Assessing the Utility of Thermodynamic Features for microRNA Target Prediction under Relaxed Seed and No Conservation Requirements
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DOI: 10.1371/journal.pone.0020622
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- Daehyun Baek & Judit Villén & Chanseok Shin & Fernando D. Camargo & Steven P. Gygi & David P. Bartel, 2008. "The impact of microRNAs on protein output," Nature, Nature, vol. 455(7209), pages 64-71, September.
- Yong Zhao & Eva Samal & Deepak Srivastava, 2005. "Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis," Nature, Nature, vol. 436(7048), pages 214-220, July.
- Kevin Chen & Jonas Maaskola & Mark L Siegal & Nikolaus Rajewsky, 2009. "Reexamining microRNA Site Accessibility in Drosophila: A Population Genomics Study," PLOS ONE, Public Library of Science, vol. 4(5), pages 1-5, May.
- Eva Gottwein & Neelanjan Mukherjee & Christoph Sachse & Corina Frenzel & William H. Majoros & Jen-Tsan A. Chi & Ravi Braich & Muthiah Manoharan & Jürgen Soutschek & Uwe Ohler & Bryan R. Cullen, 2007. "A viral microRNA functions as an orthologue of cellular miR-155," Nature, Nature, vol. 450(7172), pages 1096-1099, December.
- Matthias Selbach & Björn Schwanhäusser & Nadine Thierfelder & Zhuo Fang & Raya Khanin & Nikolaus Rajewsky, 2008. "Widespread changes in protein synthesis induced by microRNAs," Nature, Nature, vol. 455(7209), pages 58-63, September.
- Brenda J. Reinhart & Frank J. Slack & Michael Basson & Amy E. Pasquinelli & Jill C. Bettinger & Ann E. Rougvie & H. Robert Horvitz & Gary Ruvkun, 2000. "The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans," Nature, Nature, vol. 403(6772), pages 901-906, February.
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