Experimental ‘omics’ data in tree research: facing complexity

Stability criteria for complex ecosystems

(2012) Stefano Allesina et al.   NATURE

The changes that count

(2012) Monya Baker   NATURE

Apple, from genome to breeding

(2012) M. Troggio et al.   Tree Genetics & Genomes

Genomics of Fagaceae

(2012) Antoine Kremer et al.   Tree Genetics & Genomes

The genomes of the giants: a walk through the forest of tree genomes

(2012) Albert Abbott   Tree Genetics & Genomes

Citrus genomics

(2012) Fred G. Gmitter et al.   Tree Genetics & Genomes

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

(2012) Dario Grattapaglia et al.   Tree Genetics & Genomes

Metabolite profiling reveals clear metabolic changes during somatic embryo development of Norway spruce (Picea abies)

(2012) E. Businge et al.   TREE PHYSIOLOGY

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

(2012) Alisdair R. Fernie   Frontiers in Plant Science

EuroPineDB: a high-coverage web database for maritime pine transcriptome

(2011) Noé Fernández-Pozo et al.   BMC GENOMICS

Characterization of the genome of bald cypress

(2011) Wenxuan Liu et al.   BMC GENOMICS

Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

(2011) W Walter Lorenz et al.   BMC GENOMICS

A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation

(2011) Nathaniel Street et al.   BMC PLANT BIOLOGY

Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana

(2011) Ana Pop et al.   BMC Systems Biology

Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome

(2011) Peter E Larsen et al.   BMC Systems Biology

One dry summer: A leaf proteome study on the response of oak to drought exposure

(2011) Kjell Sergeant et al.   Journal of Proteomics

Proteins associated with cork formation in Quercus suber L. stem tissues

(2011) Cândido P.P. Ricardo et al.   Journal of Proteomics

Studies of variability in Holm oak (Quercus ilex subsp. ballota [Desf.] Samp.) through acorn protein profile analysis

(2011) José Valero Galván et al.   Journal of Proteomics

Green systems biology — From single genomes, proteomes and metabolomes to ecosystems research and biotechnology

(2011) Wolfram Weckwerth   Journal of Proteomics

Poplar under drought: Comparison of leaf and cambial proteomic responses

(2011) Thomas C. Durand et al.   Journal of Proteomics

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

(2011) Klára Kosová et al.   Journal of Proteomics

Metabolomics demonstrates divergent responses of two Eucalyptus species to water stress

(2011) Charles R. Warren et al.   Metabolomics

Controllability of complex networks

(2011) Yang-Yu Liu et al.   NATURE

High plant diversity is needed to maintain ecosystem services

(2011) Forest Isbell et al.   NATURE

Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome

(2011) Andrew J. Eckert et al.   NEW PHYTOLOGIST

Proteomics research on forest trees, the most recalcitrant and orphan plant species

(2011) Nieves Abril et al.   PHYTOCHEMISTRY

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

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

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

A White Spruce Gene Catalog for Conifer Genome Analyses

(2011) Philippe Rigault et al.   PLANT PHYSIOLOGY

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

(2011) Sergei A. Filichkin et al.   PLoS One

Genome-scale transcriptome analysis of the desert poplar, Populus euphratica

(2011) Q. Qiu et al.   TREE PHYSIOLOGY

Changes in the proteome of juvenile European beech following three years exposure to free-air elevated ozone

(2011) R Kerner et al.   iForest-Biogeosciences and Forestry

The Roots of Bioinformatics in Theoretical Biology

(2011) Paulien Hogeweg   PLoS Computational Biology

The limits to prediction in ecological systems

(2011) Brian Beckage et al.   Ecosphere

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

(2010) Saneyoshi Ueno et al.   BMC GENOMICS

Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes

(2010) David Cohen et al.   BMC GENOMICS

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

(2010) Thomas L Parchman et al.   BMC GENOMICS

Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms

(2010) Dennis Janz et al.   BMC PLANT BIOLOGY

The sigma profile: A formal tool to study organization and its evolution at multiple scales

(2010) Carlos Gershenson   COMPLEXITY

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

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

Symbiont genomics, our new tangled bank

(2010) M. Medina et al.   GENOMICS

Metabolomics for plant stress response

(2010) Vladimir Shulaev et al.   PHYSIOLOGIA PLANTARUM

An integrated genomic, proteomic and biochemical analysis of (+)-3-carene biosynthesis in Sitka spruce (Picea sitchensis) genotypes that are resistant or susceptible to white pine weevil

(2010) Dawn E. Hall et al.   PLANT JOURNAL

Proteomic approach to analyze dormancy breaking of tree seeds

(2010) Tomasz Andrzej Pawłowski   PLANT MOLECULAR BIOLOGY

Plant molecular stress responses face climate change

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

Genome scale transcriptome analysis of shoot organogenesis in Populus

(2009) Yanghuan Bao et al.   BMC PLANT BIOLOGY

PopulusResponses to Edaphic and Climatic Cues: Emerging Evidence from Systems Biology Research

(2009) Stan D. Wullschleger et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Poplar Genomics: State of the Science

(2009) Xiaohan Yang et al.   CRITICAL REVIEWS IN PLANT SCIENCES

PopulusRhizosphere and the Ectomycorrhizal Interactome

(2009) Gopi K. Podila et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Genomics of Secondary Metabolism inPopulus: Interactions with Biotic and Abiotic Environments

(2009) Feng Chen et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Integrated omics approaches in plant systems biology

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

Gene expression responses of paper birch (Betula papyrifera) to elevated CO2 and O3 during leaf maturation and senescence

(2009) Sari Kontunen-Soppela et al.   ENVIRONMENTAL POLLUTION

Ozone fumigation (twice ambient) reduces leaf infestation following natural and artificial inoculation by the endophytic fungus Apiognomonia errabunda of adult European beech trees

(2009) Maren Olbrich et al.   ENVIRONMENTAL POLLUTION

A Metabolic Signature of the Beneficial Interaction of the EndophytePaenibacillussp. Isolate and In Vitro–Grown Poplar Plants Revealed by Metabolomics

(2009) Christian Scherling et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

Divergence in an obligate mutualism is not explained by divergent climatic factors

(2009) William Godsoe et al.   NEW PHYTOLOGIST

Transcript responses in leaves of ozone-treated beech saplings seasons at an outdoor free air model fumigation site over two growing seasons

(2009) Maren Olbrich et al.   PLANT AND SOIL

Targeted proteomics using selected reaction monitoring reveals the induction of specific terpene synthases in a multi-level study of methyl jasmonate-treated Norway spruce (Picea abies)

(2009) Katherine G. Zulak et al.   PLANT JOURNAL

Systems Biology Uncovers the Foundation of Natural Genetic Diversity

(2009) D. J. Kliebenstein   PLANT PHYSIOLOGY

Large-Scale Assessment of the Effect of Popularity on the Reliability of Research

(2009) Thomas Pfeiffer et al.   PLoS One

Challenges in elevated CO2 experiments on forests

(2009) Carlo Calfapietra et al.   TRENDS IN PLANT SCIENCE

Gene Transcription in Lactarius quietus-Quercus petraea Ectomycorrhizas from a Forest Soil

(2008) P. E. Courty et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Complexity in biology. Exceeding the limits of reductionism and determinism using complexity theory

(2008) Fulvio Mazzocchi   EMBO REPORTS

Integrated Analysis of Transcript, Protein and Metabolite Data To Study Lignin Biosynthesis in Hybrid Aspen

(2008) Max Bylesjö et al.   JOURNAL OF PROTEOME RESEARCH

Combining Proteomics and Metabolite Analyses To Unravel Cadmium Stress-Response in Poplar Leaves

(2008) Pol Kieffer et al.   JOURNAL OF PROTEOME RESEARCH

Life, logic and information

(2008) Paul Nurse   NATURE

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

(2008) F. Martin et al.   NATURE

High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)

(2008) Andrew J. Eckert et al.   Tree Genetics & Genomes

Plant systems biology comes of age

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