Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships

(2021) Florian Huber et al.   PLoS Computational Biology

New software tools, databases, and resources in metabolomics: updates from 2020

(2021) Biswapriya B. Misra   Metabolomics

Quo Vadis Caenorhabditis elegans Metabolomics—A Review of Current Methods and Applications to Explore Metabolism in the Nematode

(2021) Liesa Salzer et al.   Metabolites

ISFrag: De Novo Recognition of In-Source Fragments for Liquid Chromatography–Mass Spectrometry Data

(2021) Jian Guo et al.   ANALYTICAL CHEMISTRY

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

(2021) Robin Schmid et al.   Nature Communications

Gut microbiome variation modulates the effects of dietary fiber on host metabolism

(2021) Sofia M. Murga-Garrido et al.   Microbiome

Investigating Global Lipidome Alterations with the Lipid Network Explorer

(2021) Nikolai Köhler et al.   Metabolites

Using nontargeted LC-MS metabolomics to identify the Association of Biomarkers in pig feces with feed efficiency

(2021) Jie Wu et al.   Porcine Health Management

Network based strategies in metabolomics data analysis and interpretation: from molecular networking to biological interpretation

(2020) Leonardo Perez de Souza et al.   Expert Review of Proteomics

An atlas of human metabolism

(2020) Jonathan L. Robinson et al.   Science Signaling

Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model

(2020) Michael Witting   Metabolites

Retrieving and Utilizing Hypothetical Neutral Losses from Tandem Mass Spectra for Spectral Similarity Analysis and Unknown Metabolite Annotation

(2020) Shipei Xing et al.   ANALYTICAL CHEMISTRY

Feature-based molecular networking in the GNPS analysis environment

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

A strategy to incorporate prior knowledge into correlation network cutoff selection

(2020) Elisa Benedetti et al.   Nature Communications

Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer

(2020) Pamela Vernocchi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2020) Kai Dührkop et al.   NATURE BIOTECHNOLOGY

CliqueMS: A computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network

(2019) Oriol Senan et al.   BIOINFORMATICS

Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics

(2019) Xiaotao Shen et al.   Nature Communications

Improving MetFrag with statistical learning of fragment annotations

(2019) Christoph Ruttkies et al.   BMC BIOINFORMATICS

NMR Spectroscopy for Metabolomics Research

(2019) Abdul-Hamid Emwas et al.   Metabolites

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

(2019) Madeleine Ernst et al.   Metabolites

MetaboRank: network-based recommendation system to interpret and enrich metabolomics results

(2018) Clément Frainay et al.   BIOINFORMATICS

Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries

(2018) Shu Pan et al.   CURRENT OPINION IN BIOTECHNOLOGY

Targeted versus untargeted omics — the CAFSA story

(2018) Maria del Mar Amador et al.   JOURNAL OF INHERITED METABOLIC DISEASE

From correlation to causation: analysis of metabolomics data using systems biology approaches

(2018) Antonio Rosato et al.   Metabolomics

MetExplore: collaborative edition and exploration of metabolic networks

(2018) Ludovic Cottret et al.   NUCLEIC ACIDS RESEARCH

MetGem Software for the Generation of Molecular Networks Based on the t-SNE Algorithm

(2018) Florent Olivon et al.   ANALYTICAL CHEMISTRY

MetNet: Metabolite Network Prediction from High-Resolution Mass Spectrometry Data in R Aiding Metabolite Annotation

(2018) Thomas Naake et al.   ANALYTICAL CHEMISTRY

A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links

(2018) Helle Krogh Pedersen et al.   Nature Protocols

Metabolomics applied to diabetes−lessons from human population studies

(2017) Sonia Liggi et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Automated pathway and reaction prediction facilitates in silico identification of unknown metabolites in human cohort studies

(2017) Jan D. Quell et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

MetaNetter 2: A Cytoscape plugin for ab initio network analysis and metabolite feature classification

(2017) K.E.V. Burgess et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Similarity of High-Resolution Tandem Mass Spectrometry Spectra of Structurally Related Micropollutants and Transformation Products

(2017) Jennifer E. Schollée et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Navigating freely-available software tools for metabolomics analysis

(2017) Rachel Spicer et al.   Metabolomics

Characterization of poplar metabotypes via mass difference enrichment analysis

(2017) Franco Moritz et al.   PLANT CELL AND ENVIRONMENT

Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data

(2017) Martin Loos et al.   Journal of Cheminformatics

Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets

(2017) Dinesh Kumar Barupal et al.   Scientific Reports

Computational methods to identify metabolic sub-networks based on metabolomic profiles

(2016) Clément Frainay et al.   BRIEFINGS IN BIOINFORMATICS

Untargeted Metabolomics Strategies—Challenges and Emerging Directions

(2016) Alexandra C. Schrimpe-Rutledge et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

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

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

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

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

(2016) Noushin Hadadi et al.   ACS Synthetic Biology

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Updates in metabolomics tools and resources: 2014-2015

(2015) Biswapriya B. Misra et al.   ELECTROPHORESIS

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

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

(2015) James G Jeffryes et al.   Journal of Cheminformatics

Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?

(2015) Dávid Bajusz et al.   Journal of Cheminformatics

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics

(2014) Ricardo R. Silva et al.   BIOINFORMATICS

Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence

(2014) Emma L. Schymanski et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Identification of gene-networks associated with specific lipid metabolites by Weighted Gene Co-Expression Network Analysis (WGCNA)

(2014) MA Osterhoff et al.   EXPERIMENTAL AND CLINICAL ENDOCRINOLOGY & DIABETES

Systematic Structural Characterization of Metabolites inArabidopsisvia Candidate Substrate-Product Pair Networks

(2014) Kris Morreel et al.   PLANT CELL

mzGroupAnalyzer-Predicting Pathways and Novel Chemical Structures from Untargeted High-Throughput Metabolomics Data

(2014) Hannes Doerfler et al.   PLoS One

Network-level architecture and the evolutionary potential of underground metabolism

(2014) R. A. Notebaart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A systematic comparison of the MetaCyc and KEGG pathway databases

(2013) Tomer Altman et al.   BMC BIOINFORMATICS

Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery

(2013) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

Computational annotation of plant metabolomics profiles via a novel network-assisted approach

(2013) Emmanuel Gaquerel et al.   Metabolomics

Equal Opportunity for Low-Degree Network Nodes: A PageRank-Based Method for Protein Target Identification in Metabolic Graphs

(2013) Dániel Bánky et al.   PLoS One

Identifying the Unknowns by Aligning Fragmentation Trees

(2012) Florian Rasche et al.   ANALYTICAL CHEMISTRY

Improving the description of metabolic networks: the TCA cycle as example

(2012) Miranda D. Stobbe et al.   FASEB JOURNAL

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

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

(2011) Jan Krumsiek et al.   BMC Systems Biology

Kendrick-Analogous Network Visualisation of Ion Cyclotron Resonance Fourier Transform Mass Spectra: Improved Options for the Assignment of Elemental Compositions and the Classification of Organic Molecular Complexity

(2011) D. Tziotis et al.   EUROPEAN JOURNAL OF MASS SPECTROMETRY

Randomizing Genome-Scale Metabolic Networks

(2011) Areejit Samal et al.   PLoS One

Weighted Correlation Network Analysis (WGCNA) Applied to the Tomato Fruit Metabolome

(2011) Matthew V. DiLeo et al.   PLoS One

Pathway discovery in metabolic networks by subgraph extraction

(2010) Karoline Faust et al.   BIOINFORMATICS

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Graph methods for the investigation of metabolic networks in parasitology

(2010) LUDOVIC COTTRET et al.   PARASITOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

An Introduction to Metabolic Networks and Their Structural Analysis

(2008) V. Lacroix et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics