A5015820535- Gene expression and cancer classification
- Circular RNAs in diseases
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Gut microbiota and health
- Metabolomics and Mass Spectrometry Studies
- Probiotics and Fermented Foods
- Genetic Associations and Epidemiology
- Infant Health and Development
- Single-cell and spatial transcriptomics
- Diet and metabolism studies
- AI in cancer detection
Technical University of Munich
2022-2024
Microbiota assembly in the infant gut is influenced by diet. Breastfeeding and human breastmilk oligosaccharides promote colonization of beneficial bifidobacteria. Infant formulas are supplemented with bifidobacteria or complex oligosaccharides, notably galacto-oligosaccharides (GOS), to mimic breast milk. To compare microbiota development across feeding modes, this randomized controlled intervention study (German Clinical Trial DRKS00012313) longitudinally sampled stool during first year...
Abstract Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs) (1–3). Existing statistical computational methods for EI detection mostly limited pairs of SNPs due combinatorial explosion higher-order EIs. With NeEDL (network-based epistasis via local search), we leverage network medicine inform selection EIs that an order...
Circular RNAs (circRNAs) are long noncoding (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline systematically assess sponging circRNAs.We developed circRNA-sponging, a nextflow (i) identifies via backsplicing junctions detected in RNA-seq data, (ii) quantifies expression...
Abstract Background Eukaryotic gene expression is controlled by cis-regulatory elements (CREs), including promoters and enhancers, which are bound transcription factors (TFs). Differential of TFs their binding affinity at putative CREs determine tissue- developmental-specific transcriptional activity. Consolidating genomic datasets can offer further insights into the accessibility CREs, TF activity, and, thus, regulation. However, integration analysis multimodal hampered considerable...
Circular RNAs (circRNAs) are long non-coding (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline systematically assess sponging circRNAs.
<p class="first" dir="auto" id="d11370333e350"> <b>Background</b>Eukaryotic gene expression is controlled by cis-regulatory elements (CREs), including promoters and enhancers, which are bound transcription factors (TFs). Differential of TFs their binding affinity at putative CREs determine tissue- developmental-specific transcriptional activity. Consolidating genomic datasets can offer further insights into the accessibility CREs, TF activity, and, thus, regulation. However, integration...
Microbiota assembly in the infant gut is influenced by time and duration of dietary exposure to breast-milk, formula solid foods. In this randomized controlled intervention study, longitudinal sampling stool (n=998) showed similar development fecal bacterial communities (16S rRNA/shallow metagenomics sequencing) between formula- breast-fed infants during first year life (N=210). Infant supplemented with galacto-oligosaccharides (GOS) was most efficient sustain high levels bifidobacteria...
Abstract Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs) 1–3 . Existing statistical computational methods for EI detection mostly limited pairs of SNPs due combinatorial explosion higher-order EIs. With NeEDL ( ne twork-based e pistasis d etection via l ocal search), we leverage network medicine inform selection EIs that...
ABSTRACT Background Eukaryotic gene expression is controlled by cis-regulatory elements (CREs), including promoters and enhancers, which are bound transcription factors (TFs). Differential of TFs their binding affinity at putative CREs determine tissue- developmental-specific transcriptional activity. Consolidating genomic data sets can offer further insights into the accessibility CREs, TF activity, and, thus, regulation. However, integration analysis multi-modal hampered considerable...