ArticlePloS one2020
RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 20 citations in OpenAlex.
- Data-driven AI system for learning how to run transcript assemblers.Genome biology · 2026Article
- Induction of Invasive Basal Phenotype in Triple-Negative Breast Cancers by Long Noncoding RNA BORG.Cancers · 2024Article
- ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs.BMC bioinformatics · 2024Article
- StringFix: an annotation-guided transcriptome assembler improves the recovery of amino acid sequences from RNA-Seq reads.Genes & genomics · 2023Article
- Efficient Minimum Flow Decomposition via Integer Linear Programming.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.The Plant journal : for cell and molecular biology · 2022Article
- Accurate assembly of multi-end RNA-seq data with Scallop2.Nature computational science · 2022Article
- An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae.Scientific reports · 2020Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
High throughput sequencing of RNA (RNA-Seq) has become a staple in modern molecular biology, with applications not only in quantifying gene expression but also in isoform-level analysis of the RNA transcripts. To enable such an isoform-level analysis, a transcriptome assembly algorithm is utilized to stitch together the observed short reads into the corresponding transcripts. This task is complicated due to the complexity of alternative splicing - a mechanism by which the same gene may generate multiple distinct RNA transcripts. We develop a novel genome-guided transcriptome assembler, RefShannon, that exploits the varying abundances of the different transcripts, in enabling an accurate reconstruction of the transcripts. Our evaluation shows RefShannon is able to improve sensitivity effectively (up to 22%) at a given specificity in comparison with other state-of-the-art assemblers. RefShannon is written in Python and is available from Github (https://github.com/shunfumao/RefShannon).
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Registered trials
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