Pierre‐Marie Allard
A5027312343- Industrial Vision Systems and Defect Detection
- Metabolomics and Mass Spectrometry Studies
- Microbial Natural Products and Biosynthesis
- Medical Imaging Techniques and Applications
- Biomedical Text Mining and Ontologies
- Computational Drug Discovery Methods
- Genetics, Bioinformatics, and Biomedical Research
- Analytical Chemistry and Chromatography
- Genomics and Phylogenetic Studies
- Plant biochemistry and biosynthesis
- X-ray Diffraction in Crystallography
- Crystallization and Solubility Studies
- Chemistry and Chemical Engineering
- Natural product bioactivities and synthesis
- Bioinformatics and Genomic Networks
- Spectroscopy and Chemometric Analyses
- Chromatography in Natural Products
- Single-cell and spatial transcriptomics
- Biotechnology and Related Fields
- Traditional and Medicinal Uses of Annonaceae
- Innovative Microfluidic and Catalytic Techniques Innovation
- Trypanosoma species research and implications
- Natural Compounds in Disease Treatment
- Wikis in Education and Collaboration
- Species Distribution and Climate Change
University of Geneva
2016-2025
University of Fribourg
2021-2025
HES-SO University of Applied Sciences and Arts Western Switzerland
2020-2023
Ono Pharmaceutical (United States)
2022
University of Lausanne
2015-2020
Universidade Federal de São Carlos
2014
Universidade de São Paulo
2014
Institut de Chimie des Substances Naturelles
2011-2012
Centre National de la Recherche Scientifique
2011-2012
Rega Institute for Medical Research
2011
Dereplication represents a key step for rapidly identifying known secondary metabolites in complex biological matrices. In this context, liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is increasingly used and, via untargeted data-dependent MS/MS experiments, massive amounts of detailed information on the chemical composition crude extracts can be generated. An efficient exploitation such data sets requires automated treatment and access dedicated fragmentation...
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 A major aim of ecology is to upscale attributes individuals understand processes at population, community and ecosystem scales. Such are typically described using functional traits, that is, standardised characteristics impact fitness via effects on survival, growth and/or reproduction. However, commonly used traits (e.g. wood density, SLA) becoming increasingly criticised for not being truly mechanistic questionable predictors ecological processes. This Special Feature reviews...
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.
Natural products represent an inexhaustible source of novel therapeutic agents. Their complex and constrained three-dimensional structures endow these molecules with exceptional biological properties, thereby giving them a major role in drug discovery programs. However, the search for new bioactive metabolites is hampered by chemical complexity matrices which they are found. The purification single constituents from such requires significant amount work that it should be ideally performed...
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...
Significance Phytochemical diversity affects plant fitness and is the source of numerous medicines. Despite this, we know remarkably little about how phytochemical distributed across kingdom environment. To address this challenge, coupled untargeted metabolomics on 416 grassland vascular species Switzerland with phylogenetic information, distribution modelling, ensemble machine learning to construct a framework for comprehensively predicting landscape-scale both known currently unclassified...
Mountain ecology under climate change Climate warming causes shifts in the distributions of organisms and different may move at rates, resulting changes composition functioning ecological communities. These effects are rarely considered forecasts about on biodiversity. Using experimental translocations, Descombes et al. investigated how differential upslope migration alpine plants their insect herbivores affects community interactions. Lowland modify three-dimensional vegetation structure...
Abstract Molecular networking has become a key method used to visualize and annotate the chemical space in non-targeted mass spectrometry-based experiments. However, distinguishing isomeric compounds quantitative interpretation are currently limited. Therefore, we created Feature-based Networking (FBMN) as new analysis Global Natural Products Social (GNPS) infrastructure. FBMN leverages feature detection alignment tools enhance analyses isomer distinction, including from ion-mobility...
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.
Abstract While analytical techniques in natural products research massively shifted to liquid chromatography-mass spectrometry, lichen chemistry remains reliant on limited methods, Thin Layer Chromatography being the gold standard. To meet modern standards of metabolomics within lichenochemistry, we announce publication an open access MS/MS library with 250 metabolites, coined LDB for Lichen DataBase, providing a comprehensive coverage chemodiversity. These were donated by Berlin Garden and...
The metabolome is the biochemical basis of plant form and function, but we know little about its macroecological variation across kingdom. Here, used functional trait concept to interpret leaf among 457 tropical 339 temperate species. Distilling metabolite chemistry into five metabolic traits reveals that plants vary on two major axes specialization-a chemical defense spectrum an expression longevity. Axes are similar for species, with many combinations being viable. However, orthogonally...
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,...
An in vitro screening of New Caledonian plants allowed the selection several species with a significant dengue virus NS5 RNA-dependent RNA polymerase (RdRp) inhibiting activity. The chemical investigation Cryptocarya chartacea led to isolation series new mono- and dialkylated flavanones named chartaceones A-F (1-6), along pinocembrin. They were isolated as racemic mixtures characterized using extensive one- two-dimensional NMR spectroscopy. Four diastereomers chartaceone A (1) separated...
To anticipate potential seedling damage, plants block seed germination under unfavorable conditions. Previous studies investigated how is controlled in response to abiotic stresses through gibberellic and abscisic acid signaling. However, little known about whether seeds respond rhizosphere bacterial pathogens. We found that Arabidopsis blocked the vicinity of plant pathogen Pseudomonas aeruginosa. identified L-2-amino-4-methoxy-trans-3-butenoic (AMB), released by P. aeruginosa, as a biotic...
Fungal co-cultivation has emerged as a promising way for activating cryptic biosynthetic pathways and discovering novel antimicrobial metabolites. For the success of such studies, key element remains development standardized methods compatible with high-throughput analytical procedures. To efficiently highlight induction processes, it is crucial to acquire holistic view intermicrobial communication at molecular level. tackle this issue, strategy was developed based on miniaturization fungal...
Abstract Metabolism is involved in both pharmacology and toxicology of most xenobiotics including drugs. Yet, visualization tools facilitating metabolism exploration are still underused, despite the availibility pertinent bioinformatics solutions. Since molecular networking appears as a suitable tool to explore structurally related molecules, we aimed investigate its interest vitro exploration. Quetiapine, widely prescribed antipsychotic drug, undergoes well-described extensive metabolism,...
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...