ReviewGenome biology2021
Best practices on the differential expression analysis of multi-species RNA-seq.
Review in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
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Who cites it
57 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Updated annotation and meta-analysis of Brugia malayi transcriptomics data reveals consistent transcriptional profiles across time and space with some study-specific differences in adult female worm transcriptional profiles.PLoS neglected tropical diseases · 2024Pooled it
- Guidelines to Study Transcriptome Remodeling by Proteins Using Deep Sequencing (RNA-Seq).Methods in molecular biology (Clifton, N.J.) · 2027Article
- Current Applications and Future Prospects of High-ThroughputAnimals : an open access journal from MDPI · 2026Review
- A deep learning and large language hybrid workflow for omics interpretation.Nature biomedical engineering · 2026Article
- Article
- Liver-Directed Cyp2e1 RNA Interference Attenuates Hepatotoxicity Induced by Triptolide, a Bioactive Diterpenoid fromPharmaceuticals (Basel, Switzerland) · 2026Article
- Unveiling the potential regulatory functions of long non-coding RNAs in potato tuberization through integrated analysis of transcriptomics and phytohormone profiles.BMC plant biology · 2026Article
- Transcriptomic Analysis Based on RNA-Seq Technology Reveals the Molecular Mechanisms of Sunflower (Genes · 2026Article
- Spi-1 proto-oncogene regulates mRNA hypertranscription and malignant progression in head and neck cancer.Signal transduction and targeted therapy · 2026Article
- RNA-seq evaluation of equine alveolar macrophages and monocyte-derived macrophages exposed to an inflammatory stimulus (short communication).BMC veterinary research · 2026Article
- Imputing missing values in single-cell RNA-sequencing data: a statistical and machine learning-based approach.Briefings in bioinformatics · 2026Article
- A dual approach to evaluate the performance of RNA-Seq data analysis pipelines with weak signals.Bioinformatics advances · 2026Article
- Association of Increased Nasal Fluids-Serum Concordance of Protein Profile with Prognosis in Nasal Polyps.Journal of inflammation research · 2026Article
- Genome-Wide Identification, Function, and Expression Analysis of the ABC Transporter Gene Family in Forest Musk Deer (Animals : an open access journal from MDPI · 2025Article
- Phillyrin prevents calcium oxalate kidney stones through the PPARγ signaling pathway.Renal failure · 2025Article
- A Scorecard for Information Synthesis in Multiple Experimental Conditions: Application to Bacterial Biofilm Matrix Transcriptomics.Current microbiology · 2025Article
- Cluefish: mining the dark matter of transcriptional data series with over-representation analysis enhanced by aggregated biological prior knowledge.NAR genomics and bioinformatics · 2025Article
- Multi-omics insights of immune cells in the risk and prognosis of idiopathic membranous nephropathy.Communications biology · 2025Article
- Core Perturbomes ofPathogens (Basel, Switzerland) · 2025Article
- Landscape transcriptomics as a tool for addressing global change effects across diverse species.Molecular ecology resources · 2025Review
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.
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