Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions

The Epigenome and Plant Development

(2011) Guangming He et al.   Annual Review of Plant Biology

PRIN: a predicted rice interactome network

(2011) Haibin Gu et al.   BMC BIOINFORMATICS

Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize

(2011) Paula Casati et al.   BMC GENOMICS

Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles

(2011) Shaogui Guo et al.   BMC GENOMICS

Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

(2011) Melissa ML Wong et al.   BMC GENOMICS

Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers

(2011) Wenliang Wei et al.   BMC GENOMICS

Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

(2011) Qing-Xin Song et al.   BMC PLANT BIOLOGY

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

(2011) Hélène Ferry-Dumazet et al.   BMC PLANT BIOLOGY

OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics

(2011) Mohamed Helmy et al.   BMC PLANT BIOLOGY

Hormone Signalling Crosstalk in Plant Growth Regulation

(2011) Stephen Depuydt et al.   CURRENT BIOLOGY

Natural diversity and adaptation in plant secondary metabolism

(2011) Juergen Kroymann   CURRENT OPINION IN PLANT BIOLOGY

High-throughput approaches for plant epigenomic studies

(2011) Robert J Schmitz et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome-Wide Survey and Expression Analysis of the Plant-Specific NAC Transcription Factor Family in Soybean During Development and Dehydration Stress

(2011) D. T. Le et al.   DNA RESEARCH

Genome-Wide Expression Profiling of Soybean Two-Component System Genes in Soybean Root and Shoot Tissues under Dehydration Stress

(2011) D. T. Le et al.   DNA RESEARCH

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

The auxin signalling network translates dynamic input into robust patterning at the shoot apex

(2011) T. Vernoux et al.   Molecular Systems Biology

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Genome-wide association study of leaf architecture in the maize nested association mapping population

(2011) Feng Tian et al.   NATURE GENETICS

Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

(2011) Kristen L Kump et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Experimental and computational approaches for the study of calmodulin interactions

(2011) A.S.N. Reddy et al.   PHYTOCHEMISTRY

Identification of EMS-Induced Causal Mutations in a Non-Reference Arabidopsis thaliana Accession by Whole Genome Sequencing

(2011) N. Uchida et al.   PLANT AND CELL PHYSIOLOGY

OrchidBase: A Collection of Sequences of the Transcriptome Derived from Orchids

(2011) C.-H. Fu et al.   PLANT AND CELL PHYSIOLOGY

Discovery of Genome-Wide DNA Polymorphisms in a Landrace Cultivar of Japonica Rice by Whole-Genome Sequencing

(2011) Yuko Arai-Kichise et al.   PLANT AND CELL PHYSIOLOGY

De Novo Assembly of Expressed Transcripts and Global Analysis of the Phalaenopsis aphrodite Transcriptome

(2011) Chun-lin Su et al.   PLANT AND CELL PHYSIOLOGY

Natural Variation of Barley Vernalization Requirements: Implication of Quantitative Variation of Winter Growth Habit as an Adaptive Trait in East Asia

(2011) Daisuke Saisho et al.   PLANT AND CELL PHYSIOLOGY

ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic Structure-Based Dynamic Expression (DSDE) Analyses

(2011) Kei Iida et al.   PLANT AND CELL PHYSIOLOGY

Global Landscape of a Co-Expressed Gene Network in Barley and its Application to Gene Discovery in Triticeae Crops

(2011) Keiichi Mochida et al.   PLANT AND CELL PHYSIOLOGY

ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants

(2011) T. Obayashi et al.   PLANT AND CELL PHYSIOLOGY

Diverse Functions of Plant Peptides: Entering a New Phase

(2011) H. Fukuda et al.   PLANT AND CELL PHYSIOLOGY

TOMATOMA: A Novel Tomato Mutant Database Distributing Micro-Tom Mutant Collections

(2011) Takeshi Saito et al.   PLANT AND CELL PHYSIOLOGY

Barley: Emergence as a New Research Material of Crop Science

(2011) D. Saisho et al.   PLANT AND CELL PHYSIOLOGY

Unlocking the Barley Genome by Chromosomal and Comparative Genomics

(2011) Klaus F.X. Mayer et al.   PLANT CELL

Functional Network Construction inArabidopsisUsing Rule-Based Machine Learning on Large-Scale Data Sets

(2011) George W. Bassel et al.   PLANT CELL

The Predicted Arabidopsis Interactome Resource and Network Topology-Based Systems Biology Analyses

(2011) M. Lin et al.   PLANT CELL

Os-GIGANTEAConfers Robust Diurnal Rhythms on the Global Transcriptome of Rice in the Field

(2011) Takeshi Izawa et al.   PLANT CELL

Evolution of C4Photosynthesis in the GenusFlaveria: How Many and Which Genes Does It Take to Make C4?

(2011) Udo Gowik et al.   PLANT CELL

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

Systems Biology Approach inChlamydomonasReveals Connections between Copper Nutrition and Multiple Metabolic Steps

(2011) Madeli Castruita et al.   PLANT CELL

Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids

(2011) Ali M. Banaei Moghaddam et al.   PLANT JOURNAL

Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light

(2011) Miyako Kusano et al.   PLANT JOURNAL

Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries

(2011) T. Matsumoto et al.   PLANT PHYSIOLOGY

Differential Molecular Responses of Rice and Wheat Coleoptiles to Anoxia Reveal Novel Metabolic Adaptations in Amino Acid Metabolism for Tissue Tolerance

(2011) R. N. Shingaki-Wells et al.   PLANT PHYSIOLOGY

Brachypodium as a Model for the Grasses: Today and the Future

(2011) Jelena Brkljacic et al.   PLANT PHYSIOLOGY

Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment

(2011) Miyako Kusano et al.   PLoS One

Metabolomics-Driven Nutraceutical Evaluation of Diverse Green Tea Cultivars

(2011) Yoshinori Fujimura et al.   PLoS One

Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions

(2011) G. W. Bassel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize

(2011) J. A. Poland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network

(2011) M. S. Mukhtar et al.   SCIENCE

Climate Trends and Global Crop Production Since 1980

(2011) D. B. Lobell et al.   SCIENCE

Towards Establishment of a Rice Stress Response Interactome

(2011) Young-Su Seo et al.   PLoS Genetics

Polycomb Repressive Complex 2 Controls the Embryo-to-Seedling Phase Transition

(2011) Daniel Bouyer et al.   PLoS Genetics

Automated analysis of protein subcellular location in time series images

(2010) Y. Hu et al.   BIOINFORMATICS

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets

(2010) Adam J Carroll et al.   BMC BIOINFORMATICS

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics

(2010) Koh Aoki et al.   BMC GENOMICS

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

(2010) Toshio Yamamoto et al.   BMC GENOMICS

Coexpression Analysis of Tomato Genes and Experimental Verification of Coordinated Expression of Genes Found in a Functionally Enriched Coexpression Module

(2010) S. Ozaki et al.   DNA RESEARCH

Sequence Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L.

(2010) S. Sato et al.   DNA RESEARCH

Genome-Wide Analysis of Two-Component Systems and Prediction of Stress-Responsive Two-Component System Members in Soybean

(2010) K. Mochida et al.   DNA RESEARCH

Functional genomics of soybean for improvement of productivity in adverse conditions

(2010) Lam-Son Phan Tran et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

(2010) R. Shoemaker et al.   GENOME RESEARCH

Proteome Analysis of Pod and Seed Development in the Model LegumeLotus japonicus

(2010) Gitte Nautrup-Pedersen et al.   JOURNAL OF PROTEOME RESEARCH

Jasmonate perception by inositol-phosphate-potentiated COI1–JAZ co-receptor

(2010) Laura B. Sheard et al.   NATURE

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution

(2010) Romain Fernandez et al.   NATURE METHODS

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis

(2010) P. Li et al.   NUCLEIC ACIDS RESEARCH

Gramene database in 2010: updates and extensions

(2010) K. Youens-Clark et al.   NUCLEIC ACIDS RESEARCH

Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics

(2010) Z. Fei et al.   NUCLEIC ACIDS RESEARCH

PAIR: the predicted Arabidopsis interactome resource

(2010) Mingzhi Lin et al.   NUCLEIC ACIDS RESEARCH

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

(2010) A. Bombarely et al.   NUCLEIC ACIDS RESEARCH

KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data

(2010) Nozomu Sakurai et al.   NUCLEIC ACIDS RESEARCH

RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions

(2010) Y. Sato et al.   NUCLEIC ACIDS RESEARCH

The Plant Organelles Database 2 (PODB2): An Updated Resource Containing Movie Data of Plant Organelle Dynamics

(2010) Shoji Mano et al.   PLANT AND CELL PHYSIOLOGY

AtCAST, a Tool for Exploring Gene Expression Similarities among DNA Microarray Experiments Using Networks

(2010) Eriko Sasaki et al.   PLANT AND CELL PHYSIOLOGY

Molecular Basis of the Core Regulatory Network in ABA Responses: Sensing, Signaling and Transport

(2010) T. Umezawa et al.   PLANT AND CELL PHYSIOLOGY

How Many Peas in a Pod? Legume Genes Responsible for Mutualistic Symbioses Underground

(2010) H. Kouchi et al.   PLANT AND CELL PHYSIOLOGY

OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

(2010) Kazuki Hamada et al.   PLANT AND CELL PHYSIOLOGY

Plant-Microbe Communications for Symbiosis

(2010) M. Kawaguchi et al.   PLANT AND CELL PHYSIOLOGY

Metabolic Alterations in Organic Acids and γ-Aminobutyric Acid in Developing Tomato (Solanum lycopersicum L.) Fruits

(2010) Yong-Gen Yin et al.   PLANT AND CELL PHYSIOLOGY

Genomics and Bioinformatics Resources for Crop Improvement

(2010) K. Mochida et al.   PLANT AND CELL PHYSIOLOGY

RiceFOX: A Database of Arabidopsis Mutant Lines Overexpressing Rice Full-Length cDNA that Contains a Wide Range of Trait Information to Facilitate Analysis of Gene Function

(2010) Tetsuya Sakurai et al.   PLANT AND CELL PHYSIOLOGY

Comparative Transcriptomic Profiling of a Salt-Tolerant Wild Tomato Species and a Salt-Sensitive Tomato Cultivar

(2010) Wei Sun et al.   PLANT AND CELL PHYSIOLOGY

Rice Expression Atlas In Reproductive Development

(2010) Masahiro Fujita et al.   PLANT AND CELL PHYSIOLOGY

Branching Hormone is Busy Both Underground and Overground

(2010) S. Yamaguchi et al.   PLANT AND CELL PHYSIOLOGY

Comprehensive Hormone Profiling in Developing Arabidopsis Seeds: Examination of the Site of ABA Biosynthesis, ABA Transport and Hormone Interactions

(2010) Yuri Kanno et al.   PLANT AND CELL PHYSIOLOGY

Community- and Genome-Based Views of Plant-Associated Bacteria: Plant–Bacterial Interactions in Soybean and Rice

(2010) Seishi Ikeda et al.   PLANT AND CELL PHYSIOLOGY

Atlas of Rice Grain Filling-Related Metabolism under High Temperature: Joint Analysis of Metabolome and Transcriptome Demonstrated Inhibition of Starch Accumulation and Induction of Amino Acid Accumulation

(2010) Hiromoto Yamakawa et al.   PLANT AND CELL PHYSIOLOGY

Distribution and characterization of more than 1000 T-DNA tags in the genome of Brachypodium distachyon community standard line Bd21

(2010) Vera Thole et al.   PLANT BIOTECHNOLOGY JOURNAL

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

AnOrange RipeningMutant Links Plastid NAD(P)H Dehydrogenase Complex Activity to Central and Specialized Metabolism during Tomato Fruit Maturation

(2010) Shai Nashilevitz et al.   PLANT CELL

Network Analysis of Enzyme Activities and Metabolite Levels and Their Relationship to Biomass in a Large Panel of Arabidopsis Accessions

(2010) R. Sulpice et al.   PLANT CELL

Natural Variation of Transcriptional Auxin Response Networks in Arabidopsis thaliana

(2010) C. Delker et al.   PLANT CELL

RNA-Seq Analysis of Sulfur-DeprivedChlamydomonasCells Reveals Aspects of Acclimation Critical for Cell Survival

(2010) David González-Ballester et al.   PLANT CELL

Integrative Transcript and Metabolite Analysis of Nutritionally EnhancedDE-ETIOLATED1Downregulated Tomato Fruit

(2010) Eugenia M.A. Enfissi et al.   PLANT CELL

Shotguns and SNPs: how fast and cheap sequencing is revolutionizing plant biology

(2010) Steven D. Rounsley et al.   PLANT JOURNAL

Mass spectrometry screening reveals widespread diversity in trichome specialized metabolites of tomato chromosomal substitution lines

(2010) Anthony Schilmiller et al.   PLANT JOURNAL

Functional analysis of a tomato salicylic acid methyl transferase and its role in synthesis of the flavor volatile methyl salicylate

(2010) Denise Tieman et al.   PLANT JOURNAL

Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

CORNET: A User-Friendly Tool for Data Mining and Integration

(2010) S. De Bodt et al.   PLANT PHYSIOLOGY

The Influence of Fruit Load on the Tomato Pericarp Metabolome in a Solanum chmielewskii Introgression Line Population

(2010) P. T. Do et al.   PLANT PHYSIOLOGY

Genetic Dissection of Barley Morphology and Development

(2010) A. Druka et al.   PLANT PHYSIOLOGY

Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants

(2010) P. Zhang et al.   PLANT PHYSIOLOGY

Increased Leaf Size: Different Means to an End

(2010) N. Gonzalez et al.   PLANT PHYSIOLOGY

Large-Scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants

(2010) H. Nakagami et al.   PLANT PHYSIOLOGY

Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances

(2010) K.-H. Kogel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Feedstocks for Lignocellulosic Biofuels

(2010) C. Somerville et al.   SCIENCE

A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2

(2010) Sylvie Lalonde   Frontiers in Physiology

Metabolomics for Functional Genomics, Systems Biology, and Biotechnology

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

LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors

(2009) Keiichi Mochida et al.   BIOINFORMATICS

Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns

(2009) Kanako Kawaura et al.   BMC GENOMICS

Correlation exploration of metabolic and genomic diversity in rice

(2009) Keiichi Mochida et al.   BMC GENOMICS

SolEST database: a "one-stop shop" approach to the study of Solanaceae transcriptomes

(2009) Nunzio D'Agostino et al.   BMC PLANT BIOLOGY

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

(2009) D. S. Horner et al.   BRIEFINGS IN BIOINFORMATICS

RNA-mediated chromatin-based silencing in plants

(2009) Marjori Matzke et al.   CURRENT OPINION IN CELL BIOLOGY

Translating Medicago truncatula genomics to crop legumes

(2009) Nevin Dale Young et al.   CURRENT OPINION IN PLANT BIOLOGY

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

(2009) Ryan Lister et al.   CURRENT OPINION IN PLANT BIOLOGY

Development of 5006 Full-Length CDNAs in Barley: A Tool for Accessing Cereal Genomics Resources

(2009) K. Sato et al.   DNA RESEARCH

In silico Analysis of Transcription Factor Repertoire and Prediction of Stress Responsive Transcription Factors in Soybean

(2009) K. Mochida et al.   DNA RESEARCH

Understanding the Evolution of Defense Metabolites in Arabidopsis thaliana Using Genome-wide Association Mapping

(2009) E. K. F. Chan et al.   GENETICS

HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination

(2009) M. I. Sigurdsson et al.   GENOME RESEARCH

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

A high-density transcript linkage map of barley derived from a single population

(2009) K Sato et al.   HEREDITY

Structural basis of abscisic acid signalling

(2009) Ken-ichi Miyazono et al.   NATURE

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Recent advances and emerging trends in plant hormone signalling

(2009) Aaron Santner et al.   NATURE

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction

(2009) M. Krallinger et al.   NUCLEIC ACIDS RESEARCH

PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

(2009) Pawel Durek et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2010

(2009) B. Aranda et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

SALAD database: a motif-based database of protein annotations for plant comparative genomics

(2009) Motohiro Mihara et al.   NUCLEIC ACIDS RESEARCH

SoyBase, the USDA-ARS soybean genetics and genomics database

(2009) David Grant et al.   NUCLEIC ACIDS RESEARCH

RESOPS: A Database for Analyzing the Correspondence of RNA Editing Sites to Protein Three-Dimensional Structures

(2009) Kei Yura et al.   PLANT AND CELL PHYSIOLOGY

Omics-Based Approaches to Methionine Side Chain Elongation in Arabidopsis: Characterization of the Genes Encoding Methylthioalkylmalate Isomerase and Methylthioalkylmalate Dehydrogenase

(2009) Yuji Sawada et al.   PLANT AND CELL PHYSIOLOGY

Phenome Analysis in Plant Species Using Loss-of-Function and Gain-of-Function Mutants

(2009) T. Kuromori et al.   PLANT AND CELL PHYSIOLOGY

Omics and Bioinformatics: An Essential Toolbox for Systems Analyses of Plant Functions Beyond 2010

(2009) K. Shinozaki et al.   PLANT AND CELL PHYSIOLOGY

Seeing Is Believing: On the Use of Image Databases for Visually Exploring Plant Organelle Dynamics

(2009) Shoji Mano et al.   PLANT AND CELL PHYSIOLOGY

PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants

(2009) Yuko Makita et al.   PLANT AND CELL PHYSIOLOGY

Physiological and Molecular Approaches to Improve Drought Resistance in Soybean

(2009) L. P. Manavalan et al.   PLANT AND CELL PHYSIOLOGY

Metabolome Analysis of Response to Oxidative Stress in Rice Suspension Cells Overexpressing Cell Death Suppressor Bax Inhibitor-1

(2009) Toshiki Ishikawa et al.   PLANT AND CELL PHYSIOLOGY

Highly Sensitive and High-Throughput Analysis of Plant Hormones Using MS-Probe Modification and Liquid Chromatography–Tandem Mass Spectrometry: An Application for Hormone Profiling in Oryza sativa

(2009) Mikiko Kojima et al.   PLANT AND CELL PHYSIOLOGY

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

(2009) X. Wang 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

Genome-Wide Medicago truncatula Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules

(2009) C. Lelandais-Briere et al.   PLANT CELL

Regulatory Features Underlying Pollination-Dependent and -Independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling

(2009) H. Wang et al.   PLANT CELL

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

(2009) S. Proost et al.   PLANT CELL

Identification of heterotic metabolite QTL inArabidopsis thalianaRIL and IL populations

(2009) Jan Lisec et al.   PLANT JOURNAL

Computational Identification of Potential Molecular Interactions in Arabidopsis

(2009) M. Lin et al.   PLANT PHYSIOLOGY

Systematic Localization of the Arabidopsis Core Cell Cycle Proteins Reveals Novel Cell Division Complexes

(2009) J. Boruc et al.   PLANT PHYSIOLOGY

AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development

(2009) F. Matsuda et al.   PLANT PHYSIOLOGY

Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology

(2009) J.-G. Joung et al.   PLANT PHYSIOLOGY

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

TILLING in Lotus japonicus Identified Large Allelic Series for Symbiosis Genes and Revealed a Bias in Functionally Defective Ethyl Methanesulfonate Alleles toward Glycine Replacements

(2009) J. Perry et al.   PLANT PHYSIOLOGY

TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics

(2009) K. Mochida et al.   PLANT PHYSIOLOGY

Large-Scale Phosphoprotein Analysis in Medicago truncatula Roots Provides Insight into in Vivo Kinase Activity in Legumes

(2009) P. A. Grimsrud et al.   PLANT PHYSIOLOGY

Metabolic Networks: How to Identify Key Components in the Regulation of Metabolism and Growth

(2009) M. Stitt et al.   PLANT PHYSIOLOGY

The Proteome of Seed Development in the Model Legume Lotus japonicus

(2009) S. Dam et al.   PLANT PHYSIOLOGY

Mutant Resources in Rice for Functional Genomics of the Grasses

(2009) A. Krishnan et al.   PLANT PHYSIOLOGY

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Next-generation sequencing technologies and their implications for crop genetics and breeding

(2009) Rajeev K. Varshney et al.   TRENDS IN BIOTECHNOLOGY

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

(2009) Carol Soderlund et al.   PLoS Genetics

10 Reasons to be Tantalized by the B73 Maize Genome

(2009) Virginia Walbot   PLoS Genetics

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

(2009) Xiaoyu Zhang et al.   GENOME BIOLOGY

TriMEDB: A database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae

(2008) Keiichi Mochida et al.   BMC PLANT BIOLOGY

Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome

(2008) Hyun-Jin Kim et al.   BMC PLANT BIOLOGY

Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?

(2008) R. Winnenburg et al.   BRIEFINGS IN BIOINFORMATICS

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Sequencing and Analysis of Approximately 40 000 Soybean cDNA Clones from a Full-Length-Enriched cDNA Library

(2008) T. Umezawa et al.   DNA RESEARCH

Genome Structure of the Legume, Lotus japonicus

(2008) S. Sato et al.   DNA RESEARCH

Analysis of systemic sulfur metabolism in plants using integrated ‘-omics’ strategies

(2008) Masami Yokota Hirai et al.   Molecular BioSystems

Structural basis for gibberellin recognition by its receptor GID1

(2008) Asako Shimada et al.   NATURE

Inhibition of shoot branching by new terpenoid plant hormones

(2008) Mikihisa Umehara et al.   NATURE

Strigolactone inhibition of shoot branching

(2008) Victoria Gomez-Roldan et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Helicos BioSciences

(2008) Patrice Milos   PHARMACOGENOMICS

Various Spatiotemporal Expression Profiles of Anther-Expressed Genes in Rice

(2008) T. Hobo et al.   PLANT AND CELL PHYSIOLOGY

In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice

(2008) Motohiro Mihara et al.   PLANT AND CELL PHYSIOLOGY

Separated Transcriptomes of Male Gametophyte and Tapetum in Rice: Validity of a Laser Microdissection (LM) Microarray

(2008) Keita Suwabe et al.   PLANT AND CELL PHYSIOLOGY

Biochemical Mechanism on GABA Accumulation During Fruit Development in Tomato

(2008) Takashi Akihiro et al.   PLANT AND CELL PHYSIOLOGY

Alterations of Lysine Modifications on the Histone H3 N-Tail under Drought Stress Conditions in Arabidopsis thaliana

(2008) Jong-Myong Kim et al.   PLANT AND CELL PHYSIOLOGY

Widely Targeted Metabolomics Based on Large-Scale MS/MS Data for Elucidating Metabolite Accumulation Patterns in Plants

(2008) Yuji Sawada 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

High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression

(2008) X. Li et al.   PLANT CELL

Comparative Genomics and Reverse Genetics Analysis Reveal Indispensable Functions of the Serine Acetyltransferase Gene Family in Arabidopsis

(2008) M. Watanabe et al.   PLANT CELL

Metabolite annotations based on the integration of mass spectral information

(2008) Yoko Iijima et al.   PLANT JOURNAL

A gene expression atlas of the model legumeMedicago truncatula

(2008) Vagner A. Benedito et al.   PLANT JOURNAL

Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula

(2008) Million Tadege et al.   PLANT JOURNAL

Systematic approaches to using the FOX hunting system to identify useful rice genes

(2008) Youichi Kondou 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

A Rice Kinase-Protein Interaction Map

(2008) X. Ding et al.   PLANT PHYSIOLOGY

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Single-molecule DNA sequencing technologies for future genomics research

(2008) Pushpendra K. Gupta   TRENDS IN BIOTECHNOLOGY

Charting plant interactomes: possibilities and challenges

(2008) Mustafa Morsy et al.   TRENDS IN PLANT SCIENCE

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

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