A5053668445- Cancer Genomics and Diagnostics
- Marine Ecology and Invasive Species
- Planarian Biology and Electrostimulation
- Single-cell and spatial transcriptomics
- Tuberculosis Research and Epidemiology
- Epigenetics and DNA Methylation
- Mycobacterium research and diagnosis
- Genomics and Chromatin Dynamics
- SARS-CoV-2 and COVID-19 Research
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- MicroRNA in disease regulation
- SARS-CoV-2 detection and testing
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- RNA modifications and cancer
- Evolution and Genetic Dynamics
- Bioinformatics and Genomic Networks
- Cancer Cells and Metastasis
- RNA Research and Splicing
- Acute Myeloid Leukemia Research
- Gene Regulatory Network Analysis
- Renal cell carcinoma treatment
- Cancer-related gene regulation
- Bacteriophages and microbial interactions
ETH Zurich
2015-2024
Board of the Swiss Federal Institutes of Technology
2007-2023
University of Basel
2021-2022
École Polytechnique Fédérale de Lausanne
2011-2014
Institute for Biomedical Engineering
2014
Institute of Molecular Biotechnology
2013
Universität Hamburg
2012
University Medical Center Hamburg-Eppendorf
2012
University of Bonn
2012
University of California, Berkeley
2009
The ability of circulating tumor cells (CTCs) to form clusters has been linked increased metastatic potential. Yet biological features and vulnerabilities CTC remain largely unknown. Here, we profile the DNA methylation landscape single CTCs from breast cancer patients mouse models on a genome-wide scale. We find that binding sites for stemness- proliferation-associated transcription factors are specifically hypomethylated in clusters, including OCT4, NANOG, SOX2, SIN3A, paralleling...
Hsp70 chaperones assist a large variety of protein folding processes within the entire lifespan proteins. Central to these activities is regulation by DnaJ cochaperones. stimulates hydrolyze ATP, key step that closes its substrate-binding cavity and thus allows stable binding substrate. We show ATP hydrolysis Escherichia coli Hsp70, DnaK, very efficiently >1000-fold, but only if present at high (micromolar) concentration. In contrast, chaperone activity DnaK in luciferase refolding was...
Epithelial-mesenchymal transition (EMT) is a transient, reversible process of cell de-differentiation where cancer cells transit between various stages an EMT continuum, including epithelial, partial EMT, and mesenchymal states. We have employed Tamoxifen-inducible dual recombinase lineage tracing systems combined with live imaging 5-cell RNA sequencing to track undergoing or full in the MMTV-PyMT mouse model metastatic breast cancer. In primary tumors, infrequently undergo mostly epithelial...
Polycomb group (PcG) proteins are major determinants of gene silencing and epigenetic memory in higher eukaryotes. Here, we systematically mapped the human PcG complexome using a robust affinity purification mass spectrometry approach. Our high-density protein interaction network uncovered diverse range complexes. Moreover, our analysis identified interactors linking them to system, thus providing insight into molecular function complexes mechanisms recruitment target genes. We two PRC2...
Genomic imprinting is an epigenetic phenomenon leading to parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, genomic has mainly been observed in the endosperm, ephemeral triploid tissue derived after fertilization diploid central cell with a haploid sperm cell. effort identify novel imprinted genes Arabidopsis thaliana, we generated deep sequencing RNA profiles F1 hybrid seeds reciprocal crosses Col-0 Bur-0 accessions. Using...
Circulating tumor cells (CTCs) are shed from solid cancers in the form of single or clustered cells, and latter display an extraordinary ability to initiate metastasis. Yet, biological phenomena that trigger shedding CTC clusters a primary cancerous lesion poorly understood. Here, when dynamically labeling breast cancer along progression, we observe majority undergoing hypoxia, while CTCs largely normoxic. Strikingly, find vascular endothelial growth factor (VEGF) targeting leads shrinkage,...
Tuberculosis (TB) affects humans and other animals is caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Previous studies have shown that there are at least nine members of MTBC infecting than humans; these also been referred to as ecotypes. However, ecology evolution animal-adapted ecotypes poorly understood. Here we screened 12,886 publicly available genomes newly sequenced 17 strains, gathering a total 529 strains. Phylogenomic comparative analyses confirm paraphyletic...
Human tuberculosis (TB) is caused by members of the Mycobacterium complex (MTBC). The MTBC comprises several human-adapted lineages known as M. sensu stricto, well two (L5 and L6) traditionally referred to africanum. Strains L5 L6 are largely limited West Africa for reasons unknown, little their genomic diversity, phylogeography evolution. Here, we analysed genomes 350 320 strains, isolated from patients 21 African countries, plus 5 related that had not been classified into any lineages. Our...
Abstract The continuing emergence of SARS-CoV-2 variants concern and interest emphasizes the need for early detection epidemiological surveillance novel variants. We used genomic sequencing 122 wastewater samples from three locations in Switzerland to monitor local spread B.1.1.7 (Alpha), B.1.351 (Beta) P.1 (Gamma) at a population level. devised bioinformatics method named COJAC (Co-Occurrence adJusted Analysis Calling) that uses read pairs carrying multiple variant-specific signature...
The Polycomb group (PcG) and Trithorax (TrxG) of proteins are required for stable heritable maintenance repressed active gene expression states. Their antagonistic function on control, repression PcG activity TrxG, is mediated by binding to chromatin subsequent epigenetic modification target loci. Despite our broad knowledge about composition enzymatic activities the protein complexes involved, understanding still lacks important mechanistic detail a comprehensive view genes. In this study...
Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or local fragments no more than a few hundred nucleotides defined by length sequence reads. To study complex heterogeneous comprehensively, novel methods are required that allow for complete reconstruction individual viral haplotypes. Here, we show assembly whole genomes ∼8600 feasible from...
Large sequence datasets are difficult to visualize and handle. Additionally, they often do not represent a random subset of the natural diversity, but result uncoordinated convenience sampling. Consequently, can suffer from redundancy sampling biases.Here we present Treemmer, simple tool evaluate phylogenetic trees reduce their complexity by eliminating leaves that contribute least tree diversity.Treemmer size with different structures levels while maintaining sub-sample is representative...
With the advent of ultra high-throughput sequencing technologies, increasingly researchers are turning to deep for gene expression studies. Here we present a set rigorous methods normalization, quantification noise, and co-expression analysis data. Using these on 122 cap (CAGE) samples transcription start sites, construct genome-wide 'promoteromes' in human mouse consisting three-tiered hierarchy clusters, regions.
Abstract Background Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that order to overcome the challenge managing those large quantitative maximise biological information extracted from them, a sound system is required. Ease integration with analysis pipelines other computational tools key requirement for it. Results have developed openBIS, an open source software framework constructing...