Category: Uncategorized

Funding of the BMBF Consortia / Spatial Map of Fibrosis

The Federal Ministry of Education and Research (BMBF) is funding the research project „Spatial Mapping of Single Cells in Fibrotic Disease“, FibroMap for short, of the Uniklinik RWTH Aachen with 3.3 million euros. The Aachen scientists Prof. Dr. med. Dr.

Postdoc on Medical Single Cell Bioinformatics

We are looking for an experienced bioinformatician for helping the creation a spatial map of fibrosis. The candidate will develop bioinformatic methods for tracking temporal changes of  single cells and integrative analysis of scRNA-seq, scATAC-seq and spatial information. This position

Imputation and footprinting for single cell ATAC-seq. New manuscript & software release!

Imputation and footprinting for single cell ATAC-seq. New manuscript & software release! scOpen deals with massive sparsity and dropout events of single cell ATAC-seq. Use of scOpen improves clustering, inference of regulators and chromatin conformation. scHINT dissect regulatory & temporal

Congrats to Joseph Kuo for his successful Ph.D. defense!

Joseph having a hard time in keeping his new hat in the head! 

Influence of western diet in immune cells with single cell sequencing

Collaborative work with Krenkel and Tacke dissect changes in immune cells of mice subjected to high fat / high sugar diets.

Footprinting in ATAC-seq published in Genome Biology

Our paper on HINT-ATAC  is finally out in Genome Biology!

Decoding the function of lncRNAs – New computational metohd & sequencing protocols for detection of RNA-DNA Triple Helices

A paper describing TDF- a framework for detection of triple helix forming RNAs  – is finally out in NAR! Moreover with Grummt Lab, we have performed computational analysis of TripleRNA-seq and TriplexDNA-seq; two novel protocols for returning DNA/RNA molecules forming

Open positions

We perform research on computational methods for analysis of epigenomics and transcriptomics data. Over the past years, we have developed methods for prediction of cell specific binding sites from open chromatin data (Gusmao et al., Bioinformatics, 2015; Nature Methods, 2016),

Decoding the function of lncRNAs – Paper in Cell Stem Cell

Together with Kurian lab, we have delineated bionformatics framework to uncover novel antisense lncRNAs during cardiomyocite differentiation. These were particularly positioned up-stream of transcription factors, and showed a high positive correlation with these anti-sense partners.In this paper, Frank and colleagues

Papers in PNAS, Leukemia and Molecular Cell

A few successful collaborative efforts were recently published in top biomedical journals. With Zirkel and colleagues we used HINT footprint analysis to characterize transcription factor binding underlying DNA looping via HMGB2. With Sonntag and colleagues, we have leveraged molecular information