Leiden University Medical Center
Room S4-36, Postzone S4-P PO Box 9600 2300 RC LEIDEN
LUMC’s Human Genetics Bioinformatics Research group focuses on the analysis, interpretation and integration of –omics data. This includes the development of new algorithms and application of existing algorithms to challenging new problems in the area of genetic and acquired human disorders. Within this group, a main interest is in the analysis and interpretation of transcriptomics data from both microarrays and RNA-seq technologies, studying general mechanisms regulating gene expression, alternative splicing, alternative promoter and 3’-UTR usage, and mRNA translation (ribosome profiling). Moreover, we develop methods for improved functional annotation of expression changes at the level of individual genes and pathways, and inference of (patho)physiological mechanisms and new hypotheses regarding disease etiology and progression.
- Human disease
- Mouse models for human disease
- Gene expression
- Alternative splicing
- Regulation of transcription and translation
Expertise and Track Record
435002022 Characterization and quantification of maternal RNAs transferred to the child through breast milk: data ingestion via extracellular vesicles With Wauben (Utrecht University).
Most experienced in different aspects of RNA-seq data analysis in the Netherlands.
Work on the regulation of gene expression internationally widely recognized.
*A pipeline for AML diagnostics based on RNA-seq (with Haematology, GenomeScan and the Sequence Analysis Support Core)
*Analysis of smallRNAs in extracellular vesicles (with ENM Nolte-‘t Hoen, UU)
*Analysis of alternative splicing in breast cancer cell lines (with Bob vd Water, LACDR)
*RNA-seq based allele specific expression in pathogenesis of breast cancer (collaboration with LUMC’s tumorgenetics group): quality control of RNA-seq data, RNA-seq data processing, development of pipeline for analysis of differential allelic expression
*Integrative ChIP-seq and microarray-based gene expression analysis to decipher the role of Tbx3 in development of the cardiac conduction system (collaboration with AMC’s department of Anatomy and Embryology): performed microarray quality control, microarray data processing, statistical analysis of differential gene expression, ChIP-seq data quality control, preprocessing, genome alignment, advised on the calling of transcription factor binding sites and integration with expression data
BBMRI – BIOS (Biobank-based Integration of Omics Study) project on integrative analysis of methylation and expression phenotypes (member of management team)
EU – FP7 project GEUVADIS on standardization of sequencing technology and data analysis (work package coordinator and one of the main data analysts)
EU – Marie Curie International Training Network TranCYST on the study of the pathophysiological mechanisms underlying polycystic kidney disease and the prioritization of biomarkers and drug targets (work package leader)
- 3 postdocs
- 12 ICT specialists / software engineers / data analysts
ENA, EGA, GEO