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Too many roads not taken: Aled M. Edwards, Ruth Isserlin, Gary D. Bader, Stephen V. Frye, Timothy M. Willson & Frank H. Yu Nature 470, 163–165 (10 February 2011) doi:10.1038/470163a. PMID: 21307913
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http://www.carismolecularintelligence.com/
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Prioritizing Potentially Druggable Mutations with dGene: An Annotation Tool for Cancer Genome Sequencing Data. Kumar RD, Chang LW, Ellis MJ, Bose R. PLoS One. 2013 Jun 27;8(6):e67980. PMID: 23826350
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High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Wagle N, Berger MF, ..., Meyerson M, Gabriel SB, Garraway LA. Cancer Discov. 2012 Jan;2(1):82-93. PMID: 22585170
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Gene ontology: tool for the unification of biology. The unification of biology. The Gene Ontology Consortium. Ashburner M, Ball CA, ..., Rubin GM, Sherlock G. Nat Genet. 2000 May;25(1):25-9. PMID: 10802651
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The druggable genome and support for target identification and validation in drug development. Finan C, Gaulton A, Kurger F, Lumbers T, Shah T, Engmann J, Galver L, Kelly R, Karlsson A, Santos R, Overington J, Hingorani A, Casas JP. Sci. Transl. Med. 2017 Mar 29;9(383):eaag1166 PMID: 28356508
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The druggable genome. Hopkins AL, Groom CR. Nat Rev Drug Discov. 2002 Sep;1(9):727-30. PMID: 12209152
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Uhlén M, Fagerberg L, Hallström BM, et al. Proteomics. Tissue-based map of the human proteome. Science. 2015;347(6220):1260419. doi:10.1126/science.1260419. PMID: 25613900
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Rodgers,G., Austin,C., Anderson,J., Pawlyk,A., Colvis,C., Margolis,R. and Baker,J. (2018) Glimmers in illuminating the druggable genome. Nat. Rev. Drug Discov., 17, 301–302. PMID: 29348682
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Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology. Cheng, Donavan T., et al. The Journal of Molecular Diagnostics 17.3 (2015): 251-264. PMID: 25801821
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"Oncomine Comprehensive Assay v3.", Thermo Fisher Scientific Inc. Accessed 8 Sep 2020. https://assets.thermofisher.com/TFS-Assets/LSG/brochures/oncomine-comprehensive-assay-v3-flyer.pdf
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Nguyen, D.-T., Mathias, S. et al, "Pharos: Collating Protein Information to Shed Light on the Druggable Genome", Nucl. Acids Res.i>, 2017, 45(D1), D995-D1002. DOI: 10.1093/nar/gkw1072. PMID: 27903890
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The druggable genome: an update. Russ AP, Lampel S. Drug Discov Today. 2005 Dec;10(23-24):1607-10. PMID: 16376820
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Beaubier, N, Tell, R, Lau, D, Parsons, JR, Bush, S, Perera, J, Sorrells, S, Baker, T, Chang, A, Michuda, J, Iguartua, C, MacNeil, S, Shah, K, Ellis, P, Yeatts, K, Mahon, B, Taxter, T, Bontrager, M, Khan, A, Huether, R, Lefkofsky, E, & White, KP. Clinical validation of the tempus xT next-generation targeted oncology sequencing assay. Oncotarget 2019 Mar 22;10(24):2384-2396. PMID: 31040929
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Mendez,D., Gaulton,A., Bento,A.P., Chambers,J., De Veij,M., Félix,E., Magariños,M.P., Mosquera,J.F., Mutowo,P., Nowotka,M., et al. (2019) ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Res., 47, D930–D940. PMID: 30398643
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Denny Vrandečić and Markus Krötzsch. 2014. Wikidata: a free collaborative knowledgebase. Commun. ACM 57, 10 (October 2014), 78–85. DOI:https://doi.org/10.1145/2629489
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Ensembl 2020. Yates, Andrew D et al. Nucleic acids research vol. 48,D1 (2020): D682-D688. PMID: 31691826
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Entrez Gene: gene-centered information at NCBI. Maglott D, Ostell J, Pruitt KD, Tatusova T. Nucleic Acids Res. 2011 Jan;39(Database issue)52-7. Epub 2010 Nov 28. PMID: 21115458
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Cancer Commons: Biomedicine in the Internet Age. Shrager J, Tenenbaum JM, and Travers M. Collaborative Computational Technologies for Biomedical Research, (Sean Elkins, Maggie Hupcey, and Antony Williams Eds). Wiley, 2010.
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Total: | 0 |
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Total: | 0 |
In Groups: | 0 |
Tamborero, D., Rubio-Perez, C., Deu-Pons, J., Schroeder, M. P., Vivancos, A., Rovira, A., Tusquets, I., Albanell, J., Rodon, J., Tabernero, J., de Torres, C., Dienstmann, R., Gonzalez-Perez, A., & Lopez-Bigas, N. (2018). Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations. Genome medicine, 10(1), 25. https://doi.org/10.1186/s13073-018-0531-8. PMID: 29592813
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Total: | 2716 |
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Total: | 7610 |
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Mendez,D., Gaulton,A., Bento,A.P., Chambers,J., De Veij,M., Félix,E., Magariños,M.P., Mosquera,J.F., Mutowo,P., Nowotka,M., et al. (2019) ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Res., 47, D930–D940. PMID: 30398643
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http://www.clearityfoundation.org/healthcare-pros/drugs-and-biomarkers.aspx
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https://www.clearityfoundation.org/form/findtrials.aspx
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DoCM: a database of curated mutations in cancer. Ainscough BJ, Griffith M, Coffman AC, Wagner AH, Kunisaki J, Choudhary MN, McMichael JF, Fulton RS, Wilson RK, Griffith OL, Mardis ER. Nat Methods. 2016;13(10):806-7. PMID: 27684579
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Total: | 0 |
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Total: | 0 |
In Groups: | 0 |
Wishart,D.S., Feunang,Y.D., Guo,A.C., Lo,E.J., Marcu,A., Grant,J.R., Sajed,T., Johnson,D., Li,C., Sayeeda,Z., et al. (2018) DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res., 46, D1074–D1082. PMID: 29126136
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Drug Target Commons 2.0: a community platform for systematic analysis of drug–target interaction profiles. Tanoli Z, Alam Z, Vähä-Koskela M, Malyutina A, Jaiswal A, Tang J, Wennerberg K, Aittokallio T. Database. 2018. PMID: 30219839
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Sara E. Patterson, Rangjiao Liu, Cara M. Statz, Daniel Durkin, Anuradha Lakshminarayana, and Susan M. Mockus. The Clinical Trial Landscape in Oncology and Connectivity of Somatic Mutational Profiles to Targeted Therapies. Human Genomics, 2016 Jan 16;10(1):4. PMID: 26772741
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Jain,N., Mittendorf,K.F., Holt,M., Lenoue-Newton,M., Maurer,I., Miller,C., Stachowiak,M., Botyrius,M., Cole,J., Micheel,C., et al. (2020) The My Cancer Genome clinical trial data model and trial curation workflow. J. Am. Med. Inform. Assoc., 27, 1057–1066. PMID: 32483629
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Jain,N., Mittendorf,K.F., Holt,M., Lenoue-Newton,M., Maurer,I., Miller,C., Stachowiak,M., Botyrius,M., Cole,J., Micheel,C., et al. (2020) The My Cancer Genome clinical trial data model and trial curation workflow. J. Am. Med. Inform. Assoc., 27, 1057–1066. PMID: 32483629
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Total: | 1519 |
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Total: | 6231 |
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https://wiki.nci.nih.gov/display/cageneindex
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Total: | 89 |
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OncoKB: A Precision Oncology Knowledge Base. Chakravarty D, Gao J, Phillips S, et. al. JCO Precision Oncology 2017 :1, 1-16. PMID: 28890946
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Total: | 1072 |
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Whirl-Carrillo,M., McDonagh,E.M., Hebert,J.M., Gong,L., Sangkuhl,K., Thorn,C.F., Altman,R.B. and Klein,T.E. (2012) Pharmacogenomics knowledge for personalized medicine. Clin. Pharmacol. Ther., 92, 414–417. PMID: 22992668
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Morgensztern,D., Campo,M.J., Dahlberg,S.E., Doebele,R.C., Garon,E., Gerber,D.E., Goldberg,S.B., Hammerman,P.S., Heist,R.S., Hensing,T., et al. (2015) Molecularly targeted therapies in non-small-cell lung cancer annual update 2014. J. Thorac. Oncol., 10, S1–63. PMID: 25535693
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Total: | 2419 |
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The druggable genome: Evaluation of drug targets in clinical trials suggests major shifts in molecular class and indication. Rask-Andersen M, Masuram S, Schioth HB. Annu Rev Pharmacol Toxicol. 2014;54:9-26. doi: 10.1146/annurev-pharmtox-011613-135943. PMID: 24016212
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Trends in the exploitation of novel drug targets. Rask-Andersen M, Almen MS, Schioth HB. Nat Rev Drug Discov. 2011 Aug 1;10(8):579-90. PMID: 21804595
Total: | 2040 |
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Total: | 12410 |
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Total: | 15245 |
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Wang,Y., Zhang,S., Li,F., Zhou,Y., Zhang,Y., Wang,Z., Zhang,R., Zhu,J., Ren,Y., Tan,Y., et al. (2020) Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. Nucleic Acids Res., 48, D1031–D1041. PMID: 31691823
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Total: | 367 |
In Groups: | 216 |
Total: | 959 |
In Groups: | 748 |
Griffith M*, Spies NC*, Krysiak K*, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH Wartman LD, Wilson RK, Mardis ER, Griffith OL†. 2016. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet. 49, 170–174 (2017); doi: doi.org/10.1038/ng.3774. PMID: 28138153
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Griffith M*, Spies NC*, Krysiak K*, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH Wartman LD, Wilson RK, Mardis ER, Griffith OL†. 2016. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet. 49, 170–174 (2017); doi: doi.org/10.1038/ng.3774. PMID: 28138153
Total: | 15 |
In Groups: | 15 |
Total: | 28 |
In Groups: | 25 |
Total: | 37 |
In Groups: | 32 |
Tate,J.G., Bamford,S., Jubb,H.C., Sondka,Z., Beare,D.M., Bindal,N., Boutselakis,H., Cole,C.G., Creatore,C., Dawson,E., et al. (2019) COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res., 47, D941–D947. PMID: 30371878
Total: | 15 |
In Groups: | 15 |
Tate,J.G., Bamford,S., Jubb,H.C., Sondka,Z., Beare,D.M., Bindal,N., Boutselakis,H., Cole,C.G., Creatore,C., Dawson,E., et al. (2019) COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res., 47, D941–D947. PMID: 30371878
Total: | 0 |
In Groups: | 0 |
Total: | 0 |
In Groups: | 0 |
Total: | 0 |
In Groups: | 0 |
Armstrong,J.F., Faccenda,E., Harding,S.D., Pawson,A.J., Southan,C., Sharman,J.L., Campo,B., Cavanagh,D.R., Alexander,S.P.H., Davenport,A.P., et al. (2020) The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. Nucleic Acids Res., 48, D1006–D1021. PMID: 31691834
Total: | 0 |
In Groups: | 0 |
Armstrong,J.F., Faccenda,E., Harding,S.D., Pawson,A.J., Southan,C., Sharman,J.L., Campo,B., Cavanagh,D.R., Alexander,S.P.H., Davenport,A.P., et al. (2020) The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. Nucleic Acids Res., 48, D1006–D1021. PMID: 31691834