Publications - Published papers

Please find below publications of our group. Currently, we list 53 papers. Some of the publications are in collaboration with the group of Peter Stadler and are also listed in the publication list for his group. Access to published papers (access) is restricted to our local network and chosen collaborators.
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©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

Pitfalls of Ascertainment Biases in Genome Annotations —Computing Comparable Protein Domain Distributions in Eukarya

Arli Aditya Parikesit, Lydia Steiner, Peter F Stadler, Sonja J Prohaska

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Malaysian Journal of Fundamental and Applied Sciences, Vol 10, No 2 (2014)

Abstract


Most investigations into the large-scale patterns of protein evolution are based on gene annotations that have been compiled in reference databases. The use of these resources for quantitative comparisons, however, is complicated by sometimes vast differences in coverage. More importantly, however, we also observe substantial ascertainment biases that cannot be removed by simple normalization procedures. A striking example is provided by the correlations between protein domains. We observe that statistics derived from different computational gene annotation procedure show dramatic discrepancies, and even qualitative changes from negative to positive correlation, when compared to statistics obtained from annotation databases.

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