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Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia.
Moder M, Velimezi G, Owusu M, Mazouzi A, Wiedner M, Ferreira da Silva J, Robinson-Garcia L, Schischlik F, Slavkovsky R, Kralovics R, Schuster M, Bock C, Ideker T, Jackson SP, Menche J, Loizou JI. Moder M, et al. Among authors: ideker t. Nat Commun. 2017 Nov 1;8(1):1238. doi: 10.1038/s41467-017-01439-x. Nat Commun. 2017. PMID: 29089570 Free PMC article.
A human MAP kinase interactome.
Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T. Bandyopadhyay S, et al. Among authors: ideker t. Nat Methods. 2010 Oct;7(10):801-5. doi: 10.1038/nmeth.1506. Nat Methods. 2010. PMID: 20936779 Free PMC article.
Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.
Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Shen JP, et al. Among authors: ideker t. Nat Methods. 2017 Jun;14(6):573-576. doi: 10.1038/nmeth.4225. Epub 2017 Mar 20. Nat Methods. 2017. PMID: 28319113 Free PMC article.
Correcting CRISPR for copy number.
Shen JP, Ideker T. Shen JP, et al. Among authors: ideker t. Nat Genet. 2017 Nov 29;49(12):1674-1675. doi: 10.1038/ng.3994. Nat Genet. 2017. PMID: 29186130
Cost-effective strategies for completing the interactome.
Schwartz AS, Yu J, Gardenour KR, Finley RL Jr, Ideker T. Schwartz AS, et al. Among authors: ideker t. Nat Methods. 2009 Jan;6(1):55-61. doi: 10.1038/nmeth.1283. Epub 2008 Dec 14. Nat Methods. 2009. PMID: 19079254 Free PMC article.
A travel guide to Cytoscape plugins.
Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. Saito R, et al. Among authors: ideker t. Nat Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6. Nat Methods. 2012. PMID: 23132118 Free PMC article.
Network-based stratification of tumor mutations.
Hofree M, Shen JP, Carter H, Gross A, Ideker T. Hofree M, et al. Among authors: ideker t. Nat Methods. 2013 Nov;10(11):1108-15. doi: 10.1038/nmeth.2651. Epub 2013 Sep 15. Nat Methods. 2013. PMID: 24037242 Free PMC article.
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.
Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. Qu K, et al. Among authors: ideker t. Nat Methods. 2016 Mar;13(3):245-247. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18. Nat Methods. 2016. PMID: 26780094 Free PMC article.
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