ArticleGenome biology2016
CIDANE: comprehensive isoform discovery and abundance estimation.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
16 citing papers in PubMed, 51 citations in OpenAlex.
- Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses.BMC genomics · 2024Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- Counting pseudoalignments to novel splicing events.Bioinformatics (Oxford, England) · 2023Article
- Efficient Minimum Flow Decomposition via Integer Linear Programming.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data.Nature biotechnology · 2022Article
- A simple guide to de novo transcriptome assembly and annotation.Briefings in bioinformatics · 2022Review
- McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data.Bioinformatics (Oxford, England) · 2021Article
- TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.Genome research · 2020Article
- DTA-SiST: de novo transcriptome assembly by using simplified suffix trees.BMC bioinformatics · 2019Article
- AIDE: annotation-assisted isoform discovery with high precision.Genome research · 2019Article
- A multi-sample approach increases the accuracy of transcript assembly.Nature communications · 2019Article
- Modeling and analysis of RNA-seq data: a review from a statistical perspective.Quantitative biology (Beijing, China) · 2018Article
- Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.G3 (Bethesda, Md.) · 2018Article
- Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.Bioinformatics (Oxford, England) · 2018Article
- Accurate assembly of transcripts through phase-preserving graph decomposition.Nature biotechnology · 2017Article
- TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs.Genome biology · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
We present CIDANE, a novel framework for genome-based transcript reconstruction and quantification from RNA-seq reads. CIDANE assembles transcripts efficiently with significantly higher sensitivity and precision than existing tools. Its algorithmic core not only reconstructs transcripts ab initio, but also allows the use of the growing annotation of known splice sites, transcription start and end sites, or full-length transcripts, which are available for most model organisms. CIDANE supports the integrated analysis of RNA-seq and additional gene-boundary data and recovers splice junctions that are invisible to other methods. CIDANE is available at http://ccb.jhu.edu/software/cidane/.
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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.