Thema der Dissertation:
Comparative Analysis of Transposable Elements and KRAB Zinc Finger Genes in Human and Non-human Primates Thema der Disputation:
Developing TEKRABber: A Cross-species Computational Pipeline for Transposable Element Analysis and Its Application to Primate Evolution
Comparative Analysis of Transposable Elements and KRAB Zinc Finger Genes in Human and Non-human Primates Thema der Disputation:
Developing TEKRABber: A Cross-species Computational Pipeline for Transposable Element Analysis and Its Application to Primate Evolution
Abstract: The content of this disputation presents my investigation into how transposable elements (TEs) and their repressors, KRAB zinc finger genes (KRAB-ZNFs), contribute to regulatory divergence among human and non-human primates. To support systematic and comparable analyses across species, I developed TEKRABber, a computational pipeline designed to standardize TE expression quantification and enable cross-species integration.
TEKRABber provides unified procedures for normalization, subfamily-level quantification, and differential expression analysis using outputs from widely used RNA-seq TE quantification tools. Using this framework, I analyzed multiple RNA-seq datasets, including brain tissues from human and non-human primates as well as human Alzheimer’s disease samples, to identify evolutionary patterns in KRAB-ZNF–TE regulatory networks. In addition, by integrating RNA-seq and KAP1 ChIP-seq data from primate B-lymphoblastoid cells, I reconstructed species-specific regulatory modules and examined TE expression at locus-specific resolution. This disputation will begin by introducing current bioinformatics approaches for TE quantification and explaining the motivation behind developing TEKRABber as a solution for robust cross-species comparison. I will then present the results of applying this pipeline to primate evolution, highlighting how the dynamic interplay between TEs and KRAB-ZNFs has shaped lineage-specific regulatory landscapes.
TEKRABber provides unified procedures for normalization, subfamily-level quantification, and differential expression analysis using outputs from widely used RNA-seq TE quantification tools. Using this framework, I analyzed multiple RNA-seq datasets, including brain tissues from human and non-human primates as well as human Alzheimer’s disease samples, to identify evolutionary patterns in KRAB-ZNF–TE regulatory networks. In addition, by integrating RNA-seq and KAP1 ChIP-seq data from primate B-lymphoblastoid cells, I reconstructed species-specific regulatory modules and examined TE expression at locus-specific resolution. This disputation will begin by introducing current bioinformatics approaches for TE quantification and explaining the motivation behind developing TEKRABber as a solution for robust cross-species comparison. I will then present the results of applying this pipeline to primate evolution, highlighting how the dynamic interplay between TEs and KRAB-ZNFs has shaped lineage-specific regulatory landscapes.
Zeit & Ort
19.12.2025 | 10:00
Seminarraum 007
(Fachbereich Mathematik und Informatik, Arnimallee 6, 14195 Berlin)
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WebEx