ArticleiScience2021
An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses.
Article in iScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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.
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Who cites it
20 citing papers in PubMed, 26 citations in OpenAlex.
- Interpretable deep generative ensemble learning for single-cell omics with Hydra.Molecular systems biology · 2026Article
- Type I IFN-dependent FcγRIV signaling in murine monocytes promotes lethal anaphylaxis during viral infections.The Journal of clinical investigation · 2026Article
- omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.Genome biology · 2026Article
- Characterization of quiescent subpopulations and proliferative compartments in glioblastoma.bioRxiv : the preprint server for biology · 2025Article
- Type 1 innate lymphoid cell-immature neutrophil axis suppresses acute tissue inflammation.Nature communications · 2025Article
- Single-cell profiling of bone metastasis ecosystems from multiple cancer types reveals convergent and divergent mechanisms of bone colonization.Cell genomics · 2025Article
- KAT5 regulates neurodevelopmental states associated with G0-like populations in glioblastoma.Nature communications · 2025Article
- scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery.Briefings in bioinformatics · 2025Article
- Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.PLoS genetics · 2025Article
- Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels.Bioinformatics (Oxford, England) · 2024Article
- Integrative Analysis by Mendelian Randomization and Large-Scale Single-Cell Transcriptomics Reveals Causal Links between B Cell Subtypes and Diabetic Kidney Disease.Kidney diseases (Basel, Switzerland) · 2024Article
- Deconvolution of the tumor-educated platelet transcriptome reveals activated platelet and inflammatory cell transcript signatures.JCI insight · 2024Article
- A multi-organ map of the human immune system across age, sex and ethnicity.bioRxiv : the preprint server for biology · 2024Article
- Mapping a New Course to Understand Lung Biology Mechanisms: LungMAP.net.American journal of respiratory cell and molecular biology · 2024Article
- Single-cell resolution of human airway epithelial cells exposed to bronchiolitis obliterans-associated chemicals.American journal of physiology. Lung cellular and molecular physiology · 2024Article
- Longitudinal whole blood transcriptomic analysis characterizes neutrophil activation and interferon signaling in moderate and severe COVID-19.Scientific reports · 2023Article
- Schizophrenia-associated NRXN1 deletions induce developmental-timing- and cell-type-specific vulnerabilities in human brain organoids.Nature communications · 2023Article
- Secreted ORF8 induces monocytic pro-inflammatory cytokines through NLRP3 pathways in patients with severe COVID-19.iScience · 2023Article
- Transcriptomics and RNA-Based Therapeutics as Potential Approaches to Manage SARS-CoV-2 Infection.International journal of molecular sciences · 2022Review
- Impacts of exposure to air pollution, radon and climate drivers on the COVID-19 pandemic in Bucharest, Romania: A time series study.Environmental research · 2022Observational
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
Numerous studies have provided single-cell transcriptome profiles of host responses to SARS-CoV-2 infection. Critically lacking however is a data mine that allows users to compare and explore cell profiles to gain insights and develop new hypotheses. To accomplish this, we harmonized datasets from COVID-19 and other control condition blood, bronchoalveolar lavage, and tissue samples, and derived a compendium of gene signature modules per cell type, subtype, clinical condition, and compartment. We demonstrate approaches to interacting with, exploring, and functional evaluating these modules via a new interactive web portal ToppCell (http://toppcell.cchmc.org/). As examples, we develop three hypotheses: (1) alternatively-differentiated monocyte-derived macrophages form a multicelllar signaling cascade that drives T cell recruitment and activation; (2) COVID-19-generated platelet subtypes exhibit dramatically altered potential to adhere, coagulate, and thrombose; and (3) extrafollicular B maturation is driven by a multilineage cell activation network that expresses an ensemble of genes strongly associated with risk for developing post-viral autoimmunity.
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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.