title: Prediction of potent shRNAs with a sequential classification algorithm.
abstract: We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel data sets, 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.
authors.affiliation: Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Raphael
authors.initials: R
authors.lastname: Pelossof
authors.affiliation: Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.|Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York, USA.
authors.forename: Lauren
authors.initials: L
authors.lastname: Fairchild
authors.affiliation: Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.|Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York, USA.
authors.forename: Chun-Hao
authors.initials: CH
authors.lastname: Huang
authors.affiliation: Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.|Machine Learning Group, Department of Computer Science, Berlin Institute of Technology, Berlin, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Widmer
authors.affiliation: Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Vipin T
authors.initials: VT
authors.lastname: Sreedharan
authors.affiliation: Mirimus Inc., Woodbury, New York, USA.
authors.forename: Nishi
authors.initials: N
authors.lastname: Sinha
authors.affiliation: Mirimus Inc., Woodbury, New York, USA.
authors.forename: Dan-Yu
authors.initials: DY
authors.lastname: Lai
authors.affiliation: Mirimus Inc., Woodbury, New York, USA.
authors.forename: Yuanzhe
authors.initials: Y
authors.lastname: Guan
authors.affiliation: Mirimus Inc., Woodbury, New York, USA.
authors.forename: Prem K
authors.initials: PK
authors.lastname: Premsrirut
authors.affiliation: Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Darjus F
authors.initials: DF
authors.lastname: Tschaharganeh
authors.affiliation: Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Hoffmann
authors.affiliation: Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Vishal
authors.initials: V
authors.lastname: Thapar
authors.affiliation: RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Xiang
authors.affiliation: RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Ralph J
authors.initials: RJ
authors.lastname: Garippa
authors.affiliation: Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.|Department of Computer Science, ETH Zurich, Zurich, Switzerland.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Rätsch
authors.affiliation: Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria.
authors.forename: Johannes
authors.initials: J
authors.lastname: Zuber
authors.affiliation: Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.|Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York, USA.|Howard Hughes Medical Institute and Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Scott W
authors.initials: SW
authors.lastname: Lowe
authors.affiliation: Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Christina S
authors.initials: CS
authors.lastname: Leslie
authors.affiliation: Mirimus Inc., Woodbury, New York, USA.|Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
authors.forename: Christof
authors.initials: C
authors.lastname: Fellmann
mesh_terms: D000465:Algorithms; D064113:CRISPR-Cas Systems / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics*; D020868:Gene Silencing; D000069550:Machine Learning; D034741:RNA, Small Interfering / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D034741:RNA, Small Interfering