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Assessment of network module identification across complex diseases.
Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R; DREAM Module Identification Challenge Consortium; Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D. Choobdar S, et al. Among authors: marbach d. Nat Methods. 2019 Sep;16(9):843-852. doi: 10.1038/s41592-019-0509-5. Epub 2019 Aug 30. Nat Methods. 2019. PMID: 31471613 Free PMC article.
Revealing strengths and weaknesses of methods for gene network inference.
Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G. Marbach D, et al. Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6286-91. doi: 10.1073/pnas.0913357107. Epub 2010 Mar 22. Proc Natl Acad Sci U S A. 2010. PMID: 20308593 Free PMC article.
Verification of systems biology research in the age of collaborative competition.
Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G. Meyer P, et al. Among authors: marbach d. Nat Biotechnol. 2011 Sep 8;29(9):811-5. doi: 10.1038/nbt.1968. Nat Biotechnol. 2011. PMID: 21904331 Free article. No abstract available.
Wisdom of crowds for robust gene network inference.
Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR; DREAM5 Consortium; Kellis M, Collins JJ, Stolovitzky G. Marbach D, et al. Nat Methods. 2012 Jul 15;9(8):796-804. doi: 10.1038/nmeth.2016. Nat Methods. 2012. PMID: 22796662 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. Among authors: marbach d. 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.
28 results