相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Cracking the Kranz enigma with systems biology
Jim P. Fouracre et al.
JOURNAL OF EXPERIMENTAL BOTANY (2014)
Plant Protein Interactomes
Pascal Braun et al.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 64 (2013)
The Flavonoid Pathway in Tomato Seedlings: Transcript Abundance and the Modeling of Metabolite Dynamics
Marian Groenenboom et al.
PLOS ONE (2013)
Population genomic and genome-wide association studies of agroclimatic traits in sorghum
Geoffrey P. Morris et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Recruitment and remodeling of an ancient gene regulatory network during land plant evolution
Nuno D. Pires et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Recent progress in the development of metabolome databases for plant systems biology
Atsushi Fukushima et al.
FRONTIERS IN PLANT SCIENCE (2013)
Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids
Guangming He et al.
GENOME BIOLOGY (2013)
Metabolomics for Secondary Metabolite Research
Rainer Breitling et al.
METABOLITES (2013)
FX: an RNA-Seq analysis tool on the cloud
Dongwan Hong et al.
BIOINFORMATICS (2012)
MetNet Online: a novel integrated resource for plant systems biology
Yves Sucaet et al.
BMC BIOINFORMATICS (2012)
Genome-wide association studies for agronomical traits in a world wide spring barley collection
Raj K. Pasam et al.
BMC PLANT BIOLOGY (2012)
The Small RNA-Based Odyssey of Epigenetic Information in Plants: From Cells to Species
Marie Mirouze
DNA AND CELL BIOLOGY (2012)
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
Nardjis Amiour et al.
JOURNAL OF EXPERIMENTAL BOTANY (2012)
CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations
Stefanie De Bodt et al.
NEW PHYTOLOGIST (2012)
PINA v2.0: mining interactome modules
Mark J. Cowley et al.
NUCLEIC ACIDS RESEARCH (2012)
MINT, the molecular interaction database: 2012 update
Luana Licata et al.
NUCLEIC ACIDS RESEARCH (2012)
KEGG for integration and interpretation of large-scale molecular data sets
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2012)
Integrated transcriptomic and proteomic profiling of white spruce stems during the transition from active growth to dormancy
Leonardo M. Galindo Gonzalez et al.
PLANT CELL AND ENVIRONMENT (2012)
Transcriptional machineries in jasmonate-elicited plant secondary metabolism
Nathan De Geyter et al.
TRENDS IN PLANT SCIENCE (2012)
Co-expression and co-responses: within and beyond transcription
Takayuki Tohge et al.
FRONTIERS IN PLANT SCIENCE (2012)
Correlation networks visualization
Nicholas Provart
FRONTIERS IN PLANT SCIENCE (2012)
Grand challenges in plant systems biology: closing the circle(s)
Alisdair R. Fernie
FRONTIERS IN PLANT SCIENCE (2012)
Toward understanding transcriptional regulatory networks in abiotic stress responses and tolerance in rice
Daisuke Todaka et al.
RICE (2012)
From systems biology to photosynthesis and whole-plant physiology A conceptual model for integrating multi-scale networks
David J. Weston et al.
PLANT SIGNALING & BEHAVIOR (2012)
The Epigenome and Plant Development
Guangming He et al.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 62 (2011)
The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
Jonathan Blakes et al.
BIOINFORMATICS (2011)
PRIN: a predicted rice interactome network
Haibin Gu et al.
BMC BIOINFORMATICS (2011)
Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize
Paula Casati et al.
BMC GENOMICS (2011)
Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing
Melissa M. L. Wong et al.
BMC GENOMICS (2011)
MEMOSys: Bioinformatics platform for genome-scale metabolic models
Stephan Pabinger et al.
BMC SYSTEMS BIOLOGY (2011)
Epigenetic modifications in plants: an evolutionary perspective
Suhua Feng et al.
CURRENT OPINION IN PLANT BIOLOGY (2011)
Sequence Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L.
Shusei Sato et al.
DNA RESEARCH (2011)
Genome sequence and analysis of the tuber crop potato
Xun Xu et al.
NATURE (2011)
An integrated semiconductor device enabling non-optical genome sequencing
Jonathan M. Rothberg et al.
NATURE (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
The genome of woodland strawberry (Fragaria vesca)
Vladimir Shulaev et al.
NATURE GENETICS (2011)
The genome of the mesopolyploid crop species Brassica rapa
Xiaowu Wang et al.
NATURE GENETICS (2011)
Computational methods for transcriptome annotation and quantification using RNA-seq
Manuel Garber et al.
NATURE METHODS (2011)
PAIR: the predicted Arabidopsis interactome resource
Mingzhi Lin et al.
NUCLEIC ACIDS RESEARCH (2011)
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Damian Szklarczyk et al.
NUCLEIC ACIDS RESEARCH (2011)
OrchidBase: A Collection of Sequences of the Transcriptome Derived from Orchids
Chih-Hsiung Fu et al.
PLANT AND CELL PHYSIOLOGY (2011)
De Novo Assembly of Expressed Transcripts and Global Analysis of the Phalaenopsis aphrodite Transcriptome
Chun-lin Su et al.
PLANT AND CELL PHYSIOLOGY (2011)
Os-GIGANTEA Confers Robust Diurnal Rhythms on the Global Transcriptome of Rice in the Field
Takeshi Izawa et al.
PLANT CELL (2011)
Evolution of C4 Photosynthesis in the Genus Flaveria: How Many and Which Genes Does It Take to Make C4?
Udo Gowik et al.
PLANT CELL (2011)
Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max
David J. Weston et al.
PLANT CELL AND ENVIRONMENT (2011)
The Regulatory Activities of Plant MicroRNAs: A More Dynamic Perspective
Yijun Meng et al.
PLANT PHYSIOLOGY (2011)
Differential Molecular Responses of Rice and Wheat Coleoptiles to Anoxia Reveal Novel Metabolic Adaptations in Amino Acid Metabolism for Tissue Tolerance
Rachel N. Shingaki-Wells et al.
PLANT PHYSIOLOGY (2011)
Systems Biology of Tomato Fruit Development: Combined Transcript, Protein, and Metabolite Analysis of Tomato Transcription Factor (nor, rin) and Ethylene Receptor (Nr) Mutants Reveals Novel Regulatory Interactions
Sonia Osorio et al.
PLANT PHYSIOLOGY (2011)
A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies
Wenyu Zhang et al.
PLOS ONE (2011)
Time to articulate a vision for the future of plant proteomics - A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO)
Ganesh Kumar Agrawal et al.
PROTEOMICS (2011)
Evidence for Network Evolution in an Arabidopsis Interactome Map
Pascal Braun et al.
SCIENCE (2011)
Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network
M. Shahid Mukhtar et al.
SCIENCE (2011)
Redefining plant systems biology: from cell to ecosystem
Joost J. B. Keurentjes et al.
TRENDS IN PLANT SCIENCE (2011)
Crop genome sequencing: lessons and rationales
Catherine Feuillet et al.
TRENDS IN PLANT SCIENCE (2011)
Fast-forward genetics enabled by new sequencing technologies
Korbinian Schneeberger et al.
TRENDS IN PLANT SCIENCE (2011)
Polycomb Repressive Complex 2 Controls the Embryo-to-Seedling Phase Transition
Daniel Bouyer et al.
PLOS GENETICS (2011)
Identification of Carcass and Meat Quality QTL in an F2 Duroc × Pietrain Pig Resource Population Using Different Least-Squares Analysis Models
Igseo Choi et al.
Frontiers in Genetics (2011)
Metabolomics for Functional Genomics, Systems Biology, and Biotechnology
Kazuki Saito et al.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 61 (2010)
Integrative platform to translate gene sets to networks
Marko Laakso et al.
BIOINFORMATICS (2010)
SynBioWave-a real-time communication platform for molecular and synthetic biology
Paul R. Staab et al.
BIOINFORMATICS (2010)
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Thomas D. Wu et al.
BIOINFORMATICS (2010)
Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress
Kil-Young Yun et al.
BMC PLANT BIOLOGY (2010)
Exploring plant transcriptomes using ultra high-throughput sequencing
Lin Wang et al.
BRIEFINGS IN FUNCTIONAL GENOMICS (2010)
Association genetics in crop improvement
J. Antoni Rafalski
CURRENT OPINION IN PLANT BIOLOGY (2010)
Genome-wide mapping of alternative splicing in Arabidopsis thaliana
Sergei A. Filichkin et al.
GENOME RESEARCH (2010)
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
Tingting Lu et al.
GENOME RESEARCH (2010)
Integration of transcriptomic and proteomic data from a single wheat cultivar provides new tools for understanding the roles of individual alpha gliadin proteins in flour quality and celiac disease
Susan B. Altenbach et al.
JOURNAL OF CEREAL SCIENCE (2010)
Metabolic profiling of Arabidopsis thaliana epidermal cells
Berit Ebert et al.
JOURNAL OF EXPERIMENTAL BOTANY (2010)
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
Susanna Atwell et al.
NATURE (2010)
Genome-wide association studies of 14 agronomic traits in rice landraces
Xuehui Huang et al.
NATURE GENETICS (2010)
Visualization of omics data for systems biology
Nils Gehlenborg et al.
NATURE METHODS (2010)
The IntAct molecular interaction database in 2010
B. Aranda et al.
NUCLEIC ACIDS RESEARCH (2010)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2010)
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
Kin Fai Au et al.
NUCLEIC ACIDS RESEARCH (2010)
An Introduction to Liquid Chromatography-Mass Spectrometry Instrumentation Applied in Plant Metabolomic Analyses
J. William Allwood et al.
PHYTOCHEMICAL ANALYSIS (2010)
Sample Preparation for Plant Metabolomics
Hye Kyong Kim et al.
PHYTOCHEMICAL ANALYSIS (2010)
Dual metabolomics: A novel approach to understanding plant-pathogen interactions
J. William Allwood et al.
PHYTOCHEMISTRY (2010)
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
Hiromoto Yamakawa et al.
PLANT AND CELL PHYSIOLOGY (2010)
Integrative Transcript and Metabolite Analysis of Nutritionally Enhanced DE-ETIOLATED1 Downregulated Tomato Fruit
Eugenia M. A. Enfissi et al.
PLANT CELL (2010)
Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus
Diego H. Sanchez et al.
PLANT CELL AND ENVIRONMENT (2010)
Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice
Huihuang Yan et al.
PLANT JOURNAL (2010)
The metabolic transition during disease following infection of Arabidopsis thaliana by Pseudomonas syringae pv. tomato
Jane L. Ward et al.
PLANT JOURNAL (2010)
VirtualPlant: A Software Platform to Support Systems Biology Research
Manpreet S. Katari et al.
PLANT PHYSIOLOGY (2010)
Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq
Sara Zenoni et al.
PLANT PHYSIOLOGY (2010)
Increased Leaf Size: Different Means to an End
Nathalie Gonzalez et al.
PLANT PHYSIOLOGY (2010)
Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances
Karl-Heinz Kogel et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Conservation and divergence of methylation patterning in plants and animals
Suhua Feng et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation
Assaf Zemach et al.
SCIENCE (2010)
Plant molecular stress responses face climate change
Ishita Ahuja et al.
TRENDS IN PLANT SCIENCE (2010)
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions
Emilie Chautard et al.
BIOINFORMATICS (2009)
TopHat: discovering splice junctions with RNA-Seq
Cole Trapnell et al.
BIOINFORMATICS (2009)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
AtPIN: Arabidopsis thaliana Protein Interaction Network
Marcelo M. Brandao et al.
BMC BIOINFORMATICS (2009)
Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response
Jamie A. O'Rourke et al.
BMC GENOMICS (2009)
De novo sequencing of plant genomes using second-generation technologies
Michael Imelfort et al.
BRIEFINGS IN BIOINFORMATICS (2009)
RNA-mediated chromatin-based silencing in plants
Marjori Matzke et al.
CURRENT OPINION IN CELL BIOLOGY (2009)
Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond
Ryan Lister et al.
CURRENT OPINION IN PLANT BIOLOGY (2009)
Microarray analysis of the interaction between the aphid Rhopalosiphum padi and host plants reveals both differences and similarities between susceptible and partially resistant barley lines
Gabriele Delp et al.
MOLECULAR GENETICS AND GENOMICS (2009)
The Sorghum bicolor genome and the diversification of grasses
Andrew H. Paterson et al.
NATURE (2009)
The genome of the cucumber, Cucumis sativus L.
Sanwen Huang et al.
NATURE GENETICS (2009)
Continuous base identification for single-molecule nanopore DNA sequencing
James Clarke et al.
NATURE NANOTECHNOLOGY (2009)
RNA-Seq: a revolutionary tool for transcriptomics
Zhong Wang et al.
NATURE REVIEWS GENETICS (2009)
Linking DNA methylation and histone modification: patterns and paradigms
Howard Cedar et al.
NATURE REVIEWS GENETICS (2009)
ChIP-seq: advantages and challenges of a maturing technology
Peter J. Park
NATURE REVIEWS GENETICS (2009)
Metabolomic analysis of the interaction between plants and herbivores
Jeroen J. Jansen et al.
METABOLOMICS (2009)
Gene expression analysis of light-modulated germination in tomato seeds
Gabriela Alejandra Auge et al.
NEW PHYTOLOGIST (2009)
PID: the Pathway Interaction Database
Carl F. Schaefer et al.
NUCLEIC ACIDS RESEARCH (2009)
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction
Martin Krallinger et al.
NUCLEIC ACIDS RESEARCH (2009)
Omics and Bioinformatics: An Essential Toolbox for Systems Analyses of Plant Functions Beyond 2010
Kazuo Shinozaki et al.
PLANT AND CELL PHYSIOLOGY (2009)
PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants
Yuko Makita et al.
PLANT AND CELL PHYSIOLOGY (2009)
Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize
Xiangfeng Wang et al.
PLANT CELL (2009)
A Chloroplastic UDP-Glucose Pyrophosphorylase from Arabidopsis Is the Committed Enzyme for the First Step of Sulfolipid Biosynthesis
Yozo Okazaki et al.
PLANT CELL (2009)
Genome-Wide Medicago truncatula Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules
Christine Lelandais-Briere et al.
PLANT CELL (2009)
Regulatory Features Underlying Pollination-Dependent and -Independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling
Hua Wang et al.
PLANT CELL (2009)
Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses
Kazuo Nakashima et al.
PLANT PHYSIOLOGY (2009)
A Rice Kinase-Protein Interaction Map
Xiaodong Ding et al.
PLANT PHYSIOLOGY (2009)
Genetic Properties of the Maize Nested Association Mapping Population
Michael D. McMullen et al.
SCIENCE (2009)
Real-Time DNA Sequencing from Single Polymerase Molecules
John Eid et al.
SCIENCE (2009)
Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting
Mary Gehring et al.
SCIENCE (2009)
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Patrick S. Schnable et al.
SCIENCE (2009)
Genome-Wide Demethylation of Arabidopsis Endosperm
Tzung-Fu Hsieh et al.
SCIENCE (2009)
Metabolomics-assisted breeding: a viable option for crop improvement?
Alisdair R. Fernie et al.
TRENDS IN GENETICS (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize
Axel A. Elling et al.
PLANT SIGNALING & BEHAVIOR (2009)
Computational challenges in systems biology
Allison P. Heath et al.
COMPUTER SCIENCE REVIEW (2009)
Systems Approaches to Identifying Gene Regulatory Networks in Plants
Terri A. Long et al.
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY (2008)
Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling
Arthur G. Hunt et al.
BMC GENOMICS (2008)
High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
Gyorgy Szittya et al.
BMC GENOMICS (2008)
Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies
Rainer Winnenburg et al.
BRIEFINGS IN BIOINFORMATICS (2008)
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
Ryan Lister et al.
CELL (2008)
Chromatin state maps: new technologies, new insights
Eric M. Mendenhall et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2008)
Quantitative genetics in the age of omics
Joost J. B. Keurentjes et al.
CURRENT OPINION IN PLANT BIOLOGY (2008)
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
Simon Moxon et al.
GENOME RESEARCH (2008)
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino et al.
GENOME RESEARCH (2008)
Ultra-performance LC/TOF MS analysis of medicinal Panax herbs for metabolomic research
Guoxiang Xie et al.
JOURNAL OF SEPARATION SCIENCE (2008)
Analysis of systemic sulfur metabolism in plants using integrated '-omics' strategies
Masami Yokota Hirai et al.
MOLECULAR BIOSYSTEMS (2008)
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
Ray Ming et al.
NATURE (2008)
Inhibition of shoot branching by new terpenoid plant hormones
Mikihisa Umehara et al.
NATURE (2008)
Strigolactone inhibition of shoot branching
Victoria Gomez-Roldan et al.
NATURE (2008)
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Shawn J. Cokus et al.
NATURE (2008)
Genome-wide approaches to studying chromatin modifications
Dustin E. Schones et al.
NATURE REVIEWS GENETICS (2008)
DNA methylation landscapes: provocative insights from epigenomics
Miho M. Suzuki et al.
NATURE REVIEWS GENETICS (2008)
Intra- and inter-metabolite correlation spectroscopy of tomato metabolomics data obtained by liquid chromatography-mass spectrometry and nuclear magnetic resonance
Sofia Moco et al.
METABOLOMICS (2008)
Metabolomics: back to basics
R. Verpoorte et al.
PHYTOCHEMISTRY REVIEWS (2008)
Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis
Keiko Yonekura-Sakakibara et al.
PLANT CELL (2008)
Comparative Genomics and Reverse Genetics Analysis Reveal Indispensable Functions of the Serine Acetyltransferase Gene Family in Arabidopsis
Mutsumi Watanabe et al.
PLANT CELL (2008)
Helicos BioSciences
Patrice Milos
PHARMACOGENOMICS (2008)
Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics
Katja Baerenfaller et al.
SCIENCE (2008)
The methylome: approaches for global DNA methylation profiling
Stephan Beck et al.
TRENDS IN GENETICS (2008)
Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'
Kazuki Saito et al.
TRENDS IN PLANT SCIENCE (2008)
Plant systems biology comes of age
Joshua S. Yuan et al.
TRENDS IN PLANT SCIENCE (2008)
Charting plant interactomes: possibilities and challenges
Mustafa Morsy et al.
TRENDS IN PLANT SCIENCE (2008)
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge
Martin Krallinger et al.
GENOME BIOLOGY (2008)
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function
Sara Mostafavi et al.
GENOME BIOLOGY (2008)
Computational epigenetics
Christoph Bock et al.
BIOINFORMATICS (2008)
Genome-wide analysis of DNA methylation patterns
Daniel Zilberman et al.
DEVELOPMENT (2007)
Quantitative proteomics in plants: Choices in abundance
Jay J. Thelen et al.
PLANT CELL (2007)
A predicted interactome for Arabidopsis
Jane Geisler-Lee et al.
PLANT PHYSIOLOGY (2007)
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
Olivier Jaillon et al.
NATURE (2007)
An Electronic Fluorescent Pictograph Browser for Exploring and Analyzing Large-Scale Biological Data Sets
Debbie Winter et al.
PLOS ONE (2007)
A tandem affinity purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana
Jelle Van Leene et al.
MOLECULAR & CELLULAR PROTEOMICS (2007)
Exploring genetic interactions and networks with yeast
Charles Boone et al.
NATURE REVIEWS GENETICS (2007)
Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis
Masami Yokota Hirai et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
An expression atlas of rice mRNAs and small RNAs
Kan Nobuta et al.
NATURE BIOTECHNOLOGY (2007)
Gene transcript and metabolite profiling of elicitor-induced opium poppy cell cultures reveals the coordinate regulation of primary and secondary metabolism
Katherine G. Zulak et al.
PLANTA (2007)
Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants
Rudy Maor et al.
MOLECULAR & CELLULAR PROTEOMICS (2007)
Interaction network of proteins associated with abiotic stress response and development in wheat
Guylaine Tardif et al.
PLANT MOLECULAR BIOLOGY (2007)
A comprehensive analysis of the 14-3-3 interactome in barley leaves using a complementary proteomics and two-hybrid approach
Peter J. Schoonheim et al.
PLANT PHYSIOLOGY (2007)
Sungear:: interactive visualization and functional analysis of genomic datasets
Christopher S. Poultney et al.
BIOINFORMATICS (2007)
Plant lipidomics: Discerning biological function by profiling plant complex lipids using mass spectrometry
Ruth Welti et al.
FRONTIERS IN BIOSCIENCE-LANDMARK (2007)
Eukaryotic genome size databases
T. Ryan Gregory et al.
NUCLEIC ACIDS RESEARCH (2007)
How many genes are there in plants (. . . and why are they there)?
Lieven Sterck et al.
CURRENT OPINION IN PLANT BIOLOGY (2007)
Profiling a plant: expression analysis in Arabidopsis
Wolfgang Busch et al.
CURRENT OPINION IN PLANT BIOLOGY (2007)
Light-regulated transcriptional networks in higher plants
Yuling Jiao et al.
NATURE REVIEWS GENETICS (2007)
COPASI- A COmplex PAthway SImulator
Stefan Hoops et al.
BIOINFORMATICS (2006)
Integration of omics data: how well does it work for bacteria?
Sigrid C. J. De Keersmaecker et al.
MOLECULAR MICROBIOLOGY (2006)
Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior
Fernando Carrari et al.
PLANT PHYSIOLOGY (2006)
A brief history of systems biology - Every object that biology studies is a system of systems. Francois Jacob (1974).
Anthony Trewavas
PLANT CELL (2006)
MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant
Cheng Lu et al.
GENOME RESEARCH (2006)
Predicting essential components of signal transduction networks: A dynamic model of guard cell abscisic acid signaling
Song Li et al.
PLOS BIOLOGY (2006)
Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis
Xiaoyu Zhang et al.
CELL (2006)
Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis
Catherine Benedict et al.
PLANT PHYSIOLOGY (2006)
OPLS discriminant analysis:: combining the strengths of PLS-DA and SIMCA classification
Max Bylesjo et al.
JOURNAL OF CHEMOMETRICS (2006)
APID: Agile Protein Interaction DataAnalyzer
Carlos Prieto et al.
NUCLEIC ACIDS RESEARCH (2006)
The genetics of plant metabolism
Joost J. B. Keurentjes et al.
NATURE GENETICS (2006)
BABELOMICS:: a systems biology perspective in the functional annotation of genome-scale experiments
Fatima Al-Shahrour et al.
NUCLEIC ACIDS RESEARCH (2006)
Challenges of detecting directional selection after a bottleneck:: Lessons from Sorghum bicolor
Martha T. Hamblin et al.
GENETICS (2006)
NMR metabolomics to revisit the tobacco mosaic virus infection in Nicotiana tabacum leaves
Young Hae Choi et al.
JOURNAL OF NATURAL PRODUCTS (2006)
Metabolomic approaches reveal that phosphatidic and phosphatidyl glycerol phospholipids are major discriminatory non-polar metabolites in responses by Brachypodium distachyon to challenge by Magnaporthe grisea
JW Allwood et al.
PLANT JOURNAL (2006)
Review - Mass spectrometry and protein analysis
B Domon et al.
SCIENCE (2006)
Gene-to-metabolite networks for terpenoid indole alkaloid biosynthesis in Catharanthus roseus cells
H Rischer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Genetic association mapping and genome organization of maize
JM Yu et al.
CURRENT OPINION IN BIOTECHNOLOGY (2006)
Post-transcriptional small RNA pathways in plants: mechanisms and regulations
H Vaucheret
GENES & DEVELOPMENT (2006)
Modeling cellular machinery through biological network comparison
R Sharan et al.
NATURE BIOTECHNOLOGY (2006)
Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement
N Schauer et al.
NATURE BIOTECHNOLOGY (2006)
The model organism as a system: integrating 'omics' data sets
AR Joyce et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2006)
The role of mass spectrometry in plant systems biology
M Glinski et al.
MASS SPECTROMETRY REVIEWS (2006)
Pyrosequencing: History, biochemistry and future
A Ahmadian et al.
CLINICA CHIMICA ACTA (2006)
Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare
KS Caldwell et al.
GENETICS (2006)
BioGRID: a general repository for interaction datasets
Chris Stark et al.
NUCLEIC ACIDS RESEARCH (2006)
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
Nicolas Le Novere et al.
NUCLEIC ACIDS RESEARCH (2006)
Plant proteomics databases: Their status in 2005
Setsuko Komatsu
CURRENT BIOINFORMATICS (2006)
Plant metabolomics: from holistic hope, to hype, to hot topic
RD Hall
NEW PHYTOLOGIST (2006)
Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis
OE Bläsing et al.
PLANT CELL (2005)
Epigenetics and its implications for plant biology. 1. The epigenetic network in plants
RT Grant-Downton et al.
ANNALS OF BOTANY (2005)
Metabolomics: from pattern recognition to biological interpretation
W Weckwerth et al.
DRUG DISCOVERY TODAY (2005)
Interactome: gateway into systems biology
ME Cusick et al.
HUMAN MOLECULAR GENETICS (2005)
Constructing transcriptional regulatory networks
A Blais et al.
GENES & DEVELOPMENT (2005)
Plant gene expression in the age of systems biology: integrating transcriptional and post-transcriptional events
DA Belostotsky et al.
TRENDS IN PLANT SCIENCE (2005)
The pattern of polymorphism in Arabidopsis thaliana
M Nordborg et al.
PLOS BIOLOGY (2005)
Toward the $1000 human genome
ST Bennett et al.
PHARMACOGENOMICS (2005)
The light-hyperresponsive high pigment-2dg mutation of tomato:: alterations in the fruit metabolome
RJ Bino et al.
NEW PHYTOLOGIST (2005)
Comprehensive interaction map of the Arabidopsis MADS box transcription factors
S de Folter et al.
PLANT CELL (2005)
Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor
T Tohge et al.
PLANT JOURNAL (2005)
iPfam:: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
RD Finn et al.
BIOINFORMATICS (2005)
DNA methylation profiling identifies CG methylation clusters Arabidopsis genes
RK Tran et al.
CURRENT BIOLOGY (2005)
Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis
RK Tran et al.
GENOME BIOLOGY (2005)
Plant bioinformatics: from genome to phenome
D Edwards et al.
TRENDS IN BIOTECHNOLOGY (2004)
Predicting gene expression from sequence
MA Beer et al.
CELL (2004)
MAPMAN:: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
O Thimm et al.
PLANT JOURNAL (2004)
Network biology:: Understanding the cell's functional organization
AL Barabási et al.
NATURE REVIEWS GENETICS (2004)
Robustness of cellular functions
J Stelling et al.
CELL (2004)
Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen
WR Scheible et al.
PLANT PHYSIOLOGY (2004)
Web-based kinetic modelling using JWS Online
BG Olivier et al.
BIOINFORMATICS (2004)
Computational approach to systems biology: From fraction to integration and beyond
PK Dhar et al.
IEEE TRANSACTIONS ON NANOBIOSCIENCE (2004)
Inferring quantitative models of regulatory networks from expression data
I. Nachman et al.
BIOINFORMATICS (2004)
Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana
MY Hirai et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo
JV Geisberg et al.
NUCLEIC ACIDS RESEARCH (2004)
DNA and histone methylation in plants
M Tariq et al.
TRENDS IN GENETICS (2004)
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service
DJ Craigon et al.
NUCLEIC ACIDS RESEARCH (2004)
RNAi in a postmodern, postgenomic era
B Baum et al.
ONCOGENE (2004)
A gene regulatory network model for cell-fate determination during Arabidopsis thalianal flower development that is robust and recovers experimental gene expression profiles
C Espinosa-soto et al.
PLANT CELL (2004)
Structure and evolution of transcriptional regulatory networks
MM Babu et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2004)
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
B Chevreux et al.
GENOME RESEARCH (2004)
Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins
IM Zimmermann et al.
PLANT JOURNAL (2004)
Analysis of the Arabidopsis nuclear proteome and its response to cold stress
MS Bae et al.
PLANT JOURNAL (2003)
Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels
AT Rosengren et al.
PROTEOMICS (2003)
The impact of genomics on the study of natural variation in Arabidopsis
JO Borevitz et al.
PLANT PHYSIOLOGY (2003)
Quantitative traits in plants: beyond the QTL
I Paran et al.
TRENDS IN GENETICS (2003)
AraCyc: A biochemical pathway database for Arabidopsis
LA Mueller et al.
PLANT PHYSIOLOGY (2003)
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
G Pertea et al.
BIOINFORMATICS (2003)
Protein analysis on a proteomic scale
E Phizicky et al.
NATURE (2003)
Plant metabolomics: large-scale phytochemistry in the functional genomics era
LW Sumner et al.
PHYTOCHEMISTRY (2003)
Proteomics: the first decade and beyond
SD Patterson et al.
NATURE GENETICS (2003)
The systems biology markup language (SBML):: a medium for representation and exchange of biochemical network models
M Hucka et al.
BIOINFORMATICS (2003)
Secretion of secondary metabolites by ATP-binding cassette transporters in plant cell suspension cultures
A Goossens et al.
PLANT PHYSIOLOGY (2003)
Cytoscape: A software environment for integrated models of biomolecular interaction networks
P Shannon et al.
GENOME RESEARCH (2003)
Osprey: a network visualization system
BJ Breitkreutz et al.
GENOME BIOLOGY (2003)
DNA methylation patterns on plant chromosomes
MR Castiglione et al.
CARYOLOGIA (2002)
Histone modifications in transcriptional regulation
SL Berger
CURRENT OPINION IN GENETICS & DEVELOPMENT (2002)
Linkage disequilibrium:: what history has to tell us
M Nordborg et al.
TRENDS IN GENETICS (2002)
Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3
R Tompa et al.
CURRENT BIOLOGY (2002)
Metabolomics - the link between genotypes and phenotypes
O Fiehn
PLANT MOLECULAR BIOLOGY (2002)
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
I Xenarios et al.
NUCLEIC ACIDS RESEARCH (2002)
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
R Edgar et al.
NUCLEIC ACIDS RESEARCH (2002)
Modeling the heart - from genes to cells to the whole organ
D Noble
SCIENCE (2002)
An automated multidimensional protein identification technology for shotgun proteomics
DA Wolters et al.
ANALYTICAL CHEMISTRY (2001)
Analysis of the Arabidopsis mitochondrial proteome
AH Millar et al.
PLANT PHYSIOLOGY (2001)
Proteomic approach to identify novel mitochondrial proteins in Arabidopsis
V Kruft et al.
PLANT PHYSIOLOGY (2001)
Bioinformatics in proteomics
M Vihinen
BIOMOLECULAR ENGINEERING (2001)
The Virtual Cell: a software environment for computational cell biology
LM Loew et al.
TRENDS IN BIOTECHNOLOGY (2001)
Challenges and prospects of plant proteomics
KJ van Wijk
PLANT PHYSIOLOGY (2001)
Identification of a 350-kDa ClpP protease complex with 10 different Clp isoforms in chloroplasts of Arabidopsis thaliana
JB Peltier et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2001)
Mass spectrometric resolution of reversible protein phosphorylation in photosynthetic membranes of Arabidopsis thaliana
AV Vener et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2001)
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
MP Washburn et al.
NATURE BIOTECHNOLOGY (2001)
Metabolite profiling for plant functional genomics
O Fiehn et al.
NATURE BIOTECHNOLOGY (2000)
Genetics and biochemistry of secondary metabolites in plants: an evolutionary perspective
E Pichersky et al.
TRENDS IN PLANT SCIENCE (2000)
Proteomics to study genes and genomes
A Pandey et al.
NATURE (2000)
Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays
A Aharoni et al.
PLANT CELL (2000)
The cell and developmental biology of alkaloid biosynthesis
V De Luca et al.
TRENDS IN PLANT SCIENCE (2000)
The 1999 SWISS-2DPAGE database update
C Hoogland et al.
NUCLEIC ACIDS RESEARCH (2000)
Proteomics of the chloroplast: Systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins
JB Peltier et al.
PLANT CELL (2000)
分享论文
