The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Quantification of cell identity from single-cell gene expression profiles
Open accessAbstract
The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify identities from single-cell RNA-seq profiles, accurately classifying cells from Arabidopsis root tips and human glioblastoma tumors. We apply our approach to single cells captured from regenerating roots following tip excision. Our technique exposes a previously uncharacterized transient collapse of identity distant from the injury site, demonstrating the biological relevance of a quantitative cell identity index.
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Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
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The Immunological Genome Project: networks of gene expression in immune cells
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Stochastic mRNA Synthesis in Mammalian Cells
Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y., & Tyagi, S. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040309 · Cited by 1,737
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
Treutlein, B., Brownfield, D. G., Wu, A. R., Neff, N. F., Mantalas, G. L., Espinoza, F. H., Desai, T. J., Krasnow, M. A., & Quake, S. R. (2014) · Nature · doi:10.1038/nature13173 · Cited by 1,342
Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
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Validation of noise models for single-cell transcriptomics
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Integrative functional genomic analysis of human brain development and neuropsychiatric risks
Li, M., Santpere, G., Imamura Kawasawa, Y., Evgrafov, O. V., Gulden, F. O., Pochareddy, S., Sunkin, S. M., Li, Z., Shin, Y., Zhu, Y., et al. (2018) · Science · doi:10.1126/science.aat7615 · Cited by 810
Denyer, T., Ma, X., Klesen, S., Scacchi, E., Nieselt, K., & Timmermans, M. C. P. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.02.022 · Cited by 608
High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types
Shulse, C. N., Cole, B. J., Ciobanu, D., Lin, J., Yoshinaga, Y., Gouran, M., Turco, G. M., Zhu, Y., O’Malley, R. C., Brady, S. M., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.054 · Cited by 432
Spatiotemporal transcriptomic divergence across human and macaque brain development
Zhu, Y., Sousa, A. M. M., Gao, T., Skarica, M., Li, M., Santpere, G., Esteller-Cucala, P., Juan, D., Ferrández-Peral, L., Gulden, F. O., et al. (2018) · Science · doi:10.1126/science.aat8077 · Cited by 414
Shahan, R., Hsu, C.-W., Nolan, T. M., Cole, B. J., Taylor, I. W., Greenstreet, L., Zhang, S., Afanassiev, A., Vlot, A. H. C., Schiebinger, G., et al. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.01.008 · Cited by 363
Metadata
- Authors
- Efroni, I., Ip, P.-L., Nawy, T., Mello, A., & Birnbaum, K. D.
- Venue
- Genome Biology
- Published
- 2015-01-22
- Volume
- 16
- Issue
- 1
- Pages
- 9-9
- ISSN
- 1465-6906 (ISSN-L)
- OpenAlex
- W2121711223
- Cited by
- 163
- References
- 9
- FWCI
- 5.02
- Type
- journal article
- Language
- en
- Open access
- gold
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- Efroni, I., Ip, P.-L., Nawy, T., Mello, A., & Birnbaum, K. D. (2015). Quantification of cell identity from single-cell gene expression profiles. Genome Biology. https://doi.org/10.1186/s13059-015-0580-x
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