Genomics and Bioinformatics Resources for Crop Improvement

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

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

(2009) John R. Yates et al.   Annual Review of Biomedical Engineering

Structure and Dynamics of Membrane Proteins by Magic Angle Spinning Solid-State NMR

(2009) Ann McDermott   Annual Review of Biophysics

Roles of Plant Small RNAs in Biotic Stress Responses

(2009) Virginia Ruiz-Ferrer et al.   Annual Review of Plant Biology

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

A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

(2009) M Carmen Marques et al.   BMC GENOMICS

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

(2009) Jingyu Zhang et al.   BMC GENOMICS

Development and implementation of high-throughput SNP genotyping in barley

(2009) Timothy J Close et al.   BMC GENOMICS

Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays

(2009) Amy N Bernardo et al.   BMC GENOMICS

A set of EST-SNPs for map saturation and cultivar identification in melon

(2009) Wim Deleu et al.   BMC PLANT BIOLOGY

Development and diversity of Andean-derived, gene-based microsatellites for common bean (Phaseolus vulgaris L.)

(2009) Matthew W Blair et al.   BMC PLANT BIOLOGY

A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

(2009) Emma S Mace et al.   BMC PLANT BIOLOGY

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL 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

A Brassica rapa Linkage Map of EST-based SNP Markers for Identification of Candidate Genes Controlling Flowering Time and Leaf Morphological Traits

(2009) F. Li et al.   DNA RESEARCH

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

Isolation and identification of ubiquitin-related proteins from Arabidopsis seedlings

(2009) Tomoko Igawa et al.   JOURNAL OF EXPERIMENTAL BOTANY

Functional genomics using RIKEN Arabidopsis thaliana full-length cDNAs

(2009) Motoaki Seki et al.   JOURNAL OF PLANT RESEARCH

Soybean Proteome Database: A Data Resource for Plant Differential Omics

(2009) Katsumi Sakata et al.   JOURNAL OF PROTEOME RESEARCH

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

A force to fight global warming

(2009) Will R. Turner et al.   NATURE

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

(2009) Yuling Jiao et al.   NATURE GENETICS

System-wide molecular evidence for phenotypic buffering in Arabidopsis

(2009) Jingyuan Fu et al.   NATURE GENETICS

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

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

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

Functional Analysis of Transcription Factors in Arabidopsis

(2009) Nobutaka Mitsuda et al.   PLANT AND CELL PHYSIOLOGY

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

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

Global Identification of Targets of the Arabidopsis MADS Domain Protein AGAMOUS-Like15

(2009) Y. Zheng 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

Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis

(2009) Yoshiharu Y. Yamamoto et al.   PLANT JOURNAL

Stress-induced changes in theArabidopsis thalianatranscriptome analyzed using whole-genome tiling arrays

(2009) Georg Zeller et al.   PLANT JOURNAL

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

(2009) K. Mochida et al.   PLANT PHYSIOLOGY

Metabolic Pathways Involved in Cold Acclimation Identified by Integrated Analysis of Metabolites and Transcripts Regulated by DREB1A and DREB2A

(2009) K. Maruyama et al.   PLANT PHYSIOLOGY

I-TASSER: Fully automated protein structure prediction in CASP8

(2009) Yang Zhang   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

New changes in the plasma-membrane-associated proteome of rice roots under salt stress

(2009) Yanwei Cheng et al.   PROTEOMICS

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

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

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

TOBFAC: the database of tobacco transcription factors

(2008) Paul J Rushton et al.   BMC BIOINFORMATICS

Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili

(2008) Norihiro Futamura et al.   BMC GENOMICS

A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis)

(2008) Steven G Ralph et al.   BMC GENOMICS

Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding

(2008) Steven G Ralph et al.   BMC GENOMICS

Relationship between metabolic and genomic diversity in sesame (Sesamum indicum L.)

(2008) Hernán Laurentin et al.   BMC GENOMICS

Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila

(2008) Teruaki Taji et al.   BMC PLANT BIOLOGY

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

(2008) Keiichi Mochida et al.   BMC PLANT BIOLOGY

Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals

(2008) N. Barkley et al.   CURRENT GENOMICS

Population, quantitative and comparative genomics of adaptation in forest trees

(2008) David B Neale et al.   CURRENT OPINION IN PLANT BIOLOGY

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Serial Analysis of Gene Expression (SAGE): 13 Years of Application in Research

(2008) Sergey Anisimov   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

SuperSAGE: A Modern Platform for Genome-Wide Quantitative Transcript Profiling

(2008) Hideo Matsumura et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943

(2008) T. Lu et al.   DNA RESEARCH

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

CE-MS in metabolomics

(2008) Rawi Ramautar et al.   ELECTROPHORESIS

De novoassembly of thePseudomonas syringaepv.syringaeB728a genome using Illumina/Solexa short sequence reads

(2008) Rhys A. Farrer et al.   FEMS MICROBIOLOGY LETTERS

Sequencing of natural strains of Arabidopsis thaliana with short reads

(2008) S. Ossowski et al.   GENOME RESEARCH

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

Applications of High-Resolution Solid-State NMR Spectroscopy in Food Science

(2008) Fabio Bertocchi et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Plant proteomics: Concepts, applications, and novel strategies for data interpretation

(2008) Sacha Baginsky   MASS SPECTROMETRY REVIEWS

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Structural genomics: from genes to structures with valuable materials and many questions in between

(2008) Brian G Fox et al.   NATURE METHODS

Genetic approaches to crop improvement: responding to environmental and population changes

(2008) Shin Takeda et al.   NATURE REVIEWS GENETICS

The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions

(2008) S. Fukuchi et al.   NUCLEIC ACIDS RESEARCH

OryGenesDB 2008 update: database interoperability for functional genomics of rice

(2008) G. Droc et al.   NUCLEIC ACIDS RESEARCH

P3DB: a plant protein phosphorylation database

(2008) J. Gao et al.   NUCLEIC ACIDS RESEARCH

ATTED-II provides coexpressed gene networks for Arabidopsis

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

NCBI GEO: archive for high-throughput functional genomic data

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

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array

(2008) A. Matsui et al.   PLANT AND CELL PHYSIOLOGY

Alterations in Detergent-Resistant Plasma Membrane Microdomains in Arabidopsis thaliana During Cold Acclimation

(2008) Anzu Minami et al.   PLANT AND CELL PHYSIOLOGY

Large-scale phenotyping of transgenic tobacco plants (Nicotiana tabacum) to identify essential leaf functions

(2008) Wolfgang Lein et al.   PLANT BIOTECHNOLOGY JOURNAL

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

Metabolite annotations based on the integration of mass spectral information

(2008) Yoko Iijima et al.   PLANT JOURNAL

The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access

(2008) Hideki Goda et al.   PLANT JOURNAL

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

(2008) Youichi Kondou et al.   PLANT JOURNAL

Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics

(2008) Kaoru Urano 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

Identification of ubiquitinated proteins in Arabidopsis

(2008) Concepción Manzano et al.   PLANT MOLECULAR BIOLOGY

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

(2008) A. Yilmaz et al.   PLANT PHYSIOLOGY

Structures and evolutionary origins of plant-specific transcription factor DNA-binding domains

(2008) Kazuhiko Yamasaki et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

(2008) K. Nobuta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Food Security Under Climate Change

(2008) M. E. Brown et al.   SCIENCE

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility

(2008) Adam Heesacker et al.   THEORETICAL AND APPLIED GENETICS

High-density genetic map of durum wheat × wild emmer wheat based on SSR and DArT markers

(2008) Zvi Peleg et al.   THEORETICAL AND APPLIED GENETICS

High-throughput genotyping with the GoldenGate assay in the complex genome of soybean

(2008) David L. Hyten et al.   THEORETICAL AND APPLIED GENETICS

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

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

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana

(2008) Sascha Laubinger et al.   GENOME BIOLOGY

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

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