A5032275529- Bioinformatics and Genomic Networks
- Protein Structure and Dynamics
- Gene Regulatory Network Analysis
- RNA Research and Splicing
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Chromatin Dynamics
- Computational Drug Discovery Methods
- Genomics and Phylogenetic Studies
- Endoplasmic Reticulum Stress and Disease
- Advanced Proteomics Techniques and Applications
- Photoreceptor and optogenetics research
- Lipid metabolism and biosynthesis
- Chemical Synthesis and Analysis
- CRISPR and Genetic Engineering
- Synthesis and Catalytic Reactions
- Cancer-related molecular mechanisms research
- RNA regulation and disease
- MicroRNA in disease regulation
- Peroxisome Proliferator-Activated Receptors
- Redox biology and oxidative stress
Saarland University
2013-2022
Institute of Bioinformatics
2015
Reactive oxygen species (ROS) are emerging as important regulators of cancer growth and metastatic spread. However, how cells integrate redox signals to affect progression is not fully understood. Mitochondria cellular hubs, which highly regulated by interactions with neighboring organelles. Here, we investigated ROS at the endoplasmic reticulum (ER)-mitochondria interface generated translated melanoma outcome. We show that TMX1 TMX3 oxidoreductases, promote ER-mitochondria communication,...
Identifying the gene regulatory networks governing workings and identity of cells is one main challenges in understanding processes such as cellular differentiation, reprogramming or cancerogenesis. One particular challenge to identify drivers master genes that control cell fate transitions. In this work, we reformulate problem optimization problems computing a Minimum Dominating Set Connected for directed graphs. Both MDS MCDS are applied well-studied model organisms E. coli S. cerevisiae...
Abstract Motivation: Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. In particular, complexation transcription factors (TFs) and other proteins a prevailing highly conserved mechanism signal integration within critical pathways enables us to infer genes as well the exerted mechanism. Common approaches for protein complex prediction only use interaction networks, however, are designed detect self-contained...
Protein-protein interaction networks are an important component of modern systems biology. Yet, comparatively few efforts have been made to tailor their topology the actual cellular condition being studied. Here, we present a network construction method that exploits expression data at transcript-level and thus reveals alterations in protein connectivity not only caused by differential gene but also alternative splicing. We achieved this establishing direct correspondence between individual...
Cellular lipid metabolism is tightly regulated and requires a sophisticated interplay of multiple subcellular organelles to adapt changing nutrient supply. PEX19 was originally described as an essential peroxisome biogenesis factor that selectively targets membrane proteins peroxisomes. Metabolic aberrations were associated with compromised functions, solely attributed the absence peroxisomes, which also considered underlying cause for Zellweger Spectrum Disorders. More recently, however, it...
Differential analysis of cellular conditions is a key approach towards understanding the consequences and driving causes behind biological processes such as developmental transitions or diseases. The progress whole-genome expression profiling enabled to conveniently capture state cell's transcriptome detect characteristic features that distinguish cells in specific conditions. In contrast, mapping physical protein interactome for many samples experimentally infeasible at moment. For whole...
Although a considerable number of proteins operate as multiprotein complexes and not on their own, organism-wide studies so far are only able to quantify individual or protein-coding genes in condition-specific manner for sizeable samples, but assemblies. Consequently, there exist large amounts transcriptomic data an increasing amount proteome abundance, quantitative knowledge complexomes is missing. This deficiency impedes the applicability powerful tool differential analysis realm...
Abstract Summary TFmiR2 is a freely available web server for constructing and analyzing integrated transcription factor (TF) microRNA (miRNA) co-regulatory networks human mouse. generates tissue- biological process-specific the set of deregulated genes miRNAs provided by user. Furthermore, service can now identify key driver in constructed utilizing graph theoretical concept minimum connected dominating set. These putative players as well newly implemented four-node TF-miRNA motifs yield...
Besides all their conformational degrees of freedom, drug‐like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation tautomerism, open free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit output a subset possible configurational space by sometimes unwanted prior assumptions complete neglection ring‐chain tautomerism. Here,...