ArticleJournal of translational medicine2020
A modular framework for the development of targeted Covid-19 blood transcript profiling panels.
Article in Journal of translational medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity.Database : the journal of biological databases and curation · 2024Trial
- Article
- ACSL1 orchestrates ferroptosis and degranulation in low-density neutrophils: a novel pathogenic mechanism and therapeutic target in systemic lupus erythematosus.Molecular and cellular biochemistry · 2026Article
- Identification of core differentially expressed genes for respiratory syncytial virus infection.Global medical genetics · 2026Article
- Identification of potential characteristic genes in sepsis utilizing RNA sequencing and gene silence.BMC immunology · 2025Article
- Automating candidate gene prioritization with large language models: from naive scoring to literature-grounded validation.Bioinformatics (Oxford, England) · 2025Article
- From gene modules to gene markers: an integrated AI-human approach selects CD38 to represent plasma cell-associated transcriptional signatures.Frontiers in medicine · 2025Article
- Human-augmented large language model-driven selection of glutathione peroxidase 4 as a candidate blood transcriptional biomarker for circulating erythroid cells.Scientific reports · 2024Article
- A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings.Database : the journal of biological databases and curation · 2024Article
- Design of a targeted blood transcriptional panel for monitoring immunological changes accompanying pregnancy.Frontiers in immunology · 2024Article
- Harnessing large language models (LLMs) for candidate gene prioritization and selection.Journal of translational medicine · 2023Article
- An artificial neural network model based on autophagy-related genes in childhood systemic lupus erythematosus.Hereditas · 2022Article
- Transcriptomic profile investigations highlight a putative role for NUDT16 in sepsis.Journal of cellular and molecular medicine · 2022Article
- Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker.F1000Research · 2022Article
- MX2: Identification and systematic mechanistic analysis of a novel immune-related biomarker for systemic lupus erythematosus.Frontiers in immunology · 2022Article
- BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R.Bioinformatics (Oxford, England) · 2021Article
- Transcriptome and Literature Mining Highlight the Differential Expression of ERLIN1 in Immune Cells during Sepsis.Biology · 2021Article
- Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data.Nature communications · 2021Article
- Integrated transcriptional-phenotypic analysis captures systemic immunomodulation following antiangiogenic therapy in renal cell carcinoma patients.Clinical and translational medicine · 2021Article
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Authors and funding
18 authors.
Funding
Abstract
backgroundCovid-19 morbidity and mortality are associated with a dysregulated immune response. Tools are needed to enhance existing immune profiling capabilities in affected patients. Here we aimed to develop an approach to support the design of targeted blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection.
methodsWe designed a pool of candidates based on a pre-existing and well-characterized repertoire of blood transcriptional modules. Available Covid-19 blood transcriptome data was also used to guide this process. Further selection steps relied on expert curation. Additionally, we developed several custom web applications to support the evaluation of candidates.
resultsAs a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: immunological relevance, therapeutic development relevance and SARS biology relevance.
conclusionAltogether the work presented here may contribute to the future expansion of immune profiling capabilities via targeted profiling of blood transcript abundance in Covid-19 patients.
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