Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function

13C Isotope-Labeled Metabolomes Allowing for Improved Compound Annotation and Relative Quantification in Liquid Chromatography-Mass Spectrometry-based Metabolomic Research

(2009) Patrick Giavalisco et al.   ANALYTICAL CHEMISTRY

Molecular Identification and Functional Characterization ofArabidopsis thalianaMitochondrial and Chloroplastic NAD+Carrier Proteins

(2009) Ferdinando Palmieri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic responses to salt stress of barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differ in salinity tolerance

(2009) Widodo et al.   JOURNAL OF EXPERIMENTAL BOTANY

A database for poplar gene co-expression analysis for systematic understanding of biological processes, including stress responses

(2009) Yoshiyuki Ogata et al.   JOURNAL OF WOOD SCIENCE

Metabolomic Screening Applied to Rice FOX Arabidopsis Lines Leads to the Identification of a Gene-Changing Nitrogen Metabolism

(2009) Doris Albinsky et al.   Molecular Plant

A Metabolic Signature of the Beneficial Interaction of the EndophytePaenibacillussp. Isolate and In Vitro–Grown Poplar Plants Revealed by Metabolomics

(2009) Christian Scherling et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Functional genomics for plant natural product biosynthesis

(2009) Keiko Yonekura-Sakakibara et al.   NATURAL PRODUCT REPORTS

Network visualization and analysis of gene expression data using BioLayout Express3D

(2009) Athanasios Theocharidis et al.   Nature Protocols

HAG2/MYB76 and HAG3/MYB29 exert a specific and coordinated control on the regulation of aliphatic glucosinolate biosynthesis inArabidopsis thaliana

(2009) Tamara Gigolashvili et al.   NEW PHYTOLOGIST

Metabolomics-oriented isolation and structure elucidation of 37 compounds including two anthocyanins from Arabidopsis thaliana

(2009) Ryo Nakabayashi et al.   PHYTOCHEMISTRY

Web-based resources for mass-spectrometry-based metabolomics: A user’s guide

(2009) Takayuki Tohge et al.   PHYTOCHEMISTRY

Drought stress increases the production of 5-hydroxynorvaline in two C4 grasses

(2009) Ana E. Carmo-Silva et al.   PHYTOCHEMISTRY

Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology

(2009) S. M. Brady et al.   PLANT CELL

MYB58 and MYB63 Are Transcriptional Activators of the Lignin Biosynthetic Pathway during Secondary Cell Wall Formation in Arabidopsis

(2009) J. Zhou et al.   PLANT CELL

A Chloroplastic UDP-Glucose Pyrophosphorylase from Arabidopsis Is the Committed Enzyme for the First Step of Sulfolipid Biosynthesis

(2009) Y. Okazaki et al.   PLANT CELL

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

A plant thiolase involved in benzoic acid biosynthesis and volatile benzenoid production

(2009) Alex Van Moerkercke et al.   PLANT JOURNAL

The LAP1 MYB transcription factor orchestrates anthocyanidin biosynthesis and glycosylation inMedicago

(2009) Gregory J. Peel et al.   PLANT JOURNAL

Identification of heterotic metabolite QTL inArabidopsis thalianaRIL and IL populations

(2009) Jan Lisec et al.   PLANT JOURNAL

Application of GC-MS for the detection of lipophilic compounds in diverse plant tissues

(2009) Anna Lytovchenko et al.   Plant Methods

RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice

(2009) T.-H. Lee et al.   PLANT PHYSIOLOGY

Plastidial Glyceraldehyde-3-Phosphate Dehydrogenase Deficiency Leads to Altered Root Development and Affects the Sugar and Amino Acid Balance in Arabidopsis

(2009) J. Munoz-Bertomeu et al.   PLANT PHYSIOLOGY

Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development

(2009) F. Mounet et al.   PLANT PHYSIOLOGY

The Grapevine R2R3-MYB Transcription Factor VvMYBF1 Regulates Flavonol Synthesis in Developing Grape Berries

(2009) S. Czemmel et al.   PLANT PHYSIOLOGY

Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination

(2009) A. Fukushima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

XCMS2: Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization

(2008) H. P. Benton et al.   ANALYTICAL CHEMISTRY

High-Resolution Direct Infusion-Based Mass Spectrometry in Combination with Whole13C Metabolome Isotope Labeling Allows Unambiguous Assignment of Chemical Sum Formulas

(2008) Patrick Giavalisco et al.   ANALYTICAL CHEMISTRY

TagFinder for the quantitative analysis of gas chromatography—mass spectrometry (GC-MS)-based metabolite profiling experiments

(2008) Alexander Luedemann et al.   BIOINFORMATICS

VitisExpDB: A database resource for grape functional genomics

(2008) Harshavardhan Doddapaneni et al.   BMC PLANT BIOLOGY

Differential gene expression profiles of red and green forms of Perilla frutescens leading to comprehensive identification of anthocyanin biosynthetic genes

(2008) Mami Yamazaki et al.   FEBS Journal

Plant breeders go back to nature

(2008) Dani Zamir   NATURE GENETICS

1H NMR metabolite fingerprinting and metabolomic analysis of perchloric acid extracts from plant tissues

(2008) Nicholas J Kruger et al.   Nature Protocols

Explanatory signal interpretation and metabolite identification strategies for nominal mass FIE-MS metabolite fingerprints

(2008) David P Overy et al.   Nature Protocols

GeneCAT—novel webtools that combine BLAST and co-expression analyses

(2008) Marek Mutwil et al.   NUCLEIC ACIDS RESEARCH

ATTED-II provides coexpressed gene networks for Arabidopsis

(2008) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH

Screening for Wound-induced Oxylipins inArabidopsis thaliana by Differential HPLC-APCI/MS Profiling of Crude Leaf Extracts and Subsequent Characterisation by Capillary-scale NMR

(2008) Aly Thiocone et al.   PHYTOCHEMICAL ANALYSIS

KAGIANA: An Excel-Based Tool for Retrieving Summary Information on Arabidopsis Genes

(2008) Y. Ogata et al.   PLANT AND CELL PHYSIOLOGY

Biochemical Networks and Epistasis Shape the Arabidopsis thaliana Metabolome

(2008) H. C. Rowe et al.   PLANT CELL

Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene-Metabolite Correlations in Arabidopsis

(2008) K. Yonekura-Sakakibara et al.   PLANT CELL

Mode of Inheritance of Primary Metabolic Traits in Tomato

(2008) N. Schauer et al.   PLANT CELL

Adjustment of growth and central metabolism to a mild but sustained nitrogen-limitation inArabidopsis

(2008) HENDRIK TSCHOEP et al.   PLANT CELL AND ENVIRONMENT

Metabolite annotations based on the integration of mass spectral information

(2008) Yoko Iijima et al.   PLANT JOURNAL

Quality control for plant metabolomics: reporting MSI-compliant studies

(2008) Oliver Fiehn et al.   PLANT JOURNAL

MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites

(2008) Fumio Matsuda et al.   PLANT JOURNAL

Metabolome Analysis of Biosynthetic Mutants Reveals a Diversity of Metabolic Changes and Allows Identification of a Large Number of New Compounds in Arabidopsis

(2008) C. Bottcher et al.   PLANT PHYSIOLOGY

Identification and Characterization of ADNT1, a Novel Mitochondrial Adenine Nucleotide Transporter from Arabidopsis

(2008) L. Palmieri et al.   PLANT PHYSIOLOGY

CressExpress: A Tool For Large-Scale Mining of Expression Data from Arabidopsis

(2008) V. Srinivasasainagendra et al.   PLANT PHYSIOLOGY

Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy

(2008) Ki-Hong Jung et al.   PLoS One

Metabolomics-assisted breeding: a viable option for crop improvement?

(2008) Alisdair R. Fernie et al.   TRENDS IN GENETICS

Getting to grips with the plant metabolic network

(2007) Lee J. Sweetlove et al.   BIOCHEMICAL JOURNAL

Decoding genes with coexpression networks and metabolomics – ‘majority report by precogs’

(2007) Kazuki Saito et al.   TRENDS IN PLANT SCIENCE