Slavica Dimitrieva

ETH Zurich | ETH Zürich

Cancer progression and response to therapy are inextricably reliant on the coevolution of a supportive tissue microenvironment. This is particularly evident in pancreatic ductal adenocarcinoma, a tumor type characterized by expansive and heterogeneous stroma. Herein, we employed single-cell RNA sequencing and spatial transcriptomics of normal, infl...

Metastases are the primary cause of cancer-related death, and improving the means of predicting and targeting their development is one of the major goals in cancer research. While surgical resection and neo-adjuvant therapy can cure well-confined primary tumors, our ability to effectively treat cancer is largely dependent on our capacity to interdi...

Cell lines and patient-derived xenografts are essential to cancer research, however, the results derived from such models often lack clinical translatability, as these models do not fully recapitulate the complex cancer biology. It is critically important to better understand the systematic differences between cell lines, xenografts and clinical tu...

Droplet-based single-cell omics, including single-cell RNA sequencing (scRNAseq), single cell CRISPR perturbations (e.g., CROP-seq) and single-cell protein and transcriptomic profiling (e.g., CITE-seq) hold great promise for comprehensive cell profiling and genetic screening at the single cell resolution, yet these technologies suffer from substant...

Peripheral nerves are organ-like structures containing diverse cell types to optimize function. This interactive assembly includes mostly axon-associated Schwann cells, but also endothelial cells of supporting blood vessels, immune system-associated cells, barrier-forming cells of the perineurium surrounding and protecting nerve fascicles, and conn...

Altered neural stem/progenitor cell (NSPC) activity and neurodevelopmental defects are linked to intellectual disability. However, it remains unclear whether altered metabolism, a key regulator of NSPC activity, disrupts human neurogenesis and potentially contributes to cognitive defects. We investigated links between lipid metabolism and cognitive...

Background Hematopoietic stem cells (HSCs) can self‐renew and/or differentiate into various functionally divergent progenitor cell types, such as common myeloid progenitors (CMPs), megakaryocyte‐erythrocyte progenitors (MEPs) or granulocyte‐macrophage progenitors (GMPs). When the process of self‐renewal and differentiation is altered, e.g. upon gen...

Background Iron deficiency anemia (IDA) is the most prevalent nutritional insufficiency worldwide. Greece has been an entry‐route to Europe due to its unique geographical position and accepts increasing number of refugees since 2015 because of the geopolitical changes in the nearby region Aims The aim of the study was to determine the prevalence o...

Physiological processes in multicellular organisms depend on the function and interactions of specialized cell types operating in context. Some of these cell types are rare and thus obtainable only in minute quantities. For example, tissue-specific stem and progenitor cells are numerically scarce, but functionally highly relevant, and fulfill criti...

Physiological processes in multicellular organisms depend on the function and interactions of a multitude of specialized cell types operating in context. Fluorescence-activated cell sorting (FACS) provides a powerful tool to determine the cell type composition of complex mixtures and to purify highly homogeneous cell populations using a small numbe...

Wnt-β-catenin signalling plays a pivotal role in the homeostasis of the intestinal epithelium by promoting stem cell renewal1,2. In the small intestine, epithelial Paneth cells secrete Wnt ligands and thus adopt the function of the stem cell niche to maintain epithelial homeostasis3,4. It is unclear which cells comprise the stem cell niche in the c...

Background Kidney renal clear cell carcinoma (KIRC) is a type of cancer that is resistant to chemotherapy and radiotherapy and has limited treatment possibilities. Large-scale molecular profiling of KIRC tumors offers a great potential to uncover the genetic and epigenetic changes underlying this disease and to improve the clinical management of KI...

In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To evaluate the extent and the nature of site-specific selection on synonymous codons, we computed...

Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) challenges were established to compare the...

UCNEbase (http://ccg.vital-it.ch/UCNEbase) is a free, web-accessible information resource on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs). It currently covers 4351 such elements in 18 different species. The majority of UCNEs are supposed to be transcriptional regulators of key developmental genes. As most of...

Genomic context analysis, also known as phylogenetic profiling, is widely used to infer functional interactions between proteins but rarely applied to non-coding cis-regulatory DNA elements. We were wondering whether this approach could provide insights about utlraconserved non-coding elements (UCNEs). These elements are organized as large clusters...

Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time O(n(3)). Recently, it has been claimed that RNA folding can be achieved in average time O(n(2)) using a sparsification technique. A proof of quadratic time compl...

Recent comparative genomic and other large-scale bioinformatics studies increasingly have been using gene annotations, functional classifications, and complimentary data from the emerging “-omics” disciplines. Indeed, such analyses have better chances to uncover hidden patterns in complex multidimensional and heterogeneous biological systems data....