? Resource Project Pathway Commons (PC) is a convenient single point of access for all publicly accessible pathway information in the standard BioPAX format. The long-term vision is to achieve a complete computable map of the cell across all species and conditions. With NHGRI funding over the past six years, we've established key Pathway Commons and BioPAX software technology and a series of web services in use by thousands of researchers. The era of big data in biology is providing amazing opportunities for better understanding of biological systems and disease, and pathway analysis plays an important role in interpreting this data. Our major aim now is to dramatically expand use of our highly developed technology to facilitate biological data analysis. This Resource Project component describes major new work to improve utility and efficiency of the Pathway Commons resource and is supported by the Resource Informatics Core and the Management, Dissemination, and Training Core components. The resource project aims to 1) facilitate biological pathway analysis among a wide range of users; 2) expand to new data types, wider genome coverage and wider pathway information distribution to the research community; and 3) develop a community based pathway annotation system for use by authors during the publication process and additional crowdsourcing opportunities.
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| Liyanage, Sanduni U; Hurren, Rose; Voisin, Veronique et al. (2017) Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML. Blood 129:2657-2666 |
| Michailidou, Kyriaki (see original citation for additional authors) (2017) Association analysis identifies 65 new breast cancer risk loci. Nature 551:92-94 |
| Milne, Roger L (see original citation for additional authors) (2017) Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer. Nat Genet 49:1767-1778 |
| Tong, Jiefei; Helmy, Mohamed; Cavalli, Florence M G et al. (2017) Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome, and tyrosine-phosphatome in acute myeloid leukemia. Proteomics 17: |
| Helmy, Mohamed; Crits-Christoph, Alexander; Bader, Gary D (2016) Ten Simple Rules for Developing Public Biological Databases. PLoS Comput Biol 12:e1005128 |
| Kusebauch, Ulrike; Campbell, David S; Deutsch, Eric W et al. (2016) Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell 166:766-778 |
| Luna, Augustin; Babur, Özgün; Aksoy, Bülent Arman et al. (2016) PaxtoolsR: pathway analysis in R using Pathway Commons. Bioinformatics 32:1262-4 |
| Jones, Robert A; Robinson, Tyler J; Liu, Jeff C et al. (2016) RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation. J Clin Invest 126:3739-3757 |
| Kucera, Mike; Isserlin, Ruth; Arkhangorodsky, Arkady et al. (2016) AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. F1000Res 5:1717 |
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