ArticleNucleic acids research2013
Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.
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 1,133 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1,133 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Antisense Versus Antigene in the Computer-Aided Design of Triplex-Forming Oligonucleotides (TFO): Insights from a Dual-Method Review, Combining Bibliometric and Systematic Review.International journal of molecular sciences · 2025Pooled it
- Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and reoxygenation.RNA biology · 2026Article
- LncPNdeep: A long non-coding RNA classifier based on large language model with peptide and nucleotide embedding.Non-coding RNA research · 2026Article
- Integrated Survival Assessment and mRNA/miRNA Transcriptomics Reveal Heat Stress Response and Recovery Mechanisms in Cultured Razor Clam Sinonovacula constricta.Marine biotechnology (New York, N.Y.) · 2026Article
- Whole-Transcriptome Landscape Deciphers a ceRNA-Mediated "De-Repression-Activation" Circuit Governing Continuous Estrus in Ovine.Animals : an open access journal from MDPI · 2026Article
- Functional characterization of lncIMF_17214 in regulating intramuscular fat deposition of yellow-feathered broilers.Poultry science · 2026Article
- Circular RNAs orchestrate integrated post-transcriptional responses to combined heat and drought stress in rice.Molecular genetics and genomics : MGG · 2026Article
- lncRNA62732 acts as an eTM of miR9778 to regulate TaHAK18-5B and mediate the potassium deficiency response in wheat.The New phytologist · 2026Article
- Cross-kingdom noncoding RNA regulation facilitatesEngineering microbiology · 2026Article
- Genome-Wide Mining of lncRNAs Reveals Their Potential Regulatory Role in the Evolution of Viviparity.Integrative zoology · 2026Article
- Identifying heat shock-responsive lncRNAs in wheat during grain filling.BMC plant biology · 2026Article
- Correlation of Long Non-Coding RNAs and Gene Expression in Response to Reverse Development of Turritopsis dohrnii.Marine biotechnology (New York, N.Y.) · 2026Article
- The Landscape of Long Non-Coding RNAs Provides Insights Into the Domestication and Improvement of Pear Fruit.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Exploring the role of differential splicing of Pekin ducks resistant to DHAV-3 based on full-length transcriptome.Poultry science · 2026Article
- Genome-wide network analysis identifies the lncRNA-92467/miR-205-5p/PTPRM/CAMs axis in a rat model of hypoxic pulmonary hypertension.Animal models and experimental medicine · 2026Article
- Large-scale exchange of RNA between parasitic plant Orobanche cumana and its host Helianthus annuus.Pest management science · 2026Article
- Functional divergence of MADS-box genes and the dual regulatory role of a long noncoding RNA underlie sex determination in Ginkgo biloba.BMC plant biology · 2026Article
- The LncRNA Expression Profile and Regulatory Network of Microsporidian During the Infection of Western Honeybee.Animals : an open access journal from MDPI · 2026Article
- Identification of differentially expressed lncRNAs in different daily weight gains of Jiangquan black pigs and functional analysis of LOC100518120.BMC genomics · 2026Article
- Integrated multi-omics analysis reveals the molecular mechanism underlying poplar 107 rootstock-mediated regulation ofHorticulture research · 2026Article
1,073 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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense-antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan. CNCI software is available at http://www.bioinfo.org/software/cnci.
Indexed as
Identifiers
What OpenQuestion holds
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.