ArticleBMC bioinformatics2014
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 272 papers, 2 of them syntheses 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
272 citing papers in PubMed, 2 syntheses or guidelines pooled it, 468 citations in OpenAlex.
- Novel Genetic Determinants of Dental Maturation in Children.Journal of dental research · 2023Pooled it
- Transcriptional landscape of human microglia implicates age, sex, and APOE-related immunometabolic pathway perturbations.Aging cell · 2022Pooled it
- Dynamics and survival associations of T cell receptor clusters in patients with pleural mesothelioma treated with immunotherapy.Journal for immunotherapy of cancer · 2023Trial
- Trial
- Identification of osteoclast-osteoblast coupling factors in humans reveals links between bone and energy metabolism.Nature communications · 2020Trial
- Molecular profiling of long-term IDH-wildtype glioblastoma survivors.Neuro-oncology · 2019Trial
- Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders.Nature communications · 2019Trial
- Gut Microbiota Alter Colonic Expression of Genes Encoding Drug Transporters and Drug-Metabolizing Enzymes in Mice.International journal of molecular sciences · 2026Article
- Malignant B-cell States Orchestrate Spatially Organized Immune Ecosystems in B-cell Lymphomas.Research square · 2026Article
- Renovascular disease induces functionally relevant, locus-specific alterations to DNA methylation and hydroxymethylation in swine scattered tubular-like cells.American journal of physiology. Renal physiology · 2026Article
- RNA-Based and DNA-Based Next-Generation Sequencing of KIT and PDGFRA Mutations in Gastrointestinal Stromal Tumors: Analytical Performance and Epidemiologic Insights.Translational oncology · 2026Article
- Article
- Activation of the endocytosis pathway stratifies subtypes and therapeutic sensitivity in colorectal cancer.Research square · 2026Article
- Amivantamab Induces Immune-Mediated Cytotoxicity in Mesothelioma Through EGFR and MET Engagement.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2026Article
- PINK1 loss in astrocytes triggers inflammatory dysfunction and neuronal death.bioRxiv : the preprint server for biology · 2026Article
- Kidney Volume and Molecular Processes are Dynamic in ADPKD.Kidney international reports · 2026Article
- Concomitant ClonalHematology reports · 2026Article
- Mutant KRAS Heterogeneity Shapes Nuclear Architecture During Pancreatic Cancer Initiation.Epigenomes · 2026Article
- Integrative epigenomic landscape of Alzheimer's Disease brains reveals oligodendrocyte molecular perturbations associated with tau.Nature communications · 2026Article
- Vascular transcriptional and metabolic changes precede progressive intrarenal microvascular rarefaction in autosomal dominant polycystic kidney disease.American journal of physiology. Renal physiology · 2026Article
212 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
15 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundAlthough the costs of next generation sequencing technology have decreased over the past years, there is still a lack of simple-to-use applications, for a comprehensive analysis of RNA sequencing data. There is no one-stop shop for transcriptomic genomics. We have developed MAP-RSeq, a comprehensive computational workflow that can be used for obtaining genomic features from transcriptomic sequencing data, for any genome.
resultsFor optimization of tools and parameters, MAP-RSeq was validated using both simulated and real datasets. MAP-RSeq workflow consists of six major modules such as alignment of reads, quality assessment of reads, gene expression assessment and exon read counting, identification of expressed single nucleotide variants (SNVs), detection of fusion transcripts, summarization of transcriptomics data and final report. This workflow is available for Human transcriptome analysis and can be easily adapted and used for other genomes. Several clinical and research projects at the Mayo Clinic have applied the MAP-RSeq workflow for RNA-Seq studies. The results from MAP-RSeq have thus far enabled clinicians and researchers to understand the transcriptomic landscape of diseases for better diagnosis and treatment of patients.
conclusionsOur software provides gene counts, exon counts, fusion candidates, expressed single nucleotide variants, mapping statistics, visualizations, and a detailed research data report for RNA-Seq. The workflow can be executed on a standalone virtual machine or on a parallel Sun Grid Engine cluster. The software can be downloaded from http://bioinformaticstools.mayo.edu/research/maprseq/.
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.