Rodriguez-Barrueco R, Nekritz EA, Bertucci F, Yu J, Sanchez-Garcia F, Zeleke TZ, Gorbatenko A, Birnbaum D, Ezhkova E, Cordon-Cardo C, Finetti P, Llobet-Navas D, Silva JM. miR-424(322)/503 is a breast cancer tumor suppressor whose loss promotes resistance to chemotherapy. Genes & Development. 2017 Mar 15;31(6):553-566.

Yu J, Silva J, Califano A. ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. Bioinformatics. 2016 Jan 15;32(2):260-7.

Putcha P, Yu J, Rodriguez-Barrueco R, Saucedo-Cuevas L, Villagrasa P, Murga-Penas E, Quayle SN, Yang M, Castro V, Llobet-Navas D, Birnbaum D, Finetti P, Woodward WA, Bertucci F, Alpaugh ML, Califano A, Silva J. HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers. Breast Cancer Research. 2015 Dec 8;17(1):149.

Saeed M, Andreo U, Chung HY, Espiritu C, Branch AD, Silva JM, Rice CM. SEC14L2 enables pan-genotype HCV replication in cell culture. Nature. 2015 Aug 27;524(7566):471-5.

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. Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers. Genes & Development. 2015 Aug 1;29(15):1631-48.

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. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Research. 2015 Feb;25(2):257-67.

Sanchez-Garcia F, Villagrasa P, Matsui J, Kotliar D, Castro V, Akavia UD, Chen BJ, Saucedo-Cuevas L, Rodriguez Barrueco R, Llobet-Navas D, Silva JM, Pe’er D. Integration of genomic data enables selective discovery of breast cancer drivers. Cell. 2014 Dec 4;159(6):1461-75.

Llobet-Navas D, Rodriguez-Barrueco R, de la Iglesia-Vicente J, Olivan M, Castro V, Saucedo-Cuevas L, Marshall N, Putcha P, Castillo-Martin M, Bardot E, Ezhkova E, Iavarone A, Cordon-Cardo C, Silva JM. The microRNA 424/503 cluster reduces CDC25A expression during cell cycle arrest imposed by transforming growth factor β in mammary epithelial cells. Molecular and Cellular Biology. 2014 Dec 1;34(23):4216-31.

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. The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes & Development. 2014 Apr 1;28(7):765-82.

Yu J, Putcha P, Califano A, Silva JM. Pooled shRNA screenings: computational analysis. Methods in Molecular Biology. 2013;980:371-84.

Domingo-Domenech J, Vidal SJ, Rodriguez-Bravo V, Castillo-Martin M, Quinn SA, Rodriguez-Barrueco R, Bonal DM, Charytonowicz E, Gladoun N, de la Iglesia-Vicente J, Petrylak DP, Benson MC, Silva JM, Cordon-Cardo C. Suppression of acquired docetaxel resistance in prostate cancer through depletion of notch- and hedgehog-dependent tumor-initiating cells. Cancer Cell. 2012 Sep 11;22(3):373-88.

Freed-Pastor WA, Mizuno H, Zhao X, Langerød A, Moon SH, Rodriguez-Barrueco R, Barsotti A, Chicas A, Li W, Polotskaia A, Bissell MJ, Osborne TF, Tian B, Lowe SW, Silva JM, Børresen-Dale AL, Levine AJ, Bargonetti J, Prives C. Mutant p53 disrupts mammary tissue architecture via the mevalonate pathway. Cell. 2012 Jan 20;148(1-2):244-58.

Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell. 2011 Oct 14;147(2):370-81.

Silva JM, Ezhkova E, Silva J, Heart S, Castillo M, Campos Y, Castro V, Bonilla F, Cordon-Cardo C, Muthuswamy SK, Powers S, Fuchs E, Hannon GJ. Cyfip1 is a putative invasion suppressor in epithelial cancers. Cell. 2009 Jun 12;137(6):1047-61.

Silva JM, Marran K, Parker JS, Silva J, Golding M, Schlabach MR, Elledge SJ, Hannon GJ, Chang K. Profiling essential genes in human mammary cells by multiplex RNAi screening. Science. 2008 Feb 1;319(5863):617-20.

Silva JM, Li MZ, Chang K, Ge W, Golding MC, Rickles RJ, Siolas D, Hu G, Paddison PJ, Schlabach MR, Sheth N, Bradshaw J, Burchard J, Kulkarni A, Cavet G, Sachidanandam R, McCombie WR, Cleary MA, Elledge SJ, Hannon GJ. Second-generation shRNA libraries covering the mouse and human genomes. Nature Genetics. 2005 Nov;37(11):1281-8.

Silva JM, Mizuno H, Brady A, Lucito R, Hannon GJ. RNA interference microarrays: high-throughput loss-of-function genetics in mammalian cells. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6548-52.

Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O’Shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, Elledge SJ, Hannon GJ. A resource for large-scale RNA-interference-based screens in mammals. Nature. 2004 Mar 25;428(6981):427-31.

Silva JM, Sachidanandam R, Hannon GJ. Free energy lights the path toward more effective RNAi. Nature Genetics. 2003 Dec;35(4):303-5.