A5045548263- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Pluripotent Stem Cells Research
- RNA Research and Splicing
- RNA Interference and Gene Delivery
- CRISPR and Genetic Engineering
- Acute Myeloid Leukemia Research
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- Single-cell and spatial transcriptomics
- interferon and immune responses
- Cancer Genomics and Diagnostics
- Cytokine Signaling Pathways and Interactions
- RNA and protein synthesis mechanisms
- Wireless Communication Networks Research
- NF-κB Signaling Pathways
- Coding theory and cryptography
- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Immune Response and Inflammation
- Metabolomics and Mass Spectrometry Studies
- Anodic Oxide Films and Nanostructures
- Advanced Wireless Communication Techniques
Heidelberg University
2023
German Cancer Research Center
2023
German Center for Diabetes Research
2020-2022
Deutsches Diabetes-Zentrum e.V.
2020-2022
Heinrich Heine University Düsseldorf
2020-2022
University of Basel
2013-2020
SIB Swiss Institute of Bioinformatics
2013-2018
Most of what is presently known about how miRNAs regulate gene expression comes from studies that characterized the regulatory effect miRNA binding sites located in 3′ untranslated regions (UTR) mRNAs. In recent years, there has been increasing evidence also bind coding region (CDS), but implication these interactions remains obscure because they have a smaller impact on mRNA stability compared with miRNA-target involve UTRs. Here we show miRNA-complementary are both CDS and 3′-UTRs under...
Abstract Background In recent years, a variety of small RNAs derived from other with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance these is largely unknown. To gain insight into the complexity snoRNA processing snoRNA-derived RNAs, we sequence long short that co-precipitate Argonaute 2 protein RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking immunoprecipitation (PAR-CLIP) core snoRNA-associated proteins. Results...
MiRNAs are post-transcriptional regulators that contribute to the establishment and maintenance of gene expression patterns. Although their biogenesis decay appear be under complex control, implications miRNA dynamics for processes they regulate not well understood. We derived a mathematical model miRNA-mediated regulation, inferred its parameters from experimental data sets, found describes time-dependent changes in mRNA, protein ribosome density levels measured upon transfection induction....
Article19 August 2020Open Access Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation Souvik Ghosh orcid.org/0000-0003-4152-4460 Computational and Systems Biology, Biozentrum, University Basel, Switzerland Search for more papers this author Joao C Guimaraes Corresponding Author [email protected] orcid.org/0000-0002-1664-472X Manuela Lanzafame Institute Pathology, Hospital Alexander Schmidt Proteomics Core Facility, Afzal Pasha Syed Beatrice...
Article27 August 2018Open Access Transparent process Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to induction Andrzej J Rzepiela Biozentrum, University Basel and Swiss Institute Bioinformatics, Basel, Switzerland Search for more papers by this author Souvik Ghosh orcid.org/0000-0003-4152-4460 Jeremie Breda Arnau Vina-Vilaseca orcid.org/0000-0003-0447-5268 Afzal P Syed Andreas Gruber Katja Eschbach Department Biosystems Science Engineering, ETH Zürich,...
Glucocorticoids such as dexamethasone (Dex) are widely used to treat both acute and chronic inflammatory conditions. They regulate immune responses by dampening cell-mediated immunity in a glucocorticoid receptor (GR)-dependent manner, suppressing the expression of pro-inflammatory cytokines chemokines stimulating anti-inflammatory mediators. Despite its evident clinical benefit, mechanistic underpinnings gene regulatory networks transcriptionally controlled GR context-specific manner remain...
The analysis of chromatin features in single cells centers around Tn5 transposase and exploits its activity to simultaneously fragment target DNA integrate adapter sequences choice. This reaction provides a direct readout the assay for transposase-accessible (scATAC-seq) map open loci. However, current limitation is sparse coverage these sites given cell by droplet-based methods. Thus, enhancing improve genomic scATAC-seq or facilitating multi-omics readouts via together with transcriptome...
Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at level RNA processing. These include expression specific transcript isoforms 3' untranslated regions. A number studies have uncovered processing factors that modulate efficiency process. However, a comprehensive evaluation involvement in mammalian cells is lacking. Here, we used data from large carried out three species, mouse, chimpanzee human, to uncover...
MiRNAs are post-transcriptional repressors of gene expression that may additionally reduce the cell-to-cell variability in protein expression, induce correlations between target levels and provide a layer through which targets can influence each other's as 'competing RNAs' (ceRNAs). Here we combined single cell sequencing human embryonic kidney cells two distinct miRNAs was induced over wide range, with mathematical modeling, to estimate Michaelis-Menten (KM)-type constants for hundreds...
Abstract The analysis of chromatin features in single cells centers around Tn5 transposase and exploits its activity to simultaneously fragment target DNA integrate adapter sequences choice. This reaction provides a direct readout the assay for transposase-accessible (scATAC-seq) map open regions. However, current limitation is sparse coverage loci that are detected given cell by droplet-based methods. Thus, enhancing improve genomic scATAC-seq or facilitating multi-omics readouts via...