The DOI matches its Crossref record; 63 of the 63 references it cites were found in a registry or an index.
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines
Open accessAbstract
Many vaccines induce protective immunity via antibodies. Systems biology approaches have been used to determine signatures that can be used to predict vaccine-induced immunity in humans, but whether there is a 'universal signature' that can be used to predict antibody responses to any vaccine is unknown. Here we did systems analyses of immune responses to the polysaccharide and conjugate vaccines against meningococcus in healthy adults, in the broader context of published studies of vaccines against yellow fever virus and influenza virus. To achieve this, we did a large-scale network integration of publicly available human blood transcriptomes and systems-scale databases in specific biological contexts and deduced a set of transcription modules in blood. Those modules revealed distinct transcriptional signatures of antibody responses to different classes of vaccines, which provided key insights into primary viral, protein recall and anti-polysaccharide responses. Our results elucidate the early transcriptional programs that orchestrate vaccine immunity in humans and demonstrate the power of integrative network modeling.
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Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Human Protein Reference Database--2009 update
Keshava Prasad, T. S., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn892 · Cited by 3,234
Margolin, A. A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Favera, R. D., & Califano, A. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-s1-s7 · Cited by 2,420
Margolin, A. A., Nemenman, I. M., Basso, K., Wiggins, C. H., Stolovitzky, G. A., Favera, R. D., & Califano, A. (2006) · BMC Bioinformatics · doi:10.7916/d8g15zbp · Cited by 2,246
Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D., & Friedman, N. (2003) · Nature Genetics · doi:10.1038/ng1165 · Cited by 1,670
PID: the Pathway Interaction Database
Schaefer, C. F., Anthony, K., Krupa, S., Buchoff, J., Day, M., Hannay, T., & Buetow, K. H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn653 · Cited by 1,603
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
Khatri, P., Sirota, M., & Butte, A. J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002375 · Cited by 1,566
Network‐based classification of breast cancer metastasis
Chuang, H., Lee, E., Liu, Y., Lee, D., & Ideker, T. (2007) · Molecular Systems Biology · doi:10.1038/msb4100180 · Cited by 1,431
Reverse engineering of regulatory networks in human B cells
Basso, K., Margolin, A. A., Stolovitzky, G., Klein, U., Dalla-Favera, R., & Califano, A. (2005) · Nature Genetics · doi:10.1038/ng1532 · Cited by 1,404
Cited by
Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A. K., Slichter, C. K., Miller, H. W., McElrath, M. J., Prlic, M., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0844-5 · Cited by 3,159
Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans
Arunachalam, P. S., Wimmers, F., Mok, C. K. P., Perera, R. A. P. M., Scott, M., Hagan, T., Sigal, N., Feng, Y., Bristow, L., Tak-Yin Tsang, O., et al. (2020) · Science · doi:10.1126/science.abc6261 · Cited by 1,186
Self-citationVariation in the Human Immune System Is Largely Driven by Non-Heritable Influences
Brodin, P., Jojic, V., Gao, T., Bhattacharya, S., Angel, C. J. L., Furman, D., Shen-Orr, S., Dekker, C. L., Swan, G. E., Butte, A. J., et al. (2015) · Cell · doi:10.1016/j.cell.2014.12.020 · Cited by 1,065
Bhattacharya, S., Dunn, P., Thomas, C. G., Smith, B., Schaefer, H., Chen, J., Hu, Z., Zalocusky, K. A., Shankar, R. D., Shen-Orr, S. S., et al. (2018) · Scientific Data · doi:10.1038/sdata.2018.15 · Cited by 786
Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans
Hagan, T., Cortese, M., Rouphael, N., Boudreau, C., Linde, C., Maddur, M. S., Das, J., Wang, H., Guthmiller, J., Zheng, N.-Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.010 · Cited by 572
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Metadata
- Authors
- Li, S., Rouphael, N., Duraisingham, S., Romero-Steiner, S., Presnell, S., Davis, C., Schmidt, D. S., Johnson, S. E., Milton, A., Rajam, G., Kasturi, S., Carlone, G. M., Quinn, C., Chaussabel, D., Palucka, A. K., Mulligan, M. J., Ahmed, R., Stephens, D. S., Nakaya, H. I., & Pulendran, B.
- Venue
- Nature Immunology
- Published
- 2013-12-15
- Volume
- 15
- Issue
- 2
- Pages
- 195-204
- ISSN
- 1529-2908 (ISSN-L)
- 1529-2916
- OpenAlex
- W1969218538
- Cited by
- 770
- References
- 63
- FWCI
- 19.82
- Type
- journal article
- Language
- en
- Open access
- green
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- Li, S., Rouphael, N., Duraisingham, S., Romero-Steiner, S., Presnell, S., Davis, C., Schmidt, D. S., Johnson, S. E., Milton, A., Rajam, G., Kasturi, S., Carlone, G. M., Quinn, C., Chaussabel, D., Palucka, A. K., Mulligan, M. J., Ahmed, R., Stephens, D. S., Nakaya, H. I., & Pulendran, B. (2014). Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. Nature Immunology. https://doi.org/10.1038/ni.2789
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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