A5029012304- Metabolomics and Mass Spectrometry Studies
- Biomedical Text Mining and Ontologies
- Microbial Natural Products and Biosynthesis
- Genetics, Bioinformatics, and Biomedical Research
- Chemistry and Chemical Engineering
- Analytical Chemistry and Chromatography
- Plant biochemistry and biosynthesis
- Open Education and E-Learning
- Semantic Web and Ontologies
- Biotechnology and Related Fields
- Innovative Microfluidic and Catalytic Techniques Innovation
- Genomics and Phylogenetic Studies
- Spectroscopy and Chemometric Analyses
- Wikis in Education and Collaboration
- Bioinformatics and Genomic Networks
- Chromatography in Natural Products
- Phytochemistry and Biological Activities
- Biochemical Analysis and Sensing Techniques
- Computational Drug Discovery Methods
- Chemical synthesis and alkaloids
- Phytochemistry and Bioactivity Studies
- Gut microbiota and health
- Natural product bioactivities and synthesis
- Traditional and Medicinal Uses of Annonaceae
- Advanced Chemical Sensor Technologies
University of Geneva
2018-2025
ETH Zurich
2023-2025
Institute for Systems Biology
2024
HES-SO University of Applied Sciences and Arts Western Switzerland
2020-2023
University of Lausanne
2019-2020
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis interpretation of data in natural products research. Currently, reliance on a disparate set non-standardized, insular, specialized databases presents series challenges for access, both within the discipline integration interoperability between related fields. The fundamental elements exchange are referenced structure-organism pairs that establish relationships distinct molecular...
Abstract microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging curated database of >60,000 monocultures, users can known and unknown MS/MS spectra link them to their respective producers via fragmentation patterns. Identification microbe-derived metabolites relative without priori knowledge will vastly enhance the understanding microorganisms’ role ecology human health.
Mass spectrometry (MS) offers unrivalled sensitivity for the metabolite profiling of complex biological matrices encountered in natural products (NP) research. The massive and sets spectral data generated by such platforms require computational approaches their interpretation. Within approaches, annotation automatically links to candidate structures via a score, which is usually established between acquired experimental or theoretical databases (DB). This process leads various each MS...
The Experimental Natural Products Knowledge Graph (ENPKG) framework combines a sample-centric approach with semantic enrichment to organize large heterogeneous metabolomics data sets as knowledge graph. Harmonization of experimental publicly available and federated queries mechanisms enable efficient information extraction the contextualization studies, thereby offering exciting opportunities for drug discovery global chemodiversity characterization.
Competition for and exchange of nutrients play crucial roles in shaping microbial community function dynamics. Although cross-feeding small metabolites is known to drive carbon among species, the importance self-produced extracellular polymeric substances (EPS), which include proteins, polysaccharides, DNA, humic-like substances, remains less understood. Utilizing chitin-degrading isolates natural seawater communities, we found that 4 7% from chitin degradation converted into EPS, accounting...
Understanding the distribution of hundreds thousands plant metabolites across kingdom presents a challenge. To address this, we curated publicly available LC-MS/MS data from 19,075 extracts and developed plantMASST reference database encompassing 246 botanical families, 1,469 genera, 2,793 species. This taxonomically focused facilitates exploration plant-derived molecules using tandem mass spectrometry (MS/MS) spectra. tool will aid in drug discovery, biosynthesis, (chemo)taxonomy,...
Abstract Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis interpretation of data in natural products research. Currently, reliance on a disparate set non-standardized, insular, specialized databases presents series challenges for access, both within the discipline integration interoperability between related fields. The fundamental elements exchange are referenced structure-organism pairs that establish relationships distinct...
Abstract As privileged structures, natural products often display potent biological activities. However, the discovery of novel bioactive scaffolds is hampered by chemical complexity matrices they are found in. Large extract collections thus extremely valuable for their novelty potential but also complicated to exploit in frame drug-discovery projects. In end, it pure substances that desired structural determination purposes and bioactivity evaluation. Researchers interested exploration...
The standardized identification of biomedical entities is a cornerstone interoperability, reuse, and data integration in the life sciences. Several registries have been developed to catalog resources maintaining identifiers for such as small molecules, proteins, cell lines, clinical trials. However, existing struggled provide sufficient coverage metadata standards that meet evolving needs modern sciences researchers. Here, we introduce Bioregistry, an integrative, open, community-driven...
ABSTRACT Bitterness is challenging to analyze due the diversity of bitter compounds, variability in sensory perception, and its interplay with other tastes. To address this, we developed an untargeted approach deconvolute taste molecular composition complex plant extracts. We applied our methodology ethanolic extract Swertia chirayita (Roxb.) H.Karst., a known for unique bitterness. Chemical characterization was performed through nuclear magnetic resonance spectroscopy experiments together...
Analyzing bitterness is challenging because of the diverse range bitter compounds, variability in sensory perception, and its complex interaction with other tastes. To address this, we developed an untargeted approach to deconvolute taste molecular composition plant extracts. We applied our methodology ethanolic extract Swertia chirayita (Roxb.) H.Karst., a recognized for distinctive bitterness. Chemical characterization was performed through nuclear magnetic resonance spectroscopy...
Sharing knowledge on chemicals in the digital age has been playground of databases such as Chemical Abstract Services and PubChem. Wikipedia complements this field by providing context to aimed at a broad audience, but is not easily read machines. Wikidata was started database service improve machine readability captured Wikipedia. an open license, application programming interfaces, strong provenance model. Scholia uses features provide access chemical knowledge. This study reviews...
Collections of natural extracts hold potential for the discovery novel products with original modes action. The prioritization from collections remains challenging due to lack a workflow that combines multiple-source information facilitate data interpretation. Results different analytical techniques and literature reports need be organized, processed, interpreted enable optimal decision-making prioritization. Here, we introduce Inventa , computational tool highlights structural novelty...
Pigments of fungi are a fertile ground inspiration: they spread across various chemical backbones, absorption ranges, and bioactivities. However, basidiomycetes with strikingly colored fruiting bodies have never been explored as agents for photodynamic therapy (PDT), even though known photoactive compound classes (e.g., anthraquinones or alkaloids) used chemotaxonomic markers. In this study, we tested the hypothesis that dyes skin-heads (dermocyboid Cortinarii) can produce singlet oxygen...
Natural products, also known as specialized or secondary metabolites, show extraordinary chemical diversity and potent biological activities. Their biosynthesis usually first encompasses scaffold generation, followed by additional tailoring maturation steps, leading to the mature compound. The latter steps are often performed accessory enzymes maturases. While knowledge about reaction substrate specificities of these is essential for natural product biosynthesis, it scattered in literature,...
Resistance in clear cell renal carcinoma (ccRCC) against sunitinib is a multifaceted process encompassing numerous molecular aberrations. This induces clinical complications, reducing the treatment success. Understanding these aberrations helps us to select an adapted strategy that surpasses resistance mechanisms, reverting insensitivity. In this regard, we investigated dominant mechanisms of and validated optimized multidrug combination overcome resistance. Human ccRCC cells were exposed...
Modern natural products (NPs) research relies on untargeted liquid chromatography coupled with mass spectrometry metabolomics. Together cutting-edge processing and computational annotation strategies, such approaches can yield extensive spectral structural information. However, current workflows require feature-alignment steps based retention time which hinders the comparison of samples originating from different batches or analyzed using instrumental setups. In addition, there is currently...
Repurposed drugs have been evaluated for the management of clear cell renal carcinoma (ccRCC), but only a few influenced overall survival patients with advanced disease. To combine repurposed non-oncology oncological drugs, we applied our validated phenotypic method, which consisted reduced experimental part and data modeling. A synergistic optimized multidrug combination (ODC) was identified to significantly reduce energy levels in cancer remaining inactive non-cancerous cells. The ODC...
Recent developments in mass spectrometry-based metabolite profiling allow unprecedented qualitative coverage of complex biological extract composition. However, the electrospray ionization used generates multiple artifactual signals for a single analyte. This leads to thousands per analysis without satisfactory means filtering those corresponding abundant constituents. Generic approaches are therefore needed and quantitative annotation broad range relevant For this, we an analytical platform...
Black dot is a blemish disease of potato tubers caused by the phytopathogenic fungus Colletotrichum coccodes. Qualitative resistance (monogenic) that leads to hypersensitive response has not been reported against black dot, but commercial cultivars show different susceptibility levels disease, indicating quantitative (polygenic) mechanisms this pathogen exist. Cytological studies are essential decipher colonization plant tissue, and untargeted metabolomics shown effective in highlighting...
Abstract MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging curated database of >60,000 monocultures, users can known and unknown MS/MS spectra link them to their respective producers via fragmentation patterns. Identification microbial-derived metabolites relative producers, without priori knowledge, will vastly enhance the understanding microorganisms’ role ecology...
A C825T polymorphism was recently identified in the gene for G-protein β3 subunit, T-allele being associated with hypertension. To better understand underlying pathophysiological mechanisms, we compared haemodynamics of young healthy males and without T-allele. In three studies, subjects were investigated regard to cardiac vascular function at rest following intravenous administration β-adrenoceptor antagonist, propranolol, α2-adrenoceptor agonist, α-methylnoradrenaline, local venous...