of splicing factor hnRNPA1 linked to amyotrophic lateral sclerosis disrupts distinct neuronal RNA splicing networks.Genes & development · 2024Article
- A pair of RNA binding proteins inhibit ion transporter expression to maintain lifespan.Genetics · 2024Article
- TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation.Nucleic acids research · 2023Article
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2 authors.
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Abstract
Alternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. Current computational analysis methods of AS from Illumina RNA-sequencing data rely on preannotated libraries of known spliced transcripts, which hinders AS analysis with poorly annotated genomes and can further mask unknown AS patterns. To address this critical bioinformatics problem, we developed a method called the junction usage model (JUM) that uses a bottom-up approach to identify, analyze, and quantitate global AS profiles without any prior transcriptome annotations. JUM accurately reports global AS changes in terms of the five conventional AS patterns and an additional "composite" category composed of inseparable combinations of conventional patterns. JUM stringently classifies the difficult and disease-relevant pattern of intron retention (IR), reducing the false positive rate of IR detection commonly seen in other annotation-based methods to near-negligible rates. When analyzing AS in RNA samples derived from
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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.