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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: silva j. 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.
HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers.
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. Putcha P, et al. Among authors: silva j. Breast Cancer Res. 2015 Dec 8;17(1):149. doi: 10.1186/s13058-015-0658-0. Breast Cancer Res. 2015. PMID: 26643555 Free PMC article.
Erratum to: HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers.
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. Putcha P, et al. Among authors: silva j. Breast Cancer Res. 2017 Apr 19;19(1):49. doi: 10.1186/s13058-017-0841-6. Breast Cancer Res. 2017. PMID: 28424080 Free PMC article. No abstract available.
The number of titrated microRNA species dictates ceRNA regulation.
Chiu HS, Martínez MR, Komissarova EV, Llobet-Navas D, Bansal M, Paull EO, Silva J, Yang X, Sumazin P, Califano A. Chiu HS, et al. Among authors: silva j. Nucleic Acids Res. 2018 May 18;46(9):4354-4369. doi: 10.1093/nar/gky286. Nucleic Acids Res. 2018. PMID: 29684207 Free PMC article.
Phase I/II trial of ruxolitinib in combination with trastuzumab in metastatic HER2 positive breast cancer.
Kearney M, Franks L, Lee S, Tiersten A, Makower DF, Cigler T, Mundi P, Chi DC, Goel A, Klein P, Andreopoulou E, Sparano J, Trivedi M, Accordino M, Califano A, Hershman DL, Silva J, Kalinsky K. Kearney M, et al. Among authors: silva j. Breast Cancer Res Treat. 2021 Aug;189(1):177-185. doi: 10.1007/s10549-021-06306-4. Epub 2021 Jun 24. Breast Cancer Res Treat. 2021. PMID: 34169393 Free PMC article. Clinical Trial.
Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer.
Zeleke TZ, Pan Q, Chiuzan C, Onishi M, Li Y, Tan H, Alvarez MJ, Honan E, Yang M, Chia PL, Mukhopadhyay P, Kelly S, Wu R, Fenn K, Trivedi MS, Accordino M, Crew KD, Hershman DL, Maurer M, Jones S, High A, Peng J, Califano A, Kalinsky K, Yu J, Silva J. Zeleke TZ, et al. Among authors: silva j. Nat Cancer. 2023 Feb;4(2):257-275. doi: 10.1038/s43018-022-00489-5. Epub 2022 Dec 30. Nat Cancer. 2023. PMID: 36585452 Free PMC article.
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