ArticleNature medicine2021
Single-cell multi-omics analysis of the immune response in COVID-19.
Open access · hybridAbstract read
In one paragraph
Article in Nature medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 481 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
481citing papers in PubMed, 2 pooled it
54.0field-weighted citation impact, top 1% of its field
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
481 citing papers in PubMed, 2 syntheses or guidelines pooled it, 812 citations in OpenAlex.
- Improving reproducibility of differentially expressed genes in single-cell transcriptomic studies of neurodegenerative diseases through meta-analysis.Nature communications · 2025Pooled it
- Systemic cytokines drive conserved severity-associated myeloid responses across bacterial and viral infections.Communications biology · 2025Pooled it
- Dynamic transcriptional immune landscape in response to NK-cell therapy combined with gemcitabine plus S-1 in advanced pancreatic cancer: a phase 1b/2 trial.Signal transduction and targeted therapy · 2025Trial
- Immunophenotyping by Single-Cell CITE-Seq.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Single-cell Transcriptomics in Autoimmune Diseases: Mechanistic Insights, Cross-disease Convergence, and Translational Challenges in Rheumatoid Arthritis, Systemic Lupus Erythematosus, Type 1 Diabetes, and Multiple Sclerosis.Clinical reviews in allergy & immunology · 2026Review
- ConvexGating infers gating strategies from clusters in single cell cytometry data.Nature communications · 2026Article
- A statistical framework for disease classification with scRNA-Seq Data.bioRxiv : the preprint server for biology · 2026Article
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- PhenoMapR: scalable mapping of sample phenotypes to single-cell, spatial, and bulk transcriptomics data.bioRxiv : the preprint server for biology · 2026Article
- The RNA cargo of plasma-derived extracellular vesicles in mCRPC patients captures cancer cells and tumor microenvironment signals.bioRxiv : the preprint server for biology · 2026Article
- Deconformer: efficient cell-type composition profiling of cfRNA across diverse cell types.Briefings in bioinformatics · 2026Article
- scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data.Briefings in bioinformatics · 2026Article
- Continual integration of single-cell multimodal data with MIRACLE.Nature computational science · 2026Article
- COBRA: cell-type-specific orthogonal batch effect removal algorithm in single cell RNA-sequencing data.Bioinformatics (Oxford, England) · 2026Article
- Serum IgA proteomics reveals clonal composition and neutralization of dimeric and monomeric IgA repertoires against human norovirus.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Sex-specific trajectories of nonlinear immune aging at single-cell level.Nature communications · 2026Article
- Article
- Discovering reference-missing cell types in bulk transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Article
- Computational identification of antigen-specific T cell groups through generative epitope modeling.iScience · 2026Article
421 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
69 authors at 16 institutions in 2 countries.
Emily Stephenson *Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Gary Reynolds *Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Rachel A Botting *Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Fernando J Calero-Nieto *Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0003-3358-8253
Michael D Morgan *European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.ORCID http://orcid.org/0000-0003-0757-0711
Zewen Kelvin Tuong *Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0002-6735-6808
Karsten Bach *European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.
Waradon Sungnak *Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-0136-4960
Kaylee B WorlockUCL Respiratory, Division of Medicine, University College London, London, UK.
Masahiro YoshidaUCL Respiratory, Division of Medicine, University College London, London, UK.ORCID http://orcid.org/0000-0002-3521-5322
Natsuhiko KumasakaWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-3557-0375
Katarzyna KaniaCancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
Justin EngelbertBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Bayanne OlabiBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Jarmila Stremenova SpegarovaTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0002-0710-9266
Nicola K WilsonWellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0003-0865-7333
Nicole MendeWellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0002-5078-2333
Laura JardineBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Louis C S GardnerBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0002-7200-978X
Issac GohBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0002-6397-3518
Dave HorsfallBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0002-8086-812X
Jim McGrathBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Simone WebbBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0003-3058-8952
Michael W MatherBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0001-7972-7111
Rik G H LindeboomWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-3660-504X
Emma DannWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-7400-7438
Ni HuangWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
Krzysztof PolanskiWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-2586-9576
Elena PrigmoreWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
Florian GotheTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
Jonathan ScottTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
Rebecca P PayneTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0002-9037-7367
Kenneth F BakerTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0002-6735-2911
Aidan T HanrathTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
Ina C D Schim van der LoeffTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0003-1196-6196
Andrew S BarrDepartment of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0002-8084-7644
Amada Sanchez-GonzalezDepartment of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK.
Laura BergamaschiCambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.
Federica MesciaCambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-2759-4027
Josephine L BarnesUCL Respiratory, Division of Medicine, University College London, London, UK.ORCID http://orcid.org/0000-0001-9938-3176
Eliz KilichUniversity College London Hospitals NHS Foundation Trust, London, UK.
Angus de WiltonUniversity College London Hospitals NHS Foundation Trust, London, UK.
Anita SaigalRoyal Free Hospital NHS Foundation Trust, London, UK.
Aarash SalehRoyal Free Hospital NHS Foundation Trust, London, UK.
Sam M JanesUCL Respiratory, Division of Medicine, University College London, London, UK.ORCID http://orcid.org/0000-0002-6634-5939
Claire M SmithUCL Great Ormond Street Institute of Child Health, London, UK.ORCID http://orcid.org/0000-0002-8913-0009
Nusayhah GopeeBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Caroline WilsonBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Paul CouplandCancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0002-2871-3374
Jonathan M CoxheadBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
Vladimir Yu KiselevWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
Stijn van DongenWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
Jaume BacarditSchool of Computing, Newcastle University, Newcastle Upon Tyne, UK.ORCID http://orcid.org/0000-0002-2692-7205
Hamish W KingWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID http://orcid.org/0000-0001-5972-8926
Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration
Anthony J RostronTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0002-9336-1723
A John SimpsonTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0003-4731-7294
Sophie HambletonTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0001-7954-3267
Elisa LaurentiWellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0002-9917-9092
Paul A LyonsCambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.ORCID http://orcid.org/0000-0001-7035-8997
Kerstin B MeyerWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID http://orcid.org/0000-0001-5906-1498
Marko Z NikolićUCL Respiratory, Division of Medicine, University College London, London, UK.ORCID http://orcid.org/0000-0001-6304-6848
Christopher J A DuncanTranslational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
Kenneth G C SmithCambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.ORCID http://orcid.org/0000-0003-3829-4326
Sarah A TeichmannWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK. st9@sanger.ac.uk.ORCID http://orcid.org/0000-0002-6294-6366
Menna R ClatworthyMolecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK. mrc38@cam.ac.uk.ORCID http://orcid.org/0000-0002-3340-9828
John C MarioniEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK. marioni@ebi.ac.uk.ORCID http://orcid.org/0000-0001-9092-0852
Berthold GöttgensWellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK. bg200@cam.ac.uk.ORCID http://orcid.org/0000-0001-6302-5705
Muzlifah HaniffaBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK. m.a.haniffa@ncl.ac.uk.ORCID http://orcid.org/0000-0002-3927-2084
Newcastle University · GBWellcome Sanger Institute · GBUniversity of Cambridge · GBNewcastle upon Tyne Hospitals NHS Foundation Trust · GBWellcome/MRC Cambridge Stem Cell Institute · GBUniversity College London Hospitals NHS Foundation Trust · GBEuropean Bioinformatics Institute · GBUniversity College London · GBRoyal Free London NHS Foundation Trust · GBGreat Ormond Street Hospital · GBLudwig-Maximilians-Universität München · DEMRC Laboratory of Molecular Biology · GBNewcastle College · GBNIHR Newcastle Biomedical Research Centre · GBQueen Mary University of London · GBSunderland Royal Hospital · GB
Funding
Medical Research Council MC_PC_17230Medical Research Council MR/K017047/1Medical Research Council MR/P008801/1Medical Research Council MR/R015635/1Medical Research Council MR/S005579/1Medical Research Council MR/S035842/1Medical Research Council MR/S036113/1Medical Research Council MR/W014556/1Wellcome Trust 204721/Z/16/ZWellcome Trust 206328/Z/17/ZWellcome Trust 207556/Z/17/Z
Abstract
Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16
Indexed as
ProteomeTranscriptomeCOVID-19Cross-Sectional StudiesHumansMonocytesReceptors, Antigen, B-CellReceptors, Antigen, T-CellSARS-CoV-2Single-Cell AnalysisT-LymphocytesProteomeReceptors, Antigen, B-CellReceptors, Antigen, T-Cell
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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.