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Authors: Karol Kozak 1 ; Sandra Kaestner 1 ; Thomas Wild 2 ; Andreas Vonderheit 1 ; Benjamin Misselwitz 3 ; Ulrike Kutay 2 and Gabor Csucs 1

Affiliations: 1 ETH Zurich, Switzerland ; 2 Institute of Biochemsitry and ETH Zurich, Switzerland ; 3 Institute of Microbiology and ETH Zurich, Switzerland

Keyword(s): RNAi, siRNA, Off-target, Transcriptome, Bioinformatics, Cell based Screening.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Sequence Analysis ; Systems Biology ; Transcriptomics

Abstract: The occurrence of RNAi side effects called “off-target effects” is still a challenging aspect in the interpretation of data from large-scale RNA interference screens. To reduce off-target effects, improved algorithms have been developed for small interfering RNA (siRNA) design, but also chemical modifications of double stranded RNA molecules were introduced by the various commercial providers. To aid the analysis of large-scale screens, we present a new algorithm and tool for the prediction of potential off-target effects that can be applied to RNAi experimental data. Our approach provides different possibilities to search for homologies between individual siRNAs of cellular mRNAs. We demonstrate our approach on a ribosomal RNAi screening dataset.

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Paper citation in several formats:
Kozak, K.; Kaestner, S.; Wild, T.; Vonderheit, A.; Misselwitz, B.; Kutay, U. and Csucs, G. (2013). New Algorithm for Analysis of Off-target Effects in siRNA Screens. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2013) - BIOINFORMATICS; ISBN 978-989-8565-35-8; ISSN 2184-4305, SciTePress, pages 253-260. DOI: 10.5220/0004185802530260

@conference{bioinformatics13,
author={Karol Kozak. and Sandra Kaestner. and Thomas Wild. and Andreas Vonderheit. and Benjamin Misselwitz. and Ulrike Kutay. and Gabor Csucs.},
title={New Algorithm for Analysis of Off-target Effects in siRNA Screens},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2013) - BIOINFORMATICS},
year={2013},
pages={253-260},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004185802530260},
isbn={978-989-8565-35-8},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2013) - BIOINFORMATICS
TI - New Algorithm for Analysis of Off-target Effects in siRNA Screens
SN - 978-989-8565-35-8
IS - 2184-4305
AU - Kozak, K.
AU - Kaestner, S.
AU - Wild, T.
AU - Vonderheit, A.
AU - Misselwitz, B.
AU - Kutay, U.
AU - Csucs, G.
PY - 2013
SP - 253
EP - 260
DO - 10.5220/0004185802530260
PB - SciTePress

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