Publications - Published papers

Please find below publications of our group. Currently, we list 508 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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Duplicated RNA Genes in Teleost Fish Genomes

Dominic Rose, Julian Jöris, Jörg Hackermüller, Kristin Reiche, Qiang LI, Peter F. Stadler

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J Bioinform Comput Biol. 2008 Dec;6(6):1157-75.

Abstract


Teleost fishes share a duplication of their entire genomes. We report here on a computational survey of structured non-coding RNAs in teleost genomes, focussing on the fate of fish-specific duplicates. As in other metazoan groups we find evidence for a large number (11,543) of structured RNAs, most of which (~86%) are clade-specific or evolve so fast that their tetrapod homologs cannot be detected. In surprising contrast to protein-coding genes, the fish-specific genome duplication did not lead to a large number of paralogous ncRNAs: only 188 candidates, mostly microRNAs, appear in a larger copy number in teleosts than in tetrapods suggesting that large-scale gene duplications do not play a major role in the expansion of the vertebrate ncRNA inventory.

Keywords


non-coding RNA, ncRNA, ncRNA evolution, ncRNA gene finding, RNA, teleost fish, teleosts, <i>Takifugu rubripes</i>, whole-genome duplication, comparative genomics, annotation