ArticleNature communications2019
A multi-sample approach increases the accuracy of transcript assembly.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed.
- Amaranth: enhanced single-cell transcript assembly via discriminative modelling of UMI reads and internal reads.Bioinformatics (Oxford, England) · 2026Article
- The Interferon-miR-146a-5p-Stat1/Nrf2 Pathway Mediates LRRK2-R1441G-induced M1 over M2 Microglia Activation.Molecular neurobiology · 2026Article
- From Adam's rib: the Siberian moth's female W chromosome is derived from its Z counterpart.Molecular biology and evolution · 2026Article
- Amaranth: Enhanced Single-Cell Transcript Assembly via Discriminative Modeling of UMI Reads and Internal Reads.bioRxiv : the preprint server for biology · 2025Article
- Transcriptome assembly at single-cell resolution with Beaver.Bioinformatics (Oxford, England) · 2025Article
- Building better genome annotations across the tree of life.Genome research · 2025Article
- Duckweed genomes and epigenomes underlie triploid hybridization and clonal reproduction.Current biology : CB · 2025Article
- Transcriptome differentiation in Cryptomeria japonica trees with different origins growing in the north and south of Japan.PloS one · 2025Article
- Response strategies to acute and chronic environmental stress in the arctic breeding Lapland longspur (Calcarius lapponicus).Communications biology · 2024Article
- YAP1 induces bladder cancer progression and promotes immune evasion through IL-6/STAT3 pathway and CXCL deregulation.The Journal of clinical investigation · 2024Article
- High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436.NAR genomics and bioinformatics · 2024Article
- The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California.G3 (Bethesda, Md.) · 2024Article
- Accurate assembly of multiple RNA-seq samples with Aletsch.Bioinformatics (Oxford, England) · 2024Article
- GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.Genome research · 2024Article
- A new gene finding tool GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.bioRxiv : the preprint server for biology · 2024Article
- Chromosome-Level Genome Assembly and Annotation of a Periodical Cicada Species: Magicicada septendecula.Genome biology and evolution · 2024Article
- Soluble PD-L1 as a diagnostic and prognostic biomarker in resectable gastric cancer patients.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2023Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- The Interaction of Borrelia burgdorferi with Human Dendritic Cells: Functional Implications.Journal of immunology (Baltimore, Md. : 1950) · 2023Article
- An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype.G3 (Bethesda, Md.) · 2023Article
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.
Funding
Abstract
Transcript assembly from RNA-seq reads is a critical step in gene expression and subsequent functional analyses. Here we present PsiCLASS, an accurate and efficient transcript assembler based on an approach that simultaneously analyzes multiple RNA-seq samples. PsiCLASS combines mixture statistical models for exonic feature selection across multiple samples with splice graph based dynamic programming algorithms and a weighted voting scheme for transcript selection. PsiCLASS achieves significantly better sensitivity-precision tradeoff, and renders precision up to 2-3 fold higher than the StringTie system and Scallop plus TACO, the two best current approaches. PsiCLASS is efficient and scalable, assembling 667 GEUVADIS samples in 9 h, and has robust accuracy with large numbers of samples.
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.