ArticleNature biotechnology2017
Accurate assembly of transcripts through phase-preserving graph decomposition.
Article in Nature biotechnology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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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.
The trial behind it
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Who cites it
125 citing papers in PubMed.
- PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery.Scientific data · 2026Article
- The Spirogyra pratensis genome illuminates the evolution of developmental programs and spiral chloroplast biology.The Plant cell · 2026Article
- Minimum flow decomposition guided by saturating subflows.bioRxiv : the preprint server for biology · 2026Article
- Amaranth: enhanced single-cell transcript assembly via discriminative modelling of UMI reads and internal reads.Bioinformatics (Oxford, England) · 2026Article
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- Reference-guided genome assembly of long non-coding rna transcripts reveals target genes associated with Crohn's disease.Scientific reports · 2026Article
- Data-driven AI system for learning how to run transcript assemblers.Genome biology · 2026Article
- The impact of transcriptome assembly algorithms on downstream quantification in RNA-seq data analysis.Briefings in bioinformatics · 2026Article
- Coordinated molecular and physiological adaptations enable activity at sub-freezing temperatures in the snow fly Chionea alexandriana.Current biology : CB · 2026Article
- ComprehensiveNon-coding RNA · 2026Article
- High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape.Cell genomics · 2026Article
- Improved reconstruction of transcripts and coding sequences from RNA-seq data.Nucleic acids research · 2026Article
- Review
- PROCA11 early activation fuels prostate cancer neuroendocrine traits by regulating cell survival and migration.iScience · 2025Article
- Reference-free RNA profiling predicts triple negative breast cancer chemoresistance to neoadjuvant treatment.NAR cancer · 2025Article
- Amaranth: Enhanced Single-Cell Transcript Assembly via Discriminative Modeling of UMI Reads and Internal Reads.bioRxiv : the preprint server for biology · 2025Article
- Conservation and Remodeling of Alternative Splicing Landscapes in the Evolution ofPlants (Basel, Switzerland) · 2025Article
- Boosting Transcript Assembly via Delineating Transcript Start and End Sites.bioRxiv : the preprint server for biology · 2025Article
- Reference-guided Genome Assembly of Long Non-coding RNA Transcripts Reveals Target Genes Associated With Crohn's Disease.bioRxiv : the preprint server for biology · 2025Article
- High-resolution genome assembly reveals retrotransposon-mediated centromere dynamics in rye.Genome biology · 2025Article
65 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 introduce Scallop, an accurate reference-based transcript assembler that improves reconstruction of multi-exon and lowly expressed transcripts. Scallop preserves long-range phasing paths extracted from reads, while producing a parsimonious set of transcripts and minimizing coverage deviation. On 10 human RNA-seq samples, Scallop produces 34.5% and 36.3% more correct multi-exon transcripts than StringTie and TransComb, and respectively identifies 67.5% and 52.3% more lowly expressed transcripts. Scallop achieves higher sensitivity and precision than previous approaches over a wide range of coverage thresholds.
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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.