Recherche et publications

• Publications
  79 publications

  The Digital Botanical Gardens Initiative
  The DBGI Consortium, Donat Agosti, Pierre-Marie Allard, Alex Blood, Ludvik Bortl, Federico Brigante, Edouard Brulhart, Renato Bruni, Luca Cappelletti, Héloïse Coen, Chiara Dall'Asta, Tito Damiani, Emmanuel Defossez, Juri Felix, Thomas Freeth, Elodie Gaille, Gaëtan Glauser, Melanie-Jayne R. Howes, Eliot Jan-Smith, Alžběta Kadlecová, Geoffrey Kite, Jiří Kohout, Gregor Kozlowski, Kateřina Kučerová, Emilie Lab, Mazzarine Laboureau, Audrey Le Cabec, Lise Lebrun, Henry Lutcke, Anne-Laure Maire, Patricia Malcolm, Anna Maliukova, Helena Mannochio-Russo, Carlos Martel, Tarcisio Mendes de Farias, Daniel Mietchen, Blaise Mulhauser, Alain Muller, Thomas Pickering, Tomáš Pluskal, Christophe Randin, Sergio Rasmann, Simon Rérat, Arnau Ribera Tort, Gabriela Říhová, Davide Rovelli, Nicolas Ruch, Adriano Rutz, Vlastimil Rybka, Marcelino Santos do Rosário, Ana-Claudia Sima, Stephanie Tamdem Guetchueng, Disha Tandon, Marco Visani, Colin Volet, China Williams, (2026) | Prépublication

  An Integrated Miniaturized Metabologenomics Workflow for High-Throughput Actinomycetes Prioritization
  Rima Ouchene, Laurent Falquet, Laurent Poirel, Pierre-Marie Allard, (2026) | Prépublication

  RO-Crate Metadata Specification 1.3.0
  Peter Sefton, Eoghan Ó Carragáin, Stian Soiland-Reyes, Oscar Corcho, Daniel Garijo, Raul Palma, Frederik Coppens, Carole Goble, José M. Fernández, Kyle Chard, Jose Manuel Gomez-Perez, Michael R. Crusoe, Ignacio Eguinoa, Nick Juty, Kristi Holmes, Jason A. Clark, Salvador Capella-Gutierrez, Alasdair J. G. Gray, Stuart Owen, Alan R. Williams, Giacomo Tartari, Finn Bacall, Thomas Thelen, Hervé Ménager, Laura Rodríguez-Navas, Paul Walk, brandon whitehead, Mark Wilkinson, Paul Groth, Erich Bremer, Leyla Jael Castro, Karl Sebby, Alexander Kanitz, Ana Trisovic, Gavin Kennedy, Mark Graves, Jasper Koehorst, Simone Leo, Marc Portier, Paul Brack, Milan Ojsteršek, Bert Droesbeke, Chenxu Niu, Kosuke Tanabe, Tomasz Miksa, Marco La Rosa, Cedric Decruw, Andreas Czerniak, Jeremy Jay, Sergio Serra, Ronald Siebes, Shaun de Witt, Shady El Damaty, Douglas Lowe, Xuanqi Li, Sveinung Gundersen, Muhammad Radifar, Rudolf Wittner, Oliver Woolland, Paul De Geest, Douglas Fils, Florian Wetzels, Raül Sirvent, Abigail Miller, Jake Emerson, Davide Fucci, Bruno P. Kinoshita, Maciek Bąk, Jens Hollunder, Martin Weise, Vartika Bisht, Toshiyuki Nishiyama Hiraki, Bram Ulrichts, Michael Falk, Eli Chadwick, Daniel Bauer, James Love, Eleni Adamidi, Josh Moore, Lars Schöbitz, Andreas Meier, Juan Fuentes, Edan Bainglass, Balázs E. Pataki, Joe Heffer, Pascal Su, Andrea Davanzo, Meznah Aloqalaa, Pierre-Marie Allard, Venkat Malladi, Esteban Gonzalez, Phil Reed, Tilo Mathes, Saurabh Dome, Niklas-Maximilian Epping, Margareta Hellström, Paul Slavin (2026) | Autre

  METRIN-KG: A knowledge graph integrating plant metabolites, traits, and biotic interactions
  GigaScience (2026) | Article

  biostat_toolbox
  Pierre-Marie Allard, emmanuel defossez (2025) | Autre

  met_annot_enhancer
  Pierre-Marie Allard (2025) | Autre

  Inhibition of rhizobial cheaters by the host Medicago truncatula involves repression of symbiotic functions and induction of defense
  New Phytologist (2025) | Article

  Anticipating the chemistry of Life
  Marco Visani, Pierre-Marie Allard, Zenodo: (7.10.2025) | Conférence

  MAPP Metabolomics Unit
  Pierre-Marie Allard, Zenodo: (29.9.2025) | Conférence

  METRIN-KG: A knowledge graph integrating plant metabolites, traits, and biotic interactions
  Disha Tandon, Tarcisio Mendes De Farias, Pierre-Marie Allard, Emmanuel Defossez, (2025) | Prépublication

  Efficient constitution of a library of rotenoid analogs active against Trypanosoma cruzi from a digitalized plant extract collection
  RSC Advances (2025) | Article

  Poster for the Bachelor and Master evening : 21 November 2024 at the University of Fribourg
  Marco Visani, Pierre-Marie Allard, Earth Metabolome Initiative, Zenodo: (18.11.2024) | Conférence

  Poster for the Bachelor and Master evening : 21 November 2024 at the University of Fribourg
  Marco Visani, Pierre-Marie Allard, Earth Metabolome Initiative, Zenodo: (18.11.2024) | Conférence

  Sanctioning of bacterial cheaters by the host plant in nitrogen-fixing symbiosis betweenMedicago truncatulaandSinorhizobium meliloti
  Min Chen, Axelle Raisin, Natalie Judkins, Pierre-Marie Allard, Emmanuel Defossez, Michael Stumpe, Inmaculada Yruela, Manuel Becana, Didier Reinhardt, Nathalie Judkins, Emmanuel Défossez, (2024) | Prépublication

  Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation
  Adriano Rutz, Jonathan BISSON, Pierre-Marie Allard (2024) | Autre

  Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation
  Adriano Rutz, Jonathan BISSON, Pierre-Marie Allard (2024) | Autre

  Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation
  Adriano Rutz, Jonathan BISSON, Pierre-Marie Allard (2024) | Autre

  Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation
  Adriano Rutz, Jonathan BISSON, Pierre-Marie Allard (2024) | Autre

  Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation
  Adriano Rutz, Jonathan BISSON, Pierre-Marie Allard (2024) | Autre

  A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery
  ACS Central Science (2024) | Article

  Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation
  Adriano Rutz, Jonathan BISSON, Pierre-Marie Allard (2024) | Autre

  Leaf metabolic traits reveal hidden dimensions of plant form and function
  Science Advances (2023) | Article

  Leaf metabolic traits reveal hidden dimensions of plant form and function
  American Association for the Advancement of Science (2023) | Article

  Leaf metabolic traits reveal hidden dimensions of plant form and function
  Tom W. N. Walker, Franziska Schrodt, Pierre-Marie Allard, Emmanuel Defossez, Vincent E. J. Jassey, Meredith C. Schuman, Jake M. Alexander, Oliver Baines, Virginie Baldy, Richard D. Bardgett, Pol Capdevila, Phyllis D. Coley, Nicole M. van Dam, Bruno David, Patrice Descombes, Maria-Jose Endara, Catherine Fernandez, Dale Forrister, Albert Gargallo-Garriga, Gaёtan Gauser, Sue Marr, Steffen Neumann, Loïc Pellissier, Kristian Peters, Sergio Rasmann, Ute Roessner, Roberto Salguero-Gómez, Jordi Sardans, Wolfram Weckwerth, Jean-Luc Wolfender, Josep Peñuelas, (2023) | Prépublication

  SBL.00073 material - Specialized Metabolism - UniFr
  Pierre-Marie Allard , Zenodo (2023) | Autre

  Open and reusable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extracts
  GigaScience (2022) | Article

  Metabolomics in Ecology and Bioactive Natural Products Discovery: Challenges and Prospects for a Comprehensive Study of the Specialised Metabolome
  CHIMIA (2022) | Article

  Metabolomic- and Molecular Networking-Based Exploration of the Chemical Responses Induced in Citrus sinensis Leaves Inoculated with Xanthomonas citri
  Journal of Agricultural and Food Chemistry (2022) | Article

  Targeted Isolation of Antibiotic Brominated Alkaloids from the Marine Sponge Pseudoceratina durissima Using Virtual Screening and Molecular Networking
  Marine Drugs (2022) | Article

  Inventa: a computational tool to discover chemical novelty in natural extracts libraries
  Luis-Manuel Quiros-Guerrero, Louis-Félix Nothias, Arnaud Gaudry, Laurence Marcourt, Pierre-Marie Allard, Adriano Rutz, Bruno David, Emerson Ferreira Queiroz, Jean-Luc Wolfender, (2022) | Prépublication

  The LOTUS initiative for open knowledge management in natural products research
  eLife (2022) | Article

  MEMO: Mass Spectrometry-Based Sample Vectorization to Explore Chemodiverse Datasets
  Frontiers in Bioinformatics (2022) | Article

  Functional Traits 2.0: The power of the metabolome for ecology
  Journal of Ecology (2022) | Article

  Functional Traits 2.0: The power of the metabolome for ecology
  Wiley-Blackwell Publishing, Inc. (2022) | Article

  MEMO: Mass Spectrometry-based Sample Vectorization to Explore Chemodiverse Datasets
  Arnaud Gaudry, Florian Huber, Louis-Félix Nothias, Sylvian Cretton, Marcel Kaiser, Jean-Luc Wolfender, Pierre-Marie Allard, (2021) | Prépublication

  From mass spectral features to molecules in molecular networks: a novel workflow for untargeted metabolomics
  Damien Olivier-Jimenez, Zakaria Bouchouireb, Simon Ollivier, Julia Mocquard, Pierre-Marie Allard, Guillaume Bernadat, Marylène Chollet-Krugler, David Rondeau, Joël Boustie, Justin J.J. van der Hooft, Jean-Luc Wolfender, (2021) | Prépublication

  Drug Repurposing to Identify a Synergistic High-Order Drug Combination to Treat Sunitinib-Resistant Renal Cell Carcinoma
  Cancers (2021) | Article

  Molecular and Functional Analysis of Sunitinib-Resistance Induction in Human Renal Cell Carcinoma Cells
  International Journal of Molecular Sciences (2021) | Article

  Open Natural Products Research: Curation and Dissemination of Biological Occurrences of Chemical Structures through Wikidata
  Rutz A and Sorokina M and Galgonek J and Mietchen D and Willighagen E and Graham J and Stephan R and Page R and Vondrášek J and Steinbeck C and Pauli GF and Wolfender J and Bisson J and Allard P, (2021) | Prépublication

  Spatial and evolutionary predictability of phytochemical diversity
  Proceedings of the National Academy of Sciences (2021) | Article

  Novel trophic interactions under climate change promote alpine plant coexistence
  Science (2020) | Article

  A Mass Spectrometry Based Metabolite Profiling Workflow for Selecting Abundant Specific Markers and Their Structurally Related Multi-Component Signatures in Traditional Chinese Medicine Multi-Herb Formulae.
  Frontiers in pharmacology (2020) | Article

  New insights into quetiapine metabolism using molecular networking.
  Scientific reports (2020) | Article

  In Silico Studies of the Biomolecular Interactions Between Natural Products and SARS-CoV-2 Main Protease
  Wilmar Puma-Zamora, Fabian Jimenez, Jesus Antonio Alvarado-Huayhuaz, Gerson Cordova-Serrano, Pierre-Marie Allard, Mariano Prado Acosta, Gustavo E. Olivos-Ramirez, Héctor Condori-Alagón, Ihosvany Camps, (2020) | Prépublication

  Feature-based molecular networking in the GNPS analysis environment.
  Nature methods (2020) | Article

  Insights on the Structural and Metabolic Resistance of Potato (Solanum tuberosum) Cultivars to Tuber Black Dot (Colletotrichum coccodes).
  Frontiers in plant science (2020) | Article

  Metabolite Profiling of Javanese Ginger Zingiber purpureum and Identification of Antiseizure Metabolites via a Low-Cost Open-Source Zebrafish Bioassay-Guided Isolation.
  Journal of agricultural and food chemistry (2020) | Article

  Surface sensing triggers a broad-spectrum antimicrobial response in Pseudomonas aeruginosa.
  Environmental microbiology (2020) | Article

  Metabolomics of Myrcia bella Populations in Brazilian Savanna Reveals Strong Influence of Environmental Factors on Its Specialized Metabolism
  Molecules (2020) | Article

  A database of high-resolution MS/MS spectra for lichen metabolites.
  Scientific data (2019) | Article

  Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation
  Frontiers in Plant Science (2019) | Article

  Feature-based Molecular Networking in the GNPS Analysis Environment
  Nothias LF and Petras D and Schmid R and Dührkop K and Rainer J and Sarvepalli A and Protsyuk I and Ernst M and Tsugawa H and Fleischauer M and Aicheler F and Aksenov A and Alka O and Dorrestein PC, (2019) | Prépublication

  Effects of Sphagnum Leachate on Competitive Sphagnum Microbiome Depend on Species and Time.
  Frontiers in microbiology (2019) | Article

  Discovery of Lipid Peroxidation Inhibitors from Bacopa Species Prioritized through Multivariate Data Analysis and Multi-Informative Molecular Networking
  Molecules (2019) | Article

  Identification of chemotypes in bitter melon by metabolomics: a plant with potential benefit for management of diabetes in traditional Chinese medicine.
  Metabolomics : Official journal of the Metabolomic Society (2019) | Article

  Application of a molecular networking approach for clinical and forensic toxicology exemplified in three cases involving 3‐MeO‐PCP, doxylamine, and chlormequat
  Drug Testing and Analysis (2019) | Article

  A case of fatal acebutolol poisoning: an illustration of the potential of molecular networking.
  International journal of legal medicine (2019) | Article

  Characterization, Diversity, and Structure-Activity Relationship Study of Lipoamino Acids from Pantoea sp. and Synthetic Analogues
  International Journal of Molecular Sciences (2019) | Article

  Pharmacognosy in the digital era: shifting to contextualized metabolomics
  Current Opinion in Biotechnology (2018) | Article

  The plant pathogen Pseudomonas aeruginosa triggers a DELLA-dependent seed germination arrest in Arabidopsis
  eLife (2018) | Article

  Lung Cancer Chemopreventive Activity of Patulin Isolated from Penicillium vulpinum
  Molecules (2018) | Article

  Searching for original natural products by molecular networking: detection, isolation and total synthesis of chloroaustralasines
  Organic Chemistry Frontiers (2018) | Article

  Targeted Isolation of Monoterpene Indole Alkaloids from Palicourea sessilis.
  Journal of natural products (2017) | Article

  Bioactive Natural Products Prioritization Using Massive Multi-informational Molecular Networks
  ACS Chemical Biology (2017) | Article

  Cytotoxic Prenylated Stilbenes Isolated from Macaranga tanarius.
  Journal of natural products (2017) | Article

  Peptidomic and transcriptomic profiling of four distinct spider venoms.
  PloS one (2017) | Article

  Deep metabolome annotation in natural products research: towards a virtuous cycle in metabolite identification
  Current Opinion in Chemical Biology (2017) | Article

  UHPLC-MS-based HDAC Assay Applied to Bio-guided Microfractionation of Fungal Extracts.
  Phytochemical analysis : PCA (2016) | Article

  Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.
  (2016) | Article

  Targeted Isolation of Indolopyridoquinazoline Alkaloids from Conchocarpus fontanesianus Based on Molecular Networks.
  Journal of natural products (2016) | Article

  Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
  Nature Biotechnology (2016) | Article

  Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication
  Analytical Chemistry (2016) | Article

  Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication.
  (2016) | Article

  Anti-Candida Cassane-Type Diterpenoids from the Root Bark of Swartzia simplex.
  (2015) | Article

  Thinking big about small beings--the (yet) underdeveloped microbial natural products chemistry in Brazil.
  (2014) | Article

  Antiviral chlorinated daphnane diterpenoid orthoesters from the bark and wood of Trigonostemon cherrieri.
  (2012) | Article

  Trigocherrin A, the first natural chlorinated daphnane diterpene orthoester from Trigonostemon cherrieri.
  (2012) | Article

  Recherche d’inhibiteurs de virus émergents au sein de la biodiversité néo-calédonienne
  (2011) | Thèse

  Alkylated flavanones from the bark of Cryptocarya chartacea as dengue virus NS5 polymerase inhibitors.
  (2011) | Article

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