RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2015 
FD February 01 
VO 25 
IS 2 
SP 257 
OP 267 
DO 10.1101/gr.178194.114 
UL http://genome.cshlp.org/content/25/2/257.abstract 
AB 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.