ArticleNucleic acids research2013
Accurate detection of differential RNA processing.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed, 45 citations in OpenAlex.
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Selecting differential splicing methods: Practical considerations for short-read RNA sequencing.F1000Research · 2025Review
- NBBt-test: a versatile method for differential analysis of multiple types of RNA-seq data.Scientific reports · 2022Article
- Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics.Frontiers in plant science · 2022Review
- ASCOT identifies key regulators of neuronal subtype-specific splicing.Nature communications · 2020Article
- Gene Regulatory Network Perturbation by Genetic and Epigenetic Variation.Trends in biochemical sciences · 2018Review
- Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages.Nature communications · 2018Article
- Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.Bioinformatics (Oxford, England) · 2018Article
- Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data.International journal of molecular sciences · 2017Article
- RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints.Bioinformatics (Oxford, England) · 2017Article
- Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis.The Plant cell · 2016Article
- RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response.BMC genomics · 2016Article
- SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data.Bioinformatics (Oxford, England) · 2016Article
- Inferring differentially expressed pathways using kernel maximum mean discrepancy-based test.BMC bioinformatics · 2016Article
- A survey of best practices for RNA-seq data analysis.Genome biology · 2016Review
- Article
- M3D: a kernel-based test for spatially correlated changes in methylation profiles.Bioinformatics (Oxford, England) · 2015Article
- Personalized- and one- medicine: bioinformatics foundation in health and its economic feasibility.Medical science monitor : international medical journal of experimental and clinical research · 2015Article
- Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems.BMC bioinformatics · 2014Article
- IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data.BMC genomics · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 5 institutions in 2 countries.
Funding
Abstract
Deep transcriptome sequencing (RNA-Seq) has become a vital tool for studying the state of cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling data enable identification of novel isoforms, quantification of known isoforms and detection of changes in transcriptional or RNA-processing activity. Existing approaches to detect differential isoform abundance between samples either require a complete isoform annotation or fall short in providing statistically robust and calibrated significance estimates. Here, we propose a suite of statistical tests to address these open needs: a parametric test that uses known isoform annotations to detect changes in relative isoform abundance and a non-parametric test that detects differential read coverages and can be applied when isoform annotations are not available. Both methods account for the discrete nature of read counts and the inherent biological variability. We demonstrate that these tests compare favorably to previous methods, both in terms of accuracy and statistical calibrations. We use these techniques to analyze RNA-Seq libraries from Arabidopsis thaliana and Drosophila melanogaster. The identified differential RNA processing events were consistent with RT-qPCR measurements and previous studies. The proposed toolkit is available from http://bioweb.me/rdiff and enables in-depth analyses of transcriptomes, with or without available isoform annotation.
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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.