The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Expression Atlas update: from tissues to single cells
Abstract
Expression Atlas is EMBL-EBI’s resource for gene and protein expression. It sources and compiles data on the abundance and localisation of RNA and proteins in various biological systems and contexts and provides open access to this data for the research community. With the increased availability of single cell RNA-Seq datasets in the public archives, we have now extended Expression Atlas with a new added-value service to display gene expression in single cells. Single Cell Expression Atlas was launched in 2018 and currently includes 123 single cell RNA-Seq studies from 12 species. The website can be searched by genes within or across species to reveal experiments, tissues and cell types where this gene is expressed or under which conditions it is a marker gene. Within each study, cells can be visualized using a pre-calculated t-SNE plot and can be coloured by different features or by cell clusters based on gene expression. Within each experiment, there are links to downloadable files, such as RNA quantification matrices, clustering results, reports on protocols and associated metadata, such as assigned cell types.
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“Existing work had to restrict their models to a small list of selected genes.”
From Large-scale foundation model on single-cell transcriptomics (2024) · cites this paper as [8]
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Self-citationLarge-scale foundation model on single-cell transcriptomics
Hao, M., Gong, J., Zeng, X., Liu, C., Guo, Y., Cheng, X., Wang, T., Ma, J., Zhang, X., & Song, L. (2024) · Nature Methods · doi:10.1038/s41592-024-02305-7 · Cited by 628
“The ablation studies (Supplementary Note 1) of taking downsampling strategy (Supplementary Table 8) and regression loss (Supplementary Fig.”
InfluentialTCRD and pharos 2021: mining the human proteome for disease biology
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Yang, X., Liu, G., Feng, G., Bu, D., Wang, P., Jiang, J., Chen, S., Yang, Q., Zhang, Y., Man, Z., et al. (2023) · doi:10.1101/2023.09.26.559542 · Cited by 148
miRNATissueAtlas2: an update to the human miRNA tissue atlas
Keller, A., Gröger, L., Tschernig, T., Solomon, J., Laham, O., Schaum, N., Wagner, V., Kern, F., Schmartz, G. P., Li, Y., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab808 · Cited by 143
Large Scale Foundation Model on Single-cell Transcriptomics
Hao, M., Gong, J., Zeng, X., Liu, C., Guo, Y., Cheng, X., Wang, T., Ma, J., Song, L., & Zhang, X. (2023) · doi:10.1101/2023.05.29.542705 · Cited by 639
The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis
Pinkney, H. R., Wright, B. M., & Diermeier, S. D. (2020) · Non-Coding RNA · doi:10.3390/ncrna6040049 · Cited by 56
Vision-related convergent gene losses reveal SERPINE3’s unknown role in the eye
Indrischek, H., Hammer, J., Machate, A., Hecker, N., Kirilenko, B., Roscito, J., Hans, S., Norden, C., Brand, M., & Hiller, M. (2022) · eLife · doi:10.7554/elife.77999 · Cited by 21
Metadata
- Authors
- Papatheodorou, I., Moreno, P., Manning, J., Fuentes, A. M.-P., George, N., Fexova, S., Fonseca, N. A., Füllgrabe, A., Green, M., Huang, N., Huerta, L., Iqbal, H., Jianu, M., Mohammed, S., Zhao, L., Jarnuczak, A. F., Jupp, S., Marioni, J., Meyer, K., Petryszak, R., Prada Medina, C. A., Talavera-López, C., Teichmann, S., Vizcaino, J. A., & Brazma, A.
- Affiliations
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-10-30
- ISSN
- 0305-1048
- 1362-4962
- PMC
- PMC7145605
- Cited by
- 224
- References
- 6
- Language
- en
- Funders
- European Molecular Biology Laboratory
- Wellcome Trust (108437/Z/15/Z, 208391/Z/17/Z)
- National Science Foundation (NSF IOS #1127112)
- BBSRC (BB/P027849/1)
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