MicroRNA target site identification by integrating sequence and binding information

William H. Majoros, Parawee Lekprasert, Neelanjan Mukherjee, Rebecca L. Skalsky, David L. Corcoran, Bryan R. Cullen, Uwe Ohler

Research output: Contribution to journalArticlepeer-review

46 Scopus citations


High-throughput sequencing has opened numerous possibilities for the identification of regulatory RNA-binding events. Cross-linking and immunoprecipitation of Argonaute proteins can pinpoint a microRNA (miRNA) target site within tens of bases but leaves the identity of the miRNA unresolved. A flexible computational framework, microMUMMIE, integrates sequence with cross-linking features and reliably identifies the miRNA family involved in each binding event. It considerably outperforms sequence-only approaches and quantifies the prevalence of noncanonical binding modes.

Original languageEnglish (US)
Pages (from-to)630-633
Number of pages4
JournalNature Methods
Issue number7
StatePublished - Jul 2013
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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