ArticleGenome biology2015
Exploiting single-molecule transcript sequencing for eukaryotic gene prediction.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 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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Who cites it
80 citing papers in PubMed, 178 citations in OpenAlex.
- Decoding the autotetraploid origin of the stress-tolerant wild beet Beta corolliflora.BMC genomics · 2026Article
- Identification of a candidate self-incompatibility locus in beet (Beta vulgaris).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Full-Length transcriptome assembly and SSR marker development for Spinibarbus hollandi using PacBio SMRT sequencing.Scientific reports · 2026Article
- Sugar beet long-read reference assembly of genotype KWS2320.NAR genomics and bioinformatics · 2025Article
- Variation analysis using random forests reveals domestication patterns and breeding trends in sugar beet.iScience · 2025Article
- Comprehensive analysis of Metacrinus rotundus full length transcriptome.Scientific reports · 2025Article
- Full-length transcriptome provides insights into the molecular regulation of seed spike number inFrontiers in plant science · 2025Article
- Sequencing and Optical Genome Mapping for the Adventurous Chemist.Chemical & biomedical imaging · 2024Review
- Transcriptome-referenced association study provides insights into the regulation of oil and fatty acid biosynthesis in Torreya grandis kernel.Journal of advanced research · 2024Article
- Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting.Plant biotechnology journal · 2024Article
- Trehalose 6-phosphate synthase gene rdtps1 contributes to thermal acclimation in Rhyzopertha dominica.BMC genomics · 2024Article
- A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes.Communications biology · 2023Article
- Article
- The sequencing of the key genes and end products in the TLR4 signaling pathway from the kidney ofOpen life sciences · 2023Article
- Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization.Scientific reports · 2022Article
- Identification of Genes and Metabolic Pathways Involved in Resin Yield in Masson Pine by Integrative Analysis of Transcriptome, Proteome and Biochemical Characteristics.International journal of molecular sciences · 2022Article
- Prediction of NB-LRR resistance genes based on full-length sequence homology.The Plant journal : for cell and molecular biology · 2022Article
- Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica.BMC plant biology · 2022Article
- Genomic distances reveal relationships of wild and cultivated beets.Nature communications · 2022Article
- Characterization of transposable elements within the Bemisia tabaci species complex.Mobile DNA · 2022Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first genome-wide gene set for spinach (Spinacia oleracea). The workflow and guidelines are a valuable resource to obtain comprehensive gene sets for newly sequenced genomes of non-model eukaryotes.
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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.