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Updated: Apr 21, 2026

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
Published on: August 21, 2019
Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
Hua-Sheng Chiu1, David Llobet-Navas2, Xuerui Yang3
1Department of Systems Biology, Center for Computational Biology and Bioinformatics, Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA; Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA;
Abstract:
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.
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