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Causal network inference using biochemical kinetics.
Oates CJ, Dondelinger F, Bayani N, Korkola J, Gray JW, Mukherjee S. Oates CJ, et al. Among authors: gray jw. Bioinformatics. 2014 Sep 1;30(17):i468-74. doi: 10.1093/bioinformatics/btu452. Bioinformatics. 2014. PMID: 25161235 Free PMC article.
Sparse combinatorial inference with an application in cancer biology.
Mukherjee S, Pelech S, Neve RM, Kuo WL, Ziyad S, Spellman PT, Gray JW, Speed TP. Mukherjee S, et al. Among authors: gray jw. Bioinformatics. 2009 Jan 15;25(2):265-71. doi: 10.1093/bioinformatics/btn611. Epub 2008 Nov 27. Bioinformatics. 2009. PMID: 19038985 Free PMC article.
Subtype and pathway specific responses to anticancer compounds in breast cancer.
Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, Jakkula L, Korkola JE, Durinck S, Pepin F, Guan Y, Purdom E, Neuvial P, Bengtsson H, Wood KW, Smith PG, Vassilev LT, Hennessy BT, Greshock J, Bachman KE, Hardwicke MA, Park JW, Marton LJ, Wolf DM, Collisson EA, Neve RM, Mills GB, Speed TP, Feiler HS, Wooster RF, Haussler D, Stuart JM, Gray JW, Spellman PT. Heiser LM, et al. Among authors: gray jw. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2724-9. doi: 10.1073/pnas.1018854108. Epub 2011 Oct 14. Proc Natl Acad Sci U S A. 2012. PMID: 22003129 Free PMC article.
Bayesian inference of signaling network topology in a cancer cell line.
Hill SM, Lu Y, Molina J, Heiser LM, Spellman PT, Speed TP, Gray JW, Mills GB, Mukherjee S. Hill SM, et al. Among authors: gray jw. Bioinformatics. 2012 Nov 1;28(21):2804-10. doi: 10.1093/bioinformatics/bts514. Epub 2012 Aug 24. Bioinformatics. 2012. PMID: 22923301 Free PMC article.
Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer.
Korkola JE, Collisson EA, Heiser M, Oates C, Bayani N, Itani S, Esch A, Thompson W, Griffith OL, Wang NJ, Kuo WL, Cooper B, Billig J, Ziyad S, Hung JL, Jakkula L, Feiler H, Lu Y, Mills GB, Spellman PT, Tomlin C, Mukherjee S, Gray JW. Korkola JE, et al. Among authors: gray jw. PLoS One. 2015 Jul 16;10(7):e0133219. doi: 10.1371/journal.pone.0133219. eCollection 2015. PLoS One. 2015. PMID: 26181325 Free PMC article.
Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling.
Hill SM, Nesser NK, Johnson-Camacho K, Jeffress M, Johnson A, Boniface C, Spencer SE, Lu Y, Heiser LM, Lawrence Y, Pande NT, Korkola JE, Gray JW, Mills GB, Mukherjee S, Spellman PT. Hill SM, et al. Among authors: gray jw. Cell Syst. 2017 Jan 25;4(1):73-83.e10. doi: 10.1016/j.cels.2016.11.013. Epub 2016 Dec 22. Cell Syst. 2017. PMID: 28017544 Free PMC article.
Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer.
Hu Z, Mao JH, Curtis C, Huang G, Gu S, Heiser L, Lenburg ME, Korkola JE, Bayani N, Samarajiwa S, Seoane JA, Dane MA, Esch A, Feiler HS, Wang NJ, Hardwicke MA, Laquerre S, Jackson J, W Wood K, Weber B, Spellman PT, Aparicio S, Wooster R, Caldas C, Gray JW. Hu Z, et al. Among authors: gray jw. Breast Cancer Res. 2016 Jul 1;18(1):70. doi: 10.1186/s13058-016-0728-y. Breast Cancer Res. 2016. PMID: 27368372 Free PMC article.
Breast cancer genomes--form and function.
Korkola J, Gray JW. Korkola J, et al. Among authors: gray jw. Curr Opin Genet Dev. 2010 Feb;20(1):4-14. doi: 10.1016/j.gde.2009.11.005. Epub 2010 Jan 7. Curr Opin Genet Dev. 2010. PMID: 20060285 Free PMC article. Review.
Inferring causal molecular networks: empirical assessment through a community-based effort.
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium; Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Hill SM, et al. Among authors: gray jw. Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22. Nat Methods. 2016. PMID: 26901648 Free PMC article.
515 results