Cargando…
Prediction of ultra-potent shRNAs with a sequential classification algorithm
We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel datasets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a given gene. Combined with an optimized miR-E backbone,...
| Autores principales: | , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
2017
|
| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5416823/ https://www.ncbi.nlm.nih.gov/pubmed/28263295 http://dx.doi.org/10.1038/nbt.3807 |
| _version_ | 1783233826508505088 |
|---|---|
| author | Pelossof, Raphael Fairchild, Lauren Huang, Chun-Hao Widmer, Christian Sreedharan, Vipin T. Sinha, Nishi Lai, Dan-Yu Guan, Yuanzhe Premsrirut, Prem K. Tschaharganeh, Darjus F. Hoffmann, Thomas Thapar, Vishal Xiang, Qing Garippa, Ralph J. Rätsch, Gunnar Zuber, Johannes Lowe, Scott W. Leslie, Christina S. Fellmann, Christof |
| author_facet | Pelossof, Raphael Fairchild, Lauren Huang, Chun-Hao Widmer, Christian Sreedharan, Vipin T. Sinha, Nishi Lai, Dan-Yu Guan, Yuanzhe Premsrirut, Prem K. Tschaharganeh, Darjus F. Hoffmann, Thomas Thapar, Vishal Xiang, Qing Garippa, Ralph J. Rätsch, Gunnar Zuber, Johannes Lowe, Scott W. Leslie, Christina S. Fellmann, Christof |
| author_sort | Pelossof, Raphael |
| collection | PubMed |
| description | We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel datasets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a given gene. Combined with an optimized miR-E backbone, >90% of high-scoring SplashRNA predictions trigger >85% protein knockdown when expressed from a single genomic integration. SplashRNA can significantly improve the accuracy of loss-of-function genetics studies and facilitates the generation of compact shRNA libraries. |
| format | Online Article Text |
| id | pubmed-5416823 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2017 |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-54168232017-09-06 Prediction of ultra-potent shRNAs with a sequential classification algorithm Pelossof, Raphael Fairchild, Lauren Huang, Chun-Hao Widmer, Christian Sreedharan, Vipin T. Sinha, Nishi Lai, Dan-Yu Guan, Yuanzhe Premsrirut, Prem K. Tschaharganeh, Darjus F. Hoffmann, Thomas Thapar, Vishal Xiang, Qing Garippa, Ralph J. Rätsch, Gunnar Zuber, Johannes Lowe, Scott W. Leslie, Christina S. Fellmann, Christof Nat Biotechnol Article We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel datasets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a given gene. Combined with an optimized miR-E backbone, >90% of high-scoring SplashRNA predictions trigger >85% protein knockdown when expressed from a single genomic integration. SplashRNA can significantly improve the accuracy of loss-of-function genetics studies and facilitates the generation of compact shRNA libraries. 2017-03-06 2017-04 /pmc/articles/PMC5416823/ /pubmed/28263295 http://dx.doi.org/10.1038/nbt.3807 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms |
| spellingShingle | Article Pelossof, Raphael Fairchild, Lauren Huang, Chun-Hao Widmer, Christian Sreedharan, Vipin T. Sinha, Nishi Lai, Dan-Yu Guan, Yuanzhe Premsrirut, Prem K. Tschaharganeh, Darjus F. Hoffmann, Thomas Thapar, Vishal Xiang, Qing Garippa, Ralph J. Rätsch, Gunnar Zuber, Johannes Lowe, Scott W. Leslie, Christina S. Fellmann, Christof Prediction of ultra-potent shRNAs with a sequential classification algorithm |
| title | Prediction of ultra-potent shRNAs with a sequential classification algorithm |
| title_full | Prediction of ultra-potent shRNAs with a sequential classification algorithm |
| title_fullStr | Prediction of ultra-potent shRNAs with a sequential classification algorithm |
| title_full_unstemmed | Prediction of ultra-potent shRNAs with a sequential classification algorithm |
| title_short | Prediction of ultra-potent shRNAs with a sequential classification algorithm |
| title_sort | prediction of ultra-potent shrnas with a sequential classification algorithm |
| topic | Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5416823/ https://www.ncbi.nlm.nih.gov/pubmed/28263295 http://dx.doi.org/10.1038/nbt.3807 |
| work_keys_str_mv | AT pelossofraphael predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT fairchildlauren predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT huangchunhao predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT widmerchristian predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT sreedharanvipint predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT sinhanishi predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT laidanyu predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT guanyuanzhe predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT premsrirutpremk predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT tschaharganehdarjusf predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT hoffmannthomas predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT thaparvishal predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT xiangqing predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT garipparalphj predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT ratschgunnar predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT zuberjohannes predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT lowescottw predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT lesliechristinas predictionofultrapotentshrnaswithasequentialclassificationalgorithm AT fellmannchristof predictionofultrapotentshrnaswithasequentialclassificationalgorithm |