ReviewNature methods2011
Computational methods for transcriptome annotation and quantification using RNA-seq.
Review in Nature methods, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 522 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
522 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach.BMC plant biology · 2020Pooled it
- Identification of anoctamin 1 (ANO1) as a key driver of esophageal epithelial proliferation in eosinophilic esophagitis.The Journal of allergy and clinical immunology · 2020Trial
- PpAPRR2 regulates chlorophyll biosynthesis and chloroplast development during early fruit development in peach.Plant cell reports · 2026Article
- Overexpression ofPlants (Basel, Switzerland) · 2026Article
- Effects of Antheraea pernyi (Lepidoptera: Saturniidae) eggs infected by Serratia marcescens (Enterobacterales: Yersiniaceae) on the fitness and transcriptome of Trichogramma chilonis (Hymenoptera: Trichogrammatidae).Journal of insect science (Online) · 2026Article
- HyDRA: A pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly.iScience · 2026Article
- Exploring the visual system of the black grouse (Lyrurus tetrix): combining experimental and molecular approaches to inform strategies for reducing collisions.The Journal of experimental biology · 2026Article
- Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution.bioRxiv : the preprint server for biology · 2026Article
- Demographic history and identification of threats under climate and anthropogenic activity provide insights into conservation for Cypripedium palangshanense.BMC plant biology · 2026Article
- Transcriptomics Reveals Cold Tolerance Maize Lines Involved in the Phenylpropanoid and Flavonoid Pathways.Plants (Basel, Switzerland) · 2026Article
- Deep learning application for genomic data analysis.BMB reports · 2026Review
- Deep structural clustering reveals hidden systematic biases in RNA sequencing data.Genome research · 2025Article
- White paper on best practices for translational research in neuroendocrine neoplasms.Journal of neuroendocrinology · 2025Article
- Transcriptomic analysis reveals differential gene expression in spleen cells of Chinese soft-shelled turtle infected with Bacillus cereus BC12.Archives of microbiology · 2025Article
- DeepDeconUQ estimates malignant cell fraction prediction intervals in bulk RNA-seq tissue.PLoS computational biology · 2025Article
- Establishment and molecular characterisation of patient-derived organoids for primary central nervous system lymphoma.Leukemia · 2025Article
- Collagen IV of basement membranes: I. Origin and diversification of COL4 genes enabling metazoan multicellularity, evolution, and adaptation.The Journal of biological chemistry · 2025Article
- Heat Acclimation Enhances Brain Resilience to Acute Thermal Stress inAnimals : an open access journal from MDPI · 2025Article
- Integrative Analysis of ATAC-Seq and RNA-Seq Identifies Key Genes Affecting Muscle Development in Ningxiang Pigs.International journal of molecular sciences · 2025Article
- Unveiling Tissue-Specific RNA Landscapes in Mouse Organs During Fasting and Feeding Using Nanopore Direct RNA Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
462 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications.
Indexed as
Identifiers
21623353What 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.