Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling

Recent advances in the reconstruction of metabolic models and integration of omics data

(2014) Rajib Saha et al.   CURRENT OPINION IN BIOTECHNOLOGY

Our nitrogen ‘footprint’: the need for increased crop nitrogen use efficiency

(2013) M. Andrews et al.   ANNALS OF APPLIED BIOLOGY

Do plants need nitrate? The mechanisms by which nitrogen form affects plants

(2013) M. Andrews et al.   ANNALS OF APPLIED BIOLOGY

Nitrogen losses from the soil/plant system: a review

(2013) K.C. Cameron et al.   ANNALS OF APPLIED BIOLOGY

Genome-wide expression profiling of maize in response to individual and combined water and nitrogen stresses

(2013) Sabrina Humbert et al.   BMC GENOMICS

Adaptation of maize source leaf metabolism to stress related disturbances in carbon, nitrogen and phosphorus balance

(2013) Urte Schlüter et al.   BMC GENOMICS

Current challenges and future potential of tomato breeding using omics approaches

(2013) Miyako Kusano et al.   BREEDING SCIENCE

Metabolic network flux analysis for engineering plant systems

(2013) Yair Shachar-Hill   CURRENT OPINION IN BIOTECHNOLOGY

Patterns and trends in nitrogen use and nitrogen recovery efficiency in world agriculture

(2013) Richard T. Conant et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Metabolomics in plant environmental physiology

(2013) Cecilia Brunetti et al.   JOURNAL OF EXPERIMENTAL BOTANY

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Nitrogen deprivation promotesPopulusroot growth through global transcriptome reprogramming and activation of hierarchical genetic networks

(2013) Hairong Wei et al.   NEW PHYTOLOGIST

ppdb: plant promoter database version 3.0

(2013) Ayaka Hieno et al.   NUCLEIC ACIDS RESEARCH

PubChem BioAssay: 2014 update

(2013) Yanli Wang et al.   NUCLEIC ACIDS RESEARCH

The global nitrogen cycle in the twenty-first century

(2013) D. Fowler et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Biological nitrogen fixation: rates, patterns and ecological controls in terrestrial ecosystems

(2013) P. M. Vitousek et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A chronology of human understanding of the nitrogen cycle

(2013) J. N. Galloway et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Consequences of human modification of the global nitrogen cycle

(2013) J. W. Erisman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Parallel Proteomic and Phosphoproteomic Analyses of Successive Stages of Maize Leaf Development

(2013) M. R. Facette et al.   PLANT CELL

Integration of Genome-Scale Modeling and Transcript Profiling Reveals Metabolic Pathways Underlying Light and Temperature Acclimation in Arabidopsis

(2013) N. Topfer et al.   PLANT CELL

The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a complex response to changes in nitrogen supply

(2013) Shyam K. Masakapalli et al.   PLANT JOURNAL

A Developmental Transcriptional Network for Maize Defines Coexpression Modules

(2013) G. S. Downs et al.   PLANT PHYSIOLOGY

Multiscale Metabolic Modeling: Dynamic Flux Balance Analysis on a Whole-Plant Scale

(2013) E. Grafahrend-Belau et al.   PLANT PHYSIOLOGY

Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism

(2013) M. G. Poolman et al.   PLANT PHYSIOLOGY

Impact of the Carbon and Nitrogen Supply on Relationships and Connectivity between Metabolism and Biomass in a Broad Panel of Arabidopsis Accessions

(2013) R. Sulpice et al.   PLANT PHYSIOLOGY

Manipulation of microRNA expression to improve nitrogen use efficiency

(2013) Jeffrey J. Fischer et al.   PLANT SCIENCE

Characterization of Peanut Germin-Like Proteins, AhGLPs in Plant Development and Defense

(2013) Tong Wang et al.   PLoS One

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

(2013) Chloé Marchive et al.   Nature Communications

Plasticity Regulators Modulate Specific Root Traits in Discrete Nitrogen Environments

(2013) Miriam L. Gifford et al.   PLoS Genetics

Comparing global warming potential, energy use and land use of organic, conventional and integrated winter wheat production

(2012) H.L. Tuomisto et al.   ANNALS OF APPLIED BIOLOGY

Plant Nitrogen Assimilation and Use Efficiency

(2012) Guohua Xu et al.   Annual Review of Plant Biology

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

(2012) Akhil Kumar et al.   BMC BIOINFORMATICS

OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize

(2012) Christian Colmsee et al.   BMC PLANT BIOLOGY

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

The use of metabolomics to dissect plant responses to abiotic stresses

(2012) Toshihiro Obata et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Transcriptome data modeling for targeted plant metabolic engineering

(2012) Keiko Yonekura-Sakakibara et al.   CURRENT OPINION IN BIOTECHNOLOGY

Plant genome-scale metabolic reconstruction and modelling

(2012) Cristiana Gomes de Oliveira Dal’Molin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Mechanisms and dynamics in the thiol/disulfide redox regulatory network: transmitters, sensors and targets

(2012) Janine König et al.   CURRENT OPINION IN PLANT BIOLOGY

Sensing nutrient and energy status by SnRK1 and TOR kinases

(2012) Christophe Robaglia et al.   CURRENT OPINION IN PLANT BIOLOGY

Comparative Transcriptome Profiling in Winter Wheat Grown under Different Agricultural Practices

(2012) Gabriela N. Tenea et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Effects of Genetics and Environment on the Metabolome of Commercial Maize Hybrids: A Multisite Study

(2012) Vincent M. Asiago et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Transcriptome response to nitrogen starvation in rice

(2012) Hongmei Cai et al.   JOURNAL OF BIOSCIENCES

Pathways and fluxes: exploring the plant metabolic network

(2012) N. J. Kruger et al.   JOURNAL OF EXPERIMENTAL BOTANY

Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies

(2012) J. O'Grady et al.   JOURNAL OF EXPERIMENTAL BOTANY

Frontiers in metabolic reconstruction and modeling of plant genomes

(2012) S. M. D. Seaver et al.   JOURNAL OF EXPERIMENTAL BOTANY

The use of metabolomics integrated with transcriptomic and proteomic studies for identifying key steps involved in the control of nitrogen metabolism in crops such as maize

(2012) Nardjis Amiour et al.   JOURNAL OF EXPERIMENTAL BOTANY

A Comprehensive Differential Proteomic Study of Nitrate Deprivation in Arabidopsis Reveals Complex Regulatory Networks of Plant Nitrogen Responses

(2012) Xu Wang et al.   JOURNAL OF PROTEOME RESEARCH

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Genomic and metabolic prediction of complex heterotic traits in hybrid maize

(2012) Christian Riedelsheimer et al.   NATURE GENETICS

SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis

(2012) Sandra K. Tanz et al.   NUCLEIC ACIDS RESEARCH

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

(2012) Ida Schomburg et al.   NUCLEIC ACIDS RESEARCH

Engineering nitrogen use efficient crop plants: the current status

(2012) Chandra H. McAllister et al.   PLANT BIOTECHNOLOGY JOURNAL

Maize Source Leaf Adaptation to Nitrogen Deficiency Affects Not Only Nitrogen and Carbon Metabolism But Also Control of Phosphate Homeostasis

(2012) U. Schluter et al.   PLANT PHYSIOLOGY

On the Discordance of Metabolomics with Proteomics and Transcriptomics: Coping with Increasing Complexity in Logic, Chemistry, and Network Interactions Scientific Correspondence

(2012) A. R. Fernie et al.   PLANT PHYSIOLOGY

Cloning and Characterization of Maize miRNAs Involved in Responses to Nitrogen Deficiency

(2012) Meng Zhao et al.   PLoS One

Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize

(2012) C. Riedelsheimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maize proteomics: An insight into the biology of an important cereal crop

(2012) Olga Pechanova et al.   PROTEOMICS

Systems Biology for Enhanced Plant Nitrogen Nutrition

(2012) R. A. Gutierrez   SCIENCE

Network analysis: tackling complex data to study plant metabolism

(2012) David Toubiana et al.   TRENDS IN BIOTECHNOLOGY

Towards multiscale plant models: integrating cellular networks

(2012) Valentina Baldazzi et al.   TRENDS IN PLANT SCIENCE

A survey of metabolic databases emphasizing the MetaCyc family

(2011) Peter D. Karp et al.   ARCHIVES OF TOXICOLOGY

An in silico compartmentalized metabolic model of Brassica napus enables the systemic study of regulatory aspects of plant central metabolism

(2011) Eleftherios Pilalis et al.   BIOTECHNOLOGY AND BIOENGINEERING

Linked gene networks involved in nitrogen and carbon metabolism and levels of water-soluble carbohydrate accumulation in wheat stems

(2011) C. Lynne McIntyre et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Metabolomic approaches toward understanding nitrogen metabolism in plants

(2011) M. Kusano et al.   JOURNAL OF EXPERIMENTAL BOTANY

Natural variation of Arabidopsis response to nitrogen availability

(2011) Sobia Ikram et al.   JOURNAL OF EXPERIMENTAL BOTANY

Plant proteome changes under abiotic stress — Contribution of proteomics studies to understanding plant stress response

(2011) Klára Kosová et al.   Journal of Proteomics

Transcriptome analysis reveals coordinated spatiotemporal regulation of hemoglobin and nitrate reductase in response to nitrate in maize roots

(2011) S. Trevisan et al.   NEW PHYTOLOGIST

Sequencing crop genomes: approaches and applications

(2011) Scott A. Jackson et al.   NEW PHYTOLOGIST

MetaCrop 2.0: managing and exploring information about crop plant metabolism

(2011) F. Schreiber et al.   NUCLEIC ACIDS RESEARCH

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Introduction of the ZmDof1 gene into rice enhances carbon and nitrogen assimilation under low-nitrogen conditions

(2011) Tomohiro Kurai et al.   PLANT BIOTECHNOLOGY JOURNAL

Responses of barley root and shoot proteomes to long-term nitrogen deficiency, short-term nitrogen starvation and ammonium

(2011) ANDERS L. B. MØLLER et al.   PLANT CELL AND ENVIRONMENT

Expression and tissue-specific localization of nitrate-responsive miRNAs in roots of maize seedlings

(2011) SARA TREVISAN et al.   PLANT CELL AND ENVIRONMENT

Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development

(2011) Johannes Rohrmann et al.   PLANT JOURNAL

Genome-wide atlas of transcription during maize development

(2011) Rajandeep S. Sekhon et al.   PLANT JOURNAL

Gene Expression Biomarkers Provide Sensitive Indicators of in Planta Nitrogen Status in Maize

(2011) X. S. Yang et al.   PLANT PHYSIOLOGY

Arabidopsis Roots and Shoots Show Distinct Temporal Adaptation Patterns toward Nitrogen Starvation

(2011) A. Krapp et al.   PLANT PHYSIOLOGY

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

(2011) Rajib Saha et al.   PLoS One

Genome-Wide Identification of MicroRNAs in Response to Low Nitrate Availability in Maize Leaves and Roots

(2011) Zhenhua Xu et al.   PLoS One

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

(2011) S. Mintz-Oron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global food demand and the sustainable intensification of agriculture

(2011) D. Tilman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fertilizing Nature: A Tragedy of Excess in the Commons

(2011) Allen G. Good et al.   PLOS BIOLOGY

Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

(2011) Gabriel Krouk et al.   GENOME BIOLOGY

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana reveals a multiple stress response and extensive reprogramming of the transcriptome

(2010) Ralph Kissen et al.   BMC GENOMICS

Tomato root transcriptome response to a nitrogen-enriched soil patch

(2010) Daniel R Ruzicka et al.   BMC PLANT BIOLOGY

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

(2010) Karin Radrich et al.   BMC Systems Biology

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks

(2010) Eytan Ruppin et al.   CURRENT OPINION IN BIOTECHNOLOGY

‘Omics’ analyses of regulatory networks in plant abiotic stress responses

(2010) Kaoru Urano et al.   CURRENT OPINION IN PLANT BIOLOGY

ChemSpider: An Online Chemical Information Resource

(2010) Harry E. Pence et al.   JOURNAL OF CHEMICAL EDUCATION

Understanding plant response to nitrogen limitation for the improvement of crop nitrogen use efficiency

(2010) S. Kant et al.   JOURNAL OF EXPERIMENTAL BOTANY

Nitrogen signalling in Arabidopsis: how to obtain insights into a complex signalling network

(2010) L. Castaings et al.   JOURNAL OF EXPERIMENTAL BOTANY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

NMR-based metabolomic analysis of plants

(2010) Hye Kyong Kim et al.   Nature Protocols

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

In folio isotopic tracing demonstrates that nitrogen assimilation into glutamate is mostly independent from current CO2 assimilation in illuminated leaves of Brassica napus

(2010) Paul P. G. Gauthier et al.   NEW PHYTOLOGIST

AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomics insights into plant signaling and development

(2010) Kerstin Kaufmann et al.   PROTEOMICS

Making the most of ‘omics’ for crop breeding

(2010) Peter Langridge et al.   TRENDS IN BIOTECHNOLOGY

Metabolomics for Functional Genomics, Systems Biology, and Biotechnology

(2009) Kazuki Saito et al.   Annual Review of Plant Biology

Inducing drought tolerance in plants: Recent advances

(2009) M. Ashraf   BIOTECHNOLOGY ADVANCES

Evaluation of protein pattern changes in roots and leaves of Zea mays plants in response to nitrate availability by two-dimensional gel electrophoresis analysis

(2009) Bhakti Prinsi et al.   BMC PLANT BIOLOGY

A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"

(2009) Damion Nero et al.   BMC Systems Biology

Integrated omics approaches in plant systems biology

(2009) Atsushi Fukushima et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Plant proteomics update (2007–2008): Second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge

(2009) Jesús V. Jorrín-Novo et al.   Journal of Proteomics

Application of NMR based metabolomics for mapping metabolite variation in European wheat

(2009) S. F. Graham et al.   Metabolomics

Resolving the Role of Plant Glutamate Dehydrogenase. I. in vivo Real Time Nuclear Magnetic Resonance Spectroscopy Experiments

(2009) Soraya Labboun et al.   PLANT AND CELL PHYSIOLOGY

Transcriptome analysis of nitrogen-efficient rice over-expressing alanine aminotransferase

(2009) Perrin H. Beatty et al.   PLANT BIOTECHNOLOGY JOURNAL

Advancing Genetic Theory and Application by Metabolic Quantitative Trait Loci Analysis

(2009) DanielJ. Kliebenstein   PLANT CELL

Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling

(2009) YONG-MEI BI et al.   PLANT CELL AND ENVIRONMENT

A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize

(2009) BJÖRN USADEL et al.   PLANT CELL AND ENVIRONMENT

VirtualPlant: A Software Platform to Support Systems Biology Research

(2009) M. S. Katari et al.   PLANT PHYSIOLOGY

A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties

(2009) M. G. Poolman et al.   PLANT PHYSIOLOGY

A Genetic Screen for Nitrate Regulatory Mutants Captures the Nitrate Transporter Gene NRT1.1

(2009) R. Wang et al.   PLANT PHYSIOLOGY

Increasing Crop Productivity to Meet Global Needs for Feed, Food, and Fuel

(2009) M. D. Edgerton   PLANT PHYSIOLOGY

A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis

(2009) Gabriel Krouk et al.   PLoS Computational Biology

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

(2009) Patrick F. Suthers et al.   PLoS Computational Biology

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

Gel-based proteomics approach for detecting low nitrogen-responsive proteins in cultivated rice species

(2009) Du Hyun Kim et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

The nodule inception-like protein 7 modulates nitrate sensing and metabolism in Arabidopsis

(2008) Loren Castaings et al.   PLANT JOURNAL

AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response

(2008) Heng-Cheng Hu et al.   PLANT JOURNAL

Flux Balance Analysis of Barley Seeds: A Computational Approach to Study Systemic Properties of Central Metabolism

(2008) E. Grafahrend-Belau et al.   PLANT PHYSIOLOGY

Genome-Enabled Approaches Shed New Light on Plant Metabolism

(2008) D. DellaPenna et al.   SCIENCE

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology