hcapca: Automated Hierarchical Clustering and Principal Component Analysis of Large Metabolomic Datasets in R

Mass spectrometry searches using MASST

(2020) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Plant Endophytes and Epiphytes: Burgeoning Sources of Known and “Unknown” Cytotoxic and Antibiotic Agents?

(2020) David J. Newman et al.   PLANTA MEDICA

Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019

(2020) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

(2019) Chase M. Clark et al.   Jove-Journal of Visualized Experiments

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

(2018) Jasmine Chong et al.   NUCLEIC ACIDS RESEARCH

Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function

(2018) Chase M. Clark et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clustering of MS 2 spectra using unsupervised methods to aid the identification of secondary metabolites from Pseudomonas aeruginosa

(2017) Tobias Depke et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Bi- and Tetracyclic Spirotetronates from the Coal Mine Fire Isolate Streptomyces sp. LC-6-2

(2017) Xiachang Wang et al.   JOURNAL OF NATURAL PRODUCTS

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites

(2017) Brett C. Covington et al.   NATURAL PRODUCT REPORTS

Points of Significance: Clustering

(2017) Naomi Altman et al.   NATURE METHODS

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics

(2017) Zijuan Lai et al.   NATURE METHODS

Points of Significance: Principal component analysis

(2017) Jake Lever et al.   NATURE METHODS

Linear Peptides Are the Major Products of a Biosynthetic Pathway That Encodes for Cyclic Depsipeptides

(2017) Thomas P. Wyche et al.   ORGANIC LETTERS

Macrotermycins A–D, Glycosylated Macrolactams from a Termite-Associated Amycolatopsis sp. M39

(2017) Christine Beemelmanns et al.   ORGANIC LETTERS

Brackish habitat dictates cultivable Actinobacterial diversity from marine sponges

(2017) Gregory A. Ellis et al.   PLoS One

Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach

(2017) Luz A. Betancur et al.   PLoS One

Spoxazomicin D and Oxachelin C, Potent Neuroprotective Carboxamides from the Appalachian Coal Fire-Associated Isolate Streptomyces sp. RM-14-6

(2016) Khaled A. Shaaban et al.   JOURNAL OF NATURAL PRODUCTS

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

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

Selvamicin, an atypical antifungal polyene from two alternative genomic contexts

(2016) Ethan B. Van Arnam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topic modeling for untargeted substructure exploration in metabolomics

(2016) Justin Johan Jozias van der Hooft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

Mapping Microbial Response Metabolomes for Induced Natural Product Discovery

(2015) Dagmara K. Derewacz et al.   ACS Chemical Biology

Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification

(2015) Qi Yang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A New Golden Age of Natural Products Drug Discovery

(2015) Ben Shen   CELL

Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps

(2015) Cody R. Goodwin et al.   CHEMISTRY & BIOLOGY

Metabolomics as a tool in nutritional research

(2015) Helena Gibbons et al.   CURRENT OPINION IN LIPIDOLOGY

Nocarimidazoles A and B from a Marine-Derived Actinomycete of the Genus Nocardiopsis

(2015) Alain S. Leutou et al.   JOURNAL OF NATURAL PRODUCTS

The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery

(2015) Paul R. Jensen et al.   NATURAL PRODUCT REPORTS

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

The re-emergence of natural products for drug discovery in the genomics era

(2015) Alan L. Harvey et al.   NATURE REVIEWS DRUG DISCOVERY

Actinobenzoquinoline and Actinophenanthrolines A–C, Unprecedented Alkaloids from a Marine Actinobacterium

(2015) Sang-Jip Nam et al.   ORGANIC LETTERS

Endophytic and epiphytic microbes as “sources” of bioactive agents

(2015) David J. Newman et al.   Frontiers in Chemistry

Phenotypic Mapping of Metabolic Profiles Using Self-Organizing Maps of High-Dimensional Mass Spectrometry Data

(2014) Cody R. Goodwin et al.   ANALYTICAL CHEMISTRY

RAMClust: A Novel Feature Clustering Method Enables Spectral-Matching-Based Annotation for Metabolomics Data

(2014) C. D. Broeckling et al.   ANALYTICAL CHEMISTRY

Forazoline A: Marine-Derived Polyketide with Antifungal In Vivo Efficacy

(2014) Thomas P. Wyche et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structure and Stereochemical Determination of Hypogeamicins from a Cave-Derived Actinomycete

(2014) Dagmara K. Derewacz et al.   JOURNAL OF NATURAL PRODUCTS

Actinomycetes from Red Sea Sponges: Sources for Chemical and Phylogenetic Diversity

(2014) Usama Abdelmohsen et al.   Marine Drugs

Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts

(2014) Lynsey Macintyre et al.   Marine Drugs

Diversity, abundance and natural products of marine sponge-associated actinomycetes

(2014) Usama Ramadan Abdelmohsen et al.   NATURAL PRODUCT REPORTS

A roadmap for natural product discovery based on large-scale genomics and metabolomics

(2014) James R Doroghazi et al.   Nature Chemical Biology

Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora

(2014) N. Ziemert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chemical dereplication of marine actinomycetes by liquid chromatography–high resolution mass spectrometry profiling and statistical analysis

(2013) David Forner et al.   ANALYTICA CHIMICA ACTA

An Emerging Role for Metabolomics in Nutrition Science

(2013) Giuseppe Astarita et al.   Journal of Nutrigenetics and Nutrigenomics

Microbial Strain Prioritization Using Metabolomics Tools for the Discovery of Natural Products

(2012) Yanpeng Hou et al.   ANALYTICAL CHEMISTRY

Isolation of Lomaiviticins C–E, Transformation of Lomaiviticin C to Lomaiviticin A, Complete Structure Elucidation of Lomaiviticin A, and Structure–Activity Analyses

(2012) Christina M. Woo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Microtermolides A and B from Termite-Associated Streptomyces sp. and Structural Revision of Vinylamycin

(2012) Gavin Carr et al.   ORGANIC LETTERS

Structure and Biosynthesis of the Antibiotic Bottromycin D

(2012) Yanpeng Hou et al.   ORGANIC LETTERS

Host-Gut Microbiota Metabolic Interactions

(2012) J. K. Nicholson et al.   SCIENCE

Geographic Distribution of Secondary Metabolite Genes in the Marine Actinomycete Salinispora arenicola

(2011) Anna Edlund et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolomics: from small molecules to big ideas

(2011) Monya Baker   NATURE METHODS

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

Application of Fuzzy c-Means Clustering in Data Analysis of Metabolomics

(2009) Xiang Li et al.   ANALYTICAL CHEMISTRY

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

(2009) W. R. Wikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps

(2008) Peter Meinicke et al.   Algorithms for Molecular Biology

Efficient mining of myxobacterial metabolite profiles enabled by liquid chromatography–electrospray ionisation-time-of-flight mass spectrometry and compound-based principal component analysis

(2008) Daniel Krug et al.   ANALYTICA CHIMICA ACTA

Discovering the Hidden Secondary Metabolome of Myxococcus xanthus: a Study of Intraspecific Diversity

(2008) D. Krug et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

What is principal component analysis?

(2008) Markus Ringnér   NATURE BIOTECHNOLOGY

Principal component analysis of genetic data

(2008) David Reich et al.   NATURE GENETICS

Clustering Millions of Tandem Mass Spectra

(2007) Ari M. Frank et al.   JOURNAL OF PROTEOME RESEARCH