A guide to systems-level immunomics

Davis, M. M., Tato, C. M. & Furman, D. Systems immunology: just getting started. Nat. Immunol. 18, 725–732 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Aderem, A. Systems biology: its practice and challenges. Cell 121, 511–513 (2005).

CAS  PubMed  Article  Google Scholar 

Wagner, A., Regev, A. & Yosef, N. Revealing the vectors of cellular identity with single-cell genomics. Nat. Biotechnol. 34, 1145–1160 (2016).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995).

CAS  PubMed  Article  Google Scholar 

Bennett, L. et al. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J. Exp. Med 197, 711–723 (2003).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Behr, M. A. et al. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284, 1520–1523 (1999).

CAS  PubMed  Article  Google Scholar 

Xue, J. et al. Transcriptome-based network analysis reveals a spectrum model of human macrophage activation. Immunity 40, 274–288 (2014).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728–1732 (2005).

CAS  PubMed  Article  Google Scholar 

Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613–619 (2008).

CAS  PubMed  Article  Google Scholar 

Carpenter, S. et al. A long noncoding RNA mediates both activation and repression of immune response genes. Science 341, 789–792 (2013).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Shalek, A. K. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236–240 (2013).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Tang, F. et al. mRNA-seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377–382 (2009).

CAS  PubMed  Article  Google Scholar 

Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Nawy, T. Single-cell epigenetics. Nat. Methods 10, 1060 (2013).

CAS  PubMed  Article  Google Scholar 

Seydel, C. Single-cell metabolomics hits its stride. Nat. Methods 18, 1452–1456 (2021).

CAS  PubMed  Article  Google Scholar 

Pai, J. A. & Satpathy, A. T. High-throughput and single-cell T cell receptor sequencing technologies. Nat. Methods 18, 881–892 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Yaari, G. & Kleinstein, S. H. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Med. 7, 121 (2015).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Liberis, E., Velickovic, P., Sormanni, P., Vendruscolo, M. & Liò, P. Parapred: antibody paratope prediction using convolutional and recurrent neural networks. Bioinformatics 34, 2944–2950 (2018).

CAS  PubMed  Article  Google Scholar 

Miho, E. et al. Computational Strategies for dissecting the high-dimensional complexity of adaptive immune repertoires. Front. Immunol. 9, 224 (2018).

PubMed  PubMed Central  Article  Google Scholar 

Ma, K.-Y. et al. High-throughput and high-dimensional single-cell analysis of antigen-specific CD8+ T cells. Nat. Immunol. 22, 1590–1598 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Schultheiß, C. et al. Next-generation sequencing of T and B cell receptor repertoires from COVID-19 patients showed signatures associated with severity of disease. Immunity 53, 442–455.e4 (2020).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Specht, H. et al. Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biol. 22, 50 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Stuart, T. & Satija, R. Integrative single-cell analysis. Nat. Rev. Genet. 20, 257–272 (2019).

CAS  PubMed  Article  Google Scholar 

Hasin, Y., Seldin, M. & Lusis, A. Multi-omics approaches to disease. Genome Biol. 18, 83 (2017).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Karczewski, K. J. & Snyder, M. P. Integrative omics for health and disease. Nat. Rev. Genet. 19, 299–310 (2018).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Van den Berge, K. et al. RNA sequencing data: hitchhiker’s guide to expression analysis. Annu. Rev. Biomed. Data Sci. 2, 139–173 (2019).

Stark, R., Grzelak, M. & Hadfield, J. RNA sequencing: the teenage years. Nat. Rev. Genet. 20, 631–656 (2019).

CAS  PubMed  Article  Google Scholar 

Svensson, V., Vento-Tormo, R. & Teichmann, S. A. Exponential scaling of single-cell RNA-seq in the past decade. Nat. Protoc. 13, 599–604 (2018).

CAS  PubMed  Article  Google Scholar 

Nakaya, H. I. et al. Systems biology of vaccination for seasonal influenza in humans. Nat. Immunol. 12, 786–795 (2011).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Rechtien, A. et al. Systems vaccinology identifies an early innate immune signature as a correlate of antibody responses to the Ebola vaccine rVSV-ZEBOV. Cell Rep. 20, 2251–2261 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Arunachalam, P. S. et al. Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Nature 596, 410–416 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181 (2014).

CAS  PubMed  Article  Google Scholar 

Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Gierahn, T. M. et al. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat. Methods 14, 395–398 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Tu, A. A. et al. TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures. Nat. Immunol. 20, 1692–1699 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Triana, S. et al. Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states. Nat. Immunol. 22, 1577–1589 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Schulte-Schrepping, J., Ferreira, H. J., Saglam, A., Hinkley, E. & Schultze, J. L. in Epigenetics of the Immune System 185–216 (Elsevier, 2020).

Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol. 109, 21.29.1–21.29.9 (2015).

Article  Google Scholar 

Dimitriu, M. A., Lazar-Contes, I., Roszkowski, M. & Mansuy, I. M. Single-cell multiomics techniques: from conception to applications. Front. Cell Dev. Biol. 10, 854317 (2022).

PubMed  PubMed Central  Article  Google Scholar 

Li, Y. et al. A functional genomics approach to understand variation in cytokine production in humans. Cell 167, 1099–1110.e14 (2016).

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