L. Nothias

发表

Learning accurate representations of microbe-metabolite interactions

James R. Foulds, Se Jin Song, James T. Morton, 2019, Nature Methods.

Revisiting microbe-metabolite interactions: doing better than random

James R. Foulds, Se Jin Song, James T. Morton, 2019, bioRxiv.

Isolation of Premyrsinane, Myrsinane, and Tigliane Diterpenoids from Euphorbia pithyusa Using a Chikungunya Virus Cell-Based Assay and Analogue Annotation by Molecular Networking.

J. Neyts, P. Retailleau, J. Paolini, 2017, Journal of natural products.

Bioactive Natural Products Prioritization Using Massive Multi-informational Molecular Networks.

C. Pannecouque, L. Marcourt, J. Neyts, 2017, ACS chemical biology.

Euphorbia dendroides Latex as a Source of Jatrophane Esters: Isolation, Structural Analysis, Conformational Study, and Anti-CHIKV Activity.

P. Retailleau, J. Paolini, Jean Costa, 2016, Journal of natural products.

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation.

Mingxun Wang, Theodore Alexandrov, Pieter C Dorrestein, 2018, Journal of natural products.

Evaluation of Jatrophane Esters from Euphorbia spp. as Modulators of Candida albicans Multidrug Transporters.

Julien Paolini, Marc Litaudon, Louis-Félix Nothias, 2017, Journal of natural products.

Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L.

Justin J. J. van der Hooft, Pieter C. Dorrestein, Marnix H. Medema, 2019, Front. Plant Sci..

Assessing specialized metabolite diversity of Alnus species by a digitized LC-MS/MS data analysis workflow.

P. Dorrestein, S. Sung, J. V. D. van der Hooft, 2020, Phytochemistry.

Sharing and community curation of mass spectrometry data with GNPS

Erin E. Carlson, Roger G. Linington, Katherine R. Duncan, 2016 .

A community resource for paired genomic and metabolomic data mining

Elizabeth I. Parkinson, Emily C. Gentry, Allegra T. Aron, 2021, Nature Chemical Biology.

Environmentally-Friendly Workflow Based on Supercritical Fluid Chromatography and Tandem Mass Spectrometry Molecular Networking For the Discovery of Potent Anti-Viral Leads From Plants

P. Dorrestein, P. Retailleau, J. Paolini, 2017, bioRxiv.

Molecular Networking [ 11 _ TD $ DIFF ] As a Drug Discovery , Drug Metabolism , and Precision Medicine Strategy

P. Dorrestein, E. Esquenazi, R. Quinn, 2016 .

Comparative Genomics and Metabolomics Analyses of Clavulanic Acid-Producing Streptomyces Species Provides Insight Into Specialized Metabolism

P. Dorrestein, F. Barona-Gómez, L. Nothias, 2019, Front. Microbiol..

NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products

Justin J. J. van der Hooft, G. Cottrell, P. Dorrestein, 2020, Journal of natural products.

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Christine M. Aceves, Emily C. Gentry, Allegra T. Aron, 2019, Nature Protocols.

Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking

P. Dorrestein, R. Ibáñez, L. Rollins-Smith, 2019, Scientific Reports.

Multi-omics profiling of Earth’s biomes reveals that microbial and metabolite composition are shaped by the environment

Se Jin Song, Luke R. Thompson, James T. Morton, 2021 .

Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts

Sneha P. Couvillion, T. Thomas, N. Webster, 2022, Microbiome.

Multi-omics profiling of Earth’s biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments

Se Jin Song, Luke R. Thompson, James T. Morton, 2022, bioRxiv.

Feature-Based Molecular Networking Analysis of the Metabolites Produced by in vitro Solid-State Fermentation Reveals Pathways for the Bioconversion of Epigallocatechin Gallate.

Zhongwen Xie, Liang Zhang, X. Wan, 2020, Journal of agricultural and food chemistry.

Reply to: Examining microbe–metabolite correlations by linear methods

James R. Foulds, Se Jin Song, James T. Morton, 2021, Nature methods.

Metabolites from Microbes Isolated from the Skin of the Panamanian Rocket Frog Colostethus panamansis (Anura: Dendrobatidae)

A. M. Caraballo-Rodríguez, P. Dorrestein, R. Ibáñez, 2020, Metabolites.

Inventa: a computational tool to discover chemical novelty in natural extracts libraries

L. Marcourt, J. Wolfender, P. Allard, 2022, bioRxiv.

Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics

Emma L. Schymanski, Andrés Mauricio Caraballo Rodríguez, Christine M. Aceves, 2022, bioRxiv.

A Convolutional Neural Network-Based Approach for the Rapid Characterization of Molecularly Diverse Natural Products.

H. H. Mao, Kelsey L. Alexander, Kelsey L Alexander, 2020, Journal of the American Chemical Society.

A Convolutional Neural Network-based approach for the Rapid Annotation of Molecularly Diverse Natural Products

H. H. Mao, Kelsey L. Alexander, Kelsey L Alexander, 2020 .

Natural Inhibitors of the RhoA-p115 Complex from the Bark of Meiogyne baillonii.

G. Ferry, J. Boutin, B. Pfeiffer, 2018, Journal of natural products.

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Se Jin Song, Luke R. Thompson, James T. Morton, 2022, Nature Microbiology.

The ant fungus garden acts as an external digestive system

Kathleen E. Kyle, Sara P. Puckett, Marcy J. Balunas, 2020, bioRxiv.

Inventa: A computational tool to discover structural novelty in natural extracts libraries

L. Marcourt, J. Wolfender, P. Allard, 2022, Frontiers in Molecular Biosciences.

4-deoxyphorbol inhibits HIV-1 infection in synergism with antiretroviral drugs and reactivates viral reservoirs through PKC/MEK activation synergizing with vorinostat.

J. Paolini, L. Nothias, M. Litaudon, 2020, Biochemical pharmacology.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Francesco Asnicar, Mingxun Wang, Yang Bai, 2019, Nature Biotechnology.

Feature-Based Molecular Networking in the GNPS Analysis Environment

Simon Rogers, Nuno Bandeira, Mingxun Wang, 2019, Nature Methods.

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Kristian Fog Nielsen, Paul Shinn, Dac-Trung Nguyen, 2016, Nature Biotechnology.

Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy.

Pieter C Dorrestein, Louis-Felix Nothias, Robert A Quinn, 2017, Trends in pharmacological sciences.

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

Joe Wandy, Simon Rogers, Mingxun Wang, 2019, bioRxiv.

Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation.

P. Dorrestein, R. D. da Silva, P. Retailleau, 2019, Journal of natural products.

Identification of four amoebicidal non-toxic compounds by a molecular docking screen of Naegleria fowleri sterol Δ8-Δ7-isomerase and phenotypic assays.

R. Abagyan, J. McKerrow, L. Nothias, 2019, ACS infectious diseases.

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra

Juho Rousu, Sebastian Böcker, Markus Fleischauer, 2020, Nature Biotechnology.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

William A. Walters, Ahmad Turan Naimey, Lasse Buur Rasmussen, 2019, Nature Biotechnology.

Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism

Kevin T. Green, P. Dorrestein, F. Rohwer, 2018, Proceedings of the Royal Society B: Biological Sciences.

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Francesco Asnicar, Mingxun Wang, Pieter C. Dorrestein, 2018 .

MEMO: Mass Spectrometry-Based Sample Vectorization to Explore Chemodiverse Datasets

J. Wolfender, L. Nothias, M. Kaiser, 2021, bioRxiv.

Antibiotic discovery is a walk in the park

R. Knight, P. Dorrestein, L. Nothias, 2016, Proceedings of the National Academy of Sciences.

Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment

Emily C. Gentry, Allegra T. Aron, Kelly C. Weldon, 2021, Nature Communications.

Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden

Kathleen E. Kyle, Sara P. Puckett, Marcy J. Balunas, 2021, mSystems.

High-confidence structural annotation of metabolites absent from spectral libraries

Emily C. Gentry, Martin A. Hoffmann, S. Böcker, 2021, Nature Biotechnology.

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC

Pieter C. Dorrestein, Sebastian Böcker, Markus Fleischauer, 2020, Nature Machine Intelligence.

Studying Charge Migration Fragmentation of Sodiated Precursor Ions in Collision-Induced Dissociation at the Library Scale.

Emma L. Schymanski, S. Böcker, P. Dorrestein, 2020, Journal of the American Society for Mass Spectrometry.

Mining the NIST Mass Spectral Library Reveals the Extent of Sodium Assisted Inductive Cleavage in Collision-Induced Fragmentation

Emma L. Schymanski, P. Dorrestein, Kai Dührkop, 2020 .

MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

Pavel A. Pevzner, Rob Knight, Pieter C. Dorrestein, 2017, bioRxiv.

ReDU: a framework to find and reanalyze public mass spectrometry data

Justin J. J. van der Hooft, Ngoc Hung Nguyen, Nuno Bandeira, 2020, Nature Methods.

Mass spectrometry searches using MASST

Justin J. J. van der Hooft, Alexander A. Aksenov, Nuno Bandeira, 2020, Nature Biotechnology.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Francesco Asnicar, Mingxun Wang, Yang Bai, 2019, Nature Biotechnology.

Genomic and Metabolomic Analysis of the Potato Common Scab Pathogen Streptomyces scabiei

P. Dorrestein, L. Nothias, K. Tahlan, 2021, ACS omega.

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

Justin J. J. van der Hooft, Mingxun Wang, Pieter C. Dorrestein, 2020, Nature Chemical Biology.

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

Justin J.J. van der Hooft, Jo Handelsman, Mingxun Wang, 2020, bioRxiv.

Phytochemical study of Alzatea verticillata, the sole species belonging to the Alzateaceae family

Mahabir P. Gupta, L. Marcourt, J. Wolfender, 2023, Frontiers in Natural Products.

MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data

Alexander A. Aksenov, Nuno Bandeira, Rob Knight, 2019, bioRxiv.

Propagating annotations of molecular networks using in silico fragmentation

Mingxun Wang, Pieter C. Dorrestein, Evan Fox, 2018, PLoS Comput. Biol..

Classes for the masses: Systematic classification of unknowns using fragmentation spectra

Juho Rousu, Pieter C. Dorrestein, Sebastian Böcker, 2020, bioRxiv.

3D molecular cartography using LC–MS facilitated by Optimus and 'ili software

Theodore Alexandrov, Pieter C Dorrestein, Alexey V Melnik, 2017, Nature Protocols.

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS

Wout Bittremieux, Alexander A. Aksenov, Yann Guitton, 2020, bioRxiv.

Significance estimation for large scale metabolomics annotations by spectral matching

S. Böcker, P. Dorrestein, Kai Dührkop, 2017, Nature Communications.

Environmentally Friendly Procedure Based on Supercritical Fluid Chromatography and Tandem Mass Spectrometry Molecular Networking for the Discovery of Potent Antiviral Compounds from Euphorbia semiperfoliata.

Pieter C Dorrestein, Julien Paolini, Marc Litaudon, 2017, Journal of natural products.

Significance estimation for large scale untargeted metabolomics annotations

Nuno Bandeira, Mingxun Wang, Pieter C Dorrestein, 2017, bioRxiv.

Tandem Mass Spectrometry Molecular Networking as a Powerful and Efficient Tool for Drug Metabolism Studies.

P. Dorrestein, H. Yoo, J. Yu, 2022, Analytical chemistry.

Ion Identity Molecular Networking in the GNPS Environment

Uwe Karst, Kelly Weldon, Mingxun Wang, 2020, bioRxiv.

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.

Hosein Mohimani, Rob Knight, Pavel A Pevzner, 2019, Cell systems.

ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules

Pieter C. Dorrestein, Sebastian Böcker, Markus Fleischauer, 2019, bioRxiv.

Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking

P. Dorrestein, R. Ibáñez, L. Reinert, 2019, Scientific Reports.

Dereplication of microbial metabolites through database search of mass spectra

Liu Cao, Hosein Mohimani, Pavel A Pevzner, 2018, Nature Communications.

Did a plant-herbivore arms race drive chemical diversity in Euphorbia?

P. Dorrestein, C. Saslis-Lagoudakis, M. Medema, 2018, bioRxiv.

Dereplication of peptidic natural products through database search of mass spectra

Neha Garg, Hosein Mohimani, Pavel A Pevzner, 2016, Nature chemical biology.

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.

Nuno Bandeira, Rob Knight, Jelena Todoric, 2016, Analytical chemistry.

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Justin J. J. van der Hooft, Nuno Bandeira, Nicole Sikora, 2020, Nature Protocols.

Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data

Ngoc Hung Nguyen, Nuno Bandeira, Kelly Weldon, 2019, bioRxiv.

Dereplication of microbial metabolites through database search of mass spectra

P. Pevzner, P. Dorrestein, A. Gurevich, 2018, Nature Communications.

Niche partitioning of a pathogenic microbiome driven by chemical gradients

Rob Knight, Pieter C. Dorrestein, Louis-Felix Nothias, 2018, Science Advances.

High-confidence structural annotation of metabolites absent from spectral libraries

Emily C. Gentry, Martin A. Hoffmann, S. Böcker, 2021, Nature Biotechnology.

Assigning confidence to structural annotations from mass spectra with COSMIC

Emily C. Gentry, Martin A. Hoffmann, S. Böcker, 2021, bioRxiv.

A multi-omics strategy for the study of microbial metabolism: application to the human skin’s microbiome

P. Dorrestein, P. Ternes, L. Nothias, 2023, bioRxiv.

Integrative analysis of multimodal mass spectrometry data in MZmine 3

Timothy R. Fallon, S. Böcker, P. Dorrestein, 2023, Nature Biotechnology.

Nerpa: A Tool for Discovering Biosynthetic Gene Clusters of Bacterial Nonribosomal Peptides

P. Dorrestein, A. Gurevich, A. Korobeynikov, 2021, Metabolites.

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data

Wout Bittremieux, Zheng Zhang, Yann Guitton, 2020, Nature Biotechnology.

Specialized Metabolites from Ribosome Engineered Strains of Streptomyces clavuligerus

P. Dorrestein, L. Nothias, K. Tahlan, 2021, Metabolites.

Distinguishing the molecular diversity, nutrient content, and energetic potential of exometabolomes produced by macroalgae and reef-building corals

Craig E. Nelson, P. Dorrestein, C. Carlson, 2022, Proceedings of the National Academy of Sciences.

INVENTA: a workflow for discovering chemical novelty in natural products extracts libraries

L. Nothias, J. Wolfender, L. Quirós-Guerrero, 2022, GA – 70th Annual Meeting 2022.

Correction to 'Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations'.

S. Böcker, P. Dorrestein, Kai Dührkop, 2023, Environmental microbiology.

Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations.

S. Böcker, P. Dorrestein, Kai Dührkop, 2022, Environmental microbiology.

DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data

Kelsey L. Alexander, G. Cottrell, P. Dorrestein, 2023, Journal of Cheminformatics.