ArticleGenome biology2014
Evaluation of de novo transcriptome assemblies from RNA-Seq data.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.
What it found
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Who cites it
139 citing papers in PubMed.
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- Comprehensive assessment of transcriptome assembly quality using CATS.Nature communications · 2026Article
- Comprehensive plastid phylogenomics reveal the phylogeny ofPhytoKeys · 2026Article
- Evolutionary Dynamics of Transposable Element Activity and Regulation in the Apennine Yellow-Bellied Toad (Bombina pachypus).Genome biology and evolution · 2025Article
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- Gut metatranscriptomics based de novo assembly reveals microbial signatures predicting immunotherapy outcomes in non-small cell lung cancer.Journal of translational medicine · 2024Article
- CARD14 signalosome formation is associated with its endosomal relocation and mTORC1-induced keratinocyte proliferation.The Biochemical journal · 2024Article
- De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide.Frontiers in zoology · 2024Review
- Integrating miRNA and full-length transcriptome profiling to elucidate the mechanism of muscle growth in Muscovy ducks reveals key roles for miR-301a-3p/ANKRD1.BMC genomics · 2024Article
- Transcriptome analysis reveals the regulatory mechanism of myofiber development in male and female black Muscovy duck at different ages.Frontiers in veterinary science · 2024Article
- Article
- Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets.Bioinformatics and biology insights · 2024Article
- Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond.Communications of the ACM · 2023Article
- Peripheral blood transcriptome analysis of patients with ovarian hyperstimulation syndrome through high-throughput sequencing.Reproductive and developmental medicine · 2023Article
- De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage.Scientific data · 2023Article
- Optimization and application of non-native Phragmites australis transcriptome assemblies.PloS one · 2023Article
- Unraveling the Biosynthesis of Carvacrol in Different Tissues ofInternational journal of molecular sciences · 2022Article
- Hypothesis-driven dragging of transcriptomic data to analyze proven targeted pathways in Rhinella arenarum larvae exposed to organophosphorus pesticides.Scientific reports · 2022Article
- Brain de novo transcriptome assembly of a toad species showing polymorphic anti-predatory behavior.Scientific data · 2022Article
- Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica).BMC plant biology · 2022Article
79 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
De novo RNA-Seq assembly facilitates the study of transcriptomes for species without sequenced genomes, but it is challenging to select the most accurate assembly in this context. To address this challenge, we developed a model-based score, RSEM-EVAL, for evaluating assemblies when the ground truth is unknown. We show that RSEM-EVAL correctly reflects assembly accuracy, as measured by REF-EVAL, a refined set of ground-truth-based scores that we also developed. Guided by RSEM-EVAL, we assembled the transcriptome of the regenerating axolotl limb; this assembly compares favorably to a previous assembly. A software package implementing our methods, DETONATE, is freely available at http://deweylab.biostat.wisc.edu/detonate.
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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.