Research and publications

• Publications
  59 publications

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

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

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

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

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

  Computational Metabolomics Workshop Material - BEFRI
  Pierre-Marie Allard , Zenodo (2023) | Other

  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) | Preprint

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

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

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

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

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

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

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

  From mass spectral features to molecules in molecular networks: a novel workflow for untargeted metabolomics
  Zakaria Bouchouireb, Damien Olivier-Jimenez, 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) | Preprint

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

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

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

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

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

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

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

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

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

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

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

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

  Discovery of Lipid Peroxidation Inhibitors from Bacopa Species Prioritized through Multivariate Data Analysis and Multi-Informative Molecular Networking.
  Molecules (Basel, Switzerland) (2019) | Journal 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) | Journal 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) | Journal article

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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