Plant systems biology: insights, advances and challenges

Cracking the Kranz enigma with systems biology

(2014) J. P. Fouracre et al.   JOURNAL OF EXPERIMENTAL BOTANY

Plant Protein Interactomes

(2013) Pascal Braun et al.   Annual Review of Plant Biology

The Flavonoid Pathway in Tomato Seedlings: Transcript Abundance and the Modeling of Metabolite Dynamics

(2013) Marian Groenenboom et al.   PLoS One

Recruitment and remodeling of an ancient gene regulatory network during land plant evolution

(2013) Nuno D. Pires et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent Progress in the Development of Metabolome Databases for Plant Systems Biology

(2013) Atsushi Fukushima et al.   Frontiers in Plant Science

FX: an RNA-Seq analysis tool on the cloud

(2012) Dongwan Hong et al.   BIOINFORMATICS

MetNet Online: a novel integrated resource for plant systems biology

(2012) Yves Sucaet et al.   BMC BIOINFORMATICS

Genome-wide association studies for agronomical traits in a world wide spring barley collection

(2012) Raj K Pasam et al.   BMC PLANT BIOLOGY

The Small RNA-Based Odyssey of Epigenetic Information in Plants: From Cells to Species

(2012) Marie Mirouze   DNA AND CELL BIOLOGY

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

CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations

(2012) Stefanie De Bodt et al.   NEW PHYTOLOGIST

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

(2012) G. P. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional machineries in jasmonate-elicited plant secondary metabolism

(2012) Nathan De Geyter et al.   TRENDS IN PLANT SCIENCE

Co-expression and co-responses: within and beyond transcription

(2012) Takayuki Tohge et al.   Frontiers in Plant Science

Correlation networks visualization

(2012) Nicholas Provart   Frontiers in Plant Science

Grand Challenges in Plant Systems Biology: Closing the Circle(s)

(2012) Alisdair R. Fernie   Frontiers in Plant Science

The Epigenome and Plant Development

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

The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology

(2011) J. Blakes et al.   BIOINFORMATICS

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

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

MEMOSys: Bioinformatics platform for genome-scale metabolic models

(2011) Stephan Pabinger et al.   BMC Systems Biology

Exploring plant transcriptomes using ultra high-throughput sequencing

(2011) L. Wang et al.   Briefings in Functional Genomics

Epigenetic modifications in plants: an evolutionary perspective

(2011) Suhua Feng et al.   CURRENT OPINION IN PLANT 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

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

PINA v2.0: mining interactome modules

(2011) Mark J. Cowley et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

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

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

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

(2011) C.-H. Fu 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

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

Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max

(2011) DAVID J. WESTON et al.   PLANT CELL AND ENVIRONMENT

Integrated transcriptomic and proteomic profiling of white spruce stems during the transition from active growth to dormancy

(2011) LEONARDO M. GALINDO GONZÁLEZ et al.   PLANT CELL AND ENVIRONMENT

The Regulatory Activities of Plant MicroRNAs: A More Dynamic Perspective

(2011) Y. Meng 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

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

(2011) Sonia Osorio et al.   PLANT PHYSIOLOGY

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

Time to articulate a vision for the future of plant proteomics - A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO)

(2011) Ganesh Kumar Agrawal et al.   PROTEOMICS

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

Redefining plant systems biology: from cell to ecosystem

(2011) Joost J.B. Keurentjes et al.   TRENDS IN PLANT SCIENCE

Fast-forward genetics enabled by new sequencing technologies

(2011) Korbinian Schneeberger et al.   TRENDS IN PLANT SCIENCE

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

(2011) Daniel Bouyer et al.   PLoS Genetics

Identification of Carcass and Meat Quality QTL in an F2 Duroc × Pietrain Pig Resource Population Using Different Least-Squares Analysis Models

(2011) Igseo Choi et al.   Frontiers in Genetics

Integrative platform to translate gene sets to networks

(2010) Marko Laakso et al.   BIOINFORMATICS

SynBioWave—a real-time communication platform for molecular and synthetic biology

(2010) Paul R. Staab et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

AtPIN: Arabidopsis thaliana Protein Interaction Network

(2010) Marcelo M Brandão et al.   BMC BIOINFORMATICS

Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress

(2010) Kil-Young Yun et al.   BMC PLANT BIOLOGY

Association genetics in crop improvement

(2010) J Antoni Rafalski   CURRENT OPINION IN PLANT BIOLOGY

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

(2010) S. Sato et al.   DNA RESEARCH

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

(2010) T. Lu et al.   GENOME RESEARCH

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

(2010) Susan B. Altenbach et al.   JOURNAL OF CEREAL SCIENCE

Metabolic profiling of Arabidopsis thaliana epidermal cells

(2010) Berit Ebert et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2010) Susanna Atwell et al.   NATURE

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

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

PAIR: the predicted Arabidopsis interactome resource

(2010) Mingzhi Lin et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Dual metabolomics: A novel approach to understanding plant–pathogen interactions

(2010) J. William Allwood et al.   PHYTOCHEMISTRY

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

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

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

Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice

(2010) Huihuang Yan et al.   PLANT JOURNAL

The metabolic transition during disease following infection of Arabidopsis thaliana by Pseudomonas syringae pv. tomato

(2010) Jane L. Ward et al.   PLANT JOURNAL

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

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

Increased Leaf Size: Different Means to an End

(2010) N. Gonzalez 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

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Plant molecular stress responses face climate change

(2010) Ishita Ahuja et al.   TRENDS IN PLANT SCIENCE

Crop genome sequencing: lessons and rationales

(2010) Catherine Feuillet et al.   TRENDS IN PLANT SCIENCE

Metabolomics for Functional Genomics, Systems Biology, and Biotechnology

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

MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions

(2009) Emilie Chautard et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response

(2009) Jamie A O'Rourke et al.   BMC GENOMICS

De novo sequencing of plant genomes using second-generation technologies

(2009) M. Imelfort et al.   BRIEFINGS IN BIOINFORMATICS

RNA-mediated chromatin-based silencing in plants

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

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

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

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Linking DNA methylation and histone modification: patterns and paradigms

(2009) Howard Cedar et al.   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Gene expression analysis of light-modulated germination in tomato seeds

(2009) Gabriela Alejandra Auge et al.   NEW PHYTOLOGIST

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

(2009) M. Krallinger 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

An introduction to liquid chromatography–mass spectrometry instrumentation applied in plant metabolomic analyses

(2009) J. William Allwood et al.   PHYTOCHEMICAL ANALYSIS

Sample preparation for plant metabolomics

(2009) Hye Kyong Kim et al.   PHYTOCHEMICAL ANALYSIS

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

(2009) K. Shinozaki 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

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

Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legumeLotus japonicus

(2009) DIEGO H. SANCHEZ et al.   PLANT CELL AND ENVIRONMENT

Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses

(2009) K. Nakashima et al.   PLANT PHYSIOLOGY

VirtualPlant: A Software Platform to Support Systems Biology Research

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

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Systems Approaches to Identifying Gene Regulatory Networks in Plants

(2008) Terri A. Long et al.   Annual Review of Cell and Developmental Biology

Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling

(2008) Arthur G Hunt et al.   BMC GENOMICS

High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families

(2008) Gyorgy Szittya et al.   BMC GENOMICS

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

Chromatin state maps: new technologies, new insights

(2008) Eric M Mendenhall et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Quantitative genetics in the age of omics

(2008) Joost JB Keurentjes et al.   CURRENT OPINION IN PLANT BIOLOGY

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

(2008) S. Moxon et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Ultra-performance LC/TOF MS analysis of medicinalPanaxherbs for metabolomic research

(2008) Guoxiang Xie et al.   JOURNAL OF SEPARATION SCIENCE

Intra- and inter-metabolite correlation spectroscopy of tomato metabolomics data obtained by liquid chromatography-mass spectrometry and nuclear magnetic resonance

(2008) Sofia Moco et al.   Metabolomics

Metabolomic analysis of the interaction between plants and herbivores

(2008) Jeroen J. Jansen et al.   Metabolomics

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

(2008) Masami Yokota Hirai et al.   Molecular BioSystems

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

(2008) Gabriele Delp et al.   MOLECULAR GENETICS AND GENOMICS

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

(2008) Ray Ming 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

Genome-wide approaches to studying chromatin modifications

(2008) Dustin E. Schones et al.   NATURE REVIEWS GENETICS

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Helicos BioSciences

(2008) Patrice Milos   PHARMACOGENOMICS

Metabolomics: back to basics

(2008) R. Verpoorte et al.   PHYTOCHEMISTRY REVIEWS

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

(2008) K. Yonekura-Sakakibara 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

A Rice Kinase-Protein Interaction Map

(2008) X. Ding et al.   PLANT PHYSIOLOGY

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

The methylome: approaches for global DNA methylation profiling

(2008) Stephan Beck et al.   TRENDS IN GENETICS

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

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

Plant systems biology comes of age

(2008) Joshua S. Yuan et al.   TRENDS IN PLANT SCIENCE

Charting plant interactomes: possibilities and challenges

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

Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge

(2008) Martin Krallinger et al.   GENOME BIOLOGY

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY

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

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