The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Dimensionality reduction by UMAP to visualize physical and genetic interactions
Open accessAbstract
Dimensionality reduction is often used to visualize complex expression profiling data. Here, we use the Uniform Manifold Approximation and Projection (UMAP) method on published transcript profiles of 1484 single gene deletions of Saccharomyces cerevisiae . Proximity in low-dimensional UMAP space identifies groups of genes that correspond to protein complexes and pathways, and finds novel protein interactions, even within well-characterized complexes. This approach is more sensitive than previous methods and should be broadly useful as additional transcriptome datasets become available for other organisms.
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Cites
UMAP: Uniform Manifold Approximation and Projection
McInnes, L., Healy, J., Saul, N., & Großberger, L. (2018) · Journal of Open Source Software · doi:10.21105/joss.00861 · Cited by 9,826
Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw937 · Cited by 6,980
The single-cell transcriptional landscape of mammalian organogenesis
Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F. J., et al. (2019) · Nature · doi:10.1038/s41586-019-0969-x · Cited by 4,490
Self-citationThree-dimensional intact-tissue sequencing of single-cell transcriptional states
Wang, X., Allen, W. E., Wright, M. A., Sylwestrak, E. L., Samusik, N., Vesuna, S., Evans, K., Liu, C., Ramakrishnan, C., Liu, J., et al. (2018) · Science · doi:10.1126/science.aat5691 · Cited by 1,620
A global genetic interaction network maps a wiring diagram of cellular function
Costanzo, M., VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., et al. (2016) · Science · doi:10.1126/science.aaf1420 · Cited by 1,240
Pooled CRISPR screening with single-cell transcriptome readout.
Datlinger, P., Rendeiro, A. F., Schmidl, C., Krausgruber, T., Traxler, P., Klughammer, J., Schuster, L. C., Kuchler, A., Alpar, D., & Bock, C. (2017) · Nature Methods · doi:10.1038/nmeth.4177 · Cited by 1,096
Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function
Shifrut, E., Carnevale, J., Tobin, V., Roth, T. L., Woo, J. M., Bui, C. T., Li, P. J., Diolaiti, M. E., Ashworth, A., & Marson, A. (2018) · Cell · doi:10.1016/j.cell.2018.10.024 · Cited by 573
Thyroid hormone regulates distinct paths to maturation in pigment cell lineages
Saunders, L. M., Mishra, A. K., Aman, A. J., Lewis, V. M., Toomey, M. B., Packer, J. S., Qiu, X., McFaline-Figueroa, J. L., Corbo, J. C., Trapnell, C., et al. (2019) · eLife · doi:10.7554/elife.45181 · Cited by 170
Self-citation
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The Specious Art of Single-Cell Genomics
Chari, T., & Pachter, L. (2021) · doi:10.1101/2021.08.25.457696 · Cited by 379
Brain mapping across 16 autism mouse models reveals a spectrum of functional connectivity subtypes
Zerbi, V., Pagani, M., Markicevic, M., Matteoli, M., Pozzi, D., Fagiolini, M., Bozzi, Y., Galbusera, A., Scattoni, M. L., Provenzano, G., et al. (2021) · Molecular Psychiatry · doi:10.1038/s41380-021-01245-4 · Cited by 102
The regulatory landscape of the yeast phosphoproteome
Leutert, M., Barente, A. S., Fukuda, N. K., Rodriguez-Mias, R. A., & Villén, J. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01115-3 · Cited by 52
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Metadata
- Authors
- Dorrity, M. W., Saunders, L. M., Queitsch, C., Fields, S., & Trapnell, C.
- Venue
- Nature Communications
- Published
- 2020-03-24
- Volume
- 11
- Issue
- 1
- Pages
- 1537-1537
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W3014040695
- Cited by
- 242
- References
- 8
- FWCI
- 9.47
- Type
- journal article
- Language
- en
- Open access
- gold
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