ArticleGenome biology2012
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models.PLoS computational biology · 2025Article
- Differential quantification of alternative splicing events on spliced pangenome graphs.PLoS computational biology · 2024Article
- A chromosome-level reference genome assembly and a full-length transcriptome assembly of the giant freshwater prawn (Macrobrachium rosenbergii).G3 (Bethesda, Md.) · 2024Article
- Article
- Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.International journal of molecular sciences · 2023Review
- Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention.Genome biology · 2023Article
- Reference genome of the nutrition-rich orphan crop chia (Frontiers in plant science · 2023Article
- Advances in alternative splicing identification: deep learning and pantranscriptome.Frontiers in plant science · 2023Article
- Therapeutic Vaccines Targeting Neoantigens to Induce T-Cell Immunity against Cancers.Pharmaceutics · 2022Review
- Article
- NeoSplice: a bioinformatics method for prediction of splice variant neoantigens.Bioinformatics advances · 2022Article
- Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.World journal of stem cells · 2021Review
- Global Survey of the Full-Length Cabbage Transcriptome (International journal of molecular sciences · 2021Article
- McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data.Bioinformatics (Oxford, England) · 2021Article
- Dynamics of the cell fate specifications during female gametophyte development in Arabidopsis.PLoS biology · 2021Article
- A Comparative Transcriptional Landscape of Two Castor Cultivars Obtained by Single-Molecule Sequencing Comparative Analysis.Frontiers in genetics · 2021Article
- Alternative Splicing Dynamics During the Lifecycle ofFrontiers in plant science · 2021Article
- Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression inFrontiers in microbiology · 2021Article
- Full-length transcriptome analysis of Phytolacca americana and its congener P. icosandra and gene expression normalization in three Phytolaccaceae species.BMC plant biology · 2020Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We propose a method for predicting splice graphs that enhances curated gene models using evidence from RNA-Seq and EST alignments. Results obtained using RNA-Seq experiments in Arabidopsis thaliana show that predictions made by our SpliceGrapher method are more consistent with current gene models than predictions made by TAU and Cufflinks. Furthermore, analysis of plant and human data indicates that the machine learning approach used by SpliceGrapher is useful for discriminating between real and spurious splice sites, and can improve the reliability of detection of alternative splicing. SpliceGrapher is available for download at http://SpliceGrapher.sf.net.
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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.