TY  - JOUR
A1  - Chiu, Hua-Sheng
A1  - Llobet-Navas, David
A1  - Yang, Xuerui
A1  - Chung, Wei-Jen
A1  - Ambesi-Impiombato, Alberto
A1  - Iyer, Archana
A1  - Kim, Hyunjae Ryan
A1  - Seviour, Elena G.
A1  - Luo, Zijun
A1  - Sehgal, Vasudha
A1  - Moss, Tyler
A1  - Lu, Yiling
A1  - Ram, Prahlad
A1  - Silva, José
A1  - Mills, Gordon B.
A1  - Califano, Andrea
A1  - Sumazin, Pavel
T1  - Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
Y1  - 2015/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 257 
EP  - 267 
DO  - 10.1101/gr.178194.114 
VL  - 25 
IS  - 2 
UR  - http://genome.cshlp.org/content/25/2/257.abstract 
N2  - We introduce a method for simultaneous prediction of microRNA–target interactions and their mediated competitive endogenous RNA (ceRNA) interactions. Using high-throughput validation assays in breast cancer cell lines, we show that our integrative approach significantly improves on microRNA–target prediction accuracy as assessed by both mRNA and protein level measurements. Our biochemical assays support nearly 500 microRNA–target interactions with evidence for regulation in breast cancer tumors. Moreover, these assays constitute the most extensive validation platform for computationally inferred networks of microRNA–target interactions in breast cancer tumors, providing a useful benchmark to ascertain future improvements. 
ER  -