ArticleBriefings in bioinformatics2018
Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments.
Article in Briefings in bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- Article
- Contact Lens Wear Alters Transcriptional Responses to Pseudomonas aeruginosa in Both the Corneal Epithelium and the Bacteria.Investigative ophthalmology & visual science · 2025Article
- Metagenomic Insights into Pigeon Gut Microbiota Characteristics and Antibiotic-Resistant Genes.Biology · 2025Article
- Contact Lens Wear Alters Transcriptional Responses tobioRxiv : the preprint server for biology · 2024Article
- Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases.Veterinary sciences · 2024Review
- The Fur-like regulatory protein MAP3773c modulates key metabolic pathways in Mycobacterium avium subsp. paratuberculosis under in-vitro iron starvation.Scientific reports · 2024Article
- RNA methylation-related inhibitors: Biological basis and therapeutic potential for cancer therapy.Clinical and translational medicine · 2024Review
- Refining dual RNA-seq mapping: sequential and combined approaches in host-parasitic plant dynamics.Frontiers in plant science · 2024Article
- Legume-rhizobia symbiosis: Translatome analysis.Genetics and molecular biology · 2024Article
- Wolbachia endosymbionts manipulate the self-renewal and differentiation of germline stem cells to reinforce fertility of their fruit fly host.PLoS biology · 2023Article
- A 3D Bioprinted Gut Anaerobic Model for Studying Bacteria-Host Interactions.Research (Washington, D.C.) · 2023Article
- dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data.Microbial genomics · 2022Article
- Role of main RNA modifications in cancer: NSignal transduction and targeted therapy · 2022Review
- Steroid-Refractory Gut Graft-Versus-Host Disease: What We Have Learned From Basic Immunology and Experimental Mouse Model.Frontiers in immunology · 2022Review
- Dual transcriptomic analysis reveals metabolic changes associated with differential persistence of human pathogenic bacteria in leaves of Arabidopsis and lettuce.G3 (Bethesda, Md.) · 2021Article
- Molecular insights into the mechanisms of susceptibility of Labeo rohita against oomycete Aphanomyces invadans.Scientific reports · 2020Article
- Stress responses, M2 macrophages, and a distinct microbial signature in fatal intestinal acute graft-versus-host disease.JCI insight · 2019Article
- Early Transcriptional Landscapes ofFrontiers in cellular and infection microbiology · 2019Article
- A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host CellsFrontiers in microbiology · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA sequencing technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. Several laboratory protocols have been presented that outline the collection, extraction and sequencing of total RNA for dRNA-Seq experiments, but there is relatively little guidance available for the detailed bioinformatic analyses required. This protocol outlines a typical dRNA-Seq experiment, based on a Chlamydia trachomatis-infected host cell, with a detailed description of the necessary bioinformatic analyses with currently available software tools.
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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.