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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: paull eo. 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.
Prophetic Granger Causality to infer gene regulatory networks.
Carlin DE, Paull EO, Graim K, Wong CK, Bivol A, Ryabinin P, Ellrott K, Sokolov A, Stuart JM. Carlin DE, et al. Among authors: paull eo. PLoS One. 2017 Dec 6;12(12):e0170340. doi: 10.1371/journal.pone.0170340. eCollection 2017. PLoS One. 2017. PMID: 29211761 Free PMC article.
The Cancer Genome Atlas Pan-Cancer analysis project.
Cancer Genome Atlas Research Network; Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. Cancer Genome Atlas Research Network, et al. Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764. Nat Genet. 2013. PMID: 24071849 Free PMC article.
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F; Broad-DREAM Community; Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA. Gönen M, et al. Cell Syst. 2017 Nov 22;5(5):485-497.e3. doi: 10.1016/j.cels.2017.09.004. Epub 2017 Oct 4. Cell Syst. 2017. PMID: 28988802 Free PMC article.
Pathway-Based Genomics Prediction using Generalized Elastic Net.
Sokolov A, Carlin DE, Paull EO, Baertsch R, Stuart JM. Sokolov A, et al. Among authors: paull eo. PLoS Comput Biol. 2016 Mar 9;12(3):e1004790. doi: 10.1371/journal.pcbi.1004790. eCollection 2016 Mar. PLoS Comput Biol. 2016. PMID: 26960204 Free PMC article.
23 results