Like other scientific communities all across the globe, the Single Cell Community is committed to contribute with its research to help win the fight against the COVID-19 pandemic. Please find below recent (single cell) publications and other useful resources for COVID-19 research within the Single Cell community.


Bernardes, J P, Mishra, N, Tran, F, Bahmer, T, Best, L, Blase, JI et al.Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories. Immunity. 2020;  S1074-7613(20)30504-5. doi: 10.1016/j.immuni.2020.11.017. PubMedbPMID: 33296687

Schulte-Schrepping, J, Reusch, N, Paclik, D, Baßler, K, Schlickeiser, S, Zhang, B et al.Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. Cell. 2020;182 (6):1419-1440.e23. doi: 10.1016/j.cell.2020.08.001. PubMed PMID:32810438

Sungnak, W, Huang, N, Bécavin, C, Berg, M, Queen, R, Litvinukova, M et al.SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat Med. 2020; 26(5):681-687. doi: 10.1038/s41591-020-0868-6. PubMed PIMD:32327758

Ziegler, CGK, Allon, SJ, Nyquist, SK, Mbano, IM, Miao, VN, Tzouanas, CN et al.SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. Cell. 2020;181 (5):1016-1035.e19. doi: 10.1016/j.cell.2020.04.035. PubMed PMID:32413319

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Türei, D, Valdeolivas, A, Gul, L, Palacio-Escat, N, Ivanova, O, Gábor, A et al.. Integrated intra-and intercellular signaling knowledge for multicelullar omics analysis. BioRxiv. 2020. doi: 10.1101/2020.08.03.221242

Lotfollahi, M, Naghipourfar, M, Luecken, MD, Khajavi, M, Buttner, M, Avsec, Z et al.. Query to reference single-cell integration with transfer learning. BioRxiv. 2020. doi: 10.1101/2020.07.16.205997

Wyler, E, Mösbauer, K, Franke, V, Diag, A, Gottula, L T, Arsie, R et al.Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention. BioRxiv. 2020. doi: 10.1101/2020.05.05.079194

Muus, C, Luecken, MD, Eraslan, G, Waghray, A, Heimberg, G, Sikkema, L et al.. Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells. BioRxiv. 2020. doi: 10.1101/2020.04.19.049254

Aschenbrenner, AC, Mouktaroudi, M, Krämer, B, Oestreich, M, Antonakos, N, Nuesch-Germano, M et al.. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. Genome Med. 2021;13 (1):7. doi: 10.1186/s13073-020-00823-5. PubMed PMID:33441124

Vinson, AJ, Chong, AS, Clegg, D, Falk, C, Foster, BJ, Halpin, A et al.. SEX MATTERS – COVID-19 IN KIDNEY TRANSPLANTATION. Kidney Int. 2021; :. doi: 10.1016/j.kint.2020.12.020. PubMed PMID:33412163

Heming, M, Li, X, Räuber, S, Mausberg, AK, Börsch, AL, Hartlehnert, M et al.. Neurological Manifestations of COVID-19 Feature T Cell Exhaustion and Dedifferentiated Monocytes in Cerebrospinal Fluid. Immunity. 2021;54 (1):164-175.e6. doi: 10.1016/j.immuni.2020.12.011. PubMed PMID:33382973

De Domenico, E, Bonaguro, L, Schulte-Schrepping, J, Becker, M, Händler, K, Schultze, JL et al.. Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19. STAR Protoc. 2020;1 (3):100233. doi: 10.1016/j.xpro.2020.100233. PubMed PMID:33377120

Woo, MS, Malsy, J, Pöttgen, J, Seddiq Zai, S, Ufer, F, Hadjilaou, A et al.. Frequent neurocognitive deficits after recovery from mild COVID-19. Brain Commun. 2020;2 (2):fcaa205. doi: 10.1093/braincomms/fcaa205. PubMed PMID:33376990

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Schulien, I, Kemming, J, Oberhardt, V, Wild, K, Seidel, L M, Killmer, S et al.. Ex vivo detection of SARS-CoV-2-specific CD8+ T cells: rapid induction, prolonged contraction, and formation of functional memory. BioRxiv. 2020. doi: 10.1101/2020.08.13.249433

Warnat-Herresthal, S, Schultze, H, Shastry, KPL, Manamohan, S, Mukherjee, S, Garg, V et al.. Swarm Learning as a privacy-preserving machine learning approach for disease classification. BioRxiv. 2020. doi: 10.1101/2020.06.25.171009

Schmidt, N, Lareau, CA, Keshishian, H, Melanson, R, Zimmer, M, Kirschner, L et al.. A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells. BioRxiv. 2020. doi: 10.1101/2020.07.15.204404

Stegmann, KM, Dickmanns, A, Gerber, S, Nikolova, V, Klemke, L, Manzini, V et al.. The folate antagonist methotrexate diminishes replication of the coronavirus SARS-CoV-2 and enhances the antiviral efficacy of remdesivir in cell culture models. BioRxiv. 2020. doi: 10.1101/2020.07.18.210013

Neufeldt, CJ, Cerikan, B, Cortese, M, Frankish, J, Lee, JY, Plociennikowska, A et al.. SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB. BioRxiv. 2020. doi: 10.1101/2020.07.21.212639

Morel, B, Barbera, P, Czech, L, Bettisworth, B, Huebner, L, Lutteropp, S et al.. Phylogenetic analysis of SARS-CoV-2 data is difficult. BioRxiv. 2020. doi: 10.1101/2020.08.05.239046

Databases, Tools and other Resources

Overview of resources for COVID-19 (single cell) research which are provided by members of the scientific community.