ReviewJournal of biomedicine & biotechnology2010
Uncovering the complexity of transcriptomes with RNA-Seq.
Review in Journal of biomedicine & biotechnology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 210 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
210 citing papers in PubMed, 1 synthesis or guideline pooled it, 450 citations in OpenAlex.
- RNA-Sequencing in Elucidating Immune Responses to Haemonchus contortus Infection in Small Ruminants: Systematic Review.Parasite immunology · 2025Pooled it
- Single-cell RNA sequencing unravels mosquito biology and host-pathogen interactions.Parasites & vectors · 2026Review
- Genomic diversification between aposematic and cryptic phenotypes of Oophaga granulifera (Anura: Dendrobatidae).Scientific reports · 2026Article
- Quantifying transcript complexity via the condition number of gene-specific random matrix.Briefings in bioinformatics · 2026Article
- Huangqin decoction disrupts energy metabolism of Trichophyton rubrum, with isocitrate lyase as a potential target.Scientific reports · 2026Article
- Multi-Omics Integration for Advancing Glioma Precision Medicine.Annals of clinical and translational neurology · 2026Review
- NOX2 Contributes to High-Frequency Outer Hair Cell Vulnerability in the Cochlea.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Deciphering transcriptomic changes in chemobrain: a comprehensive review.Acta neuropathologica communications · 2025Review
- Genome-wide analysis of the CsAP2/ERF gene family of sweet orange (Citrus sinensis) and joint analysis of transcriptional metabolism under salt stress.Annals of botany · 2025Article
- Supplementation of plant fermentation carbon sources significantly enhances the abundance of ammonia-oxidizing genes and increases nitrogen removal in a municipal wastewater treatment plant.BMC microbiology · 2025Article
- Integrated mRNA and miRNA Analysis Reveals Layer-Specific Mechanisms of Antler Yield Variation in Sika Deer.Animals : an open access journal from MDPI · 2025Article
- The Study ofJournal of fungi (Basel, Switzerland) · 2025Article
- Transcriptomics, single-cell sequencing and spatial sequencing-based studies of cerebral ischemia.European journal of medical research · 2025Review
- Disclosing antifungal activity of Huangqin decoction upon Trichophyton mentagrophytes and exploring its potential inhibitory mechanisms through transcriptome sequencing and qRT-PCR.Scientific reports · 2025Article
- Transcriptomic and Metabolomic Insights into Key Genes Involved in Kinsenoside Biosynthesis inPlants (Basel, Switzerland) · 2025Article
- Identification and Characterization of SQUAMOSA Promoter Binding Protein-like Transcription Factor Family Members inPlants (Basel, Switzerland) · 2025Article
- Differential susceptibility to prenatal stress exposure in serotonin transporter-deficient female mice-an epigenetic exploration.Frontiers in neuroscience · 2025Article
- Integrated transcriptomic and immune enzymatic analyses uncover coordinated immunometabolic responses in large yellow croaker (Frontiers in immunology · 2025Article
- Differential expression and correlation analysis of global transcriptome for obstructive sleep apnea hypopnea syndrome.Frontiers in molecular biosciences · 2025Article
- Transcriptomic Analysis Reveals the Potential Mechanism ofInternational journal of molecular sciences · 2024Article
150 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
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide variations are only some of the intriguing new applications supported by these innovative platforms. Among them RNA-Seq is perhaps the most complex NGS application. Expression levels of specific genes, differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespread hybridization-based or tag sequence-based approaches. However, the unprecedented level of sensitivity and the large amount of available data produced by NGS platforms provide clear advantages as well as new challenges and issues. This technology brings the great power to make several new biological observations and discoveries, it also requires a considerable effort in the development of new bioinformatics tools to deal with these massive data files. The paper aims to give a survey of the RNA-Seq methodology, particularly focusing on the challenges that this application presents both from a biological and a bioinformatics point of view.
Indexed as
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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.