The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
The reactome pathway knowledgebase 2022
Open accessAbstract
The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired disease processes. The processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Recent curation work has expanded our annotations of normal and disease-associated signaling processes and of the drugs that target them, in particular infections caused by the SARS-CoV-1 and SARS-CoV-2 coronaviruses and the host response to infection. New tools support better simultaneous analysis of high-throughput data from multiple sources and the placement of understudied (‘dark’) proteins from analyzed datasets in the context of Reactome’s manually curated pathways.
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Cites
UniProt: the universal protein knowledgebase in 2021
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1100 · Cited by 6,372
The Reactome pathway Knowledgebase
Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1351 · Cited by 5,605
Self-citationA SARS-CoV-2 protein interaction map reveals targets for drug repurposing
Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., et al. (2020) · Nature · doi:10.1038/s41586-020-2286-9 · Cited by 4,405
KEGG: integrating viruses and cellular organisms
Kanehisa, M., Furumichi, M., Sato, Y., Ishiguro-Watanabe, M., & Tanabe, M. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa970 · Cited by 3,436
The reactome pathway knowledgebase
Jassal, B., Matthews, L., Viteri, G., Gong, C., Lorente, P., Fabregat, A., Sidiropoulos, K., Cook, J., Gillespie, M., Haw, R., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1031 · Cited by 2,159
Self-citationDe Lean, A., Stadel, J. M., & Lefkowitz, R. J. (1980) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(20)79672-9 · Cited by 1,612
The MetaCyc database of metabolic pathways and enzymes - a 2019 update
Caspi, R., Billington, R., Keseler, I. M., Kothari, A., Krummenacker, M., Midford, P. E., Ong, W. K., Paley, S., Subhraveti, P., & Karp, P. D. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz862 · Cited by 1,395
Human Coronavirus: Host-Pathogen Interaction
Fung, T. S., & Liu, D. X. (2019) · Annual Review of Microbiology · doi:10.1146/annurev-micro-020518-115759 · Cited by 960
Reactome: a knowledge base of biologic pathways and processes
Vastrik, I., D'Eustachio, P., Schmidt, E., Joshi-Tope, G., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., et al. (2007) · Genome Biology · doi:10.1186/gb-2007-8-3-r39 · Cited by 654
Self-citationKibbe, W. A., Arze, C., Felix, V., Mitraka, E., Bolton, E., Fu, G., Mungall, C. J., Binder, J. X., Malone, J., Vasant, D., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1011 · Cited by 580
Cited by
Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A. L., Fang, T., Doncheva, N. T., Pyysalo, S., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1000 · Cited by 9,726
Kolberg, L., Raudvere, U., Kuzmin, I., Adler, P., Vilo, J., & Peterson, H. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad347 · Cited by 1,673
Best practices for single-cell analysis across modalities
Heumos, L., Schaar, A. C., Lance, C., Litinetskaya, A., Drost, F., Zappia, L., Lücken, M. D., Strobl, D. C., Henao, J., Curion, F., et al. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00586-w · Cited by 1,051
“3).”
JBrowse 2: a modular genome browser with views of synteny and structural variation
Diesh, C., Stevens, G. J., Xie, P., De Jesus Martinez, T., Hershberg, E. A., Leung, A., Guo, E., Dider, S., Zhang, J., Bridge, C., et al. (2023) · Genome Biology · doi:10.1186/s13059-023-02914-z · Cited by 853
Self-citationSpatial multi-omic map of human myocardial infarction
Kuppe, C., Ramirez Flores, R. O., Li, Z., Hayat, S., Levinson, R. T., Liao, X., Hannani, M. T., Tanevski, J., Wünnemann, F., Nagai, J. S., et al. (2022) · Nature · doi:10.1038/s41586-022-05060-x · Cited by 772
Metadata
- Authors
- Gillespie, M., Jassal, B., Stephan, R., Milacic, M., Rothfels, K., Senff-Ribeiro, A., Griss, J., Sevilla, C., Matthews, L., Gong, C., Deng, C., Varusai, T., Ragueneau, E., Haider, Y., May, B., Shamovsky, V., Weiser, J., Brunson, T., Sanati, N., Beckman, L., Shao, X., Fabregat, A., Sidiropoulos, K., Murillo, J., Viteri, G., Cook, J., Shorser, S., Bader, G., Demir, E., Sander, C., Haw, R., Wu, G., Stein, L., Hermjakob, H., & D’Eustachio, P.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-11-12
- Volume
- 50
- Issue
- D1
- Pages
- D687-D692
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W3211402536
- Cited by
- 2,339
- References
- 24
- FWCI
- 120.09
- Type
- journal article
- Language
- en
- Open access
- gold
- Funders
- National Institutes of Health (U41HG003751, U54GM114833, U01CA239069)
- European Bioinformatics Institute
- Open Targets
- University of Toronto
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- Gillespie, M., Jassal, B., Stephan, R., Milacic, M., Rothfels, K., Senff-Ribeiro, A., Griss, J., Sevilla, C., Matthews, L., Gong, C., Deng, C., Varusai, T., Ragueneau, E., Haider, Y., May, B., Shamovsky, V., Weiser, J., Brunson, T., Sanati, N., . . . D’Eustachio, P. (2022). The reactome pathway knowledgebase 2022. Nucleic Acids Research. https://doi.org/10.1093/nar/gkab1028
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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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