Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

Hierarchical clustering of MS/MS spectra from the firefly metabolome identifies new lucibufagin compounds

(2020) Catherine Rawlinson et al.   Scientific Reports

Feature-based molecular networking in the GNPS analysis environment

(2020) Louis-Félix Nothias et al.   NATURE METHODS

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

(2019) Kai Dührkop et al.   NATURE METHODS

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Untargeted Mass Spectrometry-Based Metabolomics Approach Unveils Molecular Changes in Raw and Processed Foods and Beverages

(2019) Julia M. Gauglitz et al.   FOOD CHEMISTRY

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Learning representations of microbe–metabolite interactions

(2019) James T. Morton et al.   NATURE METHODS

ChemDistiller: an engine for metabolite annotation in mass spectrometry

(2018) Ivan Laponogov et al.   BIOINFORMATICS

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

(2018) Stefan Janssen et al.   mSystems

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Assembling the Community-Scale Discoverable Human Proteome

(2018) Mingxun Wang et al.   Cell Systems

Striped UniFrac: enabling microbiome analysis at unprecedented scale

(2018) Daniel McDonald et al.   NATURE METHODS

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

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Critical Assessment of Small Molecule Identification 2016: automated methods

(2017) Emma L. Schymanski et al.   Journal of Cheminformatics

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

(2017) Alex D. Washburne et al.   PeerJ

Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies

(2016) Hendrik Treutler et al.   ANALYTICAL CHEMISTRY

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

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

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

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

(2016) Yannick Djoumbou Feunang et al.   Journal of Cheminformatics

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

(2015) Kai Dührkop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolite Profiling of a NIST Standard Reference Material for Human Plasma (SRM 1950): GC-MS, LC-MS, NMR, and Clinical Laboratory Analyses, Libraries, and Web-Based Resources

(2013) Yamil Simón-Manso et al.   ANALYTICAL CHEMISTRY

Identifying the Unknowns by Aligning Fragmentation Trees

(2012) Florian Rasche et al.   ANALYTICAL CHEMISTRY

Metabolite identification and molecular fingerprint prediction through machine learning

(2012) M. Heinonen et al.   BIOINFORMATICS

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Mass spectral molecular networking of living microbial colonies

(2012) J. Watrous et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

(2010) Justin Kuczynski et al.   NATURE METHODS