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The Reactome BioMart.

Database : the journal of biological databases and curation

Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD.
PMID: 22012987
Database (Oxford). 2011 Oct 19;2011:bar031. doi: 10.1093/database/bar031. Print 2011.

Reactome is an open source, expert-authored, manually curated and peer-reviewed database of reactions, pathways and biological processes. We provide an intuitive web-based user interface to pathway knowledge and a suite of data analysis tools. The Reactome BioMart provides biologists...

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Haw RA, Croft D, Yung CK, et al. The Reactome BioMart. Database (Oxford). 2011;2011:bar031doi: 10.1093/database/bar031.
Haw, R. A., Croft, D., Yung, C. K., Ndegwa, N., D'Eustachio, P., Hermjakob, H., & Stein, L. D. (2011). The Reactome BioMart. Database : the journal of biological databases and curation, 2011bar031. https://doi.org/10.1093/database/bar031
Haw, Robin A, et al. "The Reactome BioMart." Database : the journal of biological databases and curation vol. 2011 (2011): bar031. doi: https://doi.org/10.1093/database/bar031
Haw RA, Croft D, Yung CK, Ndegwa N, D'Eustachio P, Hermjakob H, Stein LD. The Reactome BioMart. Database (Oxford). 2011 Oct 19;2011:bar031. doi: 10.1093/database/bar031. Print 2011. PMID: 22012987; PMCID: PMC3197281.
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Using Reactome to build an autophagy mechanism knowledgebase.

Autophagy

Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D'Eustachio P, Metzakopian E, Hermjakob H.
PMID: 32486891
Autophagy. 2021 Jun;17(6):1543-1554. doi: 10.1080/15548627.2020.1761659. Epub 2020 Jun 02.

The 21st century has revealed much about the fundamental cellular process of autophagy. Autophagy controls the catabolism and recycling of various cellular components both as a constitutive process and as a response to stress and foreign material invasion. There...

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Varusai TM, Jupe S, Sevilla C, et al. Using Reactome to build an autophagy mechanism knowledgebase. Autophagy. 2020;17(6):1543-1554doi: 10.1080/15548627.2020.1761659.
Varusai, T. M., Jupe, S., Sevilla, C., Matthews, L., Gillespie, M., Stein, L., Wu, G., D'Eustachio, P., Metzakopian, E., & Hermjakob, H. (2021). Using Reactome to build an autophagy mechanism knowledgebase. Autophagy, 17(6), 1543-1554. https://doi.org/10.1080/15548627.2020.1761659
Varusai, Thawfeek Mohamed, et al. "Using Reactome to build an autophagy mechanism knowledgebase." Autophagy vol. 17,6 (2021): 1543-1554. doi: https://doi.org/10.1080/15548627.2020.1761659
Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D'Eustachio P, Metzakopian E, Hermjakob H. Using Reactome to build an autophagy mechanism knowledgebase. Autophagy. 2021 Jun;17(6):1543-1554. doi: 10.1080/15548627.2020.1761659. Epub 2020 Jun 02. PMID: 32486891; PMCID: PMC8204961.
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Perform Pathway Enrichment Analysis Using ReactomeFIViz.

Methods in molecular biology (Clifton, N.J.)

Haw R, Loney F, Ong E, He Y, Wu G.
PMID: 31583638
Methods Mol Biol. 2020;2074:165-179. doi: 10.1007/978-1-4939-9873-9_13.

Modern large-scale biological data analysis often generates a set of significant genes, frequently associated with scores. Pathway-based approaches are routinely performed to understand the functional contexts of these genes. Reactome is the most comprehensive open-access biological pathway knowledge base,...

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Haw R, Loney F, Ong E, et al. Perform Pathway Enrichment Analysis Using ReactomeFIViz. Methods Mol Biol. 2020;2074:165-179doi: 10.1007/978-1-4939-9873-9_13.
Haw, R., Loney, F., Ong, E., He, Y., & Wu, G. (2020). Perform Pathway Enrichment Analysis Using ReactomeFIViz. Methods in molecular biology (Clifton, N.J.), 2074165-179. https://doi.org/10.1007/978-1-4939-9873-9_13
Haw, Robin, et al. "Perform Pathway Enrichment Analysis Using ReactomeFIViz." Methods in molecular biology (Clifton, N.J.) vol. 2074 (2020): 165-179. doi: https://doi.org/10.1007/978-1-4939-9873-9_13
Haw R, Loney F, Ong E, He Y, Wu G. Perform Pathway Enrichment Analysis Using ReactomeFIViz. Methods Mol Biol. 2020;2074:165-179. doi: 10.1007/978-1-4939-9873-9_13. PMID: 31583638.
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Overview of the interactive task in BioCreative V.

Database : the journal of biological databases and curation

Wang Q, S Abdul S, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN.
PMID: 27589961
Database (Oxford). 2016 Sep 01;2016. doi: 10.1093/database/baw119. Print 2016.

Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more...

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Wang Q, S Abdul S, Almeida L, et al. Overview of the interactive task in BioCreative V. Database (Oxford). 2016;2016doi: 10.1093/database/baw119.
Wang, Q., S Abdul, S., Almeida, L., Ananiadou, S., Balderas-Martínez, Y. I., Batista-Navarro, R., Campos, D., Chilton, L., Chou, H. J., Contreras, G., Cooper, L., Dai, H. J., Ferrell, B., Fluck, J., Gama-Castro, S., George, N., Gkoutos, G., Irin, A. K., Jensen, L. J., Jimenez, S., Jue, T. R., Keseler, I., Madan, S., Matos, S., McQuilton, P., Milacic, M., Mort, M., Natarajan, J., Pafilis, E., Pereira, E., Rao, S., Rinaldi, F., Rothfels, K., Salgado, D., Silva, R. M., Singh, O., Stefancsik, R., Su, C. H., Subramani, S., Tadepally, H. D., Tsaprouni, L., Vasilevsky, N., Wang, X., Chatr-Aryamontri, A., Laulederkind, S. J., Matis-Mitchell, S., McEntyre, J., Orchard, S., Pundir, S., Rodriguez-Esteban, R., Van Auken, K., Lu, Z., Schaeffer, M., Wu, C. H., Hirschman, L., & Arighi, C. N. (2016). Overview of the interactive task in BioCreative V. Database : the journal of biological databases and curation, 2016. https://doi.org/10.1093/database/baw119
Wang, Qinghua, et al. "Overview of the interactive task in BioCreative V." Database : the journal of biological databases and curation vol. 2016 (2016). doi: https://doi.org/10.1093/database/baw119
Wang Q, S Abdul S, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN. Overview of the interactive task in BioCreative V. Database (Oxford). 2016 Sep 01;2016. doi: 10.1093/database/baw119. Print 2016. PMID: 27589961; PMCID: PMC5009325.
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MET network in PubMed: a text-mined network visualization and curation system.

Database : the journal of biological databases and curation

Dai HJ, Su CH, Lai PT, Huang MS, Jonnagaddala J, Rose Jue T, Rao S, Chou HJ, Milacic M, Singh O, Syed-Abdul S, Hsu WL.
PMID: 27242035
Database (Oxford). 2016 May 30;2016. doi: 10.1093/database/baw090. Print 2016.

Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis...

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Dai HJ, Su CH, Lai PT, et al. MET network in PubMed: a text-mined network visualization and curation system. Database (Oxford). 2016;2016doi: 10.1093/database/baw090.
Dai, H. J., Su, C. H., Lai, P. T., Huang, M. S., Jonnagaddala, J., Rose Jue, T., Rao, S., Chou, H. J., Milacic, M., Singh, O., Syed-Abdul, S., & Hsu, W. L. (2016). MET network in PubMed: a text-mined network visualization and curation system. Database : the journal of biological databases and curation, 2016. https://doi.org/10.1093/database/baw090
Dai, Hong-Jie, et al. "MET network in PubMed: a text-mined network visualization and curation system." Database : the journal of biological databases and curation vol. 2016 (2016). doi: https://doi.org/10.1093/database/baw090
Dai HJ, Su CH, Lai PT, Huang MS, Jonnagaddala J, Rose Jue T, Rao S, Chou HJ, Milacic M, Singh O, Syed-Abdul S, Hsu WL. MET network in PubMed: a text-mined network visualization and curation system. Database (Oxford). 2016 May 30;2016. doi: 10.1093/database/baw090. Print 2016. PMID: 27242035; PMCID: PMC4885604.
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Gramene Database: Navigating Plant Comparative Genomics Resources.

Current plant biology

Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P.
PMID: 28713666
Curr Plant Biol. 2016 Nov;7:10-15. doi: 10.1016/j.cpb.2016.12.005.

Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the...

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Gupta P, Naithani S, Tello-Ruiz MK, et al. Gramene Database: Navigating Plant Comparative Genomics Resources. Curr Plant Biol. 2016;7:10-15doi: 10.1016/j.cpb.2016.12.005.
Gupta, P., Naithani, S., Tello-Ruiz, M. K., Chougule, K., D'Eustachio, P., Fabregat, A., Jiao, Y., Keays, M., Lee, Y. K., Kumari, S., Mulvaney, J., Olson, A., Preece, J., Stein, J., Wei, S., Weiser, J., Huerta, L., Petryszak, R., Kersey, P., Stein, L. D., Ware, D., & Jaiswal, P. (2016). Gramene Database: Navigating Plant Comparative Genomics Resources. Current plant biology, 710-15. https://doi.org/10.1016/j.cpb.2016.12.005
Gupta, Parul, et al. "Gramene Database: Navigating Plant Comparative Genomics Resources." Current plant biology vol. 7 (2016): 10-15. doi: https://doi.org/10.1016/j.cpb.2016.12.005
Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P. Gramene Database: Navigating Plant Comparative Genomics Resources. Curr Plant Biol. 2016 Nov;7:10-15. doi: 10.1016/j.cpb.2016.12.005. PMID: 28713666; PMCID: PMC5509230.
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Showing 1 to 6 of 6 entries