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Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases.
Daboussi F, Zaslavskiy M, Poirot L, Loperfido M, Gouble A, Guyot V, Leduc S, Galetto R, Grizot S, Oficjalska D, Perez C, Delacôte F, Dupuy A, Chion-Sotinel I, Le Clerre D, Lebuhotel C, Danos O, Lemaire F, Oussedik K, Cédrone F, Epinat JC, Smith J, Yáñez-Muñoz RJ, Dickson G, Popplewell L, Koo T, VandenDriessche T, Chuah MK, Duclert A, Duchateau P, Pâques F. Daboussi F, et al. Among authors: zaslavskiy m. Nucleic Acids Res. 2012 Jul;40(13):6367-79. doi: 10.1093/nar/gks268. Epub 2012 Mar 29. Nucleic Acids Res. 2012. PMID: 22467209 Free PMC article.
A path following algorithm for the graph matching problem.
Zaslavskiy M, Bach F, Vert JP. Zaslavskiy M, et al. IEEE Trans Pattern Anal Mach Intell. 2009 Dec;31(12):2227-42. doi: 10.1109/TPAMI.2008.245. IEEE Trans Pattern Anal Mach Intell. 2009. PMID: 19834143
A deep learning model to predict RNA-Seq expression of tumours from whole slide images.
Schmauch B, Romagnoni A, Pronier E, Saillard C, Maillé P, Calderaro J, Kamoun A, Sefta M, Toldo S, Zaslavskiy M, Clozel T, Moarii M, Courtiol P, Wainrib G. Schmauch B, et al. Among authors: zaslavskiy m. Nat Commun. 2020 Aug 3;11(1):3877. doi: 10.1038/s41467-020-17678-4. Nat Commun. 2020. PMID: 32747659 Free PMC article.
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. 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.
Predicting Survival After Hepatocellular Carcinoma Resection Using Deep Learning on Histological Slides.
Saillard C, Schmauch B, Laifa O, Moarii M, Toldo S, Zaslavskiy M, Pronier E, Laurent A, Amaddeo G, Regnault H, Sommacale D, Ziol M, Pawlotsky JM, Mulé S, Luciani A, Wainrib G, Clozel T, Courtiol P, Calderaro J. Saillard C, et al. Among authors: zaslavskiy m. Hepatology. 2020 Dec;72(6):2000-2013. doi: 10.1002/hep.31207. Hepatology. 2020. PMID: 32108950
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M; AstraZeneca-Sanger Drug Combination DREAM Consortium; Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Menden MP, et al. Among authors: zaslavskiy m. Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2. Nat Commun. 2019. PMID: 31209238 Free PMC article.
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