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Network-based stratification of tumor mutations.
Hofree M, Shen JP, Carter H, Gross A, Ideker T. Hofree M, et al. Among authors: shen jp. 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.
Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.
Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T. Gross AM, et al. Among authors: shen jp. Nat Genet. 2014 Sep;46(9):939-43. doi: 10.1038/ng.3051. Epub 2014 Aug 3. Nat Genet. 2014. PMID: 25086664 Free PMC article.
A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy.
Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, Kollenstart L, van Attikum H, Aza-Blanc P, Sobol RW, Ideker T. Srivas R, et al. Among authors: shen jp. Mol Cell. 2016 Aug 4;63(3):514-25. doi: 10.1016/j.molcel.2016.06.022. Epub 2016 Jul 21. Mol Cell. 2016. PMID: 27453043 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. 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.
Genetic interaction mapping in mammalian cells using CRISPR interference.
Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Du D, et al. Among authors: shen jp. Nat Methods. 2017 Jun;14(6):577-580. doi: 10.1038/nmeth.4286. Epub 2017 May 8. Nat Methods. 2017. PMID: 28481362 Free PMC article.
Correcting CRISPR for copy number.
Shen JP, Ideker T. Shen JP, et al. Nat Genet. 2017 Nov 29;49(12):1674-1675. doi: 10.1038/ng.3994. Nat Genet. 2017. PMID: 29186130
A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.
Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. Zhang W, et al. Among authors: shen jp. Nat Genet. 2018 Apr;50(4):613-620. doi: 10.1038/s41588-018-0091-2. Epub 2018 Apr 2. Nat Genet. 2018. PMID: 29610481 Free PMC article.
185 results