A5007053071- RNA Research and Splicing
- RNA modifications and cancer
- MicroRNA in disease regulation
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- Chromosomal and Genetic Variations
- RNA Interference and Gene Delivery
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Adipose Tissue and Metabolism
- Advanced biosensing and bioanalysis techniques
- Pluripotent Stem Cells Research
- interferon and immune responses
- Renal and related cancers
- Gene Regulatory Network Analysis
- Circular RNAs in diseases
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Extracellular vesicles in disease
- Single-cell and spatial transcriptomics
- COVID-19 and healthcare impacts
- Plant Micronutrient Interactions and Effects
- Adipokines, Inflammation, and Metabolic Diseases
- Plant Stress Responses and Tolerance
SIB Swiss Institute of Bioinformatics
2007-2015
University of Basel
2007-2015
Unit of Virus Host Cell Interactions
2012
Université Joseph Fourier
2012
Université Grenoble Alpes
2012
Centre National de la Recherche Scientifique
2012
European Molecular Biology Laboratory
2011-2012
RNA transcripts are subjected to post-transcriptional gene regulation by interacting with hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) that often expressed in a cell-type dependently. To understand how the interplay these factors affects individual transcripts, high resolution maps vivo protein-RNA interactions necessary. A combination genetic, biochemical computational approaches typically applied identify RNA-RBP or RNA-RNP...
The cellular changes during an epithelial-mesenchymal transition (EMT) largely rely on global in gene expression orchestrated by transcription factors. Tead factors and their transcriptional co-activators Yap Taz have been previously implicated promoting EMT, however, direct target genes functional role EMT remained widely elusive. We uncovered a unanticipated of the factor Tead2 EMT. During mammary gland epithelial cells breast cancer cells, levels increase nucleus thereby directing...
RNA transcripts are subjected to post-transcriptional gene regulation by interacting with hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) that often expressed in a cell-type dependently. To understand how the interplay these factors affects individual transcripts, high resolution maps vivo protein-RNA interactions necessary1. A combination genetic, biochemical computational approaches typically applied identify RNA-RBP or RNA-RNP...
MicroRNAs (miRNAs) are short RNAs that act as guides for the degradation and translational repression of protein-coding mRNAs. A large body work showed miRNAs involved in regulation a broad range biological functions, from development to cardiac immune system function, metabolism, cancer. For most over 500 encoded human genome functions still remain be uncovered. Identifying whose expression changes between cell types or normal pathological conditions is an important step towards...
Metabolic diseases and comorbidities represent an ever-growing epidemic where multiple cell types impact tissue homeostasis. Here, the link between metabolic gene regulatory networks was studied through experimental computational analysis. Integrating regulation data with a human network prompted establishment of open-sourced web portal, IDARE (Integrated Data Nodes Regulation), for visualizing various gene-related in context pathways. Motivated by increasing availability deep sequencing...
Cellular differentiation of the T‐cell branch immune system begins with HSC, which undergoes a series stages characterized by progressive restriction in multipotency and acquisition specific lineage identity At molecular level, cell potential, commitment, to is achieved through coordinated control gene expression epigenetic mechanisms. Here, we analyzed compared profiles genome‐wide histone modification marks H3K4me3 (H3 lysine 4 trimethylation) H3K27me3 27 (i) vitro propagated HSCs, (ii)...
Introduction: Telemedicine reduces greenhouse gas emissions (CO 2 eq); however, results of studies vary extremely in dependence the setting. This is first study to focus on effects telemedicine CO imprint primary care. Methods: We conducted a comprehensive retrospective analyze total eq kilometers (km) saved by telemedical consultations. categorized prevented and provoked patient journeys, including pharmacy visits. calculated emission savings through care consultations comparison those that...
We previously showed that disease-linked metabolic genes are often under combinatorial regulation. Using the genome-wide ChIP-Seq binding profiles for 93 transcription factors in nine different cell lines, we show high regulatory load significantly enriched disease-association across types. find factor correlates with enhancer of and thereby allows identification by epigenomic mapping active enhancers. Identification 139 samples from 96 tissue types reveals a consistent enrichment...
The piRNA pathway operates in animal germ lines to ensure genome integrity through retrotransposon silencing. Piwi protein-associated small RNAs (piRNAs) guide proteins transcripts, which are degraded and thereby post-transcriptionally silenced a ping-pong amplification process. Cleavage of the transcript defines at same time 5' end secondary that will turn protein primary precursor, amplifying piRNAs. Although several studies provided evidence this mechanism is conserved among metazoa, how...
Transcription factors (TFs) represent key to establish a cellular phenotype. It is known that several TFs could play role in disease, yet less so far how their targets overlap. We focused here on identifying the most highly induced and putative during human adipogenesis. Applying chromatin immunoprecipitation coupled with deep sequencing (ChIP-Seq) SGBS pre-adipocyte cell line, we identified genes binding sites vicinity for three studied, PPARγ, CEBPα LXR. Here describe experimental design...
Obesity is an ever-growing epidemic where tissue homeostasis influenced by the differentiation of adipocytes that function in lipid metabolism, endocrine and inflammatory processes. While this process has been well-characterized mice, limited data available from human cells. Applying microarray expression profiling SGBS pre-adipocyte cell line, we identified genes with differential during combination constraint-based modeling metabolic pathway activity. Here describe experimental design...