The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Automated identification of stratifying signatures in cellular subpopulations
Open accessAbstract
Significance: Single-cell measurement technologies such as flow cytometry permit the investigation of specific cellular subpopulations. Mass cytometry currently measures >40 parameters per cell and produces phenotypically rich datasets that may be retrospectively interrogated for relevant biological signal. There are few methods that identify experimentally relevant subpopulations within these datasets, and most do not scale well to higher-dimensional measurements. To address this bottleneck, we present a data-driven method termed Citrus that identifies cell subsets associated with an experimental endpoint of interest. Citrus can test diverse experimental hypotheses and is demonstrated through the systematic identification of (i) blood cells that signal in response to experimental stimuli and (ii) T-cell subsets whose abundance is predictive of AIDS-free survival risk in patients with HIV.
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Cites
Regression shrinkage and selection via the lasso
Tibshirani, R. (1996) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1996.tb02080.x · Cited by 51,482
Self-citationBendall, S. C., Simonds, E. F., Qiu, P., Amir, E.-A. D., Krutzik, P. O., Finck, R., Bruggner, R. V., Melamed, R., Trejo, A., Ornatsky, O. I., et al. (2011) · Science · doi:10.1126/science.1198704 · Cited by 2,279
Self-citationPhenotype and function of human T lymphocyte subsets: Consensus and issues
Appay, V., van Lier, R. A. W., Sallusto, F., & Roederer, M. (2008) · Cytometry Part A · doi:10.1002/cyto.a.20643 · Cited by 729 · cited 2×
“…was also reported by Ganesan et al. and Aghaeepour et al. Of the remaining clusters frequently selected during cross-validation, two (clusters 824715 and 824971) had a phenotype of CCR7 + naive CD4 + T-cells (28), whereas the third (cluster 824823) had a similar phenotype to the Ki-67 + cluster.”
ResultMultiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators
Bodenmiller, B., Zunder, E. R., Finck, R., Chen, T. J., Savig, E. S., Bruggner, R. V., Simonds, E. F., Bendall, S. C., Sachs, K., Krutzik, P. O., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2317 · Cited by 546
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Cited by
Fraietta, J. A., Lacey, S. F., Orlando, E. J., Pruteanu-Malinici, I., Gohil, M., Lundh, S., Boesteanu, A. C., Wang, Y., O’Connor, R. S., Hwang, W.-T., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0010-1 · Cited by 1,785
Eleven grand challenges in single-cell data science
Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., Campbell, K. R., Beerenwinkel, N., Mahfouz, A., et al. (2020) · Genome Biology · doi:10.1186/s13059-020-1926-6 · Cited by 1,327
Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer’s disease
Gate, D., Saligrama, N., Leventhal, O., Yang, A. C., Unger, M. S., Middeldorp, J., Chen, K., Lehallier, B., Channappa, D., De Los Santos, M. B., et al. (2020) · Nature · doi:10.1038/s41586-019-1895-7 · Cited by 992
Systemic Immunity Is Required for Effective Cancer Immunotherapy
Spitzer, M. H., Carmi, Y., Reticker-Flynn, N. E., Kwek, S. S., Madhireddy, D., Martins, M. M., Gherardini, P. F., Prestwood, T. R., Chabon, J., Bendall, S. C., et al. (2017) · Cell · doi:10.1016/j.cell.2016.12.022 · Cited by 963
Self-citationZunder, E. R., Finck, R., Behbehani, G. K., Amir, E.-A. D., Krishnaswamy, S., Gonzalez, V. D., Lorang, C. G., Bjornson, Z., Spitzer, M. H., Bodenmiller, B., et al. (2015) · Nature Protocols · doi:10.1038/nprot.2015.020 · Cited by 596
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Metadata
- Authors
- Bruggner, R. V., Bodenmiller, B., Dill, D. L., Tibshirani, R. J., & Nolan, G. P.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2014-06-16
- Volume
- 111
- Issue
- 26
- Pages
- E2770-7
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2143451223
- Cited by
- 473
- References
- 4
- FWCI
- 11.07
- Type
- journal article
- Language
- en
- Open access
- green
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