A5050582956- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Bioinformatics and Genomic Networks
- Cancer Cells and Metastasis
- Cell Image Analysis Techniques
- Cancer Immunotherapy and Biomarkers
- Immune Cell Function and Interaction
- Cancer-related molecular mechanisms research
- Colorectal Cancer Treatments and Studies
- Esophageal Cancer Research and Treatment
- Glioma Diagnosis and Treatment
- RNA modifications and cancer
- MicroRNA in disease regulation
- Radiomics and Machine Learning in Medical Imaging
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Advanced Fluorescence Microscopy Techniques
- Genomics and Rare Diseases
- Human Health and Disease
- Biomedical and Engineering Education
- RNA Research and Splicing
- Genetics, Bioinformatics, and Biomedical Research
- Extracellular vesicles in disease
- Microtubule and mitosis dynamics
- Immune cells in cancer
German Cancer Research Center
2022-2024
Heidelberg University
2022-2024
The Francis Crick Institute
2018-2023
King's College London
2018-2023
University of Padua
2017-2020
The Network of Cancer Genes (NCG) is a manually curated repository 2372 genes whose somatic modifications have known or predicted cancer driver roles. These were collected from 275 publications, including two sources and 273 sequencing screens more than 100 types 34,905 donors multiple primary sites. This represents 1.5-fold content increase compared to the previous version. NCG also annotates properties genes, such as duplicability, evolutionary origin, RNA protein expression, miRNA...
Medulloblastomas with extensive nodularity are cerebellar tumors characterized by two distinct compartments and variable disease progression. The mechanisms governing the balance between proliferation differentiation in MBEN remain poorly understood. Here, we employ a multi-modal single cell transcriptome analysis to dissect this process. In internodular compartment, identify proliferating granular neuronal precursor-like malignant cells, along stromal, vascular, immune cells. contrast,...
Abstract Background Spatial transcriptomics ( ST ) technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within their spatial tissue context. The rapid evolution methods, each with unique features, presents a challenge in selecting most appropriate technology for specific research objectives. Here, we compare four imaging-based methods – RNAscope HiPlex, Molecular Cartography,...
Abstract Multiplexed imaging technologies enable the study of biological tissues at single-cell resolution while preserving spatial information. Currently, high-dimension data analysis is technology-specific and requires multiple tools, restricting analytical scalability result reproducibility. Here we present SIMPLI (Single-cell Identification from MultiPLexed Images), a flexible technology-agnostic software that unifies all steps multiplexed analysis. After raw image processing, performs...
Since the small RNA-sequencing (sRNA-seq) technology became available, it allowed discovery of thousands new microRNAs (miRNAs) in humans and many other species, providing data on these RNAs (sRNAs) high biological translational relevance. MiRNA has not yet reached saturation, even most studied model organisms, researchers are using sRNA-seq studies with different aims biomedicine, fundamental research applied animal sciences. We review several miRNA characterization software tools that...
Cell type identification plays an important role in the analysis and interpretation of single-cell data can be carried out via supervised or unsupervised clustering approaches. Supervised methods are best suited where we list all cell types their respective marker genes a priori, while algorithms look for groups cells with similar expression properties. This property permits both known unknown populations, making suitable discovery. Success is dependent on relative strength signature each...
ABSTRACT The Network of Cancer Genes (NCG) is a manually curated repository 2,372 genes whose somatic modifications have known or predicted cancer driver role. These were collected from 275 publications, including two sources and 273 sequencing screens 119 types in 31 primary sites 34,905 donors. This represents more than 1.5-fold increase content as compared to the previous version. NCG also annotates properties genes, such duplicability, evolutionary origin, RNA protein expression, miRNA...
MicroRNA-offset RNAs (moRNAs) are microRNA-like small generated by microRNA precursors. To date, little is known about moRNAs and bioinformatics tools to inspect their expression still missing. We developed miR&moRe2, the first method consistently characterize microRNAs, moRNAs, isoforms from RNA sequencing data. illustrate miR&moRe2 discovery power, we applied it several published datasets. MoRNAs identified were in agreement with previous research findings. Moreover, observed that...
Abstract Despite recent advances in understanding disease biology, treatment of Group 3/4 medulloblastoma remains a therapeutic challenge pediatric neuro-oncology. Bulk-omics approaches have identified considerable intertumoral heterogeneity medulloblastoma, including the presence clear single-gene oncogenic drivers only subset cases, whereas majority large-scale copy-number aberrations prevail. However, intratumoral heterogeneity, role oncogene aberrations, and broad CNVs tumor evolution...
Abstract Resolving the molecular mechanisms driving childhood brain tumors will uncover tumor-specific vulnerabilities and advance mechanism-of-action-based therapies. Here we describe a continuum of cell-states in Group 3/4 medulloblastomas, most frequent fatal cerebellar embryonal tumor subgroups, based on differential activity transcription-factor-driven gene networks derived using comprehensive single-nucleus multi-omic medulloblastoma atlas. We show that diversity stems from enriched...
Abstract Medulloblastoma with extensive nodularity (MBEN) are cerebellar tumors two histologically distinct compartments and varying disease course. In some children MBEN progresses, while others show spontaneous differentiation into more benign tumors. However, the mechanisms that control tug-of-war between proliferation not well understood. Here, we dissected this process a multi-modal single cell transcriptome analysis. We found internodular compartment comprised proliferating early...
Abstract Intra-tumor heterogeneity in brain cancers contributes to therapy resistance and relapse through positive selection of resistant tumor cell populations. Resolving the molecular mechanisms driving intra-tumor will uncover tumor-specific vulnerabilities advance effective treatment strategies. Group 3/4 medulloblastomas, most common embryonal cerebellar subgroup, are highly heterogeneous tumors with high frequency which almost certainly fatal. Here, we generated analyzed a...
During a three-day hackathon, work was performed on various topics within the field of spatial omics data analysis. The were organized in five workgroups and included benchmarking, pipelines, transcriptomics, proteomics, multi-omics cell-cell communication. Most tools methods considered context Python ecosystem for (SpatialData) single-cell (scverse)
Abstract Modern bioimaging core facilities at research institutions are essential for managing and maintaining high-end instruments, providing training support researchers in experimental design, image acquisition data analysis. An important task these is the professional management of complex multi-dimensional data, which often produced large quantity very different file formats. This article details process that led to successfully implementing OME Remote Objects system (OMERO)...
Abstract Modern bioimaging core facilities at research institutions are essential for managing and maintaining high‐end instruments, providing training support researchers in experimental design, image acquisition data analysis. An important task these is the professional management of complex multidimensional data, which often produced large quantity very different file formats. This article details process that led to successfully implementing OME Remote Objects system (OMERO)...
Abstract Background Cell type identification plays an important role in the analysis and interpretation of single-cell data can be carried out via supervised or unsupervised clustering approaches. Supervised methods are best suited where we list all cell types their respective marker genes a priori . While algorithms look for groups cells with similar expression properties. This property permits both known unknown populations, making suitable discovery.. Success is dependent on relative...
ABSTRACT Colorectal cancers (CRCs) show variable response to immune checkpoint blockade, which can only partially be explained by the variability of tumour mutational burden. To dissect cellular and molecular determinants we performed a multi-omic screen 721 cancer regions from patients treated with Pembrolizumab (KEYNOTE 177 clinical trial) or Nivolumab. Multi-regional whole exome, RNA T-cell receptor sequencing that, within hypermutated CRCs, both anti-PD1 agents is not positively...
ABSTRACT Multiplexed imaging technologies enable the study of biological tissues at single-cell resolution while preserving spatial information. Currently, high-dimension data analysis is technology-specific and requires multiple tools, restricting analytical scalability result reproducibility. Here we present SIMPLI (Single-cell Identification from MultiPlexed Images), a novel, flexible technology-agnostic software that unifies all steps multiplexed analysis. After raw image processing,...
ABSTRACT Genetic alterations of somatic cells can drive nonmalignant clone formation and promote cancer initiation. However, the link between these processes remains unclear hampering our understanding tissue homeostasis development. Here we collect a literature-based repertoire 3355 well-known or predicted drivers noncancer evolution in 122 types 12 tissues. Mapping genes 7953 pancancer samples reveals that, despite large size, known compendium is still incomplete biased towards frequently...