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CHEMICAL RESEARCH IN TOXICOLOGY (2016)
Omics data input for metabolic modeling
Amit Rai et al.
CURRENT OPINION IN BIOTECHNOLOGY (2016)
Natural Products as Sources of New Drugs from 1981 to 2014
David J. Newman et al.
JOURNAL OF NATURAL PRODUCTS (2016)
Green pathways: Metabolic network analysis of plant systems
Lisa Maria Dersch et al.
METABOLIC ENGINEERING (2016)
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
Mingxun Wang et al.
NATURE BIOTECHNOLOGY (2016)
OpenMS: a flexible open-source software platform for mass spectrometry data analysis
Hannes L. Roest et al.
NATURE METHODS (2016)
Metabolomics: beyond biomarkers and towards mechanisms
Caroline H. Johnson et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2016)
Topic modeling for untargeted substructure exploration in metabolomics
Justin Johan Jozias van der Hooft et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Cell-specific localization of alkaloids in Catharanthus roseus stem tissue measured with Imaging MS and Single-cell MS
Kotaro Yamamoto et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes
Ruiqi Huang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
Patrik L. Stahl et al.
SCIENCE (2016)
Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers
Katsuyuki Yugi et al.
TRENDS IN BIOTECHNOLOGY (2016)
Characterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae
Takayuki Tohge et al.
NATURE COMMUNICATIONS (2016)
The pangenome of an agronomically important crop plant Brassica oleracea
Agnieszka A. Golicz et al.
NATURE COMMUNICATIONS (2016)
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy
Yannick Djoumbou Feunang et al.
JOURNAL OF CHEMINFORMATICS (2016)
MetFrag relaunched: incorporating strategies beyond in silico fragmentation
Christoph Ruttkies et al.
JOURNAL OF CHEMINFORMATICS (2016)
Fragmentation trees reloaded
Sebastian Boecker et al.
JOURNAL OF CHEMINFORMATICS (2016)
Construction of an Ultrahigh Pressure Liquid Chromatography-Tandem Mass Spectral Library of Plant Natural Products and Comparative Spectral Analyses
Zhentian Lei et al.
ANALYTICAL CHEMISTRY (2015)
Metabolite-based genome-wide association studies in plants
Jie Luo
CURRENT OPINION IN PLANT BIOLOGY (2015)
Top-down Targeted Metabolomics Reveals a Sulfur-Containing Metabolite with Inhibitory Activity against Angiotensin-Converting Enzyme in Asparagus officinalis
Ryo Nakabayashi et al.
JOURNAL OF NATURAL PRODUCTS (2015)
Using Metabolomic Approaches to Explore Chemical Diversity in Rice
Miyako Kusano et al.
MOLECULAR PLANT (2015)
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Babak Alipanahi et al.
NATURE BIOTECHNOLOGY (2015)
Predicting effects of noncoding variants with deep learning-based sequence model
Jian Zhou et al.
NATURE METHODS (2015)
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis
Hiroshi Tsugawa et al.
NATURE METHODS (2015)
Direct metabolomics for plant cells by live single-cell mass spectrometry
Takashi Fujii et al.
NATURE PROTOCOLS (2015)
Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato
Saleh Alseekh et al.
PLANT CELL (2015)
Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana
Renee C. Strauch et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Searching molecular structure databases with tandem mass spectra using CSI:FingerID
Kai Duehrkop et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Illuminating the dark matter in metabolomics
Ricardo R. da Silva et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
InChI, the IUPAC International Chemical Identifier
Stephen R. Heller et al.
JOURNAL OF CHEMINFORMATICS (2015)
T3DB: the toxic exposome database
David Wishart et al.
NUCLEIC ACIDS RESEARCH (2015)
Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean
Humira Sonah et al.
PLANT BIOTECHNOLOGY JOURNAL (2015)
Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism
Fumio Matsuda et al.
PLANT JOURNAL (2015)
Current state of the art of mass spectrometry-based metabolomics studies - a review focusing on wide coverage, high throughput and easy identification
Yang Wang et al.
RSC ADVANCES (2015)
X13CMS: Global Tracking of Isotopic Labels in Untargeted Metabolomics
Xiaojing Huang et al.
ANALYTICAL CHEMISTRY (2014)
Natural Variations and Genome-Wide Association Studies in Crop Plants
Xuehui Huang et al.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 65 (2014)
Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence
Emma L. Schymanski et al.
ENVIRONMENTAL SCIENCE & TECHNOLOGY (2014)
Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism
Wei Chen et al.
NATURE GENETICS (2014)
Toward better annotation in plant metabolomics: isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses
Zhigang Yang et al.
METABOLOMICS (2014)
CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra
Felicity Allen et al.
NUCLEIC ACIDS RESEARCH (2014)
Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks
Kris Morreel et al.
PLANT CELL (2014)
Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits
Christopher Sauvage et al.
PLANT PHYSIOLOGY (2014)
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
Samuel M. D. Seaver et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Combination of Liquid Chromatography Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry with 13C-Labeling for Chemical Assignment of Sulfur-Containing Metabolites in Onion Bulbs
Ryo Nakabayashi et al.
ANALYTICAL CHEMISTRY (2013)
ECMDB: The E-coli Metabolome Database
An Chi Guo et al.
NUCLEIC ACIDS RESEARCH (2013)
The High Polyphenol Content of Grapevine Cultivar Tannat Berries Is Conferred Primarily by Genes That Are Not Shared with the Reference Genome
Cecilia Da Silva et al.
PLANT CELL (2013)
Use of Natural Products as Chemical Library for Drug Discovery and Network Pharmacology
Jiangyong Gu et al.
PLOS ONE (2013)
Genetic analysis of the metabolome exemplified using a rice population
Liang Gong et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Computational mass spectrometry for small molecules
Kerstin Scheubert et al.
JOURNAL OF CHEMINFORMATICS (2013)
XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data
Ralf Tautenhahn et al.
ANALYTICAL CHEMISTRY (2012)
Structural Annotation and Elucidation of Conjugated Phenolic Compounds in Black, Green, and White Tea Extracts
Justin J. J. van der Hooft et al.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2012)
imzML - A common data format for the flexible exchange and processing of mass spectrometry imaging data
Thorsten Schramm et al.
JOURNAL OF PROTEOMICS (2012)
YMDB: the Yeast Metabolome Database
Timothy Jewison et al.
NUCLEIC ACIDS RESEARCH (2012)
RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database
Yuji Sawada et al.
PHYTOCHEMISTRY (2012)
KNApSAcK Family Databases: Integrated Metabolite-Plant Species Databases for Multifaceted Plant Research
Farit Mochamad Afendi et al.
PLANT AND CELL PHYSIOLOGY (2012)
Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis
Fumio Matsuda et al.
PLANT JOURNAL (2012)
Natural Variation in Arabidopsis: From Molecular Genetics to Ecological Genomics
Detlef Weigel
PLANT PHYSIOLOGY (2012)
Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality
Natalia Carreno-Quintero et al.
PLANT PHYSIOLOGY (2012)
Identification of a BAHD acetyltransferase that produces protective acyl sugars in tomato trichomes
Anthony L. Schilmiller et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Polyphenol Identification Based on Systematic and Robust High-Resolution Accurate Mass Spectrometry Fragmentation
Justin J. J. van der Hooft et al.
ANALYTICAL CHEMISTRY (2011)
Convergent Evolution in Plant Specialized Metabolism
Eran Pichersky et al.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 62 (2011)
Structural and Functional Evolution of Isopropylmalate Dehydrogenases in the Leucine and Glucosinolate Pathways of Arabidopsis thaliana
Yan He et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2011)
In silico fragmentation for computer assisted identification of metabolite mass spectra
Sebastian Wolf et al.
BMC BIOINFORMATICS (2010)
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
Tomas Pluskal et al.
BMC BIOINFORMATICS (2010)
MassBank: a public repository for sharing mass spectral data for life sciences
Hisayuki Horai et al.
JOURNAL OF MASS SPECTROMETRY (2010)
SMPDB: The Small Molecule Pathway Database
Alex Frolkis et al.
NUCLEIC ACIDS RESEARCH (2010)
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data
Jianguo Xia et al.
NUCLEIC ACIDS RESEARCH (2010)
Mass spectrometry screening reveals widespread diversity in trichome specialized metabolites of tomato chromosomal substitution lines
Anthony Schilmiller et al.
PLANT JOURNAL (2010)
C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism
Cristiana Gomes de Oliveira Dal'Molin et al.
PLANT PHYSIOLOGY (2010)
Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants
Peifen Zhang et al.
PLANT PHYSIOLOGY (2010)
Chromosome Segment Substitution Lines: A Powerful Tool for the Introgression of Valuable Genes from Oryza Wild Species into Cultivated Rice (O. sativa)
M. Liakat Ali et al.
RICE (2010)
Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature
Benjamin Brachi et al.
PLOS GENETICS (2010)
Update of the LIPID MAPS comprehensive classification system for lipids
Eoin Fahy et al.
JOURNAL OF LIPID RESEARCH (2009)
Metabolomics-oriented isolation and structure elucidation of 37 compounds including two anthocyanins from Arabidopsis thaliana
Ryo Nakabayashi et al.
PHYTOCHEMISTRY (2009)
Ozone-induced dissociation: Elucidation of double bond position within mass-selected lipid ions
Michael C. Thomas et al.
ANALYTICAL CHEMISTRY (2008)
Chemical substructures that enrich for biological activity
Justin Klekota et al.
BIOINFORMATICS (2008)
A Spectral Clustering Approach to MS/MS Identification of Post-Translational Modifications
Jayson A. Falkner et al.
JOURNAL OF PROTEOME RESEARCH (2008)
Using support vector machine combined with auto covariance to predict proteinprotein interactions from protein sequences
Yanzhi Guo et al.
NUCLEIC ACIDS RESEARCH (2008)
Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis
Keiko Yonekura-Sakakibara et al.
PLANT CELL (2008)
Proposed minimum reporting standards for chemical analysis
Lloyd W. Sumner et al.
METABOLOMICS (2007)
XCMS: Processing mass spectrometry data for metabolite profiling using Nonlinear peak alignment, matching, and identification
CA Smith et al.
ANALYTICAL CHEMISTRY (2006)
The evolutionary dynamics of plant duplicate genes
RC Moore et al.
CURRENT OPINION IN PLANT BIOLOGY (2005)
Predicting protein-protein interactions using signature products
S Martin et al.
BIOINFORMATICS (2005)
Reoptimization of MDL keys for use in drug discovery
JL Durant et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2002)