Systems Biology & Biomedical Data Science Laboratory

We develop and apply data science approaches to understand gene activity regulation in health and disease.

Current Projects

100'000 Genomes Project

Analysis of whole genomes of thousands of cancers sequenced through Genomics England.

100'000 Genomes Project

Pan Prostate Cancer Group

Analysis of 1200 prostate cancers.

Pan Prostate Cancer Group

The Human Cell Atlas

Analysis of single-cell RNA sequencing data.

The Human Cell Atlas

Software, Tools & Databases

A consolidated atlas of polyadenylation sites from 3' end sequencing.

Feb 4, 2021

TECtool (Terminal Exon Characterization tool) is a machine learning-based annotation software (implemented in Python) that makes use of RNA sequencing (RNA-seq) data to identify novel terminal exons, infer novel transcript isoforms and annotate potential coding sequences.

Feb 13, 2021

The KAPAC tool enables the identification of sequence motifs that can explain changes in cellular 3' end processing from high-throughput sequencing data.

Feb 13, 2021

PAQR, standing for polyadenylation site usage quantification from RNA sequencing data, allows to quantify 3' end usage from standard RNA sequencing libraries.

Feb 13, 2021

A comprehensive repository for 3' end processing sites based on a uniform analysis of a large number of 3' end sequencing data sets.

Feb 13, 2021

The Integrated System for Motif Actitivity Response Analysis (ISMARA) is an online tool that models genome-wide expression or ChIP-seq data, in terms of computationally predicted regulatory sites for epigenetic regulators, transcription factors (TFs) and microRNAs (miRNAs).

Feb 6, 2021

Selected Publications

#Quickly discover relevant content by filtering publications. #

Alternative cleavage and polyadenylation in health and disease

Most human genes have multiple sites at which RNA 3' end cleavage and polyadenylation can occur, enabling the expression of distinct …

Alternative cleavage and polyadenylation in health and disease

Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms

Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through …

Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms

Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction

miRNAs are small RNAs that regulate gene expression post-transcriptionally. By repressing the translation and promoting the degradation …

Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction

Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC

3' Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in …

Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC

TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition

The transition between epithelial and mesenchymal phenotypes (EMT) occurs in a variety of contexts. It is critical for mammalian …

TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better …

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogenous ribonucleoprotein C on cleavage and polyadenylation

Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to …

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogenous ribonucleoprotein C on cleavage and polyadenylation

Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells

Alternative polyadenylation is a cellular mechanism that generates mRNA isoforms differing in their 3' untranslated regions (3' UTRs). …

Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways

The findings that microRNAs (miRNAs) are essential for early development in many species and that embryonic miRNAs can reprogram …

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

Accurate reconstruction of the regulatory networks that control gene expression is one of the key current challenges in molecular …

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

Pegylated ifn-alpha regulates hepatic gene expression through transient Jak/STAT activation

The use of pegylated interferon-α (pegIFN-α) has replaced unmodified recombinant IFN-α for the treatment of chronic viral hepatitis. …

Pegylated ifn-alpha regulates hepatic gene expression through transient Jak/STAT activation

Modulation of epigenetic regulators and cell fate decisions by miRNAs

Mammalian gene expression is controlled at multiple levels by a variety of regulators, including chromatin modifiers, transcription …

Modulation of epigenetic regulators and cell fate decisions by miRNAs

Contact

Universitaetsstraße 10
78464 Konstanz