Publications - Published papers

Please find below publications of our group. Currently, we list 560 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

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Automatic Curation of Large Comparative Animal MicroRNA Data Sets

Yazbeck, Ali M. and Stadler, Peter F. and Tout, Kifah and Fallmann, Jörg

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PREPRINT 19-027:   [ Supplement ]
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Bioinformatics 35: 4553-4559

Abstract


Motivation MicroRNAs form an important class of RNA regulators that has been studied extensively. The miRBase and Rfam database provide rich, frequently updated information on both pre-miRNAs and their mature forms. These data sources, however, rely on individual data submission and thus are neither complete nor consistent in their coverage across different miRNA families. Quantitative studies of miRNA evolution therefore are difficult or impossible on this basis. Results We present here a workflow and a corresponding implementation, MIRfix, that automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. MIRfix produces alignments that are comparable across families and sets the stage for improved homology search as well as quantitative analyses. Availability and implementation MIRfix can be downloaded from https://github.com/Bierinformatik/MIRfix. Supplementary information Supplementary data are available at Bioinformatics online.