Division Signaling and Functional Genomics

Bioinformatic Tools

We develop database and computational tools for the design and analysis of high-throughput screening experiments.

E-RNAi

E-RNAi is a web application to design optimized RNAi reagents. It integrates genomic context information with predicted specificity and efficiency parameters.

E-RNAi can be accessed at e-rnai.org

Please cite when using E-RNAi: Horn, T., Boutros, M. (2010). E-RNAi: a web application for the multi-species design of RNAi reagents - 2010 update. Nucleic Acids Research 38:W332-339. Fulltext

NEXT-RNAi

NEXT-RNAi is a software for the design and evaluation of genome-wide RNAi libraries. It performs all steps from the prediction of specific and efficient RNAi target sites to the visualization of designed reagents in their genomic context.

NEXT-RNAi can be accessed at www.nextrnai.org and is available for download at GitHub.

Please cite when using NEXT-RNAi: Horn, T., Sandmann, T., Boutros., M. (2010). Design and evaluation of genome-wide libraries for RNAi screens. Genome Biology 11:R61. Fulltext

GenomeRNAi Database

GenomeRNAi is a database with phenotype information from high-throughput RNAi experiments in human (cell-based) and Drosophila (cell-based or in vivo). The GenomeRNAi website features search and browse functionalities, a “frequent hitter” page, download options, and a dynamic genome browser based on a DAS server. It is well integrated with external resources. The website also provides details on RNAi reagents and associated mapping information, as well as assessments with regard to their specificity and efficiency. Direct submissions by data producers are welcome!

GenomeRNAi can be accessed at www.genomernai.org

Please cite when using GenomeRNAi: Schmidt, EE., Pelz, O., Buhlmann, S., Kerr, G., Horn, T., Boutros, M. (2013). GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. Nucleic Acids Res. 2013 Jan 1;41(D1):D1021-6. doi: 10.1093/nar/gks1170. Fulltext

cellHTS

cellHTS is a software package implemented in Bioconductor/R to analyze cell-based high-throughput RNAi screens. The cellHTS2 package is the new version of the cellHTS package, offering improved functionality for the analysis and integration of multi-channel screens and multiple screens.

More information on cellHTS can be found at: www.dkfz.de/signaling/cellHTS

Please cite when using cellHTS: Boutros, M., Bras, L., Huber, W. (2006). Analysis of cell-based RNAi screens. Genome Biology, 7:R66. Fulltext

web cellHTS

A prototype of a web-application that provides a user-friendly interface to cellHTS and a step-by-step tutorial how to use cellHTS for the analysis of high-throughput screening experiments. web cellHTS is available as open source and can be downloaded for local installation.

web cellHTS is accessible at web-cellhts2.dkfz.de and available for download at GitHub.

Please cite when using web cellHTS: Pelz., O., Gilsdorf, M., Boutros, M. (2010). web cellHTS2: A web application for the analysis of high-throughput screening data. BMC Bioinformatics 11:185. Fulltext

Booking Calendar

Please contact us with any suggestions or comments at b110-office (at) dkfz.de