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geWorkbench: an open source platform for integrative genomics.
Floratos A, Smith K, Ji Z, Watkinson J, Califano A. Floratos A, et al. Among authors: califano a. Bioinformatics. 2010 Jul 15;26(14):1779-80. doi: 10.1093/bioinformatics/btq282. Epub 2010 May 28. Bioinformatics. 2010. PMID: 20511363 Free PMC article.
Towards patient-based cancer therapeutics.
Cancer Target Discovery and Development Network; Schreiber SL, Shamji AF, Clemons PA, Hon C, Koehler AN, Munoz B, Palmer M, Stern AM, Wagner BK, Powers S, Lowe SW, Guo X, Krasnitz A, Sawey ET, Sordella R, Stein L, Trotman LC, Califano A, Dalla-Favera R, Ferrando A, Iavarone A, Pasqualucci L, Silva J, Stockwell BR, Hahn WC, Chin L, DePinho RA, Boehm JS, Gopal S, Huang A, Root DE, Weir BA, Gerhard DS, Zenklusen JC, Roth MG, White MA, Minna JD, MacMillan JB, Posner BA. Cancer Target Discovery and Development Network, et al. Among authors: califano a. Nat Biotechnol. 2010 Sep;28(9):904-6. doi: 10.1038/nbt0910-904. Nat Biotechnol. 2010. PMID: 20829823 Free PMC article.
Pooled shRNA screenings: computational analysis.
Yu J, Putcha P, Califano A, Silva JM. Yu J, et al. Among authors: califano a. Methods Mol Biol. 2013;980:371-84. doi: 10.1007/978-1-62703-287-2_22. Methods Mol Biol. 2013. PMID: 23359167
Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia.
Piovan E, Yu J, Tosello V, Herranz D, Ambesi-Impiombato A, Da Silva AC, Sanchez-Martin M, Perez-Garcia A, Rigo I, Castillo M, Indraccolo S, Cross JR, de Stanchina E, Paietta E, Racevskis J, Rowe JM, Tallman MS, Basso G, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA. Piovan E, et al. Among authors: califano a. Cancer Cell. 2013 Dec 9;24(6):766-76. doi: 10.1016/j.ccr.2013.10.022. Epub 2013 Nov 27. Cancer Cell. 2013. PMID: 24291004 Free PMC article.
The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.
Llobet-Navas D, Rodríguez-Barrueco R, Castro V, Ugalde AP, Sumazin P, Jacob-Sendler D, Demircan B, Castillo-Martín M, Putcha P, Marshall N, Villagrasa P, Chan J, Sanchez-Garcia F, Pe'er D, Rabadán R, Iavarone A, Cordón-Cardó C, Califano A, López-Otín C, Ezhkova E, Silva JM. Llobet-Navas D, et al. Among authors: califano a. Genes Dev. 2014 Apr 1;28(7):765-82. doi: 10.1101/gad.237404.114. Epub 2014 Mar 17. Genes Dev. 2014. PMID: 24636986 Free PMC article.
Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.
Chiu HS, Llobet-Navas D, Yang X, Chung WJ, Ambesi-Impiombato A, Iyer A, Kim HR, Seviour EG, Luo Z, Sehgal V, Moss T, Lu Y, Ram P, Silva J, Mills GB, Califano A, Sumazin P. Chiu HS, et al. Among authors: califano a. Genome Res. 2015 Feb;25(2):257-67. doi: 10.1101/gr.178194.114. Epub 2014 Nov 5. Genome Res. 2015. PMID: 25378249 Free PMC article.
The Cyni framework for network inference in Cytoscape.
Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B. Guitart-Pla O, et al. Among authors: califano a. Bioinformatics. 2015 May 1;31(9):1499-501. doi: 10.1093/bioinformatics/btu812. Epub 2014 Dec 18. Bioinformatics. 2015. PMID: 25527096 Free PMC article.
Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers.
Rodriguez-Barrueco R, Yu J, Saucedo-Cuevas LP, Olivan M, Llobet-Navas D, Putcha P, Castro V, Murga-Penas EM, Collazo-Lorduy A, Castillo-Martin M, Alvarez M, Cordon-Cardo C, Kalinsky K, Maurer M, Califano A, Silva JM. Rodriguez-Barrueco R, et al. Among authors: califano a. Genes Dev. 2015 Aug 1;29(15):1631-48. doi: 10.1101/gad.262642.115. Epub 2015 Jul 30. Genes Dev. 2015. PMID: 26227964 Free PMC article.
360 results