ArticleNature methods2013
Streaming fragment assignment for real-time analysis of sequencing experiments.
Article in Nature methods, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 570 papers.
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
570 citing papers in PubMed.
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- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- UDP-glycosyltransferase confers anthranilic diamide resistance in Bemisia tabaci.Journal of advanced research · 2026Article
- Integrated Transcriptomic and Metabolomic Analyses Reveal Early Concentration-Dependent Responses ofGenes · 2026Article
- Salamander-Ecology and evolution · 2026Article
- Cell size-dependent mRNA transcription drives proteome remodeling.Cell reports · 2026Article
- Multi-Omics Integration Reveals Synergistic Metabolic Rewiring Underpinning Growth Acceleration in a Hybrid Pompano "Chenhai No. 1".Animals : an open access journal from MDPI · 2026Article
- Transcriptomic analysis of Toona sinensis leaves with eight different colors at various developmental stages.BMC genomic data · 2026Article
- Computational prediction-combined proteogenomics unveils widespread non-AUG translation initiation events in plants.Nucleic acids research · 2026Article
- Spermidine stimulates hypocrellin A biosynthesis through nitric oxide signaling in Shiraia sp. S9.Bioresources and bioprocessing · 2026Article
- Metabolome and transcriptome profiling reveals distinct regulatory networks underlying high-protein and high-oil traits in soybean cultivars Wandou 28 and Zhongdou 63.BMC plant biology · 2026Article
- Fungal-fungal interaction between Sanghuangporus vaninii and its endophytic Fusarium solani rewires host secondary metabolism to boost bioactive metabolite production.Microbial cell factories · 2026Article
- Improving gene isoform quantification with miniQuant.Nature biotechnology · 2026Article
- Dynamic and Ongoing De Novo L1 Retrotransposition Contributes to Genome Plasticity and Intrapatient Heterogeneity in Ovarian Cancer.Cancer research · 2026Article
- Unveiling Transcriptional Dynamics Across Five Developmental Stages of the Edible MushroomJournal of fungi (Basel, Switzerland) · 2026Article
- Decoding Vascular Cell Diversity: Single-Cell Approaches to Mechanisms of Vascular Disease.Circulation research · 2026Review
- Photoperiod-driven gene regulation in the brain ofFrontiers in endocrinology · 2026Article
- Zhuyu pill relieves cholestasis in rats by modulating the expression of lncRNAs and circRNAs.Frontiers in pharmacology · 2026Article
510 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
2 authors.
Funding
Abstract
We present eXpress, a software package for efficient probabilistic assignment of ambiguously mapping sequenced fragments. eXpress uses a streaming algorithm with linear run time and constant memory use. It can determine abundances of sequenced molecules in real time and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. We demonstrate its use on RNA-seq data and show that eXpress achieves greater efficiency than other quantification methods.
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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.